cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13312208
title: Natural variation of the cardiac transcriptome in humans

description: We investigated the gene-expression variation among humans by analysing previously published mRNA-seq and ribosome footprint profiling of heart left-ventricles from healthy donors. We ranked the genes according to their coefficient of variation values and found that the top 5% most variable genes had special features compared to the rest of the genome, such as lower mRNA levels and shorter half-lives coupled to increased translation efficiency. We observed that these genes are mostly involved with immune response and have a pleiotropic effect on disease phenotypes, indicating that asymptomatic conditions contribute to the gene expression diversity of healthy individuals.
DOI: 10.6084/m9.figshare.13312208.v1
title: Natural variation of the cardiac transcriptome in humans

description: We investigated the gene-expression variation among humans by analysing previously published mRNA-seq and ribosome footprint profiling of heart left-ventricles from healthy donors. We ranked the genes according to their coefficient of variation values and found that the top 5% most variable genes had special features compared to the rest of the genome, such as lower mRNA levels and shorter half-lives coupled to increased translation efficiency. We observed that these genes are mostly involved with immune response and have a pleiotropic effect on disease phenotypes, indicating that asymptomatic conditions contribute to the gene expression diversity of healthy individuals.
DOI: 10.6084/m9.figshare.12851768
title: The effects of gibberellin on the expression of symbiosis-related genes in <i>Paris</i>-type arbuscular mycorrhizal symbiosis in <i>Eustoma grandiflorum</i>

description: Arbuscular mycorrhiza (AM) is a symbiotic interaction in terrestrial plants that is colonized by fungi in the Glomeromycotina. The morphological types of AM, including the <i>Arum</i>-type and <i>Paris</i>-type, are distinct, depending on the host plant species. A part of the regulatory pathways in <i>Arum</i>-type AM symbiosis has been revealed because most model plants form the <i>Arum</i>-type AM with a model AM fungus, <i>Rhizophagus irregularis</i>. Moreover, gibberellin (GA) is known to severely inhibit AM fungal colonization in <i>Arum</i>-type AM symbiosis. Recently, we showed that exogenous GA treatment significantly promoted AM fungal colonization in <i>Paris</i>-type AM symbiosis in <i>Eustoma grandiflorum</i>. In this study, we focused on the transcriptional changes in AM symbiosis-related genes in GA-treated <i>E. grandiflorum</i>. The expression levels of all examined <i>E. grandiflorum</i> genes were maintained or increased by GA treatment compared with those of the control treatment. Our new results suggest that signaling pathway(s) required for establishing AM symbiosis in <i>E. grandiflorum</i> may be distinct from the well-characterized pathway for that in model plants.
DOI: 10.6084/m9.figshare.12851768.v1
title: The effects of gibberellin on the expression of symbiosis-related genes in <i>Paris</i>-type arbuscular mycorrhizal symbiosis in <i>Eustoma grandiflorum</i>

description: Arbuscular mycorrhiza (AM) is a symbiotic interaction in terrestrial plants that is colonized by fungi in the Glomeromycotina. The morphological types of AM, including the <i>Arum</i>-type and <i>Paris</i>-type, are distinct, depending on the host plant species. A part of the regulatory pathways in <i>Arum</i>-type AM symbiosis has been revealed because most model plants form the <i>Arum</i>-type AM with a model AM fungus, <i>Rhizophagus irregularis</i>. Moreover, gibberellin (GA) is known to severely inhibit AM fungal colonization in <i>Arum</i>-type AM symbiosis. Recently, we showed that exogenous GA treatment significantly promoted AM fungal colonization in <i>Paris</i>-type AM symbiosis in <i>Eustoma grandiflorum</i>. In this study, we focused on the transcriptional changes in AM symbiosis-related genes in GA-treated <i>E. grandiflorum</i>. The expression levels of all examined <i>E. grandiflorum</i> genes were maintained or increased by GA treatment compared with those of the control treatment. Our new results suggest that signaling pathway(s) required for establishing AM symbiosis in <i>E. grandiflorum</i> may be distinct from the well-characterized pathway for that in model plants.
DOI: 10.6084/m9.figshare.13157978
title: LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients

