cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12851726.v1
title: LINC-complex mediated positioning of the vegetative nucleus is involved in calcium and ROS signaling in Arabidopsis pollen tubes

description: Nuclear movement and positioning play a role in developmental processes throughout life. Nuclear movement and positioning are mediated primarily by linker of nucleoskeleton and cytoskeleton (LINC) complexes. LINC complexes are comprised of the inner nuclear membrane SUN proteins and the outer nuclear membrane (ONM) KASH proteins. In Arabidopsis pollen tubes, the vegetative nucleus (VN) maintains a fixed distance from the pollen tube tip during growth, and the VN precedes the sperm cells (SCs). In pollen tubes of <i>wit12</i> and <i>wifi</i>, mutants deficient in the ONM component of a plant LINC complex, the SCs precede the VN during pollen tube growth and the fixed VN distance from the tip is lost. Subsequently, pollen tubes frequently fail to burst upon reception. In this study, we sought to determine if the pollen tube reception defect observed in <i>wit12</i> and <i>wifi</i> is due to decreased sensitivity to reactive oxygen species (ROS). Here, we show that <i>wit12</i> and <i>wifi</i> are hyposensitive to exogenous H<sub>2</sub>O<sub>2</sub>, and that this hyposensitivity is correlated with decreased proximity of the VN to the pollen tube tip. Additionally, we report the first instance of nuclear Ca<sup>2+</sup> peaks in growing pollen tubes, which are disrupted in the <i>wit12</i> mutant. In the <i>wit12</i> mutant, nuclear Ca<sup>2+</sup> peaks are reduced in response to exogenous ROS, but these peaks are not correlated with pollen tube burst. This study finds that VN proximity to the pollen tube tip is required for both response to exogenous ROS, as well as internal nuclear Ca<sup>2+</sup> fluctuations.
DOI: 10.6084/m9.figshare.12851720.v2
title: Characterization of t-loop formation by TRF2

description: T-loops are thought to hide telomeres from DNA damage signaling and DSB repair pathways. T-loop formation requires the shelterin component TRF2, which represses ATM signaling and NHEJ. Here we establish that TRF2 alone, in the absence of other shelterin proteins can form t-loops. Mouse and human cells contain two isoforms of TRF2, one of which is uncharacterized. We show that both isoforms protect telomeres and form t-loops. The isoforms are not cell cycle regulated and t-loops are present in G1, S, and G2. Using the DNA wrapping deficient TRF2 Topless mutant, we confirm its inability to form t-loops and repress ATM. However, since the mutant is also defective in repression of NHEJ and telomeric localization, the role of topological changes in telomere protection remains unclear. Finally, we show that Rad51 does not affect t-loop frequencies or telomere protection. Therefore, alternative models for how TRF2 forms t-loops should be explored.
DOI: 10.6084/m9.figshare.11635989.v1
title: The role of phosphorylation in the elasticity of the tethers that connect telomeres of separating anaphase chromosomes

description: Elastic tethers, connecting telomeres of all separating anaphase chromosome pairs, lose elasticity when they lengthen during anaphase. Treatment with phosphatase inhibitor CalyculinA causes anaphase chromosomes to move backwards after they reach the poles, suggesting that dephosphorylation causes loss of tether elasticity. We added 50nM CalyculinA to living anaphase crane-fly spermatocytes with different length tethers. When tethers were short, almost all partner chromosomes moved backwards after nearing the poles. When tethers were longer, fewer chromosomes moved backwards. With yet longer tethers none moved backward. This is consistent with tether elasticity being lost by dephosphorylation. 50nM CalyculinA blocks both PP1 and PP2A. To distinguish between PP1 and PP2A we treated cells with short tethers with 50nM okadaic acid which blocks solely PP2A, or with 1µM okadaic acid which blocks both PP1 and PP2A. Only 1µM okadaic acid caused chromosomes to move backward. Thus, tether elasticity is lost because of dephosphorylation by PP1.
DOI: 10.6084/m9.figshare.12851723.v1
title: Dynamics as a cause for the nanoscale organization of the genome

