cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.825474.v1
title: Network models reveal stability and structural rearrangement of signal recognition particle

description: The signal recognition particle (SRP) and its receptors (SR) mediate the cotranslational targeting of the membrane and secretory proteins in all cells. In <i>Escherichia coli</i>, SRP is composed of the Ffh protein and the 4.5S SRP RNA. Ffh is a multidomain protein comprising a methionine-rich (M) domain, a helical N domain, and a Ras-like guanine triphosphatase (GTPase) (G) domain. The N and G domains are commonly referred to as one structural unit, the NG domain. In this article, the complex structure of SRP and SR is investigated with the Gaussian network model (GNM) and anisotropic network model (ANM). GNM provides the information of structure stability. It is found that the intermolecular interactions between SRP and SR can obviously decrease the fluctuation of NG domains. Nevertheless, the large structural rearrangement will take place during the cotranslational protein targeting cycle. Hence, the moving directions of fluctuation regions are further ascertained by using cross-correlation analysis and the ANM. The NG domain of Ffh undergoes a clockwise rotation around the GM linker and the M domain of Ffh shows an opposite direction to the NG domain. These functional movements will facilitate the SRP structure to transform into the free form and the sequence-bound form. These simple coarse-grained analyses can be used as a general and quick method for the mechanism studies of protein assembly and supramolecular systems.
DOI: 10.6084/m9.figshare.825475.v1
title: Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life

description: Intrinsically disordered proteins and intrinsically disordered protein regions are highly abundant in nature. However, the quantitative and qualitative measures of protein intrinsic disorder in species with known genomes are still not available. Furthermore, although the correlation between high fraction of disordered residues and advanced species has been reported, the details of this correlation and the connection between the disorder content and proteome complexity have not been reported as of yet. To fill this gap, we analysed entire proteomes of 3484 species from three domains of life (archaea, bacteria and eukaryotes) and from viruses. Our analysis revealed that the evolution process is characterized by distinctive patterns of changes in the protein intrinsic disorder content. We are showing here that viruses are characterized by the widest spread of the proteome disorder content (the percentage of disordered residues ranges from 7.3% in human coronavirus NL63 to 77.3% in <i>Avian carcinoma virus</i>). For several organisms, a clear correlation is seen between their disorder contents and habitats. In multicellular eukaryotes, there is a weak correlation between the complexity of an organism (evaluated as a number of different cell types) and its overall disorder content. For both the prokaryotes and eukaryotes, the disorder content is generally independent of the proteome size. However, disorder shows a sharp increase associated with the transition from prokaryotic to eukaryotic cells. This suggests that the increased disorder content in eukaryotic proteomes might be used by nature to deal with the increased cell complexity due to the appearance of the various cellular compartments.
DOI: 10.6084/m9.figshare.825472.v1
title: Feeding habits and selectivity of the wide-eyed flounder, <i>Bothus podas</i> (Delaroche, 1809) (Bothidae) from the southern Tyrrhenian sea

description: In order to assess the diet composition of the wide-eyed flounder <i>Bothus podas</i>, we analysed the stomach contents of 388 specimens collected seasonally on sandy bottoms of the north-western coast of Sicily (central Mediterranean). The benthic communities in the same area were also studied in order to investigate the feeding selectivity of <i>B. podas</i>. The prey items found in the stomach contents analysed were mostly benthic organisms. The diet composition of <i>B. podas</i> was dominated by Gammaridea, Apseudidae and Cumacea that were also the most abundant categories in the benthic community. Active prey, such as benthic and epibenthic crustaceans, were highly selected, whereas molluscs and polychaetes were only occasionally ingested. Significant differences found in prey abundance by site were related to the different benthic compositions in the sites examined rather than to changes in the feeding behaviour of <i>B. podas</i>. Significant differences in diet by seasons were explained by the highest abundance of Caprellidea, Gammaridea and Cumacea in spring and summer. The observed feeding patterns were related to spatial and temporal variation of prey abundance in the benthos. As a result, <i>B. podas</i> can be considered an active opportunistic predator.
DOI: 10.6084/m9.figshare.825468
title: Scratch-digging sauropods, revisited

