262,245 research outputs found
Gigantopelta Chen & Linse & Roterman & Copley & Rogers 2015, GEN. NOV.
No full textGIGANTOPELTA GEN. NOV. <p> <i>Type species</i></p> <p> <i>Gigantopelta chessoia</i> sp. nov., by original designation.</p> <p> <i>Etymology</i></p> <p>Giganteus (Latin), gigantic; Pelta (Latin), shield. This refers to the extremely large adult shell size of the species in this genus for the family Peltospiridae. The genus name is feminine.</p> <p> <i>Zoobank registration</i> urn:lsid:zoobank.org:act: C25960CA-B974-452C-AE24- B128FF1CEA0F</p> <p> <i>Diagnosis</i></p> <p>Shell extremely large for family, reaching 45 mm in adult shell length. Shell globose, rather loosely coiled with deep suture, three to four whorls. Spire depressed. Protoconch consisting of 0.5 whorls. Aperture very large, circular, expanding rapidly. Thick, dark olive periostracum enveloping edge of aperture. Shell milky white and thin, not nacreous. Columellar folds lacking. Concentric, multispiral operculum present. Foot large. Cephalic tentacles thick, broad, triangular, thinning towards tips. Eyes lacking. Snout tapering and thick. Oesophageal gland hypertrophied. Single, bipectinate ctenidium. Sexes separate. Epipodial tentacles present surrounding operculum. Radula rhipidoglossate, formula ∼50 + 4 + 1 + 4 + ∼50. Central, lateral teeth strong, solid with smooth cusps. Marginal teeth long, slender, truncate, divided into about 20 toothlets towards distal end.</p> <p> <i>Remarks</i></p> <p> Adult <i>Gigantopelta</i> are easily distinguished from all other described peltospirids by their extremely</p> <p> <i>COI</i>, cytochrome c oxidase subunit I</p> <p> large shell size. Furthermore, <i>Gigantopelta</i> can be distinguished from the limpet-like peltospirid genera <i>Ctenopelta</i> Warén & Bouchet, 1993, <i>Echinopelta</i> McLean, 1989, <i>Hirtopelta</i> McLean, 1989, <i>Nodopelta</i> McLean, 1989, and <i>Rhynchopelta</i> McLean, 1989, by having a coiled shell with three to four whorls. It can be distinguished from the three skeneiform genera, <i>Pachydermia</i> Warén & Bouchet, 1989, <i>Depressigyra</i> Warén & Bouchet, 1989, and <i>Lirapex</i> Warén & Bouchet, 1989, by its inflated form with a much more depressed spire and larger aperture. The shell surface is nearly smooth, which differs from all peltospirid genera except <i>Depressigyra</i>. The shell roughly resembles that of <i>Peltospira</i>, but has a more tightly coiled initial whorl, and lacks lamellar sculpture. Analysis of the soft parts shows an enlarged oesophageal gland, a feature previously only known from the ‘scaly-foot gastropod’ <i>Chrysomallon squamiferum</i> Chen <i>et al</i>., 2015 (Warén <i>et al</i>., 2003; Chen <i>et al</i>., 2015), which is also the only other known peltospirid to attain a similar size. In <i>C. squamiferum</i> the oesophageal gland houses symbiotic bacteria, but it is unclear whether this is also the case for <i>Gigantopelta</i>. <i>Gigantopelta</i> can be distinguished from <i>Chrysomallon</i> easily as it does not possess dermal sclerites, has a large operculum, and a shell that is less vertically compressed, with a more circular aperture. The shell of <i>Gigantopelta</i> may be coated in a layer of sulphide, which is frequent amongst vent gastropods including the neomphalins (Hickman, 1984; Warén & Bouchet, 2001). <i>Gigantopelta</i> is also comparable to the Oligocene fossil genus <i>Elmira</i> Cooke, 1919, from a seep deposit near Bejucal, Cuba whose possible affinity to Neomphalina based on resemblance to <i>Chrysomallon</i> was remarked upon by Kiel & Peckmann (2007). Although the type species <i>Elmira cornuarietis</i> Cooke, 1919, is approximately the same size as <i>Gigantopelta</i> (> 40 mm in shell length), it carries broad revolving grooves, which <i>Gigantopelta</i> lacks. The true taxonomic affinity of <i>Elmira</i> is still unclear.