cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5658943.v1
title: Four-to-one coarse-grained polarisable water model for dissipative particle dynamics

description: An accurate description of long-ranged electrostatics in molecular simulations necessitates the solvent models that respond in accordance with the local electric fields. Given this fact, many polarisable versions of water models exist for molecular dynamics simulations. However, there is only one model of water which is polarisable available for dissipative particle dynamics (DPD) simulations, and it is based on three-to-one coarse-graining scheme. The recent coarse-grained models of lipids meant for biomembrane studies using DPD are MARTINI-like models and have level of coarse-graining four-to-one. So a polarisable model of water needed to study the biological processes in conjunction with these lipid models should also be of the same degree of coarse-graining. Therefore, we present a DPD model of polarisable water with degree of coarse-graining four-to-one. By reflecting the positions of two Drude oscillators, the model responds to local electric fields, setting up induced polarisation locally. The model parameters are to reproduce the relative dielectric permittivity and compressibility of water at room temperature. The validity and applicability of the water model have been ascertained through in-silico evidences presented.
DOI: 10.6084/m9.figshare.5657947
title: The first crocodylomorph from the Mesozoic of Turkey (Barremian of Zonguldak) and the dispersal of the eusuchians during the Cretaceous

description: A new crocodylomorph from the upper Barremian İncigez Formation of Zonguldak (NW Turkey) is described for the first time based on jaw and limb bone elements from the collection of the Istanbul Technical University. The material is attributed to <i>Turcosuchus okani</i> gen. et sp. nov. according to a unique combination of character states, such as a strong heterodonty, composed of non-spatulated teeth, a maximum of 10 teeth posterior to the symphysis, a sigmoidal dorsal margin of the dentary in lateral view, and a splenial excluded from the symphysis. An updated phylogenetic analysis of crocodylomorphs confirms that this new taxon belongs to the Hylaeochampsidae, and that it forms a relatively robust clade with the derived <i>Unasuchus</i>, <i>Acynodon</i>, <i>Iharkutosuchus</i> and <i>Hylaeochampsa</i>. <i>Turcosuchus</i> also presents some anatomical convergence with bernissartids, allodaposuchids, basal globidontans and other crocodylians. <i>Turcosuchus okani</i> is one of the earliest, but not basal hylaeochampsids, and the first known Early Cretaceous eusuchian outside Europe and North America. Our results support the clear geographical segregation between the Late Cretaceous tribodont eusuchians: basal globidontans in North America, and hylaeochampsids in the Tethyan area. http://zoobank.org/urn:lsid:zoobank.org:pub:7071FA88-2C3D-4814-8649-4ADB581E190A
DOI: 10.6084/m9.figshare.5657317
title: The identification of new ATAD2 bromodomain inhibitors: the application of combined ligand and structure-based virtual screening

description: Ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS) approaches were used to identify new inhibitors for ATAD2 bromodomain. The LBVS approach was used to search 23,129,083 clean compounds to identify compounds similar to an active compound with reported pIC<sub>50</sub> equal to 7.2. Based on LBVS results, 19 compounds were selected. To perform SBVS, by applying nine filters on 23,129,083 clean compounds, 1,057,060 compounds were selected. After performing SBVS on these selected compounds with idock software, 16 compounds with the lowest binding energies were selected. More accurate molecular docking analysis was performed on these 35 selected compounds by using iGEMDOCK software and six of them with the lowest binding energies were selected as hit compounds. These compounds were zinc36647229, zinc77969074, zinc13637358, zinc77971540, zinc12991296 and zinc19374204.
DOI: 10.6084/m9.figshare.5657317.v1
title: The identification of new ATAD2 bromodomain inhibitors: the application of combined ligand and structure-based virtual screening

description: Ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS) approaches were used to identify new inhibitors for ATAD2 bromodomain. The LBVS approach was used to search 23,129,083 clean compounds to identify compounds similar to an active compound with reported pIC<sub>50</sub> equal to 7.2. Based on LBVS results, 19 compounds were selected. To perform SBVS, by applying nine filters on 23,129,083 clean compounds, 1,057,060 compounds were selected. After performing SBVS on these selected compounds with idock software, 16 compounds with the lowest binding energies were selected. More accurate molecular docking analysis was performed on these 35 selected compounds by using iGEMDOCK software and six of them with the lowest binding energies were selected as hit compounds. These compounds were zinc36647229, zinc77969074, zinc13637358, zinc77971540, zinc12991296 and zinc19374204.
DOI: 10.6084/m9.figshare.5657305
title: Subcellular localization of aphidicolin biosynthetic enzymes heterologously expressed in <i>Aspergillus oryzae</i>

