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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Villaverde, Tamara; Global Carex Group;

    Carex (Cyperaceae), with an estimated 2000 species, nearly cosmopolitan distribution and broad range of habitats, is one of the largest angiosperm genera and the largest in the temperate zone. In this article, we provide argument and evidence for a broader circumscription of Carex to add all species currently classified in Cymophyllus (monotypic), Kobresia (c. 60 species), Schoenoxiphium (c. 15 species) and Uncinia (c. 70 species) to those currently classified as Carex. Carex and these genera comprise tribe Cariceae (subfamily Cyperoideae, Cyperaceae) and form a wellsupported monophyletic group in all molecular phylogenetic studies to date. Carex as defined here in the broad sense currently comprises at least four clades. Three are strongly supported (Siderostictae, core Vignea and core Carex), whereas the caricoid clade, which includes all the segregate genera, receives only weak to moderate support. The caricoid clade is most commonly split into two clades, one including a monophyletic Schoenoxiphium and two small clades of species of Carex s.s., and the other comprising Kobresia, Uncinia and mostly unispicate species of Carex s.s. Morphological variation is high in all but the Vignea clade, making it extremely difficult to define consistent synapomorphies for most clades. However, Carex s.l. as newly circumscribed here is clearly differentiated from the sister groups in tribe Scirpeae by the transition from bisexual flowers with a bristle perianth in the sister group to unisexual flowers without a perianth in Carex. The naked female flowers of Carex s.l. are at least partially enclosed in a flask-shaped prophyll, termed a perigynium. Carex s.s. is not only by far the largest genus in the group, but also the earliest published name. As a result, only 72 new combinations and 58 replacement names are required to treat all of tribe Cariceae as a single genus Carex. We present the required transfers here, with synonymy, and we argue that this broader monophyletic circumscription of Carex reflects the close evolutionary relationships in the group and serves the goal of nomenclatural stability better than other possible treatments. We are grateful to the John D. and Catherine T. MacArthur Foundation for funding of the Biodiversity Synthesis Group of the Encyclopedia of Life (EOL) project, which funded our BioSynC Synthesis meeting at the Field Museum in Chicago in September 2011, when the Global Carex Group was formed. We also thank the US National Science Foundation (NSF) for funding our continuing international collaborative work on the phylogeny and classification of Carex under grants DEB 1255901 to ALH and MJW, and DEB 1256033 to EHR. We also acknowledge with thanks funding for nomenclatural research and for attendance at our second meeting during the Monocots V conference in New York in July, 2013, from the Natural Sciences and Engineering Research Council, Canada (NSERC) to MJW and JRS; University of Mainz to BG; JSPS KAKENHI Grant no. 25840136 to OY; Korea National Arboretum to SK; CGL2012- 38744 project from the Spanish Ministry of Economy and Competitiveness to ML; project 30870178 from the National Natural Science Foundation of China to SRZ, and a University of Wisconsin-Madison Raper Travel Grant to DS. The figures were prepared with invaluable technical advice from H. C. Rimmer. Peer reviewed

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Recolector de Cienci...arrow_drop_down
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    Authors: Cheng-Wei Wu; Keon Wimberly; Adele Pietras; William S Dodd; +2 Authors

    Background Adaptive responses to stress are essential for cell and organismal survival. In metazoans, little is known about the impact of environmental stress on RNA homeostasis. Results By studying the regulation of a cadmium-induced gene named numr-1 in Caenorhabditis elegans, we discovered that disruption of RNA processing acts as a signal for environmental stress. We find that NUMR-1 contains motifs common to RNA splicing factors and influences RNA splicing in vivo. A genome-wide screen reveals that numr-1 is strongly and specifically induced by silencing of genes that function in basal RNA metabolism including subunits of the metazoan integrator complex. Human integrator processes snRNAs for functioning with splicing factors, and we find that silencing of C. elegans integrator subunits disrupts snRNA processing, causes aberrant pre-mRNA splicing, and induces the heat shock response. Cadmium, which also strongly induces numr-1, has similar effects on RNA and the heat shock response. Lastly, we find that heat shock factor-1 is required for full numr-1 induction by cadmium. Conclusion Our results are consistent with a model in which disruption of integrator processing of RNA acts as a molecular damage signal initiating an adaptive stress response mediated by heat shock factor-1. When numr-1 is induced via this pathway in C. elegans, its function in RNA metabolism may allow it to mitigate further damage and thereby promote tolerance to cadmium. Electronic supplementary material The online version of this article (10.1186/s12915-019-0675-z) contains supplementary material, which is available to authorized users.