</p>Published as part of <i>Chen, Chong, Linse, Katrin, Roterman, Christopher N., Copley, Jonathan T. & Rogers, Alex D., 2015, A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae), pp. 319-335 in Zoological Journal of the Linnean Society (Zool. J. Linn. Soc.) (Zool. J. Linn. Soc.) 175 (2)</i> on pages 322-323, DOI: 10.1111/zoj.12279, <a href="http://zenodo.org/record/5338416">http://zenodo.org/record/5338416</a>
Never born proteins as a test case for ab initio protein structures prediction
No full textThe number of natural proteins although large is significantly smaller than the theoretical number of proteins that can be obtained combining the 20 natural amino acids, the so-called "never born proteins" (NBPs). The study of the structure and properties of these proteins allows to investigate the sources of the natural proteins being of unique characteristics or special properties. However the structural study of NPBs can also been intended as an ideal test for evaluating the efficiency of software packages for the ab initio protein structure prediction. In this research, 10.000 three-dimensional structures of proteins of completely random sequence generated according to ROSETTA and FOD model were compared. The results show the limits of these software packages, but at the same time indicate that in many cases there is a significant agreement between the prediction obtained
Gigantopelta aegis Chen & Linse & Roterman & Copley & Rogers 2015, SP. NOV.
No full textGIGANTOPELTA AEGIS SP. NOV. (FIGS 2–7) <p> <i>Type material</i></p> <p> Holotype. Shell diameter 37.61 mm, 99% ethanol, Figure 3D–F. Longqi vent field, Southwest Indian Ridge, 37°47.03′S, 49°38.97′E (‘Tiamat’), 2785 m deep, RRS <i>James Cook</i> expedition JC67, ROV <i>Kiel 6000</i> Dive 142, 29.xi.2011, leg. J. T. Copley (NHMUK 20150070). Paratypes. One dissected specimen, 99% ethanol (shell diameter 35.24 mm, Fig. 4C, D; NHMUK 20150071); growth series of five specimens, 99% ethanol (NHMUK 20150072); growth series of five specimens, 99% ethanol OUMNH. ZC. 2013.02.003); two specimens, 99% ethanol (CAMZM 2015.3.1 -2); growth series of five specimens (SMNH Type Collection 8451). All paratypes above have the same collection data as holotype. Five specimens, 10% buffered formalin (NHMUK 20150073): Longqi vent field, Southwest Indian Ridge, 37°47.03′S, 49°38.96′E (‘Tiamat’ chimney), 2783 m deep, RRS <i>James Cook</i> expedition JC67, ROV <i>Kiel 6000</i> Dive 140, 27.xi.2011, leg. J. T. Copley (NHMUK 20150073).</p> <p> <i>Other material examined</i></p> <p>Approximately 200 specimens, same collection data as the holotype.</p> <p> <i>Etymology</i></p> <p>Aegis (Latin), the shield of Zeus and Athena. The specific name is an allusion of the thick and large sulphidecovered operculum to the mythical shield.