bluuebunny/crossref_metadata_2025_split huggingface dataset:
The RNA binding protein DAZL functions as repressor and activator of maternal mRNA translation during oocyte maturation
Authors: Yang Cai-Rong , Rajkovic Gabriel , Daldello Enrico Maria , Luong Xuan G. , Chen Jing , Conti Marco 
Published: April 2019

AbstractDeleted in azoospermia like (DAZL) is an RNA-binding protein playing critical function during gamete development. In fully-grown oocytes, DAZL protein is detected in prophase and levels increase four to five fold during reentry into the meiotic cell cycle. Here, we have investigated the functional significance of this DAZL accumulation in maturing oocytes. Oocyte depletion of DAZL prevents progression to MII. This maturation block is associated with widespread disruption in the pattern of maternal transcripts loading on ribosomes and their translation measured using a RiboTag IP/RNASeq or qPCR strategy. In addition to decreased ribosome loading of a subset of transcripts, we found that DAZL depletion causes also translational activation of distinct subset of mRNAs. DAZL binds to mRNAs whose translation is both repressed and activated during oocyte maturation. Unexpectedly, DAZL depletion also causes increased ribosome loading of a subset of mRNAs in quiescent GV-arrested oocytes. This dual role of repression and activation is recapitulated by using YFP reporters including the 3’UTR of DAZL targets. Injection of recombinant DAZL protein in DAZL-depleted oocytes rescues the translation of these targets as well as maturation to MII. Mutagenesis of putative DAZL-binding sites in these candidate mRNAs mimics the effect of DAZL depletion. These findings demonstrate that DAZL regulates translation of maternal mRNAs in mature oocytes, functioning both as translational repressor and activator.
Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles
Authors: Cho Yun Sung , Jun JeHoon , Kim Jung A , Kim Hak-Min , Chung Oksung , Kang Seung-Gu , Park Jin-Young , Kim Hwa-Jung , Kim Sunghyun , Kim Hee-Jong , Jang Jin-ho , Na Ki-Jeong , Kim Jeongho , Park Seung Gu , Lee Hwang-Yeol , Manica Andrea , Mindell David P. , Fuchs Jérôme , Edwards Jeremy S. , Weber Jessica A. , Witt Christopher C. , Yeo Joo-Hong , Kim Soonok , Bhak Jong 
Published: April 2019

AbstractBackgroundBirds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day, and owls (Strigiformes) hunting by night.ResultsHere, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops-owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identified common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems (e.g., loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems) that are probably convergent with other nocturnal avian orders. Additionally, we found that a suite of genes associated with vision and circadian rhythm were differentially expressed between nocturnal and diurnal raptors, indicating adaptive expression change during the transition to nocturnality.ConclusionsOverall, raptor genomes showed genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators.
A generalization of partial least squares regression and correspondence analysis for categorical and mixed data: An application with the ADNI data
Authors: Beaton Derek ,   ADNI, Saporta Gilbert , Abdi Hervé 
Published: April 2019

AbstractCurrent large scale studies of brain and behavior typically involve multiple populations, diverse types of data (e.g., genetics, brain structure, behavior, demographics, or “mutli-omics,” and “deep-phenotyping”) measured on various scales of measurement. To analyze these heterogeneous data sets we need simple but flexible methods able to integrate the inherent properties of these complex data sets. Here we introduce partial least squares-correspondence analysis-regression (PLS-CA-R) a method designed to address these constraints. PLS-CA-R generalizes PLS regression to most data types (e.g., continuous, ordinal, categorical, non-negative values). We also show that PLS-CA-R generalizes many “two-table” multivariate techniques and their respective algorithms, such as various PLS approaches, canonical correlation analysis, and redundancy analysis (a.k.a. reduced rank regression).
Tomato spotted wilt virusmanipulates the reproduction of its insect vector, western flower thrips (Frankliniella occidentalis), to facilitate transmission
Authors: Wan Yanran , Hussain Sabir , Xu Baoyun , Xie Wen , Wang Shaoli , Zhang Youjun , Zhou Xuguo , Wu Qingjun 
Published: April 2019