description: The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and <i>C.elegans</i>. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.
DOI: 10.6084/m9.figshare.13536389.v2
title: Nuclear SR-protein mediated mRNA quality control is continued in cytoplasmic nonsense-mediated decay

description: One important task of eukaryotic cells is to translate only mRNAs that were correctly processed to prevent the production of truncated proteins, found in neurodegenerative diseases and cancer. Nuclear quality control of splicing requires the SR-like proteins Gbp2 and Hrb1 in <i>S. cerevisiae</i>, where they promote the degradation of faulty pre-mRNAs. Here we show that Gbp2 and Hrb1 also function in nonsense mediated decay (NMD) of spliced premature termination codon (PTC)-containing mRNAs. Our data support a model in which they are in a complex with the Upf-proteins and help to transmit the Upf1-mediated PTC recognition to the transcripts ends. Most importantly they appear to promote translation repression of spliced transcripts that contain a PTC and to finally facilitate degradation of the RNA, presumably by supporting the recruitment of the degradation factors. Therefore, they seem to control mRNA quality beyond the nuclear border and may thus be global surveillance factors. Identification of SR-proteins as general cellular surveillance factors in yeast will help to understand the complex human system in which many diseases with defects in SR-proteins or NMD are known, but the proteins were not yet recognized as general RNA surveillance factors.
DOI: 10.6084/m9.figshare.13157978.v1
title: LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients

description: The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and <i>C.elegans</i>. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.
DOI: 10.6084/m9.figshare.13536389
title: Nuclear SR-protein mediated mRNA quality control is continued in cytoplasmic nonsense-mediated decay

description: One important task of eukaryotic cells is to translate only mRNAs that were correctly processed to prevent the production of truncated proteins, found in neurodegenerative diseases and cancer. Nuclear quality control of splicing requires the SR-like proteins Gbp2 and Hrb1 in <i>S. cerevisiae</i>, where they promote the degradation of faulty pre-mRNAs. Here we show that Gbp2 and Hrb1 also function in nonsense mediated decay (NMD) of spliced premature termination codon (PTC)-containing mRNAs. Our data support a model in which they are in a complex with the Upf-proteins and help to transmit the Upf1-mediated PTC recognition to the transcripts ends. Most importantly they appear to promote translation repression of spliced transcripts that contain a PTC and to finally facilitate degradation of the RNA, presumably by supporting the recruitment of the degradation factors. Therefore, they seem to control mRNA quality beyond the nuclear border and may thus be global surveillance factors. Identification of SR-proteins as general cellular surveillance factors in yeast will help to understand the complex human system in which many diseases with defects in SR-proteins or NMD are known, but the proteins were not yet recognized as general RNA surveillance factors.
DOI: 10.6084/m9.figshare.13536389.v1
title: Nuclear SR-protein mediated mRNA quality control is continued in cytoplasmic nonsense-mediated decay

description: One important task of eukaryotic cells is to translate only mRNAs that were correctly processed to prevent the production of truncated proteins, found in neurodegenerative diseases and cancer. Nuclear quality control of splicing requires the SR-like proteins Gbp2 and Hrb1 in <i>S. cerevisiae</i>, where they promote the degradation of faulty pre-mRNAs. Here we show that Gbp2 and Hrb1 also function in nonsense mediated decay (NMD) of spliced premature termination codon (PTC)-containing mRNAs. Our data support a model in which they are in a complex with the Upf-proteins and help to transmit the Upf1-mediated PTC recognition to the transcripts ends. Most importantly they appear to promote translation repression of spliced transcripts that contain a PTC and to finally facilitate degradation of the RNA, presumably by supporting the recruitment of the degradation factors. Therefore, they seem to control mRNA quality beyond the nuclear border and may thus be global surveillance factors. Identification of SR-proteins as general cellular surveillance factors in yeast will help to understand the complex human system in which many diseases with defects in SR-proteins or NMD are known, but the proteins were not yet recognized as general RNA surveillance factors.
DOI: 10.5517/ccdc.csd.cc13tvc4
title: CCDC 1037736: Experimental Crystal Structure Determination

