cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568746.v1
title: Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants

description: Plant microRNAs (miRNAs) are predominantly 21 nucleotides (nt) long but non-canonical lengths of 22 and 20 nt are commonly observed in diverse plant species. While miRNAs longer than 21 nt can be attributed to the neglect of unpaired bases within asymmetric bulges by the ruler function of DICER-LIKE 1 (DCL1), how 20-nt miRNA is generated remains obscure. Analysis of small RNA data revealed that 20-nt miRNA can be divided into 3 main groups featured by atypical 3′ overhangs or shorter duplex regions. Asymmetric bulges or mismatches at specific positions are commonly observed within each group and were shown to be crucial for 20-nt miRNA formation. Analysis of DCL1 cleavage sites on 20-nt miRNA precursors suggests that these determinants might alter precursor structure or trigger 3′-end decay of mature miRNA. The results herein advance our understanding of miRNA biogenesis and demonstrate that the effect of asymmetric bulges on miRNA length could be position-dependent.
DOI: 10.6084/m9.figshare.1568765.v7
title: Expression of dengue virus NS3 protein in <i>Drosophila</i> alters its susceptibility to infection

description: We developed a <i>Drosophila</i> model in which the dengue virus NS3 protein is expressed in a tissue specific and inducible manner. Dengue virus NS3 is a multifunctional protein playing a major role during viral replication. Both protease and helicase domains of NS3 are interacting with human and insect host proteins including innate immune components of the host machinery. We characterized the NS3 transgenic flies showing that NS3 expression did not affect fly development. To further study the links between NS3 and the innate immune response, we challenge the flies with gram-positive and gram-negative bacteria. Interestingly, the <i>Drosophila</i> transgenic flies expressing NS3 were more susceptible to bacterial infections than control flies. However ubiquitous or immune-specific NS3 expression affected neither the life span nor the response to a non-infectious stress of the flies. In conclusion, we generated a new <i>in vivo</i> system to study the functional impact of DENV NS3 protein on the innate immune response.
DOI: 10.6084/m9.figshare.1568745.v1
title: RAID3 - An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity

description: Aptamers are an emerging class of highly specific targeting ligands. They can be selected <i>in vitro</i> for a large variety of targets, ranging from small molecules to whole cells. Most aptamers selected are nucleic acid-based, allowing chemical synthesis and easy modification. Although their properties make them interesting drug candidates for a broad spectrum of applications and an interesting alternative to antibodies or fusion proteins, they are not yet broadly used. One major drawback of aptamers is their susceptibility to abundant serum nucleases, resulting in their fast degradation in biological fluids. Using modified nucleic acids has become a common strategy to overcome these disadvantages, greatly increasing their half-life under cell culture conditions or even <i>in vivo</i>. Whereas pre-selective modifications of the initial library for aptamer selection are relatively easy to obtain, post-selective modifications of already selected aptamers are still generally very labor-intensive and often compromise the aptamers ability to bind its target molecule.Here we report the selection, characterization and post-selective modification of a 34 nucleotide (nt) RNA aptamer for a non-dominant, novel target site (domain 3) of the interleukin-6 receptor (IL-6R). We performed structural analyses and investigated the affinity of the aptamer to the membrane-bound and soluble forms (sIL-6R) of the IL-6R. Further, we performed structural analyses of the aptamer in solution using small-angle X-ray scattering and determined its overall shape and oligomeric state. Post-selective exchange of all pyrimidines against their 2′-fluoro analogs increased the aptamers stability significantly without compromising its affinity for the target protein. The resulting modified aptamer could be shortened to its minimal binding motif without loss of affinity.
DOI: 10.6084/m9.figshare.1568746.v3
title: Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants

description: Plant microRNAs (miRNAs) are predominantly 21 nucleotides (nt) long but non-canonical lengths of 22 and 20 nt are commonly observed in diverse plant species. While miRNAs longer than 21 nt can be attributed to the neglect of unpaired bases within asymmetric bulges by the ruler function of DICER-LIKE 1 (DCL1), how 20-nt miRNA is generated remains obscure. Analysis of small RNA data revealed that 20-nt miRNA can be divided into 3 main groups featured by atypical 3′ overhangs or shorter duplex regions. Asymmetric bulges or mismatches at specific positions are commonly observed within each group and were shown to be crucial for 20-nt miRNA formation. Analysis of DCL1 cleavage sites on 20-nt miRNA precursors suggests that these determinants might alter precursor structure or trigger 3′-end decay of mature miRNA. The results herein advance our understanding of miRNA biogenesis and demonstrate that the effect of asymmetric bulges on miRNA length could be position-dependent.
DOI: 10.6084/m9.figshare.1568746.v2
title: Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants

description: Plant microRNAs (miRNAs) are predominantly 21 nucleotides (nt) long but non-canonical lengths of 22 and 20 nt are commonly observed in diverse plant species. While miRNAs longer than 21 nt can be attributed to the neglect of unpaired bases within asymmetric bulges by the ruler function of DICER-LIKE 1 (DCL1), how 20-nt miRNA is generated remains obscure. Analysis of small RNA data revealed that 20-nt miRNA can be divided into 3 main groups featured by atypical 3′ overhangs or shorter duplex regions. Asymmetric bulges or mismatches at specific positions are commonly observed within each group and were shown to be crucial for 20-nt miRNA formation. Analysis of DCL1 cleavage sites on 20-nt miRNA precursors suggests that these determinants might alter precursor structure or trigger 3′-end decay of mature miRNA. The results herein advance our understanding of miRNA biogenesis and demonstrate that the effect of asymmetric bulges on miRNA length could be position-dependent.
DOI: 10.6084/m9.figshare.1568744
title: An ABC transporter B family protein, ABCB19, is required for cytoplasmic streaming and gravitropism of the inflorescence stems

description: A significant feature of plant cells is the extensive motility of organelles and the cytosol, which was originally defined as cytoplasmic streaming. We suggested previously that a three-way interaction between plant-specific motor proteins myosin XIs, actin filaments, and the endoplasmic reticulum (ER) was responsible for cytoplasmic streaming.<sup>1</sup> Currently, however, there are no reports of molecular components for cytoplasmic streaming other than the actin-myosin-cytoskeleton and ER-related proteins. In the present study, we found that elongated cells of inflorescence stems of <i>Arabidopsis thaliana</i> exhibit vigorous cytoplasmic streaming. Statistical analysis showed that the maximal velocity of plastid movements is 7.26 µm/s, which is much faster than the previously reported velocities of organelles. Surprisingly, the maximal velocity of streaming in the inflorescence stem cells was significantly reduced to 1.11 µm/s in an <i>Arabidopsis</i> mutant, <i>abcb19-101</i>, which lacks ATP BINDING CASSETTE SUBFAMILY B19 (ABCB19) that mediates the polar transport of the phytohormone auxin together with PIN-FORMED (PIN) proteins. Polar auxin transport establishes the auxin concentration gradient essential for plant development and tropisms. Deficiency of ABCB19 activity eventually caused enhanced gravitropic responses of the inflorescence stems and abnormally flexed inflorescence stems. These results suggest that ABCB19-mediated auxin transport plays a role not only in tropism regulation, but also in cytoplasmic streaming.
DOI: 10.6084/m9.figshare.1568745.v3
title: RAID3 - An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity

description: Aptamers are an emerging class of highly specific targeting ligands. They can be selected <i>in vitro</i> for a large variety of targets, ranging from small molecules to whole cells. Most aptamers selected are nucleic acid-based, allowing chemical synthesis and easy modification. Although their properties make them interesting drug candidates for a broad spectrum of applications and an interesting alternative to antibodies or fusion proteins, they are not yet broadly used. One major drawback of aptamers is their susceptibility to abundant serum nucleases, resulting in their fast degradation in biological fluids. Using modified nucleic acids has become a common strategy to overcome these disadvantages, greatly increasing their half-life under cell culture conditions or even <i>in vivo</i>. Whereas pre-selective modifications of the initial library for aptamer selection are relatively easy to obtain, post-selective modifications of already selected aptamers are still generally very labor-intensive and often compromise the aptamers ability to bind its target molecule.Here we report the selection, characterization and post-selective modification of a 34 nucleotide (nt) RNA aptamer for a non-dominant, novel target site (domain 3) of the interleukin-6 receptor (IL-6R). We performed structural analyses and investigated the affinity of the aptamer to the membrane-bound and soluble forms (sIL-6R) of the IL-6R. Further, we performed structural analyses of the aptamer in solution using small-angle X-ray scattering and determined its overall shape and oligomeric state. Post-selective exchange of all pyrimidines against their 2′-fluoro analogs increased the aptamers stability significantly without compromising its affinity for the target protein. The resulting modified aptamer could be shortened to its minimal binding motif without loss of affinity.
DOI: 10.6084/m9.figshare.1568744.v1
title: An ABC transporter B family protein, ABCB19, is required for cytoplasmic streaming and gravitropism of the inflorescence stems

description: A significant feature of plant cells is the extensive motility of organelles and the cytosol, which was originally defined as cytoplasmic streaming. We suggested previously that a three-way interaction between plant-specific motor proteins myosin XIs, actin filaments, and the endoplasmic reticulum (ER) was responsible for cytoplasmic streaming.<sup>1</sup> Currently, however, there are no reports of molecular components for cytoplasmic streaming other than the actin-myosin-cytoskeleton and ER-related proteins. In the present study, we found that elongated cells of inflorescence stems of <i>Arabidopsis thaliana</i> exhibit vigorous cytoplasmic streaming. Statistical analysis showed that the maximal velocity of plastid movements is 7.26 µm/s, which is much faster than the previously reported velocities of organelles. Surprisingly, the maximal velocity of streaming in the inflorescence stem cells was significantly reduced to 1.11 µm/s in an <i>Arabidopsis</i> mutant, <i>abcb19-101</i>, which lacks ATP BINDING CASSETTE SUBFAMILY B19 (ABCB19) that mediates the polar transport of the phytohormone auxin together with PIN-FORMED (PIN) proteins. Polar auxin transport establishes the auxin concentration gradient essential for plant development and tropisms. Deficiency of ABCB19 activity eventually caused enhanced gravitropic responses of the inflorescence stems and abnormally flexed inflorescence stems. These results suggest that ABCB19-mediated auxin transport plays a role not only in tropism regulation, but also in cytoplasmic streaming.
DOI: 10.6084/m9.figshare.1568745.v2
title: RAID3 - An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity

description: Aptamers are an emerging class of highly specific targeting ligands. They can be selected <i>in vitro</i> for a large variety of targets, ranging from small molecules to whole cells. Most aptamers selected are nucleic acid-based, allowing chemical synthesis and easy modification. Although their properties make them interesting drug candidates for a broad spectrum of applications and an interesting alternative to antibodies or fusion proteins, they are not yet broadly used. One major drawback of aptamers is their susceptibility to abundant serum nucleases, resulting in their fast degradation in biological fluids. Using modified nucleic acids has become a common strategy to overcome these disadvantages, greatly increasing their half-life under cell culture conditions or even <i>in vivo</i>. Whereas pre-selective modifications of the initial library for aptamer selection are relatively easy to obtain, post-selective modifications of already selected aptamers are still generally very labor-intensive and often compromise the aptamers ability to bind its target molecule.Here we report the selection, characterization and post-selective modification of a 34 nucleotide (nt) RNA aptamer for a non-dominant, novel target site (domain 3) of the interleukin-6 receptor (IL-6R). We performed structural analyses and investigated the affinity of the aptamer to the membrane-bound and soluble forms (sIL-6R) of the IL-6R. Further, we performed structural analyses of the aptamer in solution using small-angle X-ray scattering and determined its overall shape and oligomeric state. Post-selective exchange of all pyrimidines against their 2′-fluoro analogs increased the aptamers stability significantly without compromising its affinity for the target protein. The resulting modified aptamer could be shortened to its minimal binding motif without loss of affinity.
DOI: 10.6084/m9.figshare.1568731
title: The use of navigation systems in naturalistic driving

