cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17155733.v1
title: Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves

description: Neurons have highlighted the needs for decentralized gene expression and specific RNA function in somato-dendritic and axonal compartments, as well as in intercellular communication via extracellular vesicles (EVs). Despite advances in miRNA biology, the identity and regulatory capacity of other small non-coding RNAs (sncRNAs) in neuronal models and local subdomains has been largely unexplored. We identified a highly complex and differentially localized content of sncRNAs in axons and EVs during early neuronal development of cortical primary neurons and in adult axons <i>in</i> <i>vivo</i>. This content goes far beyond miRNAs and includes most known sncRNAs and precisely processed fragments from tRNAs, sno/snRNAs, Y RNAs and vtRNAs. Although miRNAs are the major sncRNA biotype in whole-cell samples, their relative abundance is significantly decreased in axons and neuronal EVs, where specific tRNA fragments (tRFs and tRHs/tiRNAs) mainly derived from tRNAs Gly-GCC, Val-CAC and Val-AAC predominate. Notably, although 5ʹ-tRHs compose the great majority of tRNA-derived fragments observed <i>in</i> <i>vitro</i>, a shift to 3ʹ-tRNAs is observed in mature axons <i>in</i> <i>vivo</i>. The existence of these complex sncRNA populations that are specific to distinct neuronal subdomains and selectively incorporated into EVs, equip neurons with key molecular tools for spatiotemporal functional control and cell-to-cell communication.
DOI: 10.6084/m9.figshare.21776446.v1
title: Integrated multi-omics reveals common properties underlying stress granule and P-body formation

description: Non-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically and quantitatively determined the protein and mRNA composition of PBs and SGs formed before and after nutrient stress. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that we propose may act as seeds for further condensation of proteins forming mature PBs and SGs. We identify an enrichment of proteins with low complexity and RNA binding domains, as well as long, structured mRNAs that are poorly translated following nutrient stress. Many proteins and mRNAs are shared between PBs and SGs including several multivalent RNA binding proteins that promote condensate interactions during liquid-liquid phase separation. We uncover numerous common protein and RNA components across PBs and SGs that support a complex interaction profile during the maturation of these biological condensates. These interaction networks represent a tuneable response to stress, highlighting previously unrecognized condensate heterogeneity. These studies therefore provide an integrated and quantitative understanding of the dynamic nature of key biological condensates.
DOI: 10.13145/bacdive161416.20220920.7
title: <i>Sphingopyxis</i> <i>macrogoltabida</i> (Takeuchi <i>et al.</i> 1993) Takeuchi <i>et al.</i> 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.21776446
title: Integrated multi-omics reveals common properties underlying stress granule and P-body formation

description: Non-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically and quantitatively determined the protein and mRNA composition of PBs and SGs formed before and after nutrient stress. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that we propose may act as seeds for further condensation of proteins forming mature PBs and SGs. We identify an enrichment of proteins with low complexity and RNA binding domains, as well as long, structured mRNAs that are poorly translated following nutrient stress. Many proteins and mRNAs are shared between PBs and SGs including several multivalent RNA binding proteins that promote condensate interactions during liquid-liquid phase separation. We uncover numerous common protein and RNA components across PBs and SGs that support a complex interaction profile during the maturation of these biological condensates. These interaction networks represent a tuneable response to stress, highlighting previously unrecognized condensate heterogeneity. These studies therefore provide an integrated and quantitative understanding of the dynamic nature of key biological condensates.
DOI: 10.13145/bacdive161416.20221219.7.1
title: <i>Sphingopyxis</i> <i>macrogoltabida</i> (Takeuchi <i>et al.</i> 1993) Takeuchi <i>et al.</i> 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.17045676
title: A novel panel of blood-based microRNAs capable of discrimination between benign breast disease and breast cancer at early stages