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    Europe PubMed Central
    Article . 2019
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    BMC Biology
    Article . 2019
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    BMC Biology
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      Europe PubMed Central
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    Authors: Hernández, Raúl Bonne; Moteshareie, Houman; Burnside, Daniel; McKay, Bruce; +1 Authors

    AbstractManganese (Mn) is an essential element, but in humans, chronic and/or acute exposure to this metal can lead to neurotoxicity and neurodegenerative disorders including Parkinsonism and Parkinson’s Disease by unclear mechanisms. To better understand the effects that exposure to Mn2+ exert on eukaryotic cell biology, we exposed a non-essential deletion library of the yeast Saccharomyces cerevisiae to a sub-inhibitory concentration of Mn2+ followed by targeted functional analyses of the positive hits. This screen produced a set of 43 sensitive deletion mutants that were enriched for genes associated with protein biosynthesis. Our follow-up investigations demonstrated that Mn reduced total rRNA levels in a dose-dependent manner and decreased expression of a β-galactosidase reporter gene. This was subsequently supported by analysis of ribosome profiles that suggested Mn-induced toxicity was associated with a reduction in formation of active ribosomes on the mRNAs. Altogether, these findings contribute to the current understanding of the mechanism of Mn-triggered cytotoxicity. Lastly, using the Comparative Toxicogenomic Database, we revealed that Mn shared certain similarities in toxicological mechanisms with neurodegenerative disorders including amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s and Huntington’s diseases.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Europe PubMed Central
    Article . 2019
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    Scientific Reports
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    Scientific Reports
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    Scientific Reports
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    Authors: Neale, Chris; Herce, Henry D.; Pomès, Régis; García, Angel E.;

    AbstractG-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane’s cytosolic leaflet enter the empty G-protein binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency. Simulations of the receptor embedded in an anionic membrane show increased lipid binding, providing a molecular mechanism for the experimental observation that anionic lipids can enhance receptor activity. Conservation of the arginine component of the ionic lock among Rhodopsin-like G-protein-coupled receptors suggests that intracellular lipid ingression between receptor helices H6 and H7 may be a general mechanism for active-state stabilization.

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    Biophysical Journal
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    Biophysical Journal
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    Europe PubMed Central
    Other literature type . 2015
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      Biophysical Journal
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      Europe PubMed Central
      Other literature type . 2015
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    Authors: Till S. Harter; Christian Damsgaard; Matthew D. Regan;

    ABSTRACT The gill is the primary site of ionoregulation and gas exchange in adult teleost fishes. However, those characteristics that benefit diffusive gas exchange (large, thin gills) may also enhance the passive equilibration of ions and water that threaten osmotic homeostasis. Our literature review revealed that gill surface area and thickness were similar in freshwater (FW) and seawater (SW) species; however, the diffusive oxygen (O2) conductance (Gd) of the gill was lower in FW species. While a lower Gd may reduce ion losses, it also limits O2 uptake capacity and possibly aerobic performance in situations of high O2 demand (e.g. exercise) or low O2 availability (e.g. environmental hypoxia). We also found that FW fishes had significantly higher haemoglobin (Hb)–O2 binding affinities than SW species, which will increase the O2 diffusion gradient across the gills. Therefore, we hypothesized that the higher Hb–O2 affinity of FW fishes compensates, in part, for their lower Gd. Using a combined literature review and modelling approach, our results show that a higher Hb–O2 affinity in FW fishes increases the flux of O2 across their low-Gd gills. In addition, FW and SW teleosts can achieve similar maximal rates of O2 consumption (ṀO2,max) and hypoxia tolerance (Pcrit) through different combinations of Hb–O2 affinity and Gd. Our combined data identified novel patterns in gill and Hb characteristics between FW and SW fishes and our modelling approach provides mechanistic insight into the relationship between aerobic performance and species distribution ranges, generating novel hypotheses at the intersection of cardiorespiratory and ionoregulatory fish physiology.