ABSTRACTBACKGROUNDTomato spotted wilt virus(TSWV), one of the most devastating viruses of ornamental plants and vegetable crops worldwide, is transmitted by the western flower thrips,Frankliniella occidentalis(Pergande), in a persistent-propagative manner. How TSWV manipulates the reproduction of its vector to enhance transmission and whether infection with TSWV changes the mating behaviour of this thrips vector are not fully understood.RESULTSIn this study, we found that TSWV-exposed thrips, in general, had a significantly longer developmental time than did non-exposed individuals. Such an increase was predominantly seen in adults, a stage associated with dispersal and virus transmission. TSWV-exposedF. occidentalis produced substantially more progeny than did non-exposed thrips. Interestingly, most of the increase in progeny came from an increase in males, a sex with a greater dispersal and virus transmission capability. Specifically, the sex ratio of progeny shifted from female biased (2-7:1) to evenly split or male biased. Regarding mating behaviour, compared to virus-free controls, TSWV-exposedF. occidentalis had significantly longer copulation duration, were more active in males, and remated less often in females.CONCLUSIONThese combined results suggest that TSWV alters the reproductive behaviour of its insect vector,F. occidentalis, to promote virus transmission. Consequently, a monitoring program capable of earlier detection of the virus and a reduced economic threshold for vector (thrips) control should be in consideration for the long-term, sustainable management of TSWV.
Streptococcus pneumoniae evades host cell phagocytosis and limits host mortality through its cell wall anchoring protein PfbA
Authors: Yamaguchi Masaya , Hirose Yujiro , Takemura Moe , Ono Masayuki , Sumitomo Tomoko , Nakata Masanobu , Terao Yutaka , Kawabata Shigetada 
Published: April 2019

AbstractStreptococcus pneumoniae is a Gram-positive bacterium belonging to the oral streptococcus species, mitis group. This pathogen is a leading cause of community-acquired pneumonia, which often evades host immunity and causes systemic diseases, such as sepsis and meningitis. Previously, we reported that PfbA is a β-helical cell surface protein contributing to pneumococcal adhesion to and invasion of human epithelial cells in addition to its survival in blood. In the present study, we investigated the role of PfbA in pneumococcal pathogenesis. Phylogenetic analysis indicated that the pfbA gene is specific to S. pneumoniae within the mitis group. Our in vitro assays showed that PfbA inhibits neutrophil phagocytosis, leading to pneumococcal survival. We found that PfbA activates NF-κB through TLR2, but not TLR4. In addition, TLR2/4 inhibitor peptide treatment of neutrophils enhanced the survival of the S. pneumoniae ΔpfbA strain as compared to a control peptide treatment, whereas the treatment did not affect survival of a wild-type strain. In a mouse pneumonia model, the host mortality and level of TNF-α in bronchoalveolar lavage fluid were comparable between wild-type and ΔpfbA-infected mice, while deletion of pfbA increased the bacterial burden in bronchoalveolar lavage fluid. In a mouse sepsis model, the ΔpfbA strain demonstrated significantly increased host mortality and TNF-α levels in plasma, but showed reduced bacterial burden in lung and liver. These results indicate that PfbA may contribute to the success of S. pneumoniae species by inhibiting host cell phagocytosis, excess inflammation, and mortality.ImportanceStreptococcus pneumoniae is often isolated from the nasopharynx of healthy children, but the bacterium is also a leading cause of pneumonia, meningitis, and sepsis. In this study, we focused on the role of a cell wall anchoring protein, PfbA, in the pathogenesis of S. pneumoniae-related disease. We found that PfbA is a pneumococcus-specific anti-phagocytic factor that functions as a TLR2 ligand, indicating that PfbA may represent a pneumococcal-specific therapeutic target. However, a mouse pneumonia model revealed that PfbA deficiency reduced the bacterial burden, but did not decrease host mortality. Furthermore, in a mouse sepsis model, PfbA deficiency increased host mortality. These results suggest that S. pneumoniae optimizes reproduction by regulating host mortality through PfbA; therefore, PfbA inhibition would not be an effective strategy for combatting pneumococcal infection. Our findings underscore the challenges involved in drug development for a bacterium harboring both commensal and pathogenic states.
Hybridization preceded radiation in diploid wheats
Authors: Huynh Stella , Marcussen Thomas , Felber François , Parisod Christian 
Published: April 2019