description: Chromatin ‘blobs’ were recently identified by live super-resolution imaging of labeled nucleosomes as pervasive but fleeting structural entities. However, the mechanisms leading to the formation of these blobs and their functional implications are unknown. We explore here whether causal relationships exist between parameters that characterize the chromatin blob dynamics and structure, by adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals that chromatin dynamics is a key determinant for both blob area and local density. Such causality, however, could be demonstrated only in 10–20% of the nucleus, suggesting that chromatin dynamics and structure at the nanometer scale are dominated by stochasticity. We show that the theory of active semiflexible polymers can be invoked to provide potential mechanisms leading to the organization of chromatin into blobs. Our results represent a first step toward elucidating the mechanisms that govern the dynamic and stochastic organization of chromatin in the cell nucleus.
DOI: 10.6084/m9.figshare.12851726
title: LINC-complex mediated positioning of the vegetative nucleus is involved in calcium and ROS signaling in Arabidopsis pollen tubes

description: Nuclear movement and positioning play a role in developmental processes throughout life. Nuclear movement and positioning are mediated primarily by linker of nucleoskeleton and cytoskeleton (LINC) complexes. LINC complexes are comprised of the inner nuclear membrane SUN proteins and the outer nuclear membrane (ONM) KASH proteins. In Arabidopsis pollen tubes, the vegetative nucleus (VN) maintains a fixed distance from the pollen tube tip during growth, and the VN precedes the sperm cells (SCs). In pollen tubes of <i>wit12</i> and <i>wifi</i>, mutants deficient in the ONM component of a plant LINC complex, the SCs precede the VN during pollen tube growth and the fixed VN distance from the tip is lost. Subsequently, pollen tubes frequently fail to burst upon reception. In this study, we sought to determine if the pollen tube reception defect observed in <i>wit12</i> and <i>wifi</i> is due to decreased sensitivity to reactive oxygen species (ROS). Here, we show that <i>wit12</i> and <i>wifi</i> are hyposensitive to exogenous H<sub>2</sub>O<sub>2</sub>, and that this hyposensitivity is correlated with decreased proximity of the VN to the pollen tube tip. Additionally, we report the first instance of nuclear Ca<sup>2+</sup> peaks in growing pollen tubes, which are disrupted in the <i>wit12</i> mutant. In the <i>wit12</i> mutant, nuclear Ca<sup>2+</sup> peaks are reduced in response to exogenous ROS, but these peaks are not correlated with pollen tube burst. This study finds that VN proximity to the pollen tube tip is required for both response to exogenous ROS, as well as internal nuclear Ca<sup>2+</sup> fluctuations.
DOI: 10.6084/m9.figshare.13199791
title: Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0

description: NucleusJ 1.0, an ImageJ plugin, is a useful tool to analyze nuclear morphology and chromatin organization in plant and animal cells. NucleusJ 2.0 is a new release of NucleusJ, in which image processing is achieved more quickly using a command-lineuser interface. Starting with large collection of 3D nuclei, segmentation can be performed by the previously developed Otsu-modified method or by a new 3D gift-wrapping method, taking better account of nuclear indentations and unstained nucleoli. These two complementary methods are compared for their accuracy by using three types of datasets available to the community at https://www.brookes.ac.uk/indepth/images/. Finally, NucleusJ 2.0 was evaluated using original plant genetic material by assessing its efficiency on nuclei stained with DNA dyes or after 3D-DNA Fluorescence <i>in situ</i> hybridization. With these improvements, NucleusJ 2.0 permits the generation of large user-curated datasets that will be useful for software benchmarking or to train convolution neural networks.
DOI: 10.6084/m9.figshare.12851720.v1
title: Characterization of t-loop formation by TRF2

description: The telomeric t-loop structure is thought to hide chromosome ends from DNA damage signaling and repair pathways that can act on DNA ends. Previously, it was shown that t-loop formation requires the shelterin component TRF2, which represses ATM signaling and Non-Homologous End Joining (NHEJ). Here we establish that TRF2 alone, in the absence of other shelterin proteins can remodel telomeres into t-loops. Mouse and human TRF2 are expressed as two isoforms, only one of which had been studied to date. Here we characterize the expression of the TRF2 isoforms and show that they are equal in their ability to protect telomeres and form t-loops. Both isoforms are expressed throughout the cell cycle and t-loop frequencies appeared unaffected by cell cycle stage. To characterize the mechanism of t-loop formation, we analyzed the TRF2 Topless mutant which is deficient in a DNA-wrapping activity implicated in t-loop formation. We confirm that TRF2 Topless is defective in t-loop formation and repression of ATM but report that it is also defective in repression of NHEJ and shows diminished telomere localization. Therefore, the role of topological changes enforced by TRF2 remains unclear. Finally, we tested whether t-loop formation, which includes a strand-invasion step, is dependent on the Rad51 recombinase. Rad51 deletion did not affect t-loop frequencies and did not induce robust telomere damage, indicating that Rad51 is not required for this aspect of telomere protection. Therefore, alternative models for how TRF2 forms t-loops should be explored.
DOI: 10.6084/m9.figshare.12851720
title: Characterization of t-loop formation by TRF2