description: Related Article: Juan Chirinos, Darmenia Ibarra, Ángel Morillo, Ligia Llovera, Teresa González, Jeannette Zárraga, Oswaldo Larreal, Mayamarú Guerra|2021|Polyhedron|203|115232|doi:10.1016/j.poly.2021.115232
DOI: 10.5517/ccdc.csd.cc23g0sd
title: CCDC 1949893: Experimental Crystal Structure Determination

description: Related Article: Hiroaki Iwamoto, Yu Ozawa, Yuta Takenouchi, Tsuneo Imamoto, Hajime Ito|2021|J.Am.Chem.Soc.|143|6413|doi:10.1021/jacs.0c08899
DOI: 10.5517/ccdc.csd.cc23g0tf
title: CCDC 1949894: Experimental Crystal Structure Determination

description: Related Article: Hiroaki Iwamoto, Yu Ozawa, Yuta Takenouchi, Tsuneo Imamoto, Hajime Ito|2021|J.Am.Chem.Soc.|143|6413|doi:10.1021/jacs.0c08899
DOI: 10.5517/ccdc.csd.cc25k8z0
title: CCDC 2012612: Experimental Crystal Structure Determination

description: Related Article: Hiroaki Iwamoto, Yu Ozawa, Yuta Takenouchi, Tsuneo Imamoto, Hajime Ito|2021|J.Am.Chem.Soc.|143|6413|doi:10.1021/jacs.0c08899
DOI: 10.5517/ccdc.csd.cc25k902
title: CCDC 2012613: Experimental Crystal Structure Determination

description: Related Article: Hiroaki Iwamoto, Yu Ozawa, Yuta Takenouchi, Tsuneo Imamoto, Hajime Ito|2021|J.Am.Chem.Soc.|143|6413|doi:10.1021/jacs.0c08899
DOI: 10.5517/ccdc.csd.cc25ln8q
title: CCDC 2013923: Experimental Crystal Structure Determination

description: Related Article: Hiroaki Iwamoto, Yu Ozawa, Yuta Takenouchi, Tsuneo Imamoto, Hajime Ito|2021|J.Am.Chem.Soc.|143|6413|doi:10.1021/jacs.0c08899
DOI: 10.5517/ccdc.csd.cc2667f3
title: CCDC 2031784: Experimental Crystal Structure Determination

description: Related Article: Nozomi Tomioka, Tomoyo Misawa-Suzuki, Hirotaka Nagao|2021|Polyhedron|202|115193|doi:10.1016/j.poly.2021.115193
DOI: 10.5517/ccdc.csd.cc26hv0l
title: CCDC 2041009: Experimental Crystal Structure Determination

description: Related Article: Nozomi Tomioka, Tomoyo Misawa-Suzuki, Hirotaka Nagao|2021|Polyhedron|202|115193|doi:10.1016/j.poly.2021.115193
DOI: 10.5517/ccdc.csd.cc26y7l0
title: CCDC 2053892: Experimental Crystal Structure Determination

description: Related Article: Ying-Zhou Li, Zhi-Rui Yuan, Rakesh Ganguly, Yongxin Li, Deborah Roshni Rajaratnam, Weng Kee Leong|2021|J.Organomet.Chem.|942|121817|doi:10.1016/j.jorganchem.2021.121817
DOI: 10.5517/ccdc.csd.cc26y7m1
title: CCDC 2053893: Experimental Crystal Structure Determination