description: Unguals of sauropod dinosaurs are notable for their unusual shape and orientation, and differ from those of graviportal mammals to which they are often compared. Early in their evolution, sauropod manual unguals underwent severe reduction, being lost on all digits except digit (D)-I. In contrast, the pedal unguals become hypertrophied and laterally compressed with an unusual angled orientation. Recent workers dismissed an early suggestion of a scratch-digging function, supporting instead substrate-gripping during locomotion, although neither hypothesis has been adequately tested, and rejection of the scratch-digging hypothesis was based on inadequate comparison. Here, we show that sauropod nesting traces are morphologically consistent with being excavated by scratch-digging, and that this behaviour is also observed in extant tortoises, which possess flattened unguals with a functionally analogous orientation. In this initial qualitative study, we surveyed claw morphology and use in a range of tortoises, based on previously published accounts and observation of specimens and video footage. Our findings suggest that there is a good case for re-examining the scratch-digging hypothesis for sauropods, although further work is required. The influence of reproductive behaviours on morphology is discussed, including the suggestion that the single manus claw of sauropods may have functioned for mate-gripping during copulation.
DOI: 10.6084/m9.figshare.825467
title: Octocorallia (Cnidaria: Anthozoa) from Brazilian reefs

description: Brazilian reef octocorals have been relatively poorly studied. The last major review was published in the early 1960s by F.M. Bayer. The current study includes a full historical and literature review of Brazilian reef octocorals and lists 17 species. Four new species are described: <i>Muriceopsis metaclados</i>, <i>Leptogorgia pseudogracilis</i>, <i>Stephanogorgia rattoi</i> and <i>Trichogorgia brasiliensis</i>. Two new synonyms are proposed: <i>Olindagorgia gracilis</i> (Verrill, 1868) with <i>Olindagorgia marcgravii</i> (Bayer, 1961), and <i>Ellisella elongata</i> (Pallas, 1766) with <i>Ellisella barbadensis</i> (Duchassaing and Michelotti, 1864). Current knowledge on <i>Muriceopsis</i> is included, but the <i>Muriceopsis sulphurea</i> complex needs a thorough revision. Whenever there is not a recent evaluation of a species, it is fully described and illustrated, its main synonymies are included, and distributional ranges are indicated. An identification key is provided.
DOI: 10.6084/m9.figshare.825468.v1
title: Scratch-digging sauropods, revisited

description: Unguals of sauropod dinosaurs are notable for their unusual shape and orientation, and differ from those of graviportal mammals to which they are often compared. Early in their evolution, sauropod manual unguals underwent severe reduction, being lost on all digits except digit (D)-I. In contrast, the pedal unguals become hypertrophied and laterally compressed with an unusual angled orientation. Recent workers dismissed an early suggestion of a scratch-digging function, supporting instead substrate-gripping during locomotion, although neither hypothesis has been adequately tested, and rejection of the scratch-digging hypothesis was based on inadequate comparison. Here, we show that sauropod nesting traces are morphologically consistent with being excavated by scratch-digging, and that this behaviour is also observed in extant tortoises, which possess flattened unguals with a functionally analogous orientation. In this initial qualitative study, we surveyed claw morphology and use in a range of tortoises, based on previously published accounts and observation of specimens and video footage. Our findings suggest that there is a good case for re-examining the scratch-digging hypothesis for sauropods, although further work is required. The influence of reproductive behaviours on morphology is discussed, including the suggestion that the single manus claw of sauropods may have functioned for mate-gripping during copulation.
DOI: 10.6084/m9.figshare.825467.v1
title: Octocorallia (Cnidaria: Anthozoa) from Brazilian reefs

