95 research outputs found

    Phylogenetic relationships and ecological speciation in the mistletoe Tristerix (Loranthaceae): the influence of pollinators, dispersers, and hosts

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    Phylogenies can provide valuable information on biotic and abiotic factors associated with speciation. We examined species relationships in Tristerix (Loranthaceae), a genus of 11 species with an Andean distribution from Colombia to Chile. A previous classification divided Tristerix into subgenera Tristerix (two species) and Metastachys (nine species). We tested this classification by generating a molecular phylogeny of the genus using nuclear ribosomal DNA ITS and chloroplast atpB-rbcL intergenic spacer and trnL-F regions. All partitions generally gave congruent trees, thus a combined analysis was conducted. Tristerix was composed of a northern clade (six species) and a southern clade (four species). Tristerix verticillatus and T. penduliflorus (Metastachys) were strongly supported as members of the (southern) subgenus Tristerix clade. Speciation appears to be correlated with the emergence of matorral and cloud forest biomes and is driven by interactions with pollinators and seed dispersers. Tristerix aphyllus is sister to T. corymbosus of the matorral, not to neighboring temperate forest populations, thus rendering the latter species paraphyletic. This ecological speciation event may have occurred in sympatry. Tristerix provides excellent examples of how, during the orography of the Andes, many dynamic and interacting ecological factors have influenced their speciation

    Off equilibrium fluctuations in a polymer glass

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    The fluctuation-dissipation relation (FDR) is measured on the dielectric properties a polymer glass (polycarbonate). It is observed that the fluctuation dissipation theorem is strongly violated for a quench from above to below the glass transition temperature. The amplitude and the persistence time of this violation are decreasing functions of frequency. Around 1Hz1Hz it may persist for several hours. The origin of this violation is a highly intermittent dynamics characterized by large fluctuations a strongly non-Gaussian statistics. The intermittent dynamics depends on the quenching rate and it disappears after slow quenches. The relevance of these results for recent models of aging are discussed.Comment: submitted to Physica

    Melanopsin System Dysfunction in Smith-Magenis Syndrome Patients

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    PURPOSE: Smith-Magenis syndrome (SMS) causes sleep disturbance that is related to an abnormal melatonin profile. It is not clear how the genomic disorder leads to a disturbed synchronization of the sleep/wake rhythm in SMS patients. To evaluate the integrity of the intrinsically photosensitive retinal ganglion cell (ipRGC)/melanopsin system, the transducers of the light-inhibitory effect on pineal melatonin synthesis, we recorded pupillary light responses (PLR) in SMS patients. METHODS: Subjects were SMS patients (n = 5), with molecular diagnosis and melatonin levels measured for 24 hours and healthy controls (n = 4). Visual stimuli were 1-second red light flashes (640 nminsignificant direct ipRGC activation), followed by a 470-nm blue light, near the melanopsin peak absorption region (direct ipRGC activation). Blue flashes produce a sustained pupillary constriction (ipRGC driven) followed by baseline return, while red flashes produce faster recovery. RESULTS: Pupillary light responses to 640-nm red flash were normal in SMS patients. In response to 470-nm blue flash, SMS patients had altered sustained responses shown by faster recovery to baseline. SMS patients showed impairment in the expected melatonin production suppression during the day, confirming previous reports. CONCLUSIONS: SMS patients show dysfunction in the sustained component of the PLR to blue light. It could explain their well-known abnormal melatonin profile and elevated circulating melatonin levels during the day. Synchronization of daily melatonin profile and its photoinhibition are dependent on the activation of melanopsin. This retinal dysfunction might be related to a deficit in melanopsin-based photoreception, but a deficit in rod function is also possible.Sao Paulo Research Foundation (FAPESP) [2014/26818-2, 2014/50457-0, 2016/04538-3, 2014/06457-5, 2015/22227-2, 2016/22007-5]National Council for Scientific and Technological Development (CNPq) [480428/2013-4, 470785/2014-4, 404239/2016-1]CAPES [3263/2013]Janos Bolyai Scholarship of the Hungarian Academy of SciencesUniv Sao Paulo, Dept Expt Psychol, Inst Psychol, Sao Paulo, BrazilSemmelweis Univ, Dept Ophthalmol, Budapest, HungaryUniv Sao Paulo, Dept Neurol, Fac Med, Sao Paulo, BrazilBudapest Univ Technol & Econ, Dept Mechatron Opt & Engn Informat, Budapest, HungaryUniv Texas San Antonio, Dept Cellular & Struct Biol, San Antonio, TX USAUniv Fed Sao Paulo, Dept Physiol, Sao Paulo, BrazilUniv Sao Paulo, Dept Physiol & Biophys, Inst Biomed Sci, Av Lineu Prestes 1524, BR-05508000 Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Dept Physiol, Sao Paulo, BrazilFAPESP [2014/26818-2, 2014/50457-0, 2016/04538-3, 2014/06457-5, 2015/22227-2, 2016/22007-5]CNPq [480428/2013-4, 470785/2014-4, 404239/2016-1]CAPES [3263/2013]Web of Scienc

    Thermal noise properties of two aging materials

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    In this lecture we review several aspects of the thermal noise properties in two aging materials: a polymer and a colloidal glass. The measurements have been performed after a quench for the polymer and during the transition from a fluid-like to a solid-like state for the gel. Two kind of noise has been measured: the electrical noise and the mechanical noise. For both materials we have observed that the electric noise is characterized by a strong intermittency, which induces a large violation of the Fluctuation Dissipation Theorem (FDT) during the aging time, and may persist for several hours at low frequency. The statistics of these intermittent signals and their dependance on the quench speed for the polymer or on sample concentration for the gel are studied. The results are in a qualitative agreement with recent models of aging, that predict an intermittent dynamics. For the mechanical noise the results are unclear. In the polymer the mechanical thermal noise is still intermittent whereas for the gel the violation of FDT, if it exists, is extremely small.Comment: to be published in the Proceedings of the XIX Sitges Conference on ''Jammming, Yielding and Irreversible Deformation in Condensed Matter'', M.-C.Miguel and M. Rubi eds.,Springer Verlag, Berli

    Slow dynamics and aging in a non-randomly frustrated spin system

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    A simple, non-disordered spin model has been studied in an effort to understand the origin of the precipitous slowing down of dynamics observed in supercooled liquids approaching the glass transition. A combination of Monte Carlo simulations and exact calculations indicates that this model exhibits an entropy vanishing transition accompanied by a rapid divergence of time scales. Measurements of various correlation functions show that the system displays a hierarchy of time scales associated with different degrees of freedom. Extended structures, arising from the frustration in the system, are identified as the source of the slow dynamics. In the simulations, the system falls out of equilibrium at a temperature TgT_{g} higher than the entropy-vanishing transition temperature and the dynamics below TgT_{g} exhibits aging as distinct from coarsening. The cooling rate dependence of the energy is also consistent with the usual glass formation scenario.Comment: 41 pages, 16 figures. Bibliography file is correcte

    Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

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    Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

    Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

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    Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

    Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

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    This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

    Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

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    Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment
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