description: T-loops are thought to hide telomeres from DNA damage signaling and DSB repair pathways. T-loop formation requires the shelterin component TRF2, which represses ATM signaling and NHEJ. Here we establish that TRF2 alone, in the absence of other shelterin proteins can form t-loops. Mouse and human cells contain two isoforms of TRF2, one of which is uncharacterized. We show that both isoforms protect telomeres and form t-loops. The isoforms are not cell cycle regulated and t-loops are present in G1, S, and G2. Using the DNA wrapping deficient TRF2 Topless mutant, we confirm its inability to form t-loops and repress ATM. However, since the mutant is also defective in repression of NHEJ and telomeric localization, the role of topological changes in telomere protection remains unclear. Finally, we show that Rad51 does not affect t-loop frequencies or telomere protection. Therefore, alternative models for how TRF2 forms t-loops should be explored.
DOI: 10.15161/oar.it/73774
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.5281/zenodo.4025187
title: Dataset and R code - Crop functional diversity drives multiple ecosystem functions during early agroforestry succession

description: Dataset and the script of our analyses in the manuscript entitled: "<strong>Crop functional diversity drives multiple ecosystem functions during early agroforestry succession</strong>".
DOI: 10.5281/zenodo.4025186
title: Dataset and R code - Crop functional diversity drives multiple ecosystem functions during early agroforestry succession

description: Dataset and the script of our analyses in the manuscript entitled: "<strong>Crop functional diversity drives multiple ecosystem functions during early agroforestry succession</strong>".
DOI: 10.6084/m9.figshare.14561847
title: Supplementaries

description: metagenomic data, Supplementary tables, figures, dataset
DOI: 10.6084/m9.figshare.14561847.v1
title: Supplementaries

description: metagenomic data, Supplementary tables, figures, dataset
DOI: 10.34740/kaggle/dsv/2212569
title: Data set of Discriminant Analysis
DOI: 10.25646/8464
title: Tagesdaten-CSV aus dem DIVI-Intensivregister

description: Die Tagesdaten-CSV entspricht einem Auszug der Daten des DIVI-Intensivregisters. Die Datei enthält eine Aggregation der aktuellsten Meldungen pro Landkreis. Es werden die aktuell gemeldeten Anzahlen der COVID-19 Intensivfälle sowie die gemeldeten intensivmedizinischen Behandlungskapazitäten angezeigt. Die Tagesdaten-CSV liefert dabei ausschließlich einen Blick auf die Daten gemäß dem Stand des betrachteten Tages. Die Daten sind im situationsbedingten Kontext aufbereitet, damit sind verschiedene Tagesdaten-CSVs u.U. nicht direkt miteinander vergleichbar. Die aktuellsten Meldungen werden im gewählten Betrachtungszeitfenster über alle Meldebereiche und Standorte aufsummiert. Weitere Informationen sind zu finden unter https://www.intensivregister.de/#/faq
DOI: 10.6084/m9.figshare.12851747
title: Immediate targets of ETTIN suggest a key role for pectin methylesterase inhibitors in the control of <i>Arabidopsis</i> gynecium development

description: The control of gynecium development in <i>Arabidopsis thaliana</i> by the auxin response factor ETTIN (ETT) correlates with a reduction in the methylesterification of cell-wall pectins and a decrease in cell-wall stiffness in the valve tissues of the ovary. Here, we determine the list of genes rapidly regulated following the <i>in-vivo</i> activation of an ETT fusion protein, and show these to be significantly enriched in genes encoding cell-wall proteins, including several pectin methylesterases (PMEs) and pectin methylesterase inhibitors (PMEIs). We also perform a genome-wide scan for potential ETT-binding sites, and incorporate the results of this procedure into a comparison of datasets, derived using four distinct methods, to identify genes regulated directly or indirectly by ETT. We conclude from our combined analyses that PMEIs are likely to be key actors that mediate the regulation of gynecium development by ETT, while ETT may simultaneously regulate PMEs to prevent exaggerated developmental effects from the regulation of PMEIs. We also postulate the existence of one or more rapidly-acting intermediate factors in the transcriptional regulation of PMEs and PMEIs by ETT.
DOI: 10.6084/m9.figshare.12851744
title: Function analysis and stress-mediated <i>cis</i>-element identification in the promoter region of <i>VqMYB15</i>