description: Related Article: Ying-Zhou Li, Zhi-Rui Yuan, Rakesh Ganguly, Yongxin Li, Deborah Roshni Rajaratnam, Weng Kee Leong|2021|J.Organomet.Chem.|942|121817|doi:10.1016/j.jorganchem.2021.121817
DOI: 10.5517/ccdc.csd.cc26y7n2
title: CCDC 2053894: Experimental Crystal Structure Determination

description: Related Article: Ying-Zhou Li, Zhi-Rui Yuan, Rakesh Ganguly, Yongxin Li, Deborah Roshni Rajaratnam, Weng Kee Leong|2021|J.Organomet.Chem.|942|121817|doi:10.1016/j.jorganchem.2021.121817
DOI: 10.5517/ccdc.csd.cc26y7p3
title: CCDC 2053895: Experimental Crystal Structure Determination

description: Related Article: Ying-Zhou Li, Zhi-Rui Yuan, Rakesh Ganguly, Yongxin Li, Deborah Roshni Rajaratnam, Weng Kee Leong|2021|J.Organomet.Chem.|942|121817|doi:10.1016/j.jorganchem.2021.121817
DOI: 10.5517/ccdc.csd.cc26y7q4
title: CCDC 2053896: Experimental Crystal Structure Determination

description: Related Article: Ying-Zhou Li, Zhi-Rui Yuan, Rakesh Ganguly, Yongxin Li, Deborah Roshni Rajaratnam, Weng Kee Leong|2021|J.Organomet.Chem.|942|121817|doi:10.1016/j.jorganchem.2021.121817
DOI: 10.5517/ccdc.csd.cc2465dy
title: CCDC 1972139: Experimental Crystal Structure Determination

description: Related Article: Nozomi Tomioka, Tomoyo Misawa-Suzuki, Hirotaka Nagao|2021|Polyhedron|202|115193|doi:10.1016/j.poly.2021.115193
DOI: 10.5517/ccdc.csd.cc27717s
title: CCDC 2062344: Experimental Crystal Structure Determination

description: Related Article: Ying-Zhou Li, Zhi-Rui Yuan, Rakesh Ganguly, Yongxin Li, Deborah Roshni Rajaratnam, Weng Kee Leong|2021|J.Organomet.Chem.|942|121817|doi:10.1016/j.jorganchem.2021.121817
DOI: 10.5517/ccdc.csd.cc27719v
title: CCDC 2062346: Experimental Crystal Structure Determination

description: Related Article: Ying-Zhou Li, Zhi-Rui Yuan, Rakesh Ganguly, Yongxin Li, Deborah Roshni Rajaratnam, Weng Kee Leong|2021|J.Organomet.Chem.|942|121817|doi:10.1016/j.jorganchem.2021.121817
DOI: 10.5517/ccdc.csd.cc27718t
title: CCDC 2062345: Experimental Crystal Structure Determination

description: Related Article: Ying-Zhou Li, Zhi-Rui Yuan, Rakesh Ganguly, Yongxin Li, Deborah Roshni Rajaratnam, Weng Kee Leong|2021|J.Organomet.Chem.|942|121817|doi:10.1016/j.jorganchem.2021.121817
DOI: 10.5281/zenodo.4666523
title: Molecular Dynamics of Janus Nanodimers Dispersed in Lamellar Phases of a Block Copolymer (Dataset 2 of 2)

