bluuebunny/crossref_metadata_2025_split huggingface dataset:
Verticillium dahliaeinoculation andin vitropropagation modify the xylem microbiome and disease reaction to Verticillium wilt in a wild olive genotype
Authors: Anguita-Maeso Manuel , Trapero José Luis , Olivares-García Concepción , Ruano-Rosa David , Palomo-Ríos Elena , Jiménez-Díaz Rafael M. , Navas-Cortés Juan A. , Landa Blanca B. 
Published: November 2020

AbstractHost resistance is the most practical, long-term and economically efficient disease control measure for Verticillium wilt in olive caused by the xylem-invading fungusVerticillium dahliae(Vd), and it is at the core of the integrated disease management. Plant’s microbiome at the site of infection may have an influence on the host reaction to pathogens; however, the role of xylem microbial communities in the olive resistance toVdhas been overlooked and remain unexplored to date. This research was focused on elucidating whetherin vitroolive propagation may alter the diversity and composition of the xylem-inhabiting microbiome and if those changes may modify the resistance response that a wild olive clone shows to the highly virulent defoliating (D) pathotype ofVd. Results indicated that although there were differences in microbial communities among the different propagation methodologies, most substantial changes occurred when plants were inoculated withVd, regardless whether the infection process took place, with a significant increase in the diversity of bacterial communities when the pathogen was present in the soil. Furthermore, it was noticeable that olive plants multiplied underin vitroconditions developed a susceptible reaction to DVd, characterized by severe wilting symptoms and 100% vascular infection. Moreover, thosein vitropropagated plants showed an altered xylem microbiome with a decrease in total OTU numbers as compared to that of plants multiplied under non-aseptic conditions. Overall, 10 keystone bacterial genera were detected in olive xylem regardless infection byVdand the propagation procedure of plants (in vitrovs nursery), withCutibacterium(36.85%),Pseudomonas(20.93%),Anoxybacillus(6.28%),Staphylococcus(4.95%),Methylobacterium-Methylorubrum(3.91%), andBradyrhizobium(3.54%) being the most abundant.Pseudomonasspp. appeared as the most predominant bacterial group in micropropagated plants andAnoxybacillusappeared as a keystone bacterium inVd-inoculated plants irrespective of their propagation process. Our results are first to show a breakdown of resistance toVdin a wild olive that potentially maybe related to a modification of its xylem microbiome, and will help to expand our knowledge of the role of indigenous xylem microbiome on host resistance which can be of use to fight against main vascular diseases of olive.
The female (XX) and male (YY) genomes provide insights into the sex determination mechanism in spinach
Authors: She Hongbing , Liu Zhiyuan , Xu Zhaosheng , Zhang Helong , Cheng Feng , Wang Xiaowu , Qian Wei 
Published: November 2020

AbstractSexual reproduction is the primary means of reproduction for the vast majority of macroscopic organisms, including almost all animals and plants. Sex chromosomes are predicted to play a central role in sexual dimorphism. Sex determination in spinach is controlled by a pair of sex chromosomes. However, the mechanisms of sex determination in spinach remain poorly understand. Here, we assembled the genomes of both a female (XX) and a male (YY) individual of spinach, and the genome sizes were 978 Mb with 28,320 predicted genes and 926 Mb with 26,537 predicted genes, respectively. Based on reported sex-linked markers, chromosomes 4 of the female and male genome were defined as the X and Y chromosomes, and a 10 Mb male-specific region of the Y chromosome (MSY) from approximately 95– 105 Mb, was identified that contains abundant transposable elements (92.32%). Importantly, a large-scale inversion of about 13 Mb in length was detected on the X chromosome, corresponding to ~9 Mb and ~4 Mb on the Y chromosome, which were located on both sides of the MSY with two distinct evolutionary strata. Almost all sex-linked/Y-specific markers were enriched on the inversions/MSY, suggesting that the flanked inversions might result in recombination suppression between the X and Y chromosomes to maintain the MSY. Forty-nine genes within the MSY had functional homologs elsewhere in the autosomal region, suggesting movement of genes onto the MSY. The X and Y chromosomes of spinach provide a valuable resource for investigating spinach sex chromosomes evolution from wild to cultivated spinach and also provide a broader understanding of the sex determination model in the Amaranthaceae family.
Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter
Authors: Osbeck Christofer M.G. , Lundin Daniel , Karlsson Camilla , Teikari Jonna E. , Moran Mary Ann , Pinhassi Jarone 
Published: November 2020