</p> <p> <i>Zoobank registration</i> urn:lsid:zoobank.org:act: 45E3E373-E126-4179-B1EB- D583FCFB3D12)</p> <p> <i>Description/Diagnosis</i></p> <p> <i>Shell:</i> Shell (Fig. 4B) globose, three to four whorls, trochiform to neritiform. Spire depressed. Aperture holostomous. Tightly coiled. Suture deep. Aperture very large, circular, body whorl to aperture length ratio approximately 1:0.65 (average of 100 specimens). Protoconch (Fig. 5B) 0.5 whorls, about 210 μm in length, sculpture unknown (surface layer of examined specimens affect- ed by dissolution). Thick, orange to reddish sulphide layer covers periostracum. Periostracum dark olive with sulphides removed. Ostracum milky white. Ostracum thin, fragile without sulphide and periostracum. Periostracum slightly recurved at aperture. Columellar folds lacking. Callus extends extensively, covering columellar region. Area around callus flattened (dark area in Fig. 3F). Shell smooth, lacking sculpture. Fine growth lines, subtle spiral cords present under sulphide layer. Maximum shell diameter 44.2 mm.</p> <p> <i>Operculum:</i> Operculum (Fig. 3E, F) corneous, thin, flaky near the fringe, multispiral, covered by thick sulphide layer except outermost whorl, same material as those covering shell. Juvenile operculum lacking sulphide layer. Moderately thick, opaque, with concave shape (Fig. 5B).</p> <p> <i>Radula:</i> Radula (Fig. 6B) rhipidoglossate. Ribbon in adults approximately 0.5 mm wide and 4 mm long. Formula ∼50 + 4 + 1 + 4 + ∼50. Central, lateral teeth (Fig. 6D) with sharp cusps. Central tooth rectangular. Lateral teeth bear a protrusion near the base. Marginal teeth (Fig. 6F) elongate with truncate distal ending, dividing into ∼20 denticles.</p> <p> <i>Soft parts (Fig. 7B):</i> Foot muscular, large. Fully retractable. Pale white when alive. Small epipodial tentacles present, surrounding posterior two-thirds of operculum. Cephalic tentacles thick, broad at base, tapering distally. Snout tapering and thick. Oesophageal gland huge (see Fig. 7B). Intestines forming a simple loop. Ctenidium bipectinate. Sexes separate. Gonads rather displaced towards the head-foot. Shell muscle large, horse-shoe shaped.</p> <p> <i>Distribution:</i> Only known from Longqi vent field, SWIR (approximately 37°47.03′S, 49°38.96′E), around 2700 m depth. Found mostly on areas of diffuse flow but also on chimneys of active black smokers.</p> <p> <i>Remarks</i></p> <p> Similar to <i>Gigantopelta chessoia</i> sp. nov.; see Comparative remarks above for comparison. The sulphide covering of the shell and that forming the thick coating on the operculum is remarkable. The coating only covers the outer side, and can be removed from the operculum intact by inserting a blade in between. The adult shells are completely covered with sulphide. Sulphide deposition appears to start very early in development, and from the protoconch; as in young specimens (∼ 5 mm maximum diameter) sulphide is only present as a tablet on the apex and not covering the whole shell. The shell parameters are given in Table 2. The relationships between the six parameters measured were investigated, and they were linear across all life stages. Figure 8B shows a scatter plot of shell diameter against shell height.</p>Published as part of <i>Chen, Chong, Linse, Katrin, Roterman, Christopher N., Copley, Jonathan T. & Rogers, Alex D., 2015, A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae), pp. 319-335 in Zoological Journal of the Linnean Society (Zool. J. Linn. Soc.) (Zool. J. Linn. Soc.) 175 (2)</i> on pages 327-329, DOI: 10.1111/zoj.12279, <a href="http://zenodo.org/record/5338416">http://zenodo.org/record/5338416</a>
Gigantopelta chessoia Chen & Linse & Roterman & Copley & Rogers 2015, SP. NOV.