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    Authors: Ross, Cressman; Vlastimil, Krivan;

    This article verifies that the ideal free distribution (IFD) is evolutionarily stable, provided the payoff in each patch decreases with an increasing number of individuals. General frequency-dependent models of migratory dynamics that differ in the degree of animal omniscience are then developed. These models do not exclude migration at the IFD where balanced dispersal emerges. It is shown that the population distribution converges to the IFD even when animals are nonideal (i.e., they do not know the quality of all patches). In particular, the IFD emerges when animals never migrate from patches with a higher payoff to patches with a lower payoff and when some animals always migrate to the best patch. It is shown that some random migration does not necessarily lead to undermatching, provided migration occurs at the IFD. The effect of population dynamics on the IFD (and vice versa) is analyzed. Without any migration, it is shown that population dynamics alone drive the population distribution to the IFD. If animal migration tends (for each fixed population size) to the IFD, then the combined migration-population dynamics evolve to the population IFD independent of the two timescales (i.e., behavioral vs. population).

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    The American Naturalist
    Article . 2006
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      The American Naturalist
      Article . 2006
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    Authors: Justin P. Suraci; Michael Clinchy; Liana Zanette; Christopher C. Wilmers;

    AbstractApex predators such as large carnivores can have cascading, landscape‐scale impacts across wildlife communities, which could result largely from the fear they inspire, although this has yet to be experimentally demonstrated. Humans have supplanted large carnivores as apex predators in many systems, and similarly pervasive impacts may now result from fear of the human ‘super predator’. We conducted a landscape‐scale playback experiment demonstrating that the sound of humans speaking generates a landscape of fear with pervasive effects across wildlife communities. Large carnivores avoided human voices and moved more cautiously when hearing humans, while medium‐sized carnivores became more elusive and reduced foraging. Small mammals evidently benefited, increasing habitat use and foraging. Thus, just the sound of a predator can have landscape‐scale effects at multiple trophic levels. Our results indicate that many of the globally observed impacts on wildlife attributed to anthropogenic activity may be explained by fear of humans.

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    Scholarship@Western
    Article . 2019
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    Ecology Letters
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    Ecology Letters
    Article . 2019
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    Ecology Letters
    Article . 2019
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      Scholarship@Western
      Article . 2019
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      Ecology Letters
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      Ecology Letters
      Article . 2019
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      Article . 2019
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    Authors: Sabateeshan Mathavarajah; Kathleen L. Vergunst; Shelby K. Williams; Raymond He; +9 Authors

    ABSTRACTWe have uncovered a novel role for the promyelocytic leukemia (PML) gene and novel PML-like DEDDh exonucleases in the maintenance of genome stability through the restriction of LINE-1 (L1) retrotransposition in jawed vertebrates. Although the PML tumour suppressor protein in mammals is SUMOylated and forms nuclear bodies, we found that the spotted gar PML ortholog and related proteins in fish are not SUMOylated and function as cytoplasmic DEDDh exonucleases. In contrast, more closely related avian and turtle PML proteins are predicted to be SUMOylated and localized both to the cytoplasm and to nuclear bodies. We also identified PML-like exon 9 (Plex9) genes in teleost fishes that encode exonucleases sharing homology to gar PML. In an example of convergent evolution and akin to TREX1, gar PML and zebrafish Plex9 proteins suppressed L1 retrotransposition and could complement TREX1 knockout in mammalian cells. We also characterized the first non-mammalian TREX1 homologs in axolotl. Following export to the cytoplasm, the human PML-I isoform also restricted L1 through its conserved C-terminus and suppressed CGAS activation. Thus, PML first emerged as a cytoplasmic suppressor of retroelements, and this function is retained in amniotes despite its role in the assembly of nuclear bodies and the acquisition of SUMO-modification.