description: Brazilian reef octocorals have been relatively poorly studied. The last major review was published in the early 1960s by F.M. Bayer. The current study includes a full historical and literature review of Brazilian reef octocorals and lists 17 species. Four new species are described: <i>Muriceopsis metaclados</i>, <i>Leptogorgia pseudogracilis</i>, <i>Stephanogorgia rattoi</i> and <i>Trichogorgia brasiliensis</i>. Two new synonyms are proposed: <i>Olindagorgia gracilis</i> (Verrill, 1868) with <i>Olindagorgia marcgravii</i> (Bayer, 1961), and <i>Ellisella elongata</i> (Pallas, 1766) with <i>Ellisella barbadensis</i> (Duchassaing and Michelotti, 1864). Current knowledge on <i>Muriceopsis</i> is included, but the <i>Muriceopsis sulphurea</i> complex needs a thorough revision. Whenever there is not a recent evaluation of a species, it is fully described and illustrated, its main synonymies are included, and distributional ranges are indicated. An identification key is provided.
DOI: 10.6084/m9.figshare.825455
title: Hybridization network for the system of woody plant gene pools in the United States

description: Hybridization generates similarities among gene pools. This structure can be visualized and analyzed at the systems level using networks. Here we construct a network of the 315 woody plant species native or naturalized in the United States using data compiled by the Forest Service of the US Department of Agriculture (USFS). Each species is represented by a node in the network whose size is proportional to a recent census for live stems in the continental United States. Each of the 416 links between node pairs represents evidence for hybridization compiled from the USFS manual <i>Silvics of North America</i>. The total network resolved into 100 separate connected components or clusters (mean size, 3.15 species), with 44% of species linked to at least one other. <i>Betula</i> had the largest component (18 species) following by the separate <i>Quercus</i> clusters (17 red oaks and 16 white oaks); <i>Q. velutina</i> was the most genetically connected woody plant in the continental US. The number of species held together per component (i.e. size) scaled as a power–law albeit a slightly truncated one. The truncation suggests there are fewer than expected hybridizing species within the large woody genera of plants in the US.
DOI: 10.6084/m9.figshare.825455.v1
title: Hybridization network for the system of woody plant gene pools in the United States

description: Hybridization generates similarities among gene pools. This structure can be visualized and analyzed at the systems level using networks. Here we construct a network of the 315 woody plant species native or naturalized in the United States using data compiled by the Forest Service of the US Department of Agriculture (USFS). Each species is represented by a node in the network whose size is proportional to a recent census for live stems in the continental United States. Each of the 416 links between node pairs represents evidence for hybridization compiled from the USFS manual <i>Silvics of North America</i>. The total network resolved into 100 separate connected components or clusters (mean size, 3.15 species), with 44% of species linked to at least one other. <i>Betula</i> had the largest component (18 species) following by the separate <i>Quercus</i> clusters (17 red oaks and 16 white oaks); <i>Q. velutina</i> was the most genetically connected woody plant in the continental US. The number of species held together per component (i.e. size) scaled as a power–law albeit a slightly truncated one. The truncation suggests there are fewer than expected hybridizing species within the large woody genera of plants in the US.
DOI: 10.6084/m9.figshare.825447
title: Evidence-based docking of the urease activation complex

description: <sup>1</sup>Ureases require accessory proteins for their activation and proper function. In <i>Klebsiella aerogenes</i>, UreD, UreF, UreG, and UreE are sequentially complexed to UreABC as required for its activation. Until now, only low-resolution structures are available for this activation complex. To circumvent such limitation, our work intends to provide an atomic-level model for the (UreABC–UreDFG)<sub>3</sub> complex from <i>K. aerogenes</i>, by employing comparative modeling associated to sequential macromolecular dockings, validated through small-angle X-ray scattering profiles and comparison with results from cross-linking, mutagenesis, and pull-down experiments. Additionally, normal mode analyses of the obtained complex supported the characterization of the elevated flexibility of both UreD–UreF dimer and (UreABC–UreDFG)<sub>3</sub> oligomer, explaining the previously observed diffuse binding of UreD to the apoenzyme. The model shown here is the first atomic-level depiction of this complex, a required step for the unraveling of the urease activation process. <sup>1</sup>Both authors share senior authorship. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:6
DOI: 10.6084/m9.figshare.825449
title: Elucidation by NMR solution of neurotensin in small unilamellar vesicle environment: molecular surveys for neurotensin receptor recognition

