bluuebunny/crossref_metadata_2025_split huggingface dataset:
What maintains signal honesty in animal colour displays used in mate choice?
Authors: Weaver Ryan J. , Koch Rebecca E. , Hill Geoffrey E. 
Published: May 2017

Many of the colour displays of animals are proposed to have evolved in response to female mate choice for honest signals of quality, but such honest signalling requires mechanisms to prevent cheating. The most widely accepted and cited mechanisms for ensuring signal honesty are based on the costly signalling hypothesis, which posits that costs associated with ornamentation prevent low-quality males from being highly ornamented. Alternatively, by the index hypothesis, honesty can be achieved via cost-free mechanisms if ornament production is causally linked to core physiological pathways. In this essay, we review how a costly signalling framework has shaped empirical research in mate choice for colourful male ornaments and emphasize that alternative interpretations are plausible under an index signalling framework. We discuss the challenges in both empirically testing and distinguishing between the two hypotheses, noting that they need not be mutually exclusive. Finally, we advocate for a comprehensive approach to studies of colour signals that includes the explicit consideration of cost-free mechanisms for honesty.This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.
Life stage associated remodeling of lipid metabolism regulation in the duplicated Atlantic salmon genome
Authors: Gillard Gareth , Harvey Thomas N. , Gjuvsland Arne , Jin Yang , Thomassen Magny , Lien Sigbjørn , Leaver Michael , Torgersen Jacob S. , Hvidsten Torgeir R. , Vik Jon Olav , Sandve Simen R. 
Published: May 2017

AbstractAtlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. These habitat shifts require great phenotypic plasticity. To address the unresolved question of how the shift in diet between fresh and saltwater affects the regulation of metabolic function, we fed salmon contrasting diets in each of the two life stages. Combining transcriptomics with comparative genomics, we found that lipid metabolism undergoes a concerted shift between fresh- and saltwater stages. Lipogenesis and lipid transport become less active in liver after transition to saltwater, while genes for lipid uptake in gut are more expressed in lipid-rich seawater environments. We assess how the whole-genome duplication that gave rise to the salmonids has impacted the evolution of lipid metabolism, and find signatures of pathway-specific selection pressure on gene duplicates, as well as a limited number of cases of increased gene dosage.
Exact Topological Inference for Paired Brain NetworksviaPersistent Homology
Authors: Chung Moo K. , Villalta-Gil Victoria , Lee Hyekyoung , Rathouz Paul J. , Lahey Benjamin B. , Zald David H. 
Published: May 2017

AbstractWe present a novel framework for characterizing paired brain networks using techniques in hyper-networks, sparse learning and persistent homology. The framework is general enough for dealing with any type of paired images such as twins, multimodal and longitudinal images. The exact nonparametric statistical inference procedure is derived on testing monotonic graph theory features that do not rely on time consuming permutation tests. The proposed method computes the exact probability in quadratic time while the permutation tests require exponential time. As illustrations, we apply the method to simulated networks and a twin fMRI study. In case of the latter, we determine the statistical significance of the heritability index of the large-scale reward network where every voxel is a network node.
Cebranopadol blocks the escalation of cocaine intake and conditioned reinstatement of cocaine seeking in rats
Authors: de Guglielmo Giordano , Matzeu Alessandra , Kononoff Jenni , Mattioni Julia , Martin-Fardon Rémi , George Olivier 
Published: May 2017

AbstractCebranopadol is a novel agonist of nociceptin/orphanin FQ peptide (NOP) and opioid receptors with analgesic properties that is being evaluated in clinical Phase 2 and Phase 3 trials for the treatment of chronic and acute pain. Recent evidence indicates that the combination of opioid and NOP receptor agonism may be a new treatment strategy for cocaine addiction. We sought to extend these findings by examining the effects of cebranopadol on cocaine self-administration (0.5 mg/kg/infusion) and cocaine conditioned reinstatement in rats with extended access to cocaine. Oral administration of cebranopadol (0, 25, and 50 μg/kg) reversed the escalation of cocaine self-administration in rats that were given extended (6 h) access to cocaine, whereas it did not affect the self-administration of sweetened condensed milk (SCM). Cebranopadol induced conditioned place preference but did not affect locomotor activity during the conditioning sessions. Finally, cebranopadol blocked the conditioned reinstatement of cocaine seeking. These results show that oral cebranopadol treatment prevented addiction-like behaviors (i.e., the escalation of intake and reinstatement), suggesting that it may be a novel strategy for the treatment of cocaine use disorder. However, the conditioned place preference that was observed after cebranopadol administration suggests that this compound may have some intrinsic rewarding effects.
Recapitulating early development of mouse musculoskeletal precursors of the paraxial mesodermin vitro
Authors: Chal Jérome , Al Tanoury Ziad , Oginuma Masayuki , Moncuquet Philippe , Gobert Bénédicte , Miyanari Ayako , Tassy Olivier , Guevara Getzabel , Bera Agata , Sumara Olga , Garnier Jean-Marie , Kennedy Leif , Knockaert Marie , Gayraud-Morel Barbara , Tajbakhsh Shahragim , Pourquié Olivier 
Published: May 2017