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    Nucleic Acids Research
    Article . 2023
    License: CC BY NC
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      Nucleic Acids Research
      Article . 2023
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    Authors: Egan, Jocelyn E.; Bowling, David R.; Risk, David A.;

    Earth system scientists working with radiocarbon in organic samples use a stable carbon isotope (δ13C) correction to account for mass-dependent fractionation, but it has not been evaluated for the soil gas environment, wherein both diffusive gas transport and diffusive mixing are important. Using theory and an analytical soil gas transport model, we demonstrate that the conventional correction is inappropriate for interpreting the radioisotopic composition of CO2 from biological production because it does not account for important gas transport mechanisms. Based on theory used to interpret δ13C of soil production from soil CO2, we propose a new solution for radiocarbon applications in the soil gas environment that fully accounts for both mass-dependent diffusion and mass-independent diffusive mixing.

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    Biogeosciences (BG)
    Other literature type . 2019
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    Studies of animal behavior often rely on human observation, which introduces a number of limitations on sampling. Recent developments in automated logging of behaviors make it possible to circumvent some of these problems. Once verified for efficacy and accuracy, these automated systems can be used to determine optimal sampling regimes for behavioral studies. Here, we used a radio-frequency identification (RFID) system to quantify parental effort in a bi-parental songbird species: the tree swallow (Tachycineta bicolor). We found that the accuracy of the RFIDmonitoring systemwas similar to that of video-recorded behavioral observations for quantifying parental visits. Using RFID monitoring, we also quantified the optimum duration of sampling periods for male and female parental effort by looking at the relationship between nest visit rates estimated from sampling periods with different durations and the total visit numbers for the day. The optimum sampling duration (the shortest observation time that explained the most variation in total daily visits per unit time) was 1h for both sexes. These results show that RFID and other automated technologies can be used to quantify behavior when human observation is constrained, and the information fromthese monitoring technologies can be useful for evaluating the efficacy of human observation methods. Funding was provided by a U.S. National Science Foundation (NSF) grant (FB, ITM, and MFH; IOS-1145625), the Natural Sciences and Engineering Research Council of Canada, and a Banting Postdoctoral Fellowship (FB). During the preparation of the manuscript, ÁZL was supported by a Hungarian Scientific Research Fund (OTKA K113108) and JQO by a NSF postdoctoral grant (DBI-1306025).

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    Europe PubMed Central
    Article . 2015
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    Article . 2015
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    Other literature type . 2015
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    Article . 2015
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    NARCIS; PLoS ONE
    Article . 2015
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    Article . 2015
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    https://doi.org/10.7287/peerj....
    Preprint . 2015
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    https://doi.org/10.7287/peerj....
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    https://doi.org/10.7287/peerj....
    Preprint . 2015
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    https://doi.org/10.7287/peerj....
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Villaverde, Tamara; Global Carex Group;