description: Neurotensin (NT) is a tridecapeptide, hormone in the periphery and neurotransmitter in the brain. We used high-resolution nuclear magnetic resonance (NMR) to resolve the three-dimensional structure of NT in a small unilamellar vesicle (SUV) environment. We demonstrate that if the dynamic of the association–dissociation processes of peptide to SUV binding is rapid enough, structural determination can be obtained by solution NMR experiments. Thus, according to the global dynamic of the system, SUVs seem to be an effective model to mimic biological membranes, especially since the lipid composition can be modified or sterols may be added to closely mimic the biological membranes studied. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:2
DOI: 10.6084/m9.figshare.825449.v1
title: Elucidation by NMR solution of neurotensin in small unilamellar vesicle environment: molecular surveys for neurotensin receptor recognition

description: Neurotensin (NT) is a tridecapeptide, hormone in the periphery and neurotransmitter in the brain. We used high-resolution nuclear magnetic resonance (NMR) to resolve the three-dimensional structure of NT in a small unilamellar vesicle (SUV) environment. We demonstrate that if the dynamic of the association–dissociation processes of peptide to SUV binding is rapid enough, structural determination can be obtained by solution NMR experiments. Thus, according to the global dynamic of the system, SUVs seem to be an effective model to mimic biological membranes, especially since the lipid composition can be modified or sterols may be added to closely mimic the biological membranes studied. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:2
DOI: 10.6084/m9.figshare.825447.v1
title: Evidence-based docking of the urease activation complex

description: <sup>1</sup>Ureases require accessory proteins for their activation and proper function. In <i>Klebsiella aerogenes</i>, UreD, UreF, UreG, and UreE are sequentially complexed to UreABC as required for its activation. Until now, only low-resolution structures are available for this activation complex. To circumvent such limitation, our work intends to provide an atomic-level model for the (UreABC–UreDFG)<sub>3</sub> complex from <i>K. aerogenes</i>, by employing comparative modeling associated to sequential macromolecular dockings, validated through small-angle X-ray scattering profiles and comparison with results from cross-linking, mutagenesis, and pull-down experiments. Additionally, normal mode analyses of the obtained complex supported the characterization of the elevated flexibility of both UreD–UreF dimer and (UreABC–UreDFG)<sub>3</sub> oligomer, explaining the previously observed diffuse binding of UreD to the apoenzyme. The model shown here is the first atomic-level depiction of this complex, a required step for the unraveling of the urease activation process. <sup>1</sup>Both authors share senior authorship. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:6
DOI: 10.6084/m9.figshare.825444
title: Diatom diversity and ecological variables in the Arctic lakes of the Kostyanoi Nos Cape (Nenetsky Natural Reserve, Russian North)

description: We identified 185 diatom species in 87 samples collected from 17 Arctic lakes of the Kostyanoi Nos Cape in July 2003. Species richness varies from 9 to 97 per lake with <i>Aulacoseira islandica</i> (O.F. Müller) Simonsen, <i>Fragilaria</i><i>mesolepta</i> Rabenhorst, <i>Psammothidium subatomoides</i> (Hustedt) L. Bukhtiyarova and Round as dominant species. Bioindication attests to preponderance of temperate, moderately oxygenated, low-to-moderate organic-enriched alkaline, and circumneutral low saline water. Oligotrophic to mesotrophic state correlates with the type of sediments and low organic pollution (saprobity index 0.81–1.73 and Classes 2–3 of water quality). The diatom assemblages contain cosmopolitan species accompanied by the large group of 45 boreal species including 28 Arctic–alpine taxa. Canonical correspondence analysis shows conductivity and the type of sediments being the most important variables. Multivariate regression testifies to importance of depth and area of the lake. The community level analysis reveals four groups correlated with species richness, type of sediments, pH, and salinity. Potential species richness is estimated as 800 species square kilometer based on species–area relationships. Since the diatom assemblages of Arctic lakes are sensitive to climate warming and associated changes of salinity and trophic conditions, they are under high risk of extinction, the diversity losses being scarcely compensated by the rise of tolerant species.
DOI: 10.6084/m9.figshare.825444.v1
title: Diatom diversity and ecological variables in the Arctic lakes of the Kostyanoi Nos Cape (Nenetsky Natural Reserve, Russian North)