SummaryEvolutionary relationships among theAegilops-Triticumrelatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor ofAe. tauschii) originated through homoploid hybridization between the A-genome lineage (progenitor ofTriticums.str.) and the B-genome lineage (progenitor ofAe. speltoides). Scenarios of reticulation have been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution ofAegilops-Triticumdiploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyleticAegilops-Triticumlineage that began diversifying ~6.5 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 species) and T- (Ae. mutica) genome lineage. Full-parameterized phylogenies as well as patterns of tree dilation and tree compression supported a hybrid origin of the D-genome lineage from A and B ~4.1 Ma ago, and did not indicate additional hybridization events. This comprehensive and dated phylogeny of wheat relatives indicates that the origin of the hybrid D-genome was followed by intense diversification into almost all diploid as well as allopolyploid wild wheats.
Investigating Population-scale Allele Specific Expression in Wild Populations of Oithona similis (Cyclopoida, Claus 1866)
Authors: Laso-Jadart Romuald , Sugier Kevin , Petit Emmanuelle , Labadie Karine , Peterlongo Pierre , Ambroise Christophe , Wincker Patrick , Jamet Jean-Louis , Madoui Mohammed-Amin 
Published: April 2019

AbstractAllele-specific expression (ASE) is a widely studied molecular mechanism at cell, tissue and organism levels. Here, we extrapolated the concept of ASE to the population-scale (psASE), aggregating ASEs detected at smaller scales. We developed a novel approach to detect psASE based on metagenomic and metatranscriptomic data of environmental samples containing communities of organisms. This approach which measures the deviation between the frequency and the relative expression of biallelic loci, was applied on samples collected during the Tara Oceans expedition (2009-2013), in combination to new Oithona similis transcriptomes, a widespread marine copepod. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 587 (2.3%) were targeted by psASE in at least one population. The distribution of SNVs targeted by psASE in different populations is significantly shaped by population genomic differentiation (p-value = 9.3×10−9), supporting a partial genetic control of psASE. To investigate the link between evolution and psASE, loci under selection were compared to loci under psASE. A significant amount of SNVs (0.6%) were targeted by both selection and psASE (p-values < 9.89×10−3), supporting the hypothesis that natural selection and ASE may lead to the same phenotype. Population-scale ASE offers new insights into the gene regulation control in populations and its link with natural selection.
Computing wide range of protein/peptide features from their sequence and structure
Authors: Pande Akshara , Patiyal Sumeet , Lathwal Anjali , Arora Chakit , Kaur Dilraj , Dhall Anjali , Mishra Gaurav , Kaur Harpreet , Sharma Neelam , Jain Shipra , Usmani Salman Sadullah , Agrawal Piyush , Kumar Rajesh , Kumar Vinod , Raghava Gajendra P.S. 
Published: April 2019