description: Breast cancer (BC) as a leading cause of cancer death among women, exhibits a wide range of genetic heterogeneity in affected individuals. Satisfactory management of BC depends on early diagnosis and proper monitoring of patients’ response to therapy. In this study, we aimed to assess the relation between the expression patterns of blood-based microRNAs (miRNAs) with demographic characteristics of the patients with BC in an attempt to find novel diagnostic markers for BC with acceptable precision in clinical applications. To this end, we performed comprehensive statistical analysis of the data of the Cancer Genome Atlas (TCGA) database and the blood miRNome dataset (GSE31309). As a result, 21 miRNAs were selected for experimental verification by quantitative RT-PCR on blood samples of 70 BC patients and 60 normal individuals (without any lesions or benign breast diseases). Statistical one-way ANOVA revealed no significant difference in the blood levels of the selected miRNAs in BC patients compared to any lesions or benign breast diseases. However, the multi-marker panel consisting of hsa-miR-106b-5p, −126-3p, −140-3p, −193a-5p, and −10b-5p could detect early-stages of BC with 0.79 sensitivity, 0.86 specificity and 0.82 accuracy. Furthermore, this multi-marker panel showed the potential of detecting benign breast diseases from BC patients with 0.67 sensitivity, 0.80 specificity, and 0.74 accuracy. In conclusion, these data indicate that the present panel might be considered an asset in detecting benign breast disease and BC.
DOI: 10.6084/m9.figshare.17045676.v1
title: A novel panel of blood-based microRNAs capable of discrimination between benign breast disease and breast cancer at early stages

description: Breast cancer (BC) as a leading cause of cancer death among women, exhibits a wide range of genetic heterogeneity in affected individuals. Satisfactory management of BC depends on early diagnosis and proper monitoring of patients’ response to therapy. In this study, we aimed to assess the relation between the expression patterns of blood-based microRNAs (miRNAs) with demographic characteristics of the patients with BC in an attempt to find novel diagnostic markers for BC with acceptable precision in clinical applications. To this end, we performed comprehensive statistical analysis of the data of the Cancer Genome Atlas (TCGA) database and the blood miRNome dataset (GSE31309). As a result, 21 miRNAs were selected for experimental verification by quantitative RT-PCR on blood samples of 70 BC patients and 60 normal individuals (without any lesions or benign breast diseases). Statistical one-way ANOVA revealed no significant difference in the blood levels of the selected miRNAs in BC patients compared to any lesions or benign breast diseases. However, the multi-marker panel consisting of hsa-miR-106b-5p, −126-3p, −140-3p, −193a-5p, and −10b-5p could detect early-stages of BC with 0.79 sensitivity, 0.86 specificity and 0.82 accuracy. Furthermore, this multi-marker panel showed the potential of detecting benign breast diseases from BC patients with 0.67 sensitivity, 0.80 specificity, and 0.74 accuracy. In conclusion, these data indicate that the present panel might be considered an asset in detecting benign breast disease and BC.
DOI: 10.13145/bacdive161417.20220920.7
title: <i>Stenotrophomonas</i> <i>maltophilia</i> (Hugh 1981) Palleroni and Bradbury 1993

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161417.20221219.7.1
title: <i>Stenotrophomonas</i> <i>maltophilia</i> (Hugh 1981) Palleroni and Bradbury 1993

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.17708188.v1
title: Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts

description: The well-established Shine-Dalgarno model suggests that translation initiation in bacteria is regulated via base-pairing between ribosomal RNA (rRNA) and mRNA. We used novel computational analyses and modelling of 823 bacterial genomes coupled with experiments to demonstrate that rRNA-mRNA interactions are diverse and regulate all translation steps from pre-initiation to termination. Previous research has reported the significant influence of rRNA-mRNA interactions, mainly in the initiation phase of translation. The results reported in this paper suggest that, in addition to the rRNA-mRNA interactions near the start codon that trigger initiation in bacteria, rRNA-mRNA interactions affect all sub-stages of the translation process (pre-initiation, initiation, elongation, termination). As these interactions dictate translation efficiency, they serve as an evolutionary driving force for shaping transcripts in bacteria while considering trade-offs between the effects of different interactions across different transcript regions on translation efficacy and efficiency. We observed selection for strong interactions in regions where such interactions are likely to enhance initiation, regulate early elongation, and ensure translation termination fidelity. We discovered selection <i>against</i> strong interactions and <i>for</i> intermediate interactions in coding regions and presented evidence that these patterns maximize elongation efficiency while also enhancing initiation. These finding are relevant to all biomedical disciplines due to the centrality of the translation process and the effect of rRNA-mRNA interactions on transcript evolution.
DOI: 10.13145/bacdive161418.20220920.7
title: <i>Actinomadura</i> <i>maheshkhaliensis</i> Ara <i>et al.</i>