No full textGIGANTOPELTA CHESSOIA SP. NOV. (FIGS 2–7) <p> ‘Peltospiroidea n. sp. ’ – Rogers <i>et al</i>., 2012: 7, fig. 3d. ‘Undescribed species of peltospiroid gastropod’ – Marsh <i>et al</i>., 2012: 6, fig. 5c, j.</p> <p> <i>Type material</i></p> <p> Holotype. Shell diameter 36.30 mm, 99% ethanol, Figure 3A–C. E 2 segment, East Scotia Ridge, 56°05.31′S, 30°19.10′W (‘Cindy’s Castle’), 2606 m deep, RRS <i>James Cook</i> expedition JC42, ROV <i>Isis</i> Dive 130, 20.i.2010, leg. A. D. Rogers (NHMUK 20150066). Paratypes. One dissected specimen, 99% ethanol (shell diameter 31.12 mm, Fig. 4A, B; NHMUK 20150067); growth series of five specimens, 99% ethanol (NHMUK 20150068). The above two lots have same collection data as the holotype. Growth series of five specimens, 99% ethanol (OUMNH. ZC.2013.02.002); two specimens, 99% ethanol (CAMZM 2015.2.1 -2); growth series of five specimens, 99% ethanol (SMNH Type Collection 8450); five specimens, 10% buffered formalin (NHMUK 20150069). Collection data for the latter three lots: E2 segment, East Scotia Ridge, 56°05.34′S, 30°19.07′W (‘ Cindy’s Castle’), depth 2644 m, RRS <i>James Cook</i> expedition JC42, ROV <i>Isis</i> Dive 134, 24.i.2010, leg. A. D. Rogers.</p> <p> <i>Other material examined</i></p> <p> Approximately 200 specimens collected on RRS <i>James Cook</i> expedition JC42 with ROV <i>Isis</i>, on dives 130, 134, and 141. Collection data for dive 130: same as holotype; dive 134: same as listed for paratype series; dive 141: E9 segment, East Scotia Ridge, 60°02.81′S, 29°58.71′W (‘Marsh Tower’), depth 2394 m, RRS <i>James Cook</i> expedition JC42, ROV <i>Isis</i> Dive 141, 30.i.2010, leg. A. D. Rogers.</p> <p> <i>Etymology</i></p> <p>The species is named after the ChEsSo (Chemosynthetically-driven ecosystems south of the Polar Front: biogeography and ecology) Consortium (Natural Environment Research Council (NERC) Grant NE/DO 1249X/1), which led to the discovery of ESR hydrothermal vents and this species.</p> <p> <i>Zoobank registration</i> urn:lsid:zoobank.org:act: D46EB848-506D-45B7-8D05- 35535592BD1E</p> <p> <i>Description/Diagnosis</i></p> <p> <i>Shell:</i> Shell (Fig. 4A, B) globose, three to four whorls, coiled tightly with a deep suture. Spire depressed. Aperture roughly circular, very large. Ratio of shell diameter to aperture length approximately 1:0.633 (average of 100 specimens). Shell trochiform to neritiform, holostomous. Protoconch (Fig. 5A) consists of 0.5 whorls, diameter about 210 μm. Irregular reticulate ornament present initially, becoming obsolete distally. Suture around protoconch very deep. Teleoconch smooth, no distinct sculpture. Subtle growth lines, irregular protuberances present. Growth lines stronger on the body whorl, especially near the aperture. Periostracum thick, dark olive, enveloping the aperture. Ostracum and hypostracum milky white. Thin, fragile without periostracum. Columellar folds lacking. Callus extends to slightly cover columellar. Area around callous concave. Maximum shell diameter 45.7 mm.</p> <p> <i>Operculum:</i> Operculum (Fig. 3C) with central nucleus, multispiral, thin, flaky on fringe. Operculum fringe often damaged. Juveniles operculum thin, semitransparent, fringe not flaky (Fig. 5C).</p> <p> <i>Radula:</i> Radula (Fig. 6A) rhipidoglossate. Ribbon approximately 0.5 mm wide and 4 mm long in adults. Formula ∼50 + 4 + 1 + 4 + ∼50. Central, lateral teeth cusp-like, pointed (Fig. 6C). Marginal teeth long, slender, bearing ∼20 denticles at distal end (Fig. 6E). Central tooth triangular, very broad at base, tapering dis- tally, smooth, no sculpture. Lateral teeth solid, bearing a clear protrusion at base.</p> <p> <i>Soft parts (Fig. 7A):</i> Foot muscular, large. Fully retractable into shell, red when alive. Small epipodial tentacles present, surrounding posterior two-thirds of operculum. Cephalic tentacles thick, triangular, broad at base and thinning towards tips. Eyes lacking. Snout tapering, thick. Oesophageal gland huge, approximately same size as aperture. Ctenidium bipectinate. Sexes separate. Shell muscle large, horse-shoe shaped. Intestine forms a simple loop.