    Carex (Cyperaceae), with an estimated 2000 species, nearly cosmopolitan distribution and broad range of habitats, is one of the largest angiosperm genera and the largest in the temperate zone. In this article, we provide argument and evidence for a broader circumscription of Carex to add all species currently classified in Cymophyllus (monotypic), Kobresia (c. 60 species), Schoenoxiphium (c. 15 species) and Uncinia (c. 70 species) to those currently classified as Carex. Carex and these genera comprise tribe Cariceae (subfamily Cyperoideae, Cyperaceae) and form a wellsupported monophyletic group in all molecular phylogenetic studies to date. Carex as defined here in the broad sense currently comprises at least four clades. Three are strongly supported (Siderostictae, core Vignea and core Carex), whereas the caricoid clade, which includes all the segregate genera, receives only weak to moderate support. The caricoid clade is most commonly split into two clades, one including a monophyletic Schoenoxiphium and two small clades of species of Carex s.s., and the other comprising Kobresia, Uncinia and mostly unispicate species of Carex s.s. Morphological variation is high in all but the Vignea clade, making it extremely difficult to define consistent synapomorphies for most clades. However, Carex s.l. as newly circumscribed here is clearly differentiated from the sister groups in tribe Scirpeae by the transition from bisexual flowers with a bristle perianth in the sister group to unisexual flowers without a perianth in Carex. The naked female flowers of Carex s.l. are at least partially enclosed in a flask-shaped prophyll, termed a perigynium. Carex s.s. is not only by far the largest genus in the group, but also the earliest published name. As a result, only 72 new combinations and 58 replacement names are required to treat all of tribe Cariceae as a single genus Carex. We present the required transfers here, with synonymy, and we argue that this broader monophyletic circumscription of Carex reflects the close evolutionary relationships in the group and serves the goal of nomenclatural stability better than other possible treatments. We are grateful to the John D. and Catherine T. MacArthur Foundation for funding of the Biodiversity Synthesis Group of the Encyclopedia of Life (EOL) project, which funded our BioSynC Synthesis meeting at the Field Museum in Chicago in September 2011, when the Global Carex Group was formed. We also thank the US National Science Foundation (NSF) for funding our continuing international collaborative work on the phylogeny and classification of Carex under grants DEB 1255901 to ALH and MJW, and DEB 1256033 to EHR. We also acknowledge with thanks funding for nomenclatural research and for attendance at our second meeting during the Monocots V conference in New York in July, 2013, from the Natural Sciences and Engineering Research Council, Canada (NSERC) to MJW and JRS; University of Mainz to BG; JSPS KAKENHI Grant no. 25840136 to OY; Korea National Arboretum to SK; CGL2012- 38744 project from the Spanish Ministry of Economy and Competitiveness to ML; project 30870178 from the National Natural Science Foundation of China to SRZ, and a University of Wisconsin-Madison Raper Travel Grant to DS. The figures were prepared with invaluable technical advice from H. C. Rimmer. Peer reviewed

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    Authors: Cheng-Wei Wu; Keon Wimberly; Adele Pietras; William S Dodd; +2 Authors

    Background Adaptive responses to stress are essential for cell and organismal survival. In metazoans, little is known about the impact of environmental stress on RNA homeostasis. Results By studying the regulation of a cadmium-induced gene named numr-1 in Caenorhabditis elegans, we discovered that disruption of RNA processing acts as a signal for environmental stress. We find that NUMR-1 contains motifs common to RNA splicing factors and influences RNA splicing in vivo. A genome-wide screen reveals that numr-1 is strongly and specifically induced by silencing of genes that function in basal RNA metabolism including subunits of the metazoan integrator complex. Human integrator processes snRNAs for functioning with splicing factors, and we find that silencing of C. elegans integrator subunits disrupts snRNA processing, causes aberrant pre-mRNA splicing, and induces the heat shock response. Cadmium, which also strongly induces numr-1, has similar effects on RNA and the heat shock response. Lastly, we find that heat shock factor-1 is required for full numr-1 induction by cadmium. Conclusion Our results are consistent with a model in which disruption of integrator processing of RNA acts as a molecular damage signal initiating an adaptive stress response mediated by heat shock factor-1. When numr-1 is induced via this pathway in C. elegans, its function in RNA metabolism may allow it to mitigate further damage and thereby promote tolerance to cadmium. Electronic supplementary material The online version of this article (10.1186/s12915-019-0675-z) contains supplementary material, which is available to authorized users.

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    Europe PubMed Central
    Article . 2019
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      Europe PubMed Central
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    Authors: Hernández, Raúl Bonne; Moteshareie, Houman; Burnside, Daniel; McKay, Bruce; +1 Authors