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.17068359
title: Maturation of 23S rRNA includes removal of helix H1 in many bacteria

description: In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as the nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails ribosomal protein binding, rRNA folding, rRNA modification, and rRNA processing. In the model organisms <i>Escherichia coli</i> and <i>Bacillus subtilis</i>, rRNA processing results in similar mature rRNAs, despite substantial differences in the cohort of RNAses involved. A recent study of <i>Flavobacterium johnsoniae</i>, a member of the phylum Bacteroidota (formerly Bacteroidetes), revealed that helix H1 of 23S rRNA is absent from ribosomes, apparently a consequence of rRNA maturation. In this work, we mined RNA-seq data from 19 individual organisms and ocean metatranscriptomic samples to compare rRNA processing across diverse bacterial lineages. We found that mature ribosomes from multiple clades lack H1, and typically these ribosomes also lack an encoded H98. For all groups analysed, H1 is predicted to form in precursor rRNA as part of a longer leader-trailer helix. Hence, we infer that evolutionary loss of H98 sets the stage for H1 removal during 50S subunit maturation.
DOI: 10.6084/m9.figshare.17068359.v1
title: Maturation of 23S rRNA includes removal of helix H1 in many bacteria

description: In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as the nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails ribosomal protein binding, rRNA folding, rRNA modification, and rRNA processing. In the model organisms <i>Escherichia coli</i> and <i>Bacillus subtilis</i>, rRNA processing results in similar mature rRNAs, despite substantial differences in the cohort of RNAses involved. A recent study of <i>Flavobacterium johnsoniae</i>, a member of the phylum Bacteroidota (formerly Bacteroidetes), revealed that helix H1 of 23S rRNA is absent from ribosomes, apparently a consequence of rRNA maturation. In this work, we mined RNA-seq data from 19 individual organisms and ocean metatranscriptomic samples to compare rRNA processing across diverse bacterial lineages. We found that mature ribosomes from multiple clades lack H1, and typically these ribosomes also lack an encoded H98. For all groups analysed, H1 is predicted to form in precursor rRNA as part of a longer leader-trailer helix. Hence, we infer that evolutionary loss of H98 sets the stage for H1 removal during 50S subunit maturation.
DOI: 10.6084/m9.figshare.17708188
title: Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts

description: The well-established Shine-Dalgarno model suggests that translation initiation in bacteria is regulated via base-pairing between ribosomal RNA (rRNA) and mRNA. We used novel computational analyses and modelling of 823 bacterial genomes coupled with experiments to demonstrate that rRNA-mRNA interactions are diverse and regulate all translation steps from pre-initiation to termination. Previous research has reported the significant influence of rRNA-mRNA interactions, mainly in the initiation phase of translation. The results reported in this paper suggest that, in addition to the rRNA-mRNA interactions near the start codon that trigger initiation in bacteria, rRNA-mRNA interactions affect all sub-stages of the translation process (pre-initiation, initiation, elongation, termination). As these interactions dictate translation efficiency, they serve as an evolutionary driving force for shaping transcripts in bacteria while considering trade-offs between the effects of different interactions across different transcript regions on translation efficacy and efficiency. We observed selection for strong interactions in regions where such interactions are likely to enhance initiation, regulate early elongation, and ensure translation termination fidelity. We discovered selection <i>against</i> strong interactions and <i>for</i> intermediate interactions in coding regions and presented evidence that these patterns maximize elongation efficiency while also enhancing initiation. These finding are relevant to all biomedical disciplines due to the centrality of the translation process and the effect of rRNA-mRNA interactions on transcript evolution.
DOI: 10.13145/bacdive161418.20221219.7.1
title: <i>Actinomadura</i> <i>maheshkhaliensis</i> Ara <i>et al.</i>

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161419.20220920.7
title: <i>Planococcus</i> <i>bengal</i> Chowdhury <i>et al.</i>

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.17198317
title: Poly C Binding Protein 2 dependent nuclear retention of the utrophin-A mRNA in C2C12 cells

description: Upregulation of utrophin, the autosomal homologue of dystrophin, can compensate dystrophin deficiency in Duchenne Muscular Dystrophy (DMD) although the therapeutic success is yet to be achieved. The present study has identified Poly (C) binding protein 2 (PCBP2) as a post-transcriptional suppresser for the expression of utrophin-A, the muscle-specific utrophin isoform. This study confirms nuclear retention of utrophin-A mRNA in C2C12 cells, which is mediated by PCBP2. Further investigation demonstrates PCBP2-dependent nuclear retention of follistatin mRNA as well. Its involvement in nuclear retention of mRNA sheds light on a novel function of PCBP2 that makes utrophin-A mRNA less available in cytosol. PCBP2, therefore, may be a target to de-repress utrophin-A expression in DMD.
DOI: 10.6084/m9.figshare.17198317.v1
title: Poly C Binding Protein 2 dependent nuclear retention of the utrophin-A mRNA in C2C12 cells