description: <b>Objective:</b> In this study, we assessed the use of portable navigation systems in everyday driving by applying in-vehicle naturalistic driving. <b>Method:</b> Experienced users of navigation systems, 7 females and 14 males, were provided with a specially equipped vehicle for approximately 1 month. Their trips were recorded using 4 cameras, Global Positioning System (GPS) data, and other sensor data. The drivers’ navigation system use data were coded from the video recordings, which showed how often and for how long the system was activated and how often and for how long a driver operated the system. <b>Results:</b> The system was activated for 23% of trips, predominantly on longer and unique trips. Analyses of the percentage of time for which the speed limit was exceeded showed no evidence of differences between trips for which the navigation system was used or not used. On trips for which the navigation system was activated, participants spent about 5% of trip time interacting with the device. About 40% of interacting behavior took place in the first 10% of the trip time, and about 35% took place while the car was standing still or moving at a very low speed; that is, 0–10 km/h. <b>Conclusion:</b> These results shed light on how and when drivers use navigation systems. They suggest that although drivers regulate their use of such systems to some extent, they often perform risky tasks while driving.
DOI: 10.6084/m9.figshare.1568731.v2
title: The use of navigation systems in naturalistic driving

description: <b>Objective:</b> In this study, we assessed the use of portable navigation systems in everyday driving by applying in-vehicle naturalistic driving. <b>Method:</b> Experienced users of navigation systems, 7 females and 14 males, were provided with a specially equipped vehicle for approximately 1 month. Their trips were recorded using 4 cameras, Global Positioning System (GPS) data, and other sensor data. The drivers’ navigation system use data were coded from the video recordings, which showed how often and for how long the system was activated and how often and for how long a driver operated the system. <b>Results:</b> The system was activated for 23% of trips, predominantly on longer and unique trips. Analyses of the percentage of time for which the speed limit was exceeded showed no evidence of differences between trips for which the navigation system was used or not used. On trips for which the navigation system was activated, participants spent about 5% of trip time interacting with the device. About 40% of interacting behavior took place in the first 10% of the trip time, and about 35% took place while the car was standing still or moving at a very low speed; that is, 0–10 km/h. <b>Conclusion:</b> These results shed light on how and when drivers use navigation systems. They suggest that although drivers regulate their use of such systems to some extent, they often perform risky tasks while driving.
DOI: 10.6084/m9.figshare.1568731.v1
title: The Use of Navigation Systems in Naturalistic Driving

description: ABSTRACTObjective: In this study we assessed the use of portable navigation systems in everyday driving by applying in-vehicle naturalistic driving. Method: Experienced users of navigation systems, seven female and fourteen male, were provided with a specially equipped vehicle for approximately one month. Their trips were recorded using four cameras, GPS data and other sensor data. The drivers' navigation-system use data were coded from the video recordings, which showed how often and for how long the system was activated and how often and for how long a driver operated the system. Results: The system was activated for 23% of trips, predominantly on longer and unique trips. Analyses of the percentage of time for which the speed limit was exceeded showed no evidence of differences between trips for which the navigation system was used or not used. On trips for which the navigation system was activated, participants spent about 5% of trip time interacting with the device. About 40% of interacting behaviour took place in the first 10% of the trip time, and about 35% took place while the car was standing still or moving at a very low speed, i.e. 0–10 km/h. Conclusion: These results shed light on how and when drivers use navigation systems. They suggest that although drivers regulate their use of such systems to some extent, they often perform risky tasks while driving.
DOI: 10.6084/m9.figshare.1568727
title: Mixture Modeling for Longitudinal Data