</p> <p> <i>Distribution</i></p> <p>Only known from hydrothermal vents on segment E2 (56°05.2′S to 56°05.4S, 30°19.00′W to 30°19.35′W) and E9 (60°02.50′S to 60°03.00′S, 29°58.60′W to 29°59.00′W) of ESR. This species forms dense aggregations rather close to vent effluents.</p> <p> <i>Remarks</i></p> <p> The dispersal mechanism is inferred to be nonplanktotrophic from the protoconch, presumably with a planktonic dispersal stage. Table 2 shows the shell parameters of <i>G. chessoia</i>. The relationships between the six shell parameters measured were investigated and they were all linear across all life stages. Figure 8 shows a scatter plot of shell diameter against shell height. See Rogers <i>et al</i>. (2012) for details on location of hydrothermal vent sites.</p> <p> <i>Comparative remarks</i></p> <p> Similar to <i>Gigantopelta aegis</i> sp. nov. described below. <i>Gigantopelta chessoia</i> can be distinguished as it has a taller spire, less extensive callus, and area around callus is concave and not flattened as in <i>G. aegis</i>. Differences are seen in the structure of the radula. The central tooth of <i>G. chessoia</i> is much wider at the base and triangular compared with that of <i>G. aegis</i>, which is rectangular. Lateral teeth are sculptured in both species, but the marks occur nearer to the base of the teeth in <i>G. aegis</i>. <i>Gigantopelta chessoia</i> can also be easily distinguished by the lack of sulphide deposits on the shell and operculum, at least from <i>G. aegis</i> found in Longqi Field, the only known habitat to date. Similarly, the operculum in <i>G. aegis</i> is much thicker than <i>G. chessoia</i> at all life stages.</p>Published as part of <i>Chen, Chong, Linse, Katrin, Roterman, Christopher N., Copley, Jonathan T. & Rogers, Alex D., 2015, A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae), pp. 319-335 in Zoological Journal of the Linnean Society (Zool. J. Linn. Soc.) (Zool. J. Linn. Soc.) 175 (2)</i> on pages 323-327, DOI: 10.1111/zoj.12279, <a href="http://zenodo.org/record/5338416">http://zenodo.org/record/5338416</a>
A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)
No full textRecently discovered hydrothermal vent fields on the East Scotia Ridge (ESR, 56–60°S, 30°W), Southern Ocean, and the South West Indian Ridge (SWIR, 37°S 49°E), Indian Ocean, host two closely related new species of peltospirid gastropods. Morphological and molecular (mitochondrial cytochrome c oxidase subunit I, COI) characterization justify the erection of Gigantopelta gen. nov. within the Peltospiroidae with two new species, Gigantopelta chessoia sp. nov. from ESR and Gigantopelta aegis sp. nov. from SWIR. They attain an extremely large size for the clade Neomphalina, reaching 45.7?mm in shell diameter. The oesophageal gland of both species is markedly enlarged. Gigantopelta aegis has a thick sulphide coating on both the shell and the operculum of unknown function. The analysis of a 579-bp fragment of the COI gene resulted in 19–28% pairwise distance between Gigantopelta and six other genera in Peltospiridae, whereas the range amongst those six genera was 12–28%. The COI divergence between the two newly described species of Gigantopelta was 4.43%. Population genetics analyses using COI (370?bp) of 30 individuals of each species confirmed their genetic isolation and indicate recent rapid demographic expansion in both species. <br/
Connectivity in the cold: the comparative population genetics of vent-endemic fauna in the Scotia Sea, Southern Ocean