AbstractMotivationIn last three decades, a wide range of protein descriptors/features have been discovered to annotate a protein with high precision. A wide range of features have been integrated in numerous software packages (e.g., PROFEAT, PyBioMed, iFeature, protr, Rcpi, propy) to predict function of a protein. These features are not suitable to predict function of a protein at residue level such as prediction of ligand binding residues, DNA interacting residues, post translational modification etc.ResultsIn order to facilitate scientific community, we have developed a software package that computes more than 50,000 features, important for predicting function of a protein and its residues. It has five major modules for computing; composition-based features, binary profiles, evolutionary information, structure-based features and patterns. The composition-based module allows user to compute; i) simple compositions like amino acid, dipeptide, tripeptide; ii) Properties based compositions; iii) Repeats and distribution of amino acids; iv) Shannon entropy to measure the low complexity regions; iv) Miscellaneous compositions like pseudo amino acid, autocorrelation, conjoint triad, quasi-sequence order. Binary profile of amino acid sequences provides complete information including order of residues or type of residues; specifically, suitable to predict function of a protein at residue level. Pfeature allows one to compute evolutionary information-based features in form of PSSM profile generated using PSIBLAST. Structure based module allows computing structure-based features, specifically suitable to annotate chemically modified peptides/proteins. Pfeature also allows generating overlapping patterns and feature from whole protein or its parts (e.g., N-terminal, C-terminal). In summary, Pfeature comprises of almost all features used till now, for predicting function of a protein/peptide including its residues.AvailabilityIt is available in form of a web server, named as Pfeature (https://webs.iiitd.edu.in/raghava/pfeature/), as well as python library and standalone package (https://github.com/raghavagps/Pfeature) suitable for Windows, Ubuntu, Fedora, MacOS and Centos based operating system.
Unique Neurophysiological Vulnerability of Visual Attention Networks to Acute Inflammation
Authors: Balter Leonie JT , Bosch Jos A , Aldred Sarah , Drayson Mark T , van Zanten Jet JCS Veldhuijzen , Higgs Suzanne , Raymond Jane E , Mazaheri Ali 
Published: April 2019

ABSTRACTIllness is often accompanied by perceived cognitive sluggishness, a symptom that may stem from immune system activation. The current study used electroencephalography (EEG) to assess how inflammation affected three different distinct attentional processes: alerting, orienting and executive control. In a double-blinded placebo-controlled within-subjects design (20 healthy males, mean age = 24.5, SD = 3.4), Salmonella typhoid vaccination (0.025 mg; Typhim Vi, SanofiPasteur) was used to induce transient mild inflammation, while a saline injection served as a placebo-control. Participants completed the Attention Network Test with concurrent EEG recorded six hours post-injection. Analyses focused on behavioral task performance and on modulation of oscillatory EEG activity in the alpha band (9-12 Hz) for alerting as well as orienting attention and frontal theta band (4-8 Hz) for executive control. Vaccination induced mild systemic inflammation, as assessed by interleukin-6 (IL-6) levels. While no behavioral task performance differences between the inflammation and placebo condition were evident, inflammation caused significant alterations to task-related brain activity. Specifically, inflammation produced greater cue-induced suppression of alpha power in the alerting aspect of attention while individual variation in the inflammatory response was significantly correlated with the degree of alpha power suppression. Notably, inflammation did not affect orienting (i.e., alpha lateralization) or executive control (i.e., frontal theta activity). These results reveal a unique neurophysiological vulnerability to acute mild inflammation of the neural network that underpins attentional alerting functions. Observed in the absence of performance decrements, these novel findings suggest that acute inflammation requires individuals to exert greater cognitive effort when preparing for a task in order to maintain adequate behavioral performance.HighlightsTyphoid vaccination induced a transient mild inflammatory stateMild inflammation alters neurophysiological process associated with attentionMild inflammation selectively increased alerting-related alpha suppression while behavior was unaffectedA greater inflammatory response was correlated with more alpha suppression
Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Authors: Zhang Rui , Varela Monica , Forn-Cuni Gabriel , Torraca Vincenzo , van der Vaart Michiel , Meijer Annemarie H. 
Published: April 2019