description: <strong>Abstract:</strong> We investigate structural and dynamical properties of Janus nanodimers (NDs) dispersed in lamellar phases of a diblock copolymer. By performing Molecular Dynamics simulations, we show that an accurate tuning of the interactions between NDs and copolymer blocks can lead to a close control of NDs' space distribution and orientation. In particular, NDs are preferentially found within the lamellae if enthalpy-driven forces offset their entropic counterpart. By contrast, when enthalpic interactions are relatively mild, then excluded-volume effects become dominant and NDs are essentially observed within the inter-lamellar spacing. Not only does the degree of affinity between host and guest species drive the ND's distribution in the polymer matrix, but it also determines their space orientation. In turns, these key structural properties influence the long-time dynamics and the ability of NDs to diffuse through the polymer matrix. <strong>Dataset (2/2):</strong> <strong>Systems included:</strong> H0-NDs (wpc1.NH0.*.zip, wpc5.NH0.*.zip, and wpc10.NH0.*.zip) HT-NDs (wpc1.NHT.*.zip, wpc5.NHT.*.zip, and wpc10.NHT.*.zip) <strong>Data included:</strong> Lin-spaced trajectories: \(t=10^8\,\delta t\), \(\Delta t=5\cdot10^5\,\delta t\) (*.lintraj.zip). Log-spaced trajectories: \(t=10^8\,\delta t\). 74 configurations, i.e. 8 decades. (*.logtraj.zip). Results obtained from trajectories and LAMMPS log files (*.results.zip). Structural results were obtained from a file containing some ignored duplicated configurations that have been removed from the uploaded files. Dynamical results were obtained from 100 files containing 55 configurations, i.e. 6 decades, too big to be uploaded to this repository (instead, a minimal log-scaled trajectory with 74 configurations encompassing the same time length of time has been uploaded; this file should reproduce a noisy version of the MSDs included in the results).* LAMMPS files (*.inlammps_prod.zip), including script and data file to reproduce the trajectories, as well as log file from the production run * The interested reader can contact the authors for the complete set of log-scaled trajectories (~3TB).
DOI: 10.5281/zenodo.4666522
title: Molecular Dynamics of Janus Nanodimers Dispersed in Lamellar Phases of a Block Copolymer (Dataset 2 of 2)

description: <strong>Abstract:</strong> We investigate structural and dynamical properties of Janus nanodimers (NDs) dispersed in lamellar phases of a diblock copolymer. By performing Molecular Dynamics simulations, we show that an accurate tuning of the interactions between NDs and copolymer blocks can lead to a close control of NDs' space distribution and orientation. In particular, NDs are preferentially found within the lamellae if enthalpy-driven forces offset their entropic counterpart. By contrast, when enthalpic interactions are relatively mild, then excluded-volume effects become dominant and NDs are essentially observed within the inter-lamellar spacing. Not only does the degree of affinity between host and guest species drive the ND's distribution in the polymer matrix, but it also determines their space orientation. In turns, these key structural properties influence the long-time dynamics and the ability of NDs to diffuse through the polymer matrix. <strong>Dataset (2/2):</strong> <strong>Systems included:</strong> H0-NDs (wpc1.NH0.*.zip, wpc5.NH0.*.zip, and wpc10.NH0.*.zip) HT-NDs (wpc1.NHT.*.zip, wpc5.NHT.*.zip, and wpc10.NHT.*.zip) <strong>Data included:</strong> Lin-spaced trajectories: \(t=10^8\,\delta t\), \(\Delta t=5\cdot10^5\,\delta t\) (*.lintraj.zip). Log-spaced trajectories: \(t=10^8\,\delta t\). 74 configurations, i.e. 8 decades. (*.logtraj.zip). Results obtained from trajectories and LAMMPS log files (*.results.zip). Structural results were obtained from a file containing some ignored duplicated configurations that have been removed from the uploaded files. Dynamical results were obtained from 100 files containing 55 configurations, i.e. 6 decades, too big to be uploaded to this repository (instead, a minimal log-scaled trajectory with 74 configurations encompassing the same time length of time has been uploaded; this file should reproduce a noisy version of the MSDs included in the results).* LAMMPS files (*.inlammps_prod.zip), including script and data file to reproduce the trajectories, as well as log file from the production run * The interested reader can contact the authors for the complete set of log-scaled trajectories (~3TB).