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opencc-by-4.0Sep 2019View details →

Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions"

Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions" Multiple sclerosis (MS) is the most common neurological disorder in young adults. Despite extensive studies, only a fraction of MS heritability has been explained, with association studies focusing primarily on protein-coding genes, essentially for the difficulty of interpreting non-coding features. However, non-coding RNAs (ncRNAs) and functional elements, such as super-enhancers (SE), are crucial regulators of many pathways and cellular mechanisms, and they have been implicated in a growing number of diseases. In this work, we searched for possible enrichments in non-coding elements at MS genome-wide associated loci, with the aim to highlight their possible involvement in the susceptibility to the disease. We first reconstructed the linkage disequilibrium (LD) structure of the Italian population using data of 727,478 single-nucleotide polymorphisms (SNPs) from 1,668 healthy individuals. The genomic coordinates of the obtained LD blocks were intersected with those of the top hits identified in previously published MS genome-wide association studies (GWAS). By a bootstrapping approach, we hence demonstrated a striking enrichment of non-coding elements, especially of circular RNAs (circRNAs) mapping in the 73 LD blocks harboring MS-associated SNPs. In particular, we found a total of 482 circRNAs (annotated in publicly available databases) vs. a mean of 194 ± 65 in the random sets of LD blocks, using 1,000 iterations. As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the STAT3 gene, can be modulated by the three genotypes at the disease-associated SNP. Finally, by evaluating RNA-seq data of two cell lines, SH-SY5Y and Jurkat cells, representing tissues relevant for MS, we identified 18 (two novel) circRNAs derived from MS-associated genes. In conclusion, this work showed for the first time that MS-GWAS top hits map in LD blocks enriched in circRNAs, suggesting circRNAs as possible novel contributors to the disease pathogenesis. GEO database URL: <a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a> Numero di accesso del dataset: GSE110525

opencc-by-4.0Sep 2019View details →

Link to dataset related to article "Sustained activation of detoxification pathways promotes liver carcinogenesis in response to chronic bile acid-mediated damage"

This record contains link to raw data related to article "Sustained activation of detoxification pathways promotes liver carcinogenesis in response to chronic bile acid-mediated damage" Chronic inflammation promotes oncogenic transformation and tumor progression. Many inflammatory agents also generate a toxic microenvironment, implying that adaptive mechanisms must be deployed for cells to survive and undergo transformation in such unfavorable contexts. A paradigmatic case is represented by cancers occurring in pediatric patients with genetic defects of hepatocyte phosphatidylcholine transporters and in the corresponding mouse model (Mdr2-/- mice), in which impaired bile salt emulsification leads to chronic hepatocyte damage and inflammation, eventually resulting in oncogenic transformation. By combining genomics and metabolomics, we found that the transition from inflammation to cancer in Mdr2-/- mice was linked to the sustained transcriptional activation of metabolic detoxification systems and transporters by the Constitutive Androstane Receptor (CAR), a hepatocyte-specific nuclear receptor. Activation of CAR-dependent gene expression programs coincided with reduced content of toxic bile acids in cancer nodules relative to inflamed livers. Treatment of Mdr2-/- mice with a CAR inhibitor blocked cancer progression and caused a partial regression of existing tumors. These results indicate that the acquisition of resistance to endo- or xeno-biotic toxicity is critical for cancers that develop in toxic microenvironments. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80777 under the accession GSE80777, which comprises ChIP-seq data (GSE80775) and expression data (GSE80776).

opencc-by-4.0Oct 2019View details →

Zenodo data and software citation links captured by the Asclepias Broker

The dataset was retrieved from the Asclepias Broker early January 2019 after having performed a full harvesting and deduplication cycle from a clean database with zero citation links. The dataset contains citation links from three discovery systems: the NASA Astrophysics Datasystem (ADS), Crossref Event Data and Europe PMC. Only citation links with a target DOI in the DOI prefix 10.5281 (Zenodo’s DOI prefix) were kept.

Fig. 4 in A Marrella-like arthropod from the Cambrian of Australia: A new link between "Orsten"-type and Burgess Shale assemblages

Fig. 4. Localities, in which Marrellomorpha (sensu Kühl et al. 2008) have been found. 1, Monastery Creek Phosphorite Formation, Late Templetonian– Early Floran, Australia: Austromarrella klausmuelleri gen. et sp. nov. 2, Kaili, early middle Cambrian, China: Marrella sp. (Zhao et al. 2003). 3, Burgess Shale, middle Cambrian, British Columbia, Canada: Marrella splendens Walcott, 1912 (Whittington 1971; García−Bellido and Collins 2006). 4, Fezouata biota, Ordovician, Morocco: Furca spp. (Van Roy 2006a, b; Van Roy et al. 2010). 5, Letná Formation, Ordovican, Czech Republic: Furca bohemica Fritsch, 1908 (Chlupáč 1999; Van Roy 2006a, b; Rak 2009; Rak et al. 2013). 6, Herefordshire, Silurian, England: Xylokoris chledophilia Siveter, Fortey, Sutton, Briggs and Siveter, 2007 (Siveter et al. 2007). 7, Hunsrück slate, Lower Devonian, Germany: Vachonisia rogeri Lehmann, 1955 (Kühl et al. 2008); Mimetaster hexagonalis Gürich, 1931 (Kühl and Rust 2010). Table indicates occurrences.