No full textWe report the first comparative population genetics study for vent fauna in the Southern Ocean using cytochrome C oxidase I and microsatellite markers. Three species are examined: the kiwaid squat lobster, Kiwa tyleri, the peltospirid gastropod, Gigantopelta chessoia, and a lepetodrilid limpet, Lepetodrilus sp., collected from vent fields 440 km apart on the East Scotia Ridge (ESR) and from the Kemp Caldera on the South Sandwich Island Arc, ~95 km eastwards. We report no differentiation for all species across the ESR, consistent with panmixia or recent range expansions. A lack of differentiation is notable for Kiwa tyleri, which exhibits extremely abbreviated lecithotrophic larval development, suggestive of a very limited dispersal range. Larval lifespans may, however, be extended by low temperature-induced metabolic rate reduction in the Southern Ocean, muting the impact of dispersal strategy on patterns of population structure. COI diversity patterns suggest all species experienced demographic bottlenecks or selective sweeps in the past million years and possibly at different times. ESR and Kemp limpets are divergent, although with evidence of very recent ESR-Kemp immigration. Their divergence, possibility indicative of incipient speciation, along with the absence of the other two species at Kemp, may be the consequence of differing dispersal capabilities across a ~1000 m depth range and/or different selective regimes between the two areas. Estimates of historic and recent limpet gene flow between the ESR and Kemp are consistent with predominantly easterly currents and potentially therefore, cross-axis currents on the ESR, with biogeographic implications for the region
Figure 9. Consensus tree reconstructed from a 489 in A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)
No full textFigure 9. Consensus tree reconstructed from a 489-bp fragment of the cytochrome c oxidase subunit I gene using Bayesian inference. Node values represent Bayesian posterior probabilities.Published as part of Chen, Chong, Linse, Katrin, Roterman, Christopher N., Copley, Jonathan T. & Rogers, Alex D., 2015, A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae), pp. 319-335 in Zoological Journal of the Linnean Society (Zool. J. Linn. Soc.) 175 (2) on page 330, DOI: 10.1111/zoj.12279, http://zenodo.org/record/533841
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Figure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I in A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)
No full textFigure 10. Haplotype parsimonious networks constructed from cytochrome c oxidase subunit I sequences of 30 specimens of: A, Gigantopelta chessoia sp. nov.; B, Gigantopelta aegis sp. nov. Open circles are represented haplotypes, number inside the circles and sizes of the circles correspond to number of individuals sharing the haplotype. Filled circles are hypothesized intermediate haplotypes that are not represented by sequences.Published as part of Chen, Chong, Linse, Katrin, Roterman, Christopher N., Copley, Jonathan T. & Rogers, Alex D., 2015, A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae), pp. 319-335 in Zoological Journal of the Linnean Society (Zool. J. Linn. Soc.) 175 (2) on page 331, DOI: 10.1111/zoj.12279, http://zenodo.org/record/533841
SERPENT Cruise Reports 2008 to 2010
No full textThe SERPENT Project, Scientific & Environmental ROV Partnership using Existing iNdustrialTechnology, is a collaboration between world leading scientific institutions and companiesassociated with the oil and gas industry. SERPENT is hosted at the National OceanographyCentre, Southampton (NOCS), one of the worlds’ largest research and teaching organisationsspecialising in deep-sea science and oceanography. SERPENT encompasses a scientific networkof academic partners across the world (USA, Canada, Brazil, Africa, Australia), linked to anetwork of major oil and gas operators and contractors. The project centres around theopportunistic use of ROVs (Remotely Operated Vehicles) in operational settings during periods ofstand-by time. The project also aims to maximise the scientific benefit of environmental datacollected as part of routine offshore operations and environmental surveys. Through access toROVs and such environmental data scientists at NOCS and from the wider SERPENT partnershipaim to improve the scientific understanding of the deep-sea's biodiversity in all its aspects. Thisdocument presents the cruise reports for SERPENT missions carried out from 2008 to 2010 andincludes a history of all previous SERPENT missions
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