AbstractPhytoplankton release massive amounts of dissolved organic matter (DOM) into the water column during recurring blooms in coastal waters and inland seas. The released DOM encompasses a complex mixture of both known and unknown compounds, and is a rich nutrient source for heterotrophic bacteria. The metabolic activity of bacteria during and after phytoplankton blooms can hence be expected to reflect the characteristics of the released DOM. We therefore investigated if bacterioplankton could be used as “living sensors” of phytoplankton DOM quantity and/or quality, by applying gene expression analyses to identify bacterial metabolisms induced by DOM. We used transcriptional analysis of two Baltic Sea bacterial isolates (Polaribactersp. BAL334 [Flavobacteriia] andBrevundimonassp. BAL450 [Alphaproteobacteria]) growing with DOM from axenic cultures of the dinoflagellateProrocentrum minimum. We observed pronounced differences between the two bacteria both in bacterial growth and the expressed metabolic pathways in cultures exposed to dinoflagellate DOM compared with controls. Differences in metabolic responses between the two isolates were caused both by differences in gene repertoire between them (e.g. in the SEED categories for membrane transport, motility and photoheterotrophy) and the regulation of expression (e.g. fatty acid metabolism), emphasizing the importance of separating the responses of different taxa in analyses of community sequence data. Similarities between the bacteria included substantially increased expression of genes for Ton and Tol transport systems in both isolates, which are commonly associated with uptake of complex organic molecules.Polaribactersp. BAL334 showed stronger metabolic responses to DOM harvested from exponential than stationary phase dinoflagellates (128 compared to 26 differentially expressed genes), whereasBrevundimonassp. BAL450 responded more to the DOM from stationary than exponential phase dinoflagellates (33 compared to 6 differentially expressed genes). These findings suggest that shifts in bacterial metabolisms during different phases of phytoplankton blooms can be detected in individual bacterial species and can provide insights into their involvement in DOM transformations.
Relationship between serum bilirubin levels, urinary biopyrrin levels, and retinopathy in patients with diabetes
Authors: Kudo Kana , Inoue Tomoaki , Sonoda Noriyuki , Ogawa Yoshihiro , Inoguchi Toyoshi 
Published: November 2020

ABSTRACTAims/IntroductionPrevious reports have indicated that serum bilirubin levels may be associated with diabetic retinopathy. However, the detailed mechanism is not fully understood. In this study, we evaluated the relationship between the severity of diabetic retinopathy and various factors including bilirubin levels and factors influencing bilirubin metabolism.MethodsThe study participants consisted of 94 consecutive patients with diabetes mellitus admitted to Kyushu University Hospital from April 2011 to July 2012. The patients were classified into three groups: no retinopathy (NDR), simple retinopathy (SDR), and pre-proliferative or proliferative retinopathy (PDR). The relationship between the severity of retinopathy and various factors was evaluated using univariate and logistic regression analyses. In addition, multivariate regression analysis was performed to evaluate the significant determinants for bilirubin levels.ResultsIn univariate analysis, a significant difference was found among NDR, SDR and PDR in bilirubin levels, duration of diabetes, systolic blood pressure, and macroalbuminuria. Logistic regression analysis showed that PDR was significantly associated with bilirubin levels, duration of diabetes, and systolic blood pressure (OR 0.737, 95% CI 0.570–0.952, P=0.012; OR 1.085, 95% CI 1.024–1.149, P=0.006; OR 1.036, 95% CI 1.011–1.062, P=0.005, respectively). In turn, multivariate regression analysis showed that bilirubin levels were negatively associated with high-sensitivity Creactive protein levels and PDR, but positively correlated with urinary biopyrrin levels, oxidized metabolites of bilirubin.ConclusionsPDR was negatively associated with bilirubin levels. This negative association may be due to a decreased production of bilirubin rather than its increased consumption considering the positive association between bilirubin and biopyrrin levels.
Fine-scale population structure reveals high genetic heterogeneity of the Kuwaiti population in the Arabian Peninsula
Authors: Eaaswarkhanth Muthukrishnan , Pathak Ajai K , Ongaro Linda , Montinaro Francesco , Hebbar Prashantha , Alsmadi Osama , Metspalu Mait , Al-Mulla Fahd , Thanaraj Thangavel Alphonse 
Published: November 2020