Fig. 3. Marrellomorph Marrella splendens Walcott, 1912 in A Marrella-like arthropod from the Cambrian of Australia: A new link between "Orsten"-type and Burgess Shale assemblages

Fig. 3. Marrellomorph Marrella splendens Walcott, 1912, for comparison with Austromarrella klausmuelleri gen. et sp. nov., Mount Murray, Western Queensland, Australia; Series 3 of the Cambrian. A. Dorsal view on a rendered 3D model, based on own observations. B–E. Micrographs under polarized light. B. Beautifully preserved specimen USNM 83486f with the exopods in a "rusty" preservation (cf. García−Bellido and Collins 2006). C. Stereo image of specimen USNM 139665. Exopods of preceding limbs are super−imposing each other, separated by a thin layer of sediment. D. Detail of specimen ROM 56766A in "rusty" preservation. Here the spines on the lateral side of the exopod ringlets are well preserved. E. One of the smallest specimens of M. splendens USNM 219817e that possesses preserved appendage remains. The single fragmentary specimen of A. klausmuelleri could, based on its size, belong to an entire specimen of a comparable size.

Fig. 1 in A Marrella-like arthropod from the Cambrian of Australia: A new link between "Orsten"-type and Burgess Shale assemblages

Fig. 1. SEM images of the holotype and single specimen CPC 30719 of marrellomorph Austromarrella klausmuelleri gen. et sp. nov., Mount Murray, Western Queensland, Australia; Series 3 of the Cambrian. A. Median or lateral view, exposing the more or less lanceolate lamellae. B. Anterior or posterior view. The 16 ringlets are well separated from each other. Letters indicate the direction of view in images D–F. C. Median or lateral view, opposing to side displayed in A. Here the insertion of the most proximal preserved ringlet is well apparent. D–F. Details of the stout spines on the most distal preserved annuli viewed as indicated in image B. D. View from latero/medio−proximal on the distal tip. E. View from lateral/median, same spine as in D. F. View from medio/latero−proximal. Spine on the other side of the same ringlet as in D and E.

Fig. 2 in A Marrella-like arthropod from the Cambrian of Australia: A new link between "Orsten"-type and Burgess Shale assemblages

Fig. 2. Examples of multi−annulated exopods of fossil and extant representatives of the taxa Agnostina and Crustacea sensu lato. A. SEM image of the exopod of the second head appendage of Agnostus pisiformis (Wahlenberg, 1818) composed of nine articles. Each of the six distal articles bears a pair of long, outwardly directed setae, a short spinule close to the base of the setae and a short seta opposite of the long setae (cf. Müller and Walossek 1987: pl. 18.1). Series 3 of the Cambrian (Agnostus pisiformis Zone), UB 832. B. SEM image of appendages two and three of a stage two larva of the fossil micro−predator Goticaris longispinosa Walossek and Müller, 1990. Series 3 of the Cambrian (Agnostus pisiformis Zone), UB 98. Detail of pl. 2.5 of Haug et al. (2009b). C. SEM image of the appendages two to four of the phosphatocopine Vestrogothia spinata Müller, 1964, Furongian, Cambrian, UB 622. D. Light microscopic image (processed according to Haug et al. 2009a) of a putative thecostracan larva (E_G2010_16_2_1), from the Devonian Windyfield Chert (cf. Fayers and Trewin 2004). E. Composite fluorescence image (cf. Haug et al. 2008) of an undetermined natant decapod from the Solnhofen Lithographic Limestones, Upper Jurassic, Southern Germany (SMNS 70149, ex coll. Gebert, Iphofen). F. SEM image of the second antenna of the Recent mystacocarid Derocheilocaris remanei Delamare−Deboutteville and Chappuis, 1951 (cf. Olesen 2001; Haug et al. 2011). Specimen from the collection of the Zoological Museum, Copenhagen. G. SEM image of a pleomeric segment with a pair of pleopods of the Recent amphipod Gammarus roeselii Gervais, 1835. Image courtesy Gerd Mayer, Ulm.

opencc-by-4.0Mar 2012View details →

Fig. 1 in A new basal osmylid neuropteran insect from the Middle Jurassic of China linking Osmylidae to the Permian-Triassic Archeosmylidae

Fig. 1. Forewing of osmylid neuropteran insect Archaeosmylidia fusca gen. et sp. nov. (Osmylidae) from the Jiulongshan Formation of Daohugou, China. Holotype CNU−NEU−NN2009103. Photograph (A) and line drawing of venation (B). Scale bars 5 mm. Abbreviations: 1A, 2A, anal veins; C, costa; CuA, anterior cubitus; CuP, posterior cubitus; MA and MP, anterior and posterior branches of media (M); ng, nygma; R1, first branch of radius (R); Rs, radial sector; Sc, subcosta.

