cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23360574
title: PlmCas12e (CasX2) cleavage of CCR5: impact of guide RNA spacer length and PAM sequence on cleavage activity

description: Gene editing using CRISPR/Cas (clustered regularly interspaced palindromic repeats/CRISPR-associated) is under development as a therapeutic tool for the modification of genes in eukaryotic cells. While much effort has focused on CRISPR/Cas9 systems from <i>Streptococcus pyogenes</i> and <i>Staphylococcus aureus</i>, alternative CRISPR systems have been identified from non-pathogenic microbes, including previously unknown class 2 systems, adding to a diverse toolbox of CRISPR/Cas enzymes. The Cas12e enzymes from non-pathogenic Deltaproteobacteria (CasX1, DpeCas12e) and Planctomycetes (CasX2, PlmCas12e) are smaller than Cas9, have a selective protospacer adjacent motif (PAM), and deliver a staggered cleavage cut with a 5–7 nucleotide overhang. We investigated the impact of guide RNA spacer length and alternative PAM sequences on cleavage activity to determine optimal conditions for PlmCas12e cleavage of the cellular gene <i>CCR5</i> (CC-Chemokine receptor-5). <i>CCR5</i> encodes the CCR5 coreceptor used by human immunodeficiency virus-type 1 (HIV-1) to infect target cells. A 32 base-pair deletion in <i>CCR5</i> (<i>CCR5-Δ32</i>) is responsible for HIV-1 resistance and reported cures following bone marrow transplantation. Consequently, <i>CCR5</i> has been an important target for gene editing utilizing CRISPR/Cas. We determined that <i>CCR5</i> cleavage activity varied with the target site, spacer length, and the fourth nucleotide in the previously described PAM sequence, TTCN. Our analyses demonstrated a PAM preference for purines (adenine, guanine) over pyrimidines (thymidine, cytosine) in the fourth position of the CasX2 PAM. This improved understanding of CasX2 cleavage requirements facilitates the development of therapeutic strategies to recreate the <i>CCR5-Δ32</i> mutation in haematopoietic stem cells.
DOI: 10.6084/m9.figshare.23360574.v1
title: PlmCas12e (CasX2) cleavage of CCR5: impact of guide RNA spacer length and PAM sequence on cleavage activity

description: Gene editing using CRISPR/Cas (clustered regularly interspaced palindromic repeats/CRISPR-associated) is under development as a therapeutic tool for the modification of genes in eukaryotic cells. While much effort has focused on CRISPR/Cas9 systems from <i>Streptococcus pyogenes</i> and <i>Staphylococcus aureus</i>, alternative CRISPR systems have been identified from non-pathogenic microbes, including previously unknown class 2 systems, adding to a diverse toolbox of CRISPR/Cas enzymes. The Cas12e enzymes from non-pathogenic Deltaproteobacteria (CasX1, DpeCas12e) and Planctomycetes (CasX2, PlmCas12e) are smaller than Cas9, have a selective protospacer adjacent motif (PAM), and deliver a staggered cleavage cut with a 5–7 nucleotide overhang. We investigated the impact of guide RNA spacer length and alternative PAM sequences on cleavage activity to determine optimal conditions for PlmCas12e cleavage of the cellular gene <i>CCR5</i> (CC-Chemokine receptor-5). <i>CCR5</i> encodes the CCR5 coreceptor used by human immunodeficiency virus-type 1 (HIV-1) to infect target cells. A 32 base-pair deletion in <i>CCR5</i> (<i>CCR5-Δ32</i>) is responsible for HIV-1 resistance and reported cures following bone marrow transplantation. Consequently, <i>CCR5</i> has been an important target for gene editing utilizing CRISPR/Cas. We determined that <i>CCR5</i> cleavage activity varied with the target site, spacer length, and the fourth nucleotide in the previously described PAM sequence, TTCN. Our analyses demonstrated a PAM preference for purines (adenine, guanine) over pyrimidines (thymidine, cytosine) in the fourth position of the CasX2 PAM. This improved understanding of CasX2 cleavage requirements facilitates the development of therapeutic strategies to recreate the <i>CCR5-Δ32</i> mutation in haematopoietic stem cells.
DOI: 10.6084/m9.figshare.22683584
title: MiR-2b-2-5p regulates lipid metabolism and reproduction by targeting <i>CREB</i> in <i>Bactrocera dorsalis</i>