AbstractRecent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide polymorphisms data from 583 Kuwaiti individuals sorted into three subgroups. We envisage a diverse demographic genetic history among the three subgroups based on drift and allelic sharing with modern and ancient individuals. Furthermore, our comprehensive haplotype-based analyses disclose a high genetic heterogeneity among the Kuwaiti populations. We infer the major sources of ancestry within the newly defined groups; one with an obvious predominance of sub-Saharan/Western Africa mostly comprising Kuwait-B individuals, and other with West Eurasia including Kuwait-P and Kuwait-S individuals. Overall, our results recapitulate the historical population movements and reaffirm the genetic imprints of the legacy of continental trading in the region. Such deciphering of fine-scale population structure and their regional genetic heterogeneity would provide clues to the uncharted areas of disease-gene discovery and related associations in populations inhabiting the Arabian Peninsula.
Bone marrow stromal cell transplantation ameliorates cytopenia caused by depletion FAP-α expressing cells
Authors: Camarillo-Retamosa Eva , Watson Luke , Loftus Paul , Alagesan Senthil , O’Donoghue Yvonne , Deedigan Laura M. , O’Flynn Lisa , Barkley Laura R. , J.Elliman Stephen 
Published: November 2020

AbstractThe marrow microenvironment is a complex and heterogeneous mixture of hematopoietic and stromal progenitors necessary for haematopoiesis. Whilst the hematopoietic progenitors are well described, the stromal cellular composition is not fully elucidated due to the low cells numbers, localisation-distribution-accessibility, and the lack of specific biomarkers. Cellular taxonomy studies have recently identified new populations of stromal subsets with distinct gene signature and regulatory properties of hematopoietic regeneration. Fibroblast activation protein-α (FAP), a stromal cell type first identified in cancer is also rarely found in normal tissues but might play an essential role in tissue homeostasis. Using FAPDM2transgenic mouse in which FAP-expressing cells can be ablated with Diphtheria Toxin (DTX) FAP+cells were depleted in healthy mice. Whilst FAP+cells constituted 5% of all marrow cells; its ablation caused a rapid loss of PDGFR-α, Leptin-R, gp38 and SDC2 stromal cells populations, endothelial cells and vascular disruption. These resulted in anaemia, thrombocytopenia and neutropenia in peripheral blood (PB) and extreme hypo-cellularity in marrow with abnormalities within the hematopoietic progenitors. In an effort to reverse the phenotypes caused by FAP+cell loss, a single intravenous injection of syngeneic bone marrow-derived stromal cells was administered. In a short-term evaluation, anaemia, thrombocytopenia and neutropenia ameliorated in PB and the numbers of marrow hematopoietic progenitors increased. Our data suggest FAP-expressing cells are a non-redundant component of the marrow microenvironment, necessary for marrow homeostasis and haematopoiesis. These data also provided evidence that stromal cell ablation can be rescued by stromal cell therapy.Significance StatementFAP-expressing cells depletion led to collateral damage in PB and marrow, including haematological defects that can be ameliorated by adoptive transfer of low-dose,ex-vivoexpanded FAP-expressing marrow stromal cells. We suggest that stromal cell loss is a feature of severe immune-mediated inflammatory diseases – such as Graft versus Host Disease and sepsis - and that FAPDM2model represents a novel tool to explore the native function of the recently identified stromal cell sub-populations.
A ferredoxin bridge connects the two arms of plant mitochondrial complex I
Authors: Klusch Niklas , Senkler Jennifer , Yildiz Özkan , Kühlbrandt Werner , Braun Hans-Peter 
Published: November 2020

SUMMARYMitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. It is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I fromArabidopsis thalianaand from the green algaPolytomellasp. at 3.2 and 3.3 Å resolution. In both, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved inA. thalianacomplex I, with different angles between the two arms and different conformations of the ND1 loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We suggest that the bridge domain regulates complex I activity.One sentence summaryThe activity of complex I depends on the angel between its two arms, which, in plants, is adjusted by a protein bridge that includes an unusual ferredoxin.
Improve Concentration of Frequency and Time (Conceft) by Novel Complex Spherical Designs
Authors: Sourisseau Matt , Wang Yu Guang , Womersley Robert S. , Wu Hau-Tieng , Yu Wei-Hsuan 
Published: November 2020

AbstractConcentration of frequency and time (ConceFT) is a generalized multitaper algorithm introduced to analyze complicated non-stationary time series. To avoid the randomness in the original ConceFT algorithm, we apply the novel complex spherical design technique to standardize ConceFT, which we coinCQU-ConceFT.The proposed CQU-ConceFT is applied to visualize the spindle structure in the electroencephalogram signal during the N2 sleep stage and other physiological time series.
An equilibrium constant pH molecular dynamics method for accurate prediction of pH-dependence in protein systems: Theory and application
Authors: Kots Ekaterina , Shore Derek M. , Weinstein Harel 
Published: November 2020

ABSTRACTComputational modeling and simulation of biomolecular systems at their functional pH ranges requires an accurate approach to exploring the pH dependence of conformations and interactions. Here we present a new approach – the Equilibrium Constant pH (ECpH) method – to perform conformational sampling of protein systems in the framework of molecular dynamics simulations in anN, P, T-thermodynamic ensemble. The performance of ECpH is illustrated for two proteins with experimentally determined conformational responses to pH change: the small globular water-soluble bovine b-lactoglobulin (BBL), and the dimer transmembrane antiporter CLC-ec1 Cl−/H+. We show that with computational speeds comparable to equivalent canonical MD simulations we performed, the ECpH trajectories reproduce accurately the pH-dependent conformational changes observed experimentally in these two protein systems, some of which were not seen in the corresponding canonical MD simulations.Abstract FigureTable of Contents artwork
Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET
Authors: Peter Martin F. , Gebhardt Christian , Mächtel Rebecca , Glaenzer Janin , Thomas Gavin H. , Cordes Thorben , Hagelueken Gregor 
Published: November 2020

AbstractPulsed electron-electron double resonance spectroscopy (PELDOR or DEER) and single molecule Förster resonance energy transfer spectroscopy (smFRET) are recent additions to the toolbox of integrative structural biology. Both methods are frequently used to visualize conformational changes and to determine nanometer-scale distances in biomacromolecules including proteins and nucleic acids. A prerequisite for the application of PELDOR/DEER and smFRET is the presence of suitable spin centers or fluorophores in the target molecule, which are usually introduced via chemical biology methods. The application portfolio of the two methods is overlapping: each allows determination of distances, to monitor distance changes and to visualize conformational heterogeneity and -dynamics. Both methods can provide qualitative information that facilitates mechanistic understanding, for instance on conformational changes, as well as quantitative data for structural modelling. Despite their broad application, a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET is still missing and we set out here to fill this gap. For this purpose, we prepared a library of double cysteine mutants of three well-studied substrate binding proteins that undergo large-scale conformational changes upon ligand binding. The distances between the introduced spin- or fluorescence labels were determined via PELDOR/DEER and smFRET, using established standard experimental protocols and data analysis routines. The experiments were conducted in the presence and absence of the natural ligands to investigate how well the ligand-induced conformational changes could be detected by the two methods. Overall, we found good agreement for the determined distances, yet some surprising inconsistencies occurred. In our set of experiments, we identified the source of discrepancies as the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. Our study highlights strength and weaknesses of both methods and paves the way for a higher confidence in quantitative comparison of PELDOR/DEER and smFRET results in the future.
Short linear motif based interactions and dynamics of the ezrin, radixin, moesin and merlin FERM domains
Authors: Ali Muhammad , Khramushin Alisa , Yadav Vikash K , Schueler-Furman Ora , Ivarsson Ylva 
Published: November 2020