Figure 3 in Observations of a rapid decline in invasive macroalgal cover linked to green turtle grazing in a Hawaiian marine reserve

Figure 3. Mean hourly temperatures (°C) (a.), total rainfall (mm h-1) (b.), wind (km h−1) (c.), and PAR (µmol photons m−2) (d.) in 2015 (red triangle), 2016 (blue square), and 2017 (black circle). Data was obtained from Hawai'i Institute of Marine Biology Weather Station (http://www.pacioos.hawaii.edu/weather/obs-mokuoloe/).

Figure 1 in Observations of a rapid decline in invasive macroalgal cover linked to green turtle grazing in a Hawaiian marine reserve

Figure 1. Green turtle, Chelonia mydas, feeding on Gracilaria salicornia in the back lagoon of Moku o Lo'e, Kāneʻohe Bay, Oʻahu, Hawaiʻi in March 2017. Photo by KD Bahr.

Figure 2. Surveyed sites around Moku o in Observations of a rapid decline in invasive macroalgal cover linked to green turtle grazing in a Hawaiian marine reserve

Figure 2. Surveyed sites around Moku o Loʻe, Kāneʻohe Bay, Oʻahu, Hawaiʻi in April (left) and May (right) depicting proportion of substratum classified as coral (brown), rubble (grey), sand (yellow), or Gracilaria salicornia (green). Numbers within pie charts indicate number of turtles observed at each site during the survey. Red outlined pie charts denote areas with limited accessability (only during high tides) to Chelonia mydas.

Figure 5 in Observations of a rapid decline in invasive macroalgal cover linked to green turtle grazing in a Hawaiian marine reserve

Figure 5. Back lagoon of Moku o Loʻe, Kāneʻohe Bay, Oʻahu, Hawaiʻi adjacent to a fenced enclosure on 13 April 2017 (top) and same area 21 days later on 4 May 2017 (bottom). Photo by KD Bahr.

Fig. 6 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula

Fig. 6. Phylogenetic tree based on the Maximum Likelihood analysis of the species of the Order Onchoproteocephalidea found in Octopus maya constructed on partial large subunit ribosomal gene (28S) (likelihood = – 9067.566753). Bootstrap support values for ML are provided at the nodes; ex = host; the stage of development of the cestode in parentheses.

Fig. 4 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula

Fig. 4. Phylogenetic tree based on the Maximum Likelihood (ML) analysis of the species of the Order Trypanorhyncha found in Octopus maya constructed on partial large subunit ribosomal gene (28S) (likelihood = – 15209.189111). Bootstrap support values for ML are provided at the nodes; ex = host; the stage of development of the cestode in parentheses.

Fig. 3 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula

Fig. 3. Scanning electron microscopy of whole specimens and the detail of scolecis of the cestodes found as parasites of Octopus maya. Trypanorhyncha (A–L): A-C Eutetrarhynchus sp.; D-F Kotorella pronosoma; G-I Nybelinia sp.; J-L Prochristianella sp. Onchoproteocephalidea (M–R): M-N Acanthobothrium sp. O–P Phoreiobothrium sp.; Q-R Prosobothrium sp.

Fig. 2 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula

Fig. 2. Schematic drawings and photographs of the stained specimens of cestode parasitizing Octopus maya. Trypanorhyncha (A–D): A- Eutetrarhynchus sp.; B. Kotorella pronosoma; C- Nybelinia sp.; D- Prochristianella sp. Onchoproteocephalidea (E–G): E- Acanthobothrium sp.; F- Phoreiobothrium sp.; G- Prosobothrium sp.- Abbreviations: as = apical sucker; bot = bothridia cc = calcareous corpuscles; lo = loculi; pb = pars bulbosa; pbo = pars bothrialis; ppb = pars postbulbosa; ps = pedunculus scolecis; pv = pars vaginalis; sc = scolex; sp = septa; st = strobilo; vel = velum.

Fig. 5 in Linking phenotypic to genotypic metacestodes from Octopus maya of the Yucatan Peninsula

Fig. 5. Phylogenetic tree based on the Maximum Likelihood analysis of the species of the Order Trypanorhyncha found in Octopus maya constructed on partial small subunit ribosomal gene (18S) (likelihood = – 7987.787948). Bootstrap support values for ML are provided at the nodes; ex = host; the stage of development of the cestode in parentheses.

opencc-by-4.0Sep 2016View details →

FIGURE 6 in Biting midges (Diptera: Ceratopogonidae) in Fushun amber reveal further biotic links between Asia and Europe during the Eocene

FIGURE 6. Palaeogeographic locations of early Eocene insect faunas in (approximately 50 Ma) Baltic amber (B) from Europe and Fushun amber (F) from China (modified after Blakey, 2015).

opencc-by-4.0Sep 2016View details →

FIGURE 1 in Biting midges (Diptera: Ceratopogonidae) in Fushun amber reveal further biotic links between Asia and Europe during the Eocene

FIGURE 1. Photograph of Mantohelea sinica n. sp. from lower Eocene Fushun amber. 1. Mantohelea sinica n. sp., Holotype female NIGP156996. 2. Mantohelea sinica n. sp., head.