description: In this article, we propose an unbiased estimating equation approach for a two-component mixture model with correlated response data. We adapt the mixture-of-experts model and a generalized linear model for component distribution and mixing proportion, respectively. The new approach only requires marginal distributions of both component densities and latent variables. We use serial correlations from subjects’ subgroup memberships, which improves estimation efficiency and classification accuracy, and show that estimation consistency does not depend on the choice of the working correlation matrix. The proposed estimating equation is solved by an expectation-estimating-equation (EEE) algorithm. In the E-step of the EEE algorithm, we propose a joint imputation based on the conditional linear property for the multivariate Bernoulli distribution. In addition, we establish asymptotic properties for the proposed estimators and the convergence property using the EEE algorithm. Our method is compared to an existing competitive mixture model approach in both simulation studies and an election data application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568727.v1
title: Mixture Modeling for Longitudinal Data

description: In this article, we propose an unbiased estimating equation approach for a two-component mixture model with correlated response data. We adapt the mixture-of-experts model and a generalized linear model for component distribution and mixing proportion, respectively. The new approach only requires marginal distributions of both component densities and latent variables. We use serial correlations from subjects’ subgroup memberships, which improves estimation efficiency and classification accuracy, and show that estimation consistency does not depend on the choice of the working correlation matrix. The proposed estimating equation is solved by an expectation-estimating-equation (EEE) algorithm. In the E-step of the EEE algorithm, we propose a joint imputation based on the conditional linear property for the multivariate Bernoulli distribution. In addition, we establish asymptotic properties for the proposed estimators and the convergence property using the EEE algorithm. Our method is compared to an existing competitive mixture model approach in both simulation studies and an election data application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568725
title: Elaborate uORF/IRES features control expression and localization of human glycyl-tRNA synthetase

description: ABSTRACTThe canonical activity of glycyl-tRNA synthetase (GARS) is to charge glycine onto its cognate tRNAs. However, outside translation, GARS also participates in many other functions. A single gene encodes both the cytosolic and mitochondrial forms of GARS but two mRNA isoforms were identified. Using immunolocalization assays, <i>in vitro</i> translation assays and bicistronic constructs we provide experimental evidence that one of these mRNAs tightly controls expression and localization of human GARS. An intricate regulatory domain was found in its 5′-UTR which displays a functional Internal Ribosome Entry Site and an upstream Open Reading Frame. Together, these elements hinder the synthesis of the mitochondrial GARS and target the translation of the cytosolic enzyme to ER-bound ribosomes. This finding reveals a complex picture of GARS translation and localization in mammals. In this context, we discuss how human GARS expression could influence its moonlighting activities and its involvement in diseases.
DOI: 10.6084/m9.figshare.1568725.v1
title: Elaborate uORF/IRES features control expression and localization of human glycyl-tRNA synthetase

description: ABSTRACTThe canonical activity of glycyl-tRNA synthetase (GARS) is to charge glycine onto its cognate tRNAs. However, outside translation, GARS also participates in many other functions. A single gene encodes both the cytosolic and mitochondrial forms of GARS but two mRNA isoforms were identified. Using immunolocalization assays, <i>in vitro</i> translation assays and bicistronic constructs we provide experimental evidence that one of these mRNAs tightly controls expression and localization of human GARS. An intricate regulatory domain was found in its 5′-UTR which displays a functional Internal Ribosome Entry Site and an upstream Open Reading Frame. Together, these elements hinder the synthesis of the mitochondrial GARS and target the translation of the cytosolic enzyme to ER-bound ribosomes. This finding reveals a complex picture of GARS translation and localization in mammals. In this context, we discuss how human GARS expression could influence its moonlighting activities and its involvement in diseases.