description: The transcription factor <i>MYB15</i> plays an important role in grape basal immunity, and its promoter can be used as a potential target in resistance breeding. However, the regulatory mechanisms of <i>cis</i>-elements in its promoter region under a variety of stresses remain unclear. In this study, we identified some putative <i>cis</i>-regulatory elements present upstream of <i>MYB15</i> in <i>Vitis quinquangularis</i> Shanyang (<i>pVqMYB15</i>_SY) and subsequently characterized the function of these elements using reporter assays. Our results showed that TCA-elements 1 and 2, ABRE, MYC and 3-AF1 binding site 1 are key <i>cis</i>-regulatory elements in <i>pVqMYB15</i>_SY and play important roles in plant bio/abiotic stress resistance.
DOI: 10.6084/m9.figshare.12851747.v1
title: Immediate targets of ETTIN suggest a key role for pectin methylesterase inhibitors in the control of <i>Arabidopsis</i> gynecium development

description: The control of gynecium development in <i>Arabidopsis thaliana</i> by the auxin response factor ETTIN (ETT) correlates with a reduction in the methylesterification of cell-wall pectins and a decrease in cell-wall stiffness in the valve tissues of the ovary. Here, we determine the list of genes rapidly regulated following the <i>in-vivo</i> activation of an ETT fusion protein, and show these to be significantly enriched in genes encoding cell-wall proteins, including several pectin methylesterases (PMEs) and pectin methylesterase inhibitors (PMEIs). We also perform a genome-wide scan for potential ETT-binding sites, and incorporate the results of this procedure into a comparison of datasets, derived using four distinct methods, to identify genes regulated directly or indirectly by ETT. We conclude from our combined analyses that PMEIs are likely to be key actors that mediate the regulation of gynecium development by ETT, while ETT may simultaneously regulate PMEs to prevent exaggerated developmental effects from the regulation of PMEIs. We also postulate the existence of one or more rapidly-acting intermediate factors in the transcriptional regulation of PMEs and PMEIs by ETT.
DOI: 10.6084/m9.figshare.12851744.v1
title: Function analysis and stress-mediated <i>cis</i>-element identification in the promoter region of <i>VqMYB15</i>

description: The transcription factor <i>MYB15</i> plays an important role in grape basal immunity, and its promoter can be used as a potential target in resistance breeding. However, the regulatory mechanisms of <i>cis</i>-elements in its promoter region under a variety of stresses remain unclear. In this study, we identified some putative <i>cis</i>-regulatory elements present upstream of <i>MYB15</i> in <i>Vitis quinquangularis</i> Shanyang (<i>pVqMYB15</i>_SY) and subsequently characterized the function of these elements using reporter assays. Our results showed that TCA-elements 1 and 2, ABRE, MYC and 3-AF1 binding site 1 are key <i>cis</i>-regulatory elements in <i>pVqMYB15</i>_SY and play important roles in plant bio/abiotic stress resistance.
DOI: 10.6084/m9.figshare.12851771
title: Identification and characterization of a female gametophyte defect in <i>sdk1-7 +/- abi3-6 +/-</i> heterozygotes of <i>Arabidopsis thaliana</i>

description: Successful reproduction in angiosperms is dependent on the highly synchronous development of their male and female gametophytes and the ensuing fusion of the gametes from these reproductive tissue types. When crossing a T-DNA insertion line <i>sdk1-7-/-</i>(Salk_024564), one of the S-domain receptor kinases involved in ABA responses with a fast neutron deletion line <i>abi3-6-/-</i>, the F1 heterozygotes (<i>sdk1-7+/-abi3-6</i> +/-) displayed 50% ovule abortion suggesting a likely gametophytic defects. We identified and characterized an early stage female gametophyte developmental defect in the heterozygous mutant ovules. Recombination frequency analysis of the F2 progenies from selfed heterozygotes revealed a possible pseudo-linkage of <i>sdk1-7</i> and <i>abi3-6</i> suggesting a reciprocal translocation event in the heterozygote. Our study emphasizes the importance of robust analysis to distinguish gametophytic defect phenotypes caused by genetic interactions and that resulting from possible chromosomal translocation events.
DOI: 10.6084/m9.figshare.12851771.v1
title: Identification and characterization of a female gametophyte defect in <i>sdk1-7 +/- abi3-6 +/-</i> heterozygotes of <i>Arabidopsis thaliana</i>