description: Upregulation of utrophin, the autosomal homologue of dystrophin, can compensate dystrophin deficiency in Duchenne Muscular Dystrophy (DMD) although the therapeutic success is yet to be achieved. The present study has identified Poly (C) binding protein 2 (PCBP2) as a post-transcriptional suppresser for the expression of utrophin-A, the muscle-specific utrophin isoform. This study confirms nuclear retention of utrophin-A mRNA in C2C12 cells, which is mediated by PCBP2. Further investigation demonstrates PCBP2-dependent nuclear retention of follistatin mRNA as well. Its involvement in nuclear retention of mRNA sheds light on a novel function of PCBP2 that makes utrophin-A mRNA less available in cytosol. PCBP2, therefore, may be a target to de-repress utrophin-A expression in DMD.
DOI: 10.13145/bacdive161419.20221219.7.1
title: <i>Planococcus</i> <i>bengal</i> Chowdhury <i>et al.</i>

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161420.20220920.7
title: <i>Pseudomonas</i> <i>aeruginosa</i> (Schroeter 1872) Migula 1900

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161420.20221219.7.1
title: <i>Pseudomonas</i> <i>aeruginosa</i> (Schroeter 1872) Migula 1900

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161421.20220920.7
title: <i>Pseudomonas</i> <i>aeruginosa</i> (Schroeter 1872) Migula 1900

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161421.20221219.7.1
title: <i>Pseudomonas</i> <i>aeruginosa</i> (Schroeter 1872) Migula 1900

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161422.20220920.7
title: <i>Pseudomonas</i> <i>aeruginosa</i> (Schroeter 1872) Migula 1900

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161422.20221219.7.1
title: <i>Pseudomonas</i> <i>aeruginosa</i> (Schroeter 1872) Migula 1900

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161423.20220920.7
title: <i>Pseudomonas</i> <i>alcaliphila</i> Yumoto <i>et al.</i> 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161423.20221219.7.1
title: <i>Pseudomonas</i> <i>alcaliphila</i> Yumoto <i>et al.</i> 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.21482326
title: Analysing the spatial syntax of Aldo van Eyck’s place-making in the Amsterdam playgrounds

description: Aldo van Eyck is attributed with designing more than 700 playgrounds which engendered revolutionary spatial concepts such as the ‘twin phenomena’ and ‘in-between.’ These concepts are examined in the literature through the definition of place alongside its ethnographic origins; however, a limited number of studies address place-making through quantitative measures. This research project investigates the correlation between van Eyck’s playgrounds and his place-making depending on the spatial configuration. It analyses the planning of 70 playgrounds based on space syntax techniques and clusters them into six groups. It discusses the playgrounds’ spatial properties through their corresponding genotypes and phenotypes. The results show that the playgrounds represent a spectrum of place-making concepts ranging from relativity to labyrinthian clarity with the twin phenomena and in-between as intermediate spatial concepts. The results augment quantitively the claims in the literature and identify each playground’s dominant place-making concept and its particular intricacies.
DOI: 10.6084/m9.figshare.21482326.v1
title: Analysing the spatial syntax of Aldo van Eyck’s place-making in the Amsterdam playgrounds

description: Aldo van Eyck is attributed with designing more than 700 playgrounds which engendered revolutionary spatial concepts such as the ‘twin phenomena’ and ‘in-between.’ These concepts are examined in the literature through the definition of place alongside its ethnographic origins; however, a limited number of studies address place-making through quantitative measures. This research project investigates the correlation between van Eyck’s playgrounds and his place-making depending on the spatial configuration. It analyses the planning of 70 playgrounds based on space syntax techniques and clusters them into six groups. It discusses the playgrounds’ spatial properties through their corresponding genotypes and phenotypes. The results show that the playgrounds represent a spectrum of place-making concepts ranging from relativity to labyrinthian clarity with the twin phenomena and in-between as intermediate spatial concepts. The results augment quantitively the claims in the literature and identify each playground’s dominant place-making concept and its particular intricacies.
DOI: 10.13145/bacdive161424.20220920.7
title: <i>Pseudomonas</i> <i>alcaliphila</i> Yumoto <i>et al.</i> 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161424.20221219.7.1
title: <i>Pseudomonas</i> <i>alcaliphila</i> Yumoto <i>et al.</i> 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161425.20220920.7
title: <i>Pseudomonas</i> <i>monteilii</i> Elomari <i>et al.</i> 1997

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161425.20221219.7.1
title: <i>Pseudomonas</i> <i>monteilii</i> Elomari <i>et al.</i> 1997

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive161426.20220920.7
title: <i>Pseudomonas</i> <i>monteilii</i> Elomari <i>et al.</i> 1997

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.