AbstractIn vertebrates, body skeletal muscles and axial skeleton derive from the paraxial mesoderm which flanks the neural tube and notochord. The paraxial mesoderm forms in the posterior region of the embryo as presomitic mesoderm (PSM), which generates the embryonic segments called somites. Here, we characterized gene signatures identified using microarray series from the mouse PSM and compared the PSM transcriptome dynamics to that of the developing neural tube. In contrast to the PSM where an abrupt transcriptome reorganisation occurs at the level of the determination front, we show that transcriptome changes are progressive during parallel stages of neural tube differentiation. We show that these early differentiation stages of the paraxial mesoderm can be efficiently recapitulated in monolayer culturein vitrousing murine Embryonic Stem (ES) cells. We describe a serum-containing protocol which parallelsin vivotissue maturation allowing differentiation of ES cells towards a paraxial mesoderm fate. We show that R-spondin treatment or Wnt activation alone can induce posterior PSM markers in both mouse and human ES/iPS cells but acquisition of a committed posterior PSM fate requires BMP inhibition to prevent induced cells to drift to a lateral plate mesoderm identity. We show that posterior PSM-like cells induced from mouse ES cells can be further differentiatedin vitroto acquire an anterior PSMPax3-positive identity. When grafted into injured adult muscle, these induced PSM-like precursors generated large numbers of immature muscle fibers. We further show that exposing ES-derived PSM-like cells to a brief FGF inhibition step followed by culture in horse serum-containing medium allows efficient recapitulation of the myogenic program. Differentiating ES cells first produce mononucleated embryonic myocytes and subsequently multinucleated myotubes, as well as Pax7-positive cells. The protocol described here results in improved differentiation and maturation of mouse muscle fibers differentiatedin vitroover serum-free protocols. It provides an efficient system for the study of myogenic processes otherwise difficult to studyin vivosuch as fusion or satellite cell differentiation.
Differential associations of various depression-related phenotypes with cardiometabolic risks: Identification of shared genetic factors and implications for drug repositioning
Authors: Wong Brian Chi-Fung , Chau Carlos Kwan-Long , Ao Fu-Kiu , Mo Cheuk-Hei , Wong Sze-Yung , Wong Yui-Hang , So Hon-Cheong 
Published: May 2017

AbstractNumerous studies have suggested associations between depression and cardiometabolic abnormalities or diseases, such as coronary artery disease and type 2 diabetes. However, little is known about the mechanism underlying this comorbidity, and whether the relationship differs by depression subtypes. Using the polygenic risk score (PRS) approach and linkage disequilibrium (LD) score regression, we investigated the genetic overlap of various depression-related phenotypes with a comprehensive panel of 20 cardiometabolic traits. GWAS results for major depressive disorder (MDD) were taken from the PGC and CONVERGE studies, with the latter focusing on severe melancholic depression. GWAS results on general depressive symptoms (DS) and neuroticism were also included. We also identified the shared genetic variants and inferred enriched pathways. In addition, we looked for drugs over-represented among the top shared genes, with an aim to finding repositioning opportunities for comorbidities.We found significant polygenic sharing between MDD, DS and neuroticism with various cardiometabolic traits. In general, positive polygenic associations with CV risks were observed for most depression phenotypes except MDD-CONVERGE. Counterintuitively, PRS representing severe melancholic depression was associated with reduced CV risks. Enrichment analyses of shared SNPs revealed many interesting pathways, such as those related to inflammation, that underlie the comorbidity of depressive and cardiometabolic traits. Using a gene-set analysis approach, we also revealed a number of repositioning candidates, some of which were supported by prior studies, such as bupropion and glutathione. Our study highlights shared genetic bases of depression with cardiometabolic traits, and suggests the associations vary by depression subtypes. To our knowledge, this is the also first study to make use of human genomic data to guide drug discovery or repositioning for comorbid disorders.
The genetic intractability ofSymbiodinium microadriaticumto standard algal transformation methods
Authors: Chen Jit Ern , Barbrook Adrian C. , Cui Guoxin , Howe Christopher J. , Aranda Manuel 
Published: May 2017