description: Successful reproduction in angiosperms is dependent on the highly synchronous development of their male and female gametophytes and the ensuing fusion of the gametes from these reproductive tissue types. When crossing a T-DNA insertion line <i>sdk1-7-/-</i>(Salk_024564), one of the S-domain receptor kinases involved in ABA responses with a fast neutron deletion line <i>abi3-6-/-</i>, the F1 heterozygotes (<i>sdk1-7+/-abi3-6</i> +/-) displayed 50% ovule abortion suggesting a likely gametophytic defects. We identified and characterized an early stage female gametophyte developmental defect in the heterozygous mutant ovules. Recombination frequency analysis of the F2 progenies from selfed heterozygotes revealed a possible pseudo-linkage of <i>sdk1-7</i> and <i>abi3-6</i> suggesting a reciprocal translocation event in the heterozygote. Our study emphasizes the importance of robust analysis to distinguish gametophytic defect phenotypes caused by genetic interactions and that resulting from possible chromosomal translocation events.
DOI: 10.6084/m9.figshare.12851762
title: Identification and characterization of caleosin in <i>Cycas revoluta</i> pollen

description: Oil bodies are essential energy storage organelles that are generally present in the seeds of plants. Caleosin protein has been identified in the seed oil bodies of <i>Cycas revoluta</i>seed. In this study, mature <i>Cycas revoluta</i> pollen grains were collected from cycad elliptical cones. However, the isolation and identification of oil bodies protein from mature <i>Cycas revoluta</i> grains have never been experimentally determined. Ultrastructural studies have shown that the oil bodies were present in pollen <i>Cycas revoluta</i> grains. Lipid analysis showed that oil bodies are predominantly composed of triacylglycerol. Complete cDNA fragments encoding the caleosin were obtained by PCR cloning. Phylogenetic tree analyzes showed that cycad pollen caleosin is closely related to the caleosin of <i>Cycas revoluta</i> seeds. Fresh <i>Cycas revoluta</i> pollen grains were allowed to germinate for 48 h in a germination medium containing 2% sucrose and 0.01% H<sub>3</sub>BO<sub>3.</sub> Pollen germination were recorded periodically from day one to day 10 and the results showed that the <i>Cycas revoluta</i> pollen elongate the tube and increasing of triacylglycerol(TAG) after 4 days.
DOI: 10.6084/m9.figshare.11530662
title: Spatial regulation of alpha-galactosidase activity and its influence on raffinose family oligosaccharides during seed maturation and germination in <i>Cicer arietinum</i>

description: Alpha-galactosides or Raffinose Family Oligosaccharides (RFOs) are enriched in legumes and are considered as anti-nutritional factors responsible for inducing flatulence. Due to a lack of alpha-galactosidases in the stomachs of humans and other monogastric animals, these RFOs are not metabolized and are passed to the intestines to be processed by gut bacteria leading to distressing flatulence. In plants, alpha(α)-galactosides are involved in desiccation tolerance during seed maturation and act as a source of stored energy utilized by germinating seeds. The hydrolytic enzyme alpha-galactosidase (α-GAL) can break down RFOs into sucrose and galactose releasing the monosaccharide α-galactose back into the system. Through characterization of RFOs, sucrose, reducing sugars, and α-GAL activity in maturing and germinating chickpeas, we show that stored RFOs are likely required to maintain a steady-state level of reducing sugars. These reducing sugars can then be readily converted to generate energy required for the high energy-demanding germination process. Our observations indicate that RFO levels are lowest in imbibed seeds and rapidly increase post-imbibition. Both RFOs and the α-GAL activity are possibly required to maintain a steady-state level of the reducing monosaccharide sugars, starting from dry seeds all the way through post-germination, to provide the energy for increased germination vigor.