description: The secondary metabolite aphidicolin has previously been produced by <i>Aspergillus oryzae</i> after the heterologous expression of four biosynthetic enzymes isolated from <i>Phoma betae</i>. In this study, we examined the subcellular localization of aphidicolin biosynthetic enzymes in <i>A. oryzae</i>. Fusion of green fluorescent protein to each enzyme showed that geranylgeranyl diphosphate synthase and terpene cyclase are localized to the cytoplasm and the two monooxygenases (PbP450-1 and PbP450-2) are localized to the endoplasmic reticulum (ER). Protease protection assays revealed that the catalytic domain of both PbP450s was cytoplasmic. Deletion of transmembrane domains from both PbP450s resulted in the loss of ER localization. Particularly, a PbP450-1 mutant lacking the transmembrane domain was localized to dot-like structures, but did not colocalize with any known organelle markers. Aphidicolin biosynthesis was nearly abrogated by deletion of the transmembrane domain from PbP450-1. These results suggest that ER localization of PbP450-1 is important for aphidicolin biosynthesis. Schematic representation of localization of aphidicolin biosynthetic machinery in <i>A. oryzae.</i>
DOI: 10.6084/m9.figshare.5657305.v1
title: Subcellular localization of aphidicolin biosynthetic enzymes heterologously expressed in <i>Aspergillus oryzae</i>

description: The secondary metabolite aphidicolin has previously been produced by <i>Aspergillus oryzae</i> after the heterologous expression of four biosynthetic enzymes isolated from <i>Phoma betae</i>. In this study, we examined the subcellular localization of aphidicolin biosynthetic enzymes in <i>A. oryzae</i>. Fusion of green fluorescent protein to each enzyme showed that geranylgeranyl diphosphate synthase and terpene cyclase are localized to the cytoplasm and the two monooxygenases (PbP450-1 and PbP450-2) are localized to the endoplasmic reticulum (ER). Protease protection assays revealed that the catalytic domain of both PbP450s was cytoplasmic. Deletion of transmembrane domains from both PbP450s resulted in the loss of ER localization. Particularly, a PbP450-1 mutant lacking the transmembrane domain was localized to dot-like structures, but did not colocalize with any known organelle markers. Aphidicolin biosynthesis was nearly abrogated by deletion of the transmembrane domain from PbP450-1. These results suggest that ER localization of PbP450-1 is important for aphidicolin biosynthesis. Schematic representation of localization of aphidicolin biosynthetic machinery in <i>A. oryzae.</i>
DOI: 10.6084/m9.figshare.5657299
title: The delaying effect of alpha-glycerophosphocholine on senescence, transthyretin deposition, and osteoarthritis in senescence-accelerated mouse prone 8 mice

description: Administration of alpha-glycerophosphocholine (GPC), a choline compound in food, is expected to contribute to human health. In this study, we evaluated its effect on aging in senescence-accelerated mouse prone 8 (SAMP8) mice. Male SAMP8 mice had free access to a commercial stock diet and drinking water with or without GPC (0.07 mg/ml). Mice in the GPC group had significantly lower total senescence grading score than that of the control group at 36 weeks of age. Administration of GPC decreased the deposition of transthyretin (TTR), an amyloidogenic protein, in the brain. Aggregated TTR activated microglia and led to neuroinflammation. Thus, GPC would protect the brain by reducing TTR deposition and preventing neuroinflammation. In a histological study of knee joints, it was found that SAMP8 mice administered GPC showed decreased joint degeneration. These results suggest that GPC delays the aging process and may be a useful compound in anti-aging functional food development. Transthyretin (TTR) deposition was reduced by administration of alpha-glycerophosphocholine in senescence-accelerated mouse prone 8 mice.
DOI: 10.6084/m9.figshare.5657299.v1
title: The delaying effect of alpha-glycerophosphocholine on senescence, transthyretin deposition, and osteoarthritis in senescence-accelerated mouse prone 8 mice