description: We identified 185 diatom species in 87 samples collected from 17 Arctic lakes of the Kostyanoi Nos Cape in July 2003. Species richness varies from 9 to 97 per lake with <i>Aulacoseira islandica</i> (O.F. Müller) Simonsen, <i>Fragilaria</i><i>mesolepta</i> Rabenhorst, <i>Psammothidium subatomoides</i> (Hustedt) L. Bukhtiyarova and Round as dominant species. Bioindication attests to preponderance of temperate, moderately oxygenated, low-to-moderate organic-enriched alkaline, and circumneutral low saline water. Oligotrophic to mesotrophic state correlates with the type of sediments and low organic pollution (saprobity index 0.81–1.73 and Classes 2–3 of water quality). The diatom assemblages contain cosmopolitan species accompanied by the large group of 45 boreal species including 28 Arctic–alpine taxa. Canonical correspondence analysis shows conductivity and the type of sediments being the most important variables. Multivariate regression testifies to importance of depth and area of the lake. The community level analysis reveals four groups correlated with species richness, type of sediments, pH, and salinity. Potential species richness is estimated as 800 species square kilometer based on species–area relationships. Since the diatom assemblages of Arctic lakes are sensitive to climate warming and associated changes of salinity and trophic conditions, they are under high risk of extinction, the diversity losses being scarcely compensated by the rise of tolerant species.
DOI: 10.6084/m9.figshare.825441
title: Global survey on sequence characteristics of plant microRNA genes: <i>Cis</i>-regulatory SNPs in promoters and microRNA precursors

description: MicroRNAs (miRNAs) are tiny molecules with multiple essential roles in plant growth and development. So far, numerous miRNA families, both highly conserved and species-specific, have been identified and functionally characterized. However, we are still far from a thorough understanding of these molecules, including their sequence characteristics. In this bioinformatics study, <i>cis</i>-acting regulatory elements located within plant miRNA promoters were predicted, and a comprehensive list of single nucleotide polymorphisms (SNPs) residing within these <i>cis</i>-elements, designated as <i>cis</i>-regulatory SNPs, was identified. These SNPs potentially contribute to the distinct expression patterns of miRNA genes in various Arabidopsis (<i>Arabidopsis thaliana</i>) or rice (<i>Oryza sativa</i>) subspecies. Additionally, sequence conservation analysis was carried out for all the currently miRBase-registered pre-miRNAs (precursor miRNAs) belonging to numerous plant species. Together, these analyses provide a basis to gain deeper insights into the biological role of miRNA sequence characteristics.
DOI: 10.6084/m9.figshare.825441.v1
title: Global survey on sequence characteristics of plant microRNA genes: <i>Cis</i>-regulatory SNPs in promoters and microRNA precursors

description: MicroRNAs (miRNAs) are tiny molecules with multiple essential roles in plant growth and development. So far, numerous miRNA families, both highly conserved and species-specific, have been identified and functionally characterized. However, we are still far from a thorough understanding of these molecules, including their sequence characteristics. In this bioinformatics study, <i>cis</i>-acting regulatory elements located within plant miRNA promoters were predicted, and a comprehensive list of single nucleotide polymorphisms (SNPs) residing within these <i>cis</i>-elements, designated as <i>cis</i>-regulatory SNPs, was identified. These SNPs potentially contribute to the distinct expression patterns of miRNA genes in various Arabidopsis (<i>Arabidopsis thaliana</i>) or rice (<i>Oryza sativa</i>) subspecies. Additionally, sequence conservation analysis was carried out for all the currently miRBase-registered pre-miRNAs (precursor miRNAs) belonging to numerous plant species. Together, these analyses provide a basis to gain deeper insights into the biological role of miRNA sequence characteristics.