AbstractThe ERM (ezrin, radixin and moesin) family of proteins and the related protein merlin participate in signaling events at the cell cortex. The proteins share an N-terminal FERM (band Four-point-one (4.1) ERM) domain comprised of three subdomains (F1, F2, and F3) that hold multiple binding sites for short linear peptide motifs. By screening the FERM domains of the ERMs and merlin against a phage library that display peptides representing the intrinsically disordered regions of the human proteome we identified more than 220 FERM binding peptides. The majority of the peptides contained an apparent Yx[FILV] motif, but ligands with alternative motifs were also found. Interactions with thirteen peptides were validated using a fluorescence polarization assay, and interactions with seven full-length proteins were validated through pull-down experiments. We investigated the energy landscapes of interactions between the moesin FERM domain and representative set of ligands using Rosetta FlexPepDock computational peptide docking protocols, which provide a detailed molecular understanding of the binding of peptides with distinct motifs (YxV and E[Y/F]xDFYDF) to different sites on the F3 subdomain. A third motif (FY[D/E]L(4-5x)PLxxx[L/V]) was proposed to bind more diffusely. By combining competition and modeling experiments, we further uncovered interdependencies between different types of ligands. The study expands the motif-based interactomes of the ERMs and merlin, and suggests that the FERM domain acts as a switchable interaction hub where one class of ligands to the F3 subdomain allosterically regulates binding of other F3 ligands.
The Drosophila Baramicin polypeptide gene protects against fungal infection
Authors: Hanson M.A. , Cohen L.B. , Marra A. , Iatsenko I. , Wasserman S.A. , Lemaitre B. 
Published: November 2020

AbstractThe fruit flyDrososphila melanogastercombats microbial infection by producing a battery of effector peptides that are secreted into the haemolymph. Technical difficulties prevented the investigation of these short effector genes until the recent advent of the CRISPR/CAS era. As a consequence, many putative immune effectors remain to be characterized and exactly how each of these effectors contributes to survival is not well characterized. Here we describe a novelDrosophilaantifungal peptide gene that we nameBaramicin A. We show thatBaraAencodes a precursor protein cleaved into multiple peptides via furin cleavage sites.BaraAis strongly immune-induced in the fat body downstream of the Toll pathway, but also exhibits expression in the nervous system. Importantly, we show that flies lackingBaraAare viable but susceptible to the enomopathogenic fungusBeauveria bassiana. Consistent withBaraAbeing directly antimicrobial, overexpression ofBaraApromotes resistance to fungi and the IM10-like peptides produced byBaraAsynergistically inhibit growth of fungi in vitro when combined with a membrane-disrupting antifungal. Surprisingly,BaraAmales but not females display an erect wing phenotype upon infection. Collectively, we identify a new antifungal immune effector downstream of Toll signalling, improving our knowledge of theDrosophilaantimicrobial response.
Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis
Authors: Pradhan Saurabh J. , Reddy Puli Chandramouli , Smutny Michael , Sharma Ankita , Sako Keisuke , Oak Meghana S. , Shah Rini , Pal Mrinmoy , Deshpande Ojas , Tang Yin , Mishra Rakesh , Deshpande Girish , Giraldez Antonio J. , Sonawane Mahendra , Heisenberg Carl-Philipp , Galande Sanjeev 
Published: November 2020

AbstractZygotic genome activation (ZGA) initiates regionalized transcription responsible for the acquisition of distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, whether the tissue-specific transcription is mechanistically linked with the onset of ZGA is unknown. Here, we have addressed the involvement of chromatin organizer SATB2 in orchestrating these processes during vertebrate embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility revealed contrasting molecular functions of maternal and zygotic pools of Satb2. Maternal Satb2 represses zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented. We discuss the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.