description: Administration of alpha-glycerophosphocholine (GPC), a choline compound in food, is expected to contribute to human health. In this study, we evaluated its effect on aging in senescence-accelerated mouse prone 8 (SAMP8) mice. Male SAMP8 mice had free access to a commercial stock diet and drinking water with or without GPC (0.07 mg/ml). Mice in the GPC group had significantly lower total senescence grading score than that of the control group at 36 weeks of age. Administration of GPC decreased the deposition of transthyretin (TTR), an amyloidogenic protein, in the brain. Aggregated TTR activated microglia and led to neuroinflammation. Thus, GPC would protect the brain by reducing TTR deposition and preventing neuroinflammation. In a histological study of knee joints, it was found that SAMP8 mice administered GPC showed decreased joint degeneration. These results suggest that GPC delays the aging process and may be a useful compound in anti-aging functional food development. Transthyretin (TTR) deposition was reduced by administration of alpha-glycerophosphocholine in senescence-accelerated mouse prone 8 mice.
DOI: 10.6084/m9.figshare.5657293
title: A crude sword bean (<i>Canavalia gladiata</i>) extract is gelated by cooling

description: White sword bean (<i>Canavalia gladiata</i>) seeds have the potential to be utilized in the manufacturing of processed foods owing to their high protein and carbohydrate content. Our previous reports explored the use of the sword bean as a source of food materials by preparing extracts in distilled water. In the present study, we found that one such extract can be gelated by cooling. The gelling substances were extracted by boiling and simultaneously stirring a suspension containing ground beans. Few proteins were present in the gelated extract. We also examined the conditions under which gelation occurred and the gel melting temperature. The extract gelated at temperatures below 10 °C, and the resulting gel melted at those above 65 °C. This is the first report that gelling substances can be extracted from sword beans in large quantities. We expect that this gelling agent can be used for the production of processed foods. A crude sword bean (<i>Canavalia gladiata</i>) extract is gelated by cooling.
DOI: 10.6084/m9.figshare.5657293.v1
title: A crude sword bean (<i>Canavalia gladiata</i>) extract is gelated by cooling

description: White sword bean (<i>Canavalia gladiata</i>) seeds have the potential to be utilized in the manufacturing of processed foods owing to their high protein and carbohydrate content. Our previous reports explored the use of the sword bean as a source of food materials by preparing extracts in distilled water. In the present study, we found that one such extract can be gelated by cooling. The gelling substances were extracted by boiling and simultaneously stirring a suspension containing ground beans. Few proteins were present in the gelated extract. We also examined the conditions under which gelation occurred and the gel melting temperature. The extract gelated at temperatures below 10 °C, and the resulting gel melted at those above 65 °C. This is the first report that gelling substances can be extracted from sword beans in large quantities. We expect that this gelling agent can be used for the production of processed foods. A crude sword bean (<i>Canavalia gladiata</i>) extract is gelated by cooling.
DOI: 10.6084/m9.figshare.5657287
title: Characterization of <i>cis</i>-4-hydroxy-D-proline dehydrogenase from <i>Sinorhizobium meliloti</i>

description: The <i>hypO</i> gene from <i>Sinorhizobium meliloti</i>, located within the <i>trans</i>-4-hydroxy-L-proline metabolic gene cluster, was first successfully expressed in the host <i>Pseudomonas putida</i>. Purified HypO protein functioned as a FAD-containing <i>cis</i>-4-hydroxy-D-proline dehydrogenase with a homomeric structure. In contrast to other known enzymes, significant activity for D-proline was found, confirming a previously proposed potential involvement in D-proline metabolism.
DOI: 10.6084/m9.figshare.5657287.v1
title: Characterization of <i>cis</i>-4-hydroxy-D-proline dehydrogenase from <i>Sinorhizobium meliloti</i>

description: The <i>hypO</i> gene from <i>Sinorhizobium meliloti</i>, located within the <i>trans</i>-4-hydroxy-L-proline metabolic gene cluster, was first successfully expressed in the host <i>Pseudomonas putida</i>. Purified HypO protein functioned as a FAD-containing <i>cis</i>-4-hydroxy-D-proline dehydrogenase with a homomeric structure. In contrast to other known enzymes, significant activity for D-proline was found, confirming a previously proposed potential involvement in D-proline metabolism.
DOI: 10.15156/bio/sh3296737.08fu
title: SH3296737.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3296738.08fu
title: SH3296738.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3296739.08fu
title: SH3296739.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3296740.08fu
title: SH3296740.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3296741.08fu
title: SH3296741.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3296742.08fu
title: SH3296742.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3296743.08fu
title: SH3296743.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3296744.08fu
title: SH3296744.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.