AbstractDNA Damage Regulated Autophagy Modulator 1 (DRAM1) is a stress-inducible regulator of autophagy and cell death. DRAM1 has been implicated in cancer, myocardial infarction, and infectious diseases, but the molecular and cellular functions of this transmembrane protein remain poorly understood. Previously, we have proposed DRAM1 as a host resistance factor for tuberculosis (TB) and a potential target for host-directed anti-infective therapies. In this study, we generated a zebrafish dram1 mutant and investigated its loss-of-function effects during Mycobacterium marinum (Mm) infection, a widely used model in TB research. In agreement with previous knockdown analysis, dram1 mutation increased the susceptibility of zebrafish larvae to Mm infection. RNA sequencing revealed major effects of Dram1 deficiency on metabolic, immune response, and cell death pathways during Mm infection, whereas only minor effects on proteinase and metabolic pathways were found under uninfected conditions. Furthermore, unchallenged dram1 mutants did not display overt autophagic defects, but autophagic targeting of Mm was reduced in absence of Dram1. The phagocytic ability of macrophages in dram1 mutants was unaffected, but acidification of Mm-containing vesicles was strongly reduced, indicating that Dram1 is required for phagosome maturation. By in vivo imaging we observed that Dram1-deficient macrophages fail to restrict Mm during early stages of infection. The resulting increase in bacterial burden could be reverted by knockdown of inflammatory caspase a (caspa) and gasdermin Eb (gsdmeb), demonstrating pyroptosis as the mechanism underlying premature cell death of Mm-infected macrophages in dram1 mutants. Collectively, these data demonstrate that dissemination of mycobacterial infection in zebrafish larvae is promoted in absence of Dram1 due to reduced maturation of mycobacteria-containing vesicles, failed intracellular containment, and consequent pyroptotic cell death of infected macrophages. These results provide new evidence that Dram1 plays a central role in host resistance to intracellular infection, acting at the crossroad of autophagy and cell death.
Sequence Analysis and Homology Modelling of SmHQT Protein, a Key Player in Chlorogenic Acid Pathway of Eggplant
Authors: Kaushik Prashant , Saini Dinesh Kumar 
Published: April 2019

AbstractEggplant is an important vegetable that belongs to family Solanaceae. Fruits of eggplant are rich in phenolic acids. Chlorogenic acid makes up to 90 per cent of total phenolic acids present in the eggplants fruit flesh. Eggplant hydroxycinnamoyl CoA-quinate (SmHQT) is the central enzyme that modulates the last step of the chlorogenic acid pathway of eggplant. Here, we have analysed the sequence of eggplant SmHQT protein in eggplant. The sequence obtained from the NCBI was aligned using MUSCLE. After that, homology modelling was performed using MODELLER 9v15. Model with Dope Z-Score of −1.596 was selected and verified for viability under real conditions using several online tools. Also, the docking was performed with this model. Overall, this could be useful in developing eggplant varieties rich in phenolic acids especially chlorogenic acid.
Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain
Authors: DeKraker J. , Lau J.C. , Ferko K.M. , Khan A.R. , Köhler S. 
Published: April 2019

AbstractThe internal structure of the human hippocampus is challenging to map using histology or neuroimaging due to its complex archicortical folding. Here, we aimed to overcome this challenge using a unique combination of three methods. First, we leveraged a histological dataset with unprecedented 3D coverage, 3D BigBrain. Second, we imposed a computational unfolding framework that respects the topological continuity of hippocampal subfields, which are traditionally defined by laminar composition. Third, we adapted neocortical parcellation techniques to map the hippocampus with respect to not only laminar but also morphological features. Unsupervised clustering of these features revealed subdivisions that closely resemble ground-truth manual subfield segmentations. Critically, we also show that morphological features alone are sufficient to derive most hippocampal subfield boundaries. Moreover, some features showed differences within subfields along the hippocampal longitudinal axis. Our findings highlight new characteristics of internal hippocampal structure, and offer new avenues for its characterization with in-vivo neuroimaging.