AbstractModern transformation and genome editing techniques have shown great success across a broad variety of organisms. However, no study of successfully applied genome editing has been reported in a dinoflagellate despite the first genetic transformation ofSymbiodiniumbeing published about 20 years ago. Using an array of different available transformation techniques, we attempted to transformSymbiodinium microadriaticum(CCMP2467), a dinoflagellate symbiont of reef-building corals, with the view to performing subsequent CRISPR-Cas9 mediated genome editing. Plasmid vectors designed for nuclear transformation containing the chloramphenicol resistance gene under the control of the CaMV p35S promoter as well as several putative endogenous promoters were used to test a variety of transformation techniques including biolistics, electroporation and silicon carbide whiskers. Chloroplast-targeted transformation were attempted using an engineeredSymbiodiniumchloroplast minicircle encoding a modified PsbA protein that confers atrazine resistance. We report that we have been unable to confer chloramphenicol or atrazine resistance toSymbiodinium microadriaticumstrain CCMP2467.
Insuperable problems of the genetic code initially emerging in an RNA World
Authors: Wills Peter R , Carter Charles W 
Published: May 2017

AbstractDifferential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide•RNA world.
A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination
Authors: Collins Caitlin , Didelot Xavier 
Published: May 2017

AbstractGenome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications toNeisseria meningitidisillustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available athttps://github.com/caitiecollins/treeWAS.
Cloning, molecular evolution and functional characterization of ZmbHLHl6, the maize ortholog of OsTIP2 (OsbHLH142)
Authors: Liu Yongming , Li Jia , Wei Gui , Sun Yonghao , Lu Yanli , Lan Hai , Li Chuan , Zhang Suzhi , Cao Moju 
Published: May 2017

AbstractAbstract Basic helix-loop-helix (bHLH) transcription factors play key roles in plant male reproduction. More than 14 bHLH proteins related to pollen development have been cloned from rice andArabidopsis. However, little is known about the role of the bHLH family in maize microspore development. In this study, the bHLH transcription factor ZmbHLH16 was cloned. ZmbHLH16 shares high similarity with the OsTIP2 (OsbHLH142) protein, a master regulator of the developmental coordination of male reproduction in rice. Expression characterization analysis showed that ZmbHLH16 is preferentially expressed in male reproductive organs and is located in the nucleus. Through nucleotide variation analysis, 36 polymorphic sites in ZmbHLH16, including 23 SNPs and 13 InDels, were detected among 78 maize inbred lines. Neutrality tests and linkage disequilibrium analysis showed that ZmbHLH16 experienced no significant evolutionary pressure. A yeast one-hybrid experiment showed that the first 80 residues in the N-terminus of ZmbHLH16 had transactivation activity, whereas the full length did not. To identify potential ZmbHLH16 interactors, 395 genes that shared similar expression patterns in a genome-wide search were obtained through coexpression analysis. Among these genes, the transcription factor ZmbHLH51 had an expression pattern and subcellular localization similar to those of ZmbHLH16. The interaction between ZmbHLH51 and ZmbHLH16 was verified in yeast cells. In addition to the typical bHLH domain, other regions of ZmbHLH16 were necessary and adequate for its heterodimerization with ZmbHLH51. Our results contribute to a solid foundation for further understanding the functions and mechanisms of ZmbHLH16.
An RNA Virome associated to the Golden Orb-weaver SpiderNephila clavipes
Authors: Debat Humberto J. 
Published: May 2017