description: In female animals, metabolic homoeostasis and reproductive fitness are critical to population expansion. The trade-off between lipid storage and reproduction inevitably occurs. However, most studies have focused on the complex network of relationships between reproductive and metabolic physiology at the transcriptional level. In this study, we identified a microRNA, miR-2b-2-5p, in a highly invasive quarantine pest, <i>Bactrocera dorsalis</i>. Knockdown of miR-2b-2-5p by antagomiR microinjection impaired ovarian development, reduced fecundity, and decreased triglyceride (TAG) storage in the fat body, whereas overexpression of miR-2b-2-5p by injection of its mimic caused reproductive defects similar to knockdown but increased TAG. Bioinformatics analysis and dual luciferase assay indicated that cyclic AMP response element (CRE)-binding protein (CREB) was the target gene of miR-2b-2-5p. RNAi-mediated knockdown of <i>CREB</i> led to excessive lipid storage and reproductive defects. Further starvation treatment revealed that miR-2b-2-5p functions by fine-tuning <i>CREB</i> expression in response to dietary stimuli. These results suggest that miR-2b-2-5p acts as a monitor to regulate <i>CREB</i> mRNA levels in the fat body, maintaining lipid homoeostasis and keeping the reproductive system on track. Thus, our study not only provides new insights into the interaction between metabolism and reproduction at the posttranscriptional level in <i>B. dorsalis</i>, but also providing a potential eco-friendly control strategy (RNAi-based biopesticides targeting essential miRNAs) for this notorious agricultural pest.
DOI: 10.6084/m9.figshare.22683584.v1
title: MiR-2b-2-5p regulates lipid metabolism and reproduction by targeting <i>CREB</i> in <i>Bactrocera dorsalis</i>

description: In female animals, metabolic homoeostasis and reproductive fitness are critical to population expansion. The trade-off between lipid storage and reproduction inevitably occurs. However, most studies have focused on the complex network of relationships between reproductive and metabolic physiology at the transcriptional level. In this study, we identified a microRNA, miR-2b-2-5p, in a highly invasive quarantine pest, <i>Bactrocera dorsalis</i>. Knockdown of miR-2b-2-5p by antagomiR microinjection impaired ovarian development, reduced fecundity, and decreased triglyceride (TAG) storage in the fat body, whereas overexpression of miR-2b-2-5p by injection of its mimic caused reproductive defects similar to knockdown but increased TAG. Bioinformatics analysis and dual luciferase assay indicated that cyclic AMP response element (CRE)-binding protein (CREB) was the target gene of miR-2b-2-5p. RNAi-mediated knockdown of <i>CREB</i> led to excessive lipid storage and reproductive defects. Further starvation treatment revealed that miR-2b-2-5p functions by fine-tuning <i>CREB</i> expression in response to dietary stimuli. These results suggest that miR-2b-2-5p acts as a monitor to regulate <i>CREB</i> mRNA levels in the fat body, maintaining lipid homoeostasis and keeping the reproductive system on track. Thus, our study not only provides new insights into the interaction between metabolism and reproduction at the posttranscriptional level in <i>B. dorsalis</i>, but also providing a potential eco-friendly control strategy (RNAi-based biopesticides targeting essential miRNAs) for this notorious agricultural pest.
DOI: 10.6084/m9.figshare.23896732
title: Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse

description: Recent reports show that long non-coding RNAs (lncRNAs) have inefficient splicing and fewer alternative splice variants than mRNAs. Here, we have explored the efficiency of lncRNAs and mRNAs in producing various splice variants, given the number of exons in humans and mice. Intriguingly, lncRNAs produce more splice variants per exon, referred to as Transcript Complexity, than mRNAs. Most lncRNA splice variants are the product of the alternative last exon and exon skipping. LncRNAs and mRNAs with higher transcript complexity have shorter intron lengths. Longer exon length and GC/AG at 5’/3’ splice sites are associated with higher transcript complexity in lncRNAs. Lastly, our results indicate that inefficient splicing of lncRNAs may facilitate multiple introns splicing and, thus, more spliced products per exon.
DOI: 10.6084/m9.figshare.23896732.v1
title: Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse

description: Recent reports show that long non-coding RNAs (lncRNAs) have inefficient splicing and fewer alternative splice variants than mRNAs. Here, we have explored the efficiency of lncRNAs and mRNAs in producing various splice variants, given the number of exons in humans and mice. Intriguingly, lncRNAs produce more splice variants per exon, referred to as Transcript Complexity, than mRNAs. Most lncRNA splice variants are the product of the alternative last exon and exon skipping. LncRNAs and mRNAs with higher transcript complexity have shorter intron lengths. Longer exon length and GC/AG at 5’/3’ splice sites are associated with higher transcript complexity in lncRNAs. Lastly, our results indicate that inefficient splicing of lncRNAs may facilitate multiple introns splicing and, thus, more spliced products per exon.
DOI: 10.6084/m9.figshare.23210832
title: PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes

description: Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from <i>Arabidopsis thaliana</i>. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.
DOI: 10.6084/m9.figshare.23210832.v1
title: PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes

description: Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from <i>Arabidopsis thaliana</i>. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.
DOI: 10.6084/m9.figshare.21770945
title: A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity

description: Riboswitches are regulatory RNAs that specifically bind a small molecule or ion. Like metabolite-binding proteins, riboswitches can evolve new ligand specificities, and some examples of this phenomenon have been validated. As part of work based on comparative genomics to discover novel riboswitches, we encountered a candidate riboswitch with striking similarities to the recently identified guanidine-IV riboswitch. This candidate riboswitch, the Gd4v motif, is predicted in four distinct bacterial phyla, thus almost as widespread as the guanidine-IV riboswitch. Bioinformatic and experimental analysis suggest that the Gd4v motif is a riboswitch that binds a ligand other than guanidine. It is found associated with gene classes that differ from genes regulated by confirmed guanidine riboswitches. In inline-probing assays, we showed that free guanidine binds only weakly to one of the tested sequences of the variant. Further tested compounds did not show binding, attenuation of transcription termination, or activation of a genetic reporter construct. We characterized an N-acetyltransferase frequently associated with the Gd4v motif and compared its substrate preference to an N-acetyltransferase that occurs under control of guanidine-IV riboswitches. The substrates of this Gd4v-motif-associated enzyme did not show activity for Gd4v RNA binding or transcription termination. Hence, the ligand of the candidate riboswitch motif remains unidentified. The variant RNA motif is predominantly found in gut metagenome sequences, hinting at a ligand that is highly relevant in this environment. This finding is a first step to determining the identity of this unknown ligand, and understanding how guanidine-IV-riboswitch-like structures can evolve to bind different ligands.
DOI: 10.6084/m9.figshare.21770945.v1
title: A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity

description: Riboswitches are regulatory RNAs that specifically bind a small molecule or ion. Like metabolite-binding proteins, riboswitches can evolve new ligand specificities, and some examples of this phenomenon have been validated. As part of work based on comparative genomics to discover novel riboswitches, we encountered a candidate riboswitch with striking similarities to the recently identified guanidine-IV riboswitch. This candidate riboswitch, the Gd4v motif, is predicted in four distinct bacterial phyla, thus almost as widespread as the guanidine-IV riboswitch. Bioinformatic and experimental analysis suggest that the Gd4v motif is a riboswitch that binds a ligand other than guanidine. It is found associated with gene classes that differ from genes regulated by confirmed guanidine riboswitches. In inline-probing assays, we showed that free guanidine binds only weakly to one of the tested sequences of the variant. Further tested compounds did not show binding, attenuation of transcription termination, or activation of a genetic reporter construct. We characterized an N-acetyltransferase frequently associated with the Gd4v motif and compared its substrate preference to an N-acetyltransferase that occurs under control of guanidine-IV riboswitches. The substrates of this Gd4v-motif-associated enzyme did not show activity for Gd4v RNA binding or transcription termination. Hence, the ligand of the candidate riboswitch motif remains unidentified. The variant RNA motif is predominantly found in gut metagenome sequences, hinting at a ligand that is highly relevant in this environment. This finding is a first step to determining the identity of this unknown ligand, and understanding how guanidine-IV-riboswitch-like structures can evolve to bind different ligands.
DOI: 10.6084/m9.figshare.23909520
title: Cup is essential for <i>oskar</i> mRNA translational repression during early <i>Drosophila</i> oogenesis

description: Study of the timing and location for mRNA translation across model systems has begun to shed light on molecular events fundamental to such processes as intercellular communication, morphogenesis, and body pattern formation. In <i>D. melanogaster</i>, the posterior mRNA determinant, <i>oskar</i>, is transcribed maternally but translated only when properly localized at the oocyte’s posterior cortex. Two effector proteins, Bruno1 and Cup, mediate steps of <i>oskar</i> mRNA regulation. The current model in the field identifies Bruno1 as necessary for Cup’s recruitment to <i>oskar</i> mRNA and indispensable for <i>oskar</i>’s translational repression. We now report that this Bruno1-Cup interaction leads to precise <i>oskar</i> mRNA regulation during early oogenesis and, importantly, the two proteins mutually influence each other’s mRNA expression and protein distribution in the egg chamber. We show that these factors stably associate with <i>oskar</i> mRNA <i>in vivo</i>. Cup associates with <i>oskar</i> mRNA without Bruno1, while surprisingly Bruno1’s stable association with <i>oskar</i> mRNA depends on Cup. We demonstrate that the essential factor for <i>oskar</i> mRNA repression in early oogenesis is Cup, not Bruno1. Furthermore, we find that Cup is a key P-body component that maintains functional P-body morphology during oogenesis and is necessary for <i>oskar</i> mRNA’s association with P-bodies. Therefore, Cup drives the translational repression and stability of <i>oskar</i> mRNA. These experimental results point to a regulatory feedback loop between Bruno 1 and Cup in early oogenesis that appears crucial for <i>oskar</i> mRNA to reach the posterior pole and its expression in the egg chamber for accurate embryo development.
DOI: 10.6084/m9.figshare.23909520.v1
title: Cup is essential for <i>oskar</i> mRNA translational repression during early <i>Drosophila</i> oogenesis