AbstractThe golden orb-weaver spiderNephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploringN. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource forN. clavipesRNA survey. Here, I present evidence of viral sequences corresponding to the first 10 extant virus species associated toN. clavipesand indeed, nephilids. The putatively new species are linked to ssRNA positive-strand viruses, such asPicornavirales, and to ssRNA negative-strand and dsRNA viruses. In addition, I detected sequence data of new strains of two recently reported arthropod viruses, which complemented and extended the corresponding sequence references. The identified viruses appear to be complete, potentially functional, and presenting the typical architecture and consistent viral domains. The intrinsic nature of the detected sequences and their absence in the recently generated genome assembly, suggest that they correspond tobona fideRNA virus sequences. The available RNA data allowed for the first time to address a tissue/organ specific analysis of virus loads/presence in spiders, suggesting a complex spatial and differential distribution of the tentative viruses, encompassing the spider brain and also silk and venom glands. Until recently, the virus landscape associated to spiders remained elusive. The discovered viruses described here provide only a fragmented glimpse of the potential magnitude of theAraneavirosphere. Future studies should focus not only on complementing and expanding these findings, but also on addressing the potential ecological role of these viruses, which might influence the biology of these outstanding arthropod species.Funding statementThe author received no specific funding for this study.Ethics statements(Authors are required to state the ethical considerations of their study in the manuscript, including for cases where the study was exempt from ethical approval procedures)
Selective inhibitory control of pyramidal neuron ensembles and cortical subnetworks by chandelier cells
Authors: Lu Jiangteng , Tucciarone Jason , Padilla-Coreano Nancy , He Miao , Gordon Joshua A. , Huang Z. Josh 
Published: May 2017

ABSTRACTThe neocortex comprises multiple information processing streams mediated by subsets of glutamatergic pyramidal cells (PCs) that receive diverse inputs and project to distinct targets. How GABAergic interneurons regulate the segregation and communication among intermingled PC subsets that contribute to separate brain networks remains unclear. Here we demonstrate that a subset of GABAergic chandelier cells (ChCs) in the prelimbic cortex (PL), which innervate PCs at spike initiation site, selectively control PCs projecting to the basolateral amygdala (BLAPC) compared to those projecting to contralateral cortex (ccPC). These ChCs in turn receive preferential input from local and contralateralCCPCs as opposed toBLAPCs and BLA neurons (the PL-BLA network). Accordingly, optogenetic activation of ChCs rapidly suppressesBLAPCs and BLA activity in freely behaving mice. Thus, the exquisite connectivity of ChCs not only mediates directional inhibition between local PC ensembles but may also shape communication hierarchies between global networks.
Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low cost microfluidic instrumentation
Authors: Stephenson William , Donlin Laura T. , Butler Andrew , Rozo Cristina , Rashidfarrokhi Ali , Goodman Susan M. , Ivashkiv Lionel B. , Bykerk Vivian P. , Orange DE , Darnell Robert B. , Swerdlow Harold P. , Satija Rahul 
Published: May 2017

AbstractDroplet-based single cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While these approaches offer the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective, reliable, and user-friendly instrumentation has hindered widespread adoption of droplet microfluidic techniques. To address this, we have developed a microfluidic control instrument that can be easily assembled from 3D printed parts and commercially available components costing approximately $540. We adapted this instrument for massively parallel scRNA-seq and deployed it in a clinical environment to perform single cell transcriptome profiling of disaggregated synovial tissue from a rheumatoid arthritis patient. We sequenced 8,716 single cells from a synovectomy, revealing 16 transcriptomically distinct clusters. These encompass a comprehensive and unbiased characterization of the autoimmune infiltrate, including inflammatory T and NK subsets that contribute to disease biology. Additionally, we identified fibroblast subpopulations that are demarcated viaTHY1(CD90) andCD55expression. Further experiments confirm that these represent synovial fibroblasts residing within the synovial intimal lining and subintimal lining, respectively, each under the influence of differing microenvironments. We envision that this instrument will have broad utility in basic and clinical settings, enabling low-cost and routine application of microfluidic techniques, and in particular single-cell transcriptome profiling.
FiberNET: An ensemble deep learning framework for clustering white matter fibers
Authors: Gupta Vikash , Thomopoulos Sophia I. , Rashid Faisal M. , Thompson Paul M. 
Published: May 2017

AbstractWhite matter tracts are commonly analyzed in studies of micro-structural integrity and anatomical connectivity in the brain. Over the last decade, it has been an open problem as to how best to cluster white matter fibers, extracted from whole-brain tractography, into anatomically meaningful groups. Some existing techniques use region of interest (ROI) based clustering, atlas-based labeling, or unsupervised spectral clustering. ROI-based clustering is popular for analyzing anatomical connectivity among a set of ROIs, but it does not always partition the brain into recognizable fiber bundles. Here we propose an approach using convolutional neural networks (CNNs) to learn shape features of the fiber bundles, which are then exploited to cluster white matter fibers. To achieve such clustering, we first need to re-parameterize the fibers in an intrinsic space. The clustering is performed in induced parameterized coordinates. To our knowledge, this is one of the first approaches for fiber clustering using deep learning techniques. The results show strong accuracy - on a par with or better than other state-of-the-art methods.