description: Study of the timing and location for mRNA translation across model systems has begun to shed light on molecular events fundamental to such processes as intercellular communication, morphogenesis, and body pattern formation. In <i>D. melanogaster</i>, the posterior mRNA determinant, <i>oskar</i>, is transcribed maternally but translated only when properly localized at the oocyte’s posterior cortex. Two effector proteins, Bruno1 and Cup, mediate steps of <i>oskar</i> mRNA regulation. The current model in the field identifies Bruno1 as necessary for Cup’s recruitment to <i>oskar</i> mRNA and indispensable for <i>oskar</i>’s translational repression. We now report that this Bruno1-Cup interaction leads to precise <i>oskar</i> mRNA regulation during early oogenesis and, importantly, the two proteins mutually influence each other’s mRNA expression and protein distribution in the egg chamber. We show that these factors stably associate with <i>oskar</i> mRNA <i>in vivo</i>. Cup associates with <i>oskar</i> mRNA without Bruno1, while surprisingly Bruno1’s stable association with <i>oskar</i> mRNA depends on Cup. We demonstrate that the essential factor for <i>oskar</i> mRNA repression in early oogenesis is Cup, not Bruno1. Furthermore, we find that Cup is a key P-body component that maintains functional P-body morphology during oogenesis and is necessary for <i>oskar</i> mRNA’s association with P-bodies. Therefore, Cup drives the translational repression and stability of <i>oskar</i> mRNA. These experimental results point to a regulatory feedback loop between Bruno 1 and Cup in early oogenesis that appears crucial for <i>oskar</i> mRNA to reach the posterior pole and its expression in the egg chamber for accurate embryo development.
DOI: 10.22003/xfel.eu-data-900430-00
title: Jungfrau at SPB  commissioning and calibration
DOI: 10.22003/xfel.eu-data-900462-00
title: Jungfrau at SPB  commissioning and calibration
DOI: 10.5281/zenodo.14853266
title: [Title removed]

description: [Description removed]
DOI: 10.5281/zenodo.14853267
title: OCHIN Database View S848

description: This dataset view was created for the following project:

Project Title: Unpacking Rural Disparities in Obesity through AI-enabled Social Determinants of Health Analysis 

Aim 1: automatic identification of SDOH information from existing limited, unstructured clinical notes in EHRs

Aim 2: efficient integration and linkage of external diverse individual and community-level SDOH data

Aim 3: sharing knowledge across multiple collaborative sites (e.g., rural hospitals) to augment and enhance their capabilities of addressing local SDOH while protecting patient privacy.

To learn more about the OCHIN data, including how to request access to the dataset, please visit: https://www.aim-ahead.net/data-and-research-core/about-ochin-ochin-data/
DOI: 10.5281/zenodo.14853305
title: [Title removed]

description: [Description removed]
DOI: 10.5281/zenodo.14853306
title: [Title removed]

description: [Description removed]
DOI: 10.5281/zenodo.14853385
title: [Title removed]

description: [Description removed]
DOI: 10.5281/zenodo.14853238
title: [Title removed]

description: [Description removed]
DOI: 10.5281/zenodo.14853239
title: [Title removed]

description: [Description removed]
DOI: 10.15468/dl.eqvzcu
title: Occurrence Download

description: A dataset containing 3743 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Anaxyrus microscaphus (Cope, 1867))"
 ]
}

 The dataset includes 3743 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000708-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14728404
title: Johan Sverdrup Oil Field | well 16/2-6 | Opensource Drilling Data

description: This dataset contains well log data, sonic signal audio, and a site map for the Johan Sverdrup well 16/2-6, drilled to a total depth of 2,131 meters in the North Sea. It includes a variety of well log measurements recorded at 50-meter intervals, such as Gamma Ray (API), Resistivity (RT), Sonic (DT), Density (RHOB), Neutron (NPHI), Porosity (PHI), Caliper (CAL), Photoelectric (PEF), Water Saturation (SW), and Permeability (mD), which provide insights into the geological and petrophysical properties of the formation. The sonic signal audio captures acoustic responses during drilling, useful for real-time analysis of subsurface conditions and potential drilling challenges. Additionally, the dataset includes a site map showing the location of the well in relation to nearby geological features and infrastructure, aiding in visualizing the well's position within the broader exploration field. This dataset is valuable for reservoir characterization, formation evaluation, and monitoring drilling conditions, and is intended for research, education, and industry analysis.