cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16437005.v3
title: Exogenous carbon source supplementation counteracts root and hypocotyl growth limitations under increased cotyledon shading, with glucose and sucrose differentially modulating growth curves

description: Plant growth is continuously modulated by endogenous and exogenous stimuli. By no means the only, but well described, signaling molecules produced in plants and distributed through the plant body to orchestrate efficient growth are photosynthates. Light is a potent exogenous stimulus that determines, first, the rate of photosynthesis, but also the rate of plant growth. Root meristem activity is reduced with direct illumination but enhanced with increased sugar levels. With reduced cotyledon illumination, the seedling increases hypocotyl elongation until adequate light exposure is again provided. If endogenous carbon sources are limited, this leads to a temporary inhibition of root growth. Experimental growth conditions include exogenous supplementation of sucrose or glucose in addition to culturing seedlings under light exposure in Petri dishes. We compared total root length and hypocotyl elongation of <i>Arabidopsis thaliana</i> wild type <i>Col-0</i> in response to illumination status and carbon source in the growth medium. Overall, sucrose supplementation promoted hypocotyl and root length to a greater extent than glucose supplementation. Glucose promoted root length compared to non-supplemented seedlings especially when cotyledon illumination was greatly reduced.
DOI: 10.6084/m9.figshare.15090125
title: Identification and molecular characterization of propionylcholinesterase, a novel pseudocholinesterase in rice

description: Cholinesterase is consisting of acetylcholinesterase (AChE) and pseudocholinesterase in vertebrates and invertebrates. <i>AChE</i> gene has been identified in several plant species, while pseudocholinesterase gene has not yet been found in any plant species. In this study, we report that the <i>AChE</i> gene paralog encodes propionylcholinesterase (PChE), a pseudocholinesterase in rice. <i>PChE</i> was found to be located adjacent to <i>AChE</i> (Os07g0586200) on rice chromosome 7 and designated as Os07g0586100. Phylogenetic tree analysis showed a close relationship between rice <i>AChE</i> and <i>PChE. PChE</i>-overexpressing rice had higher hydrolytic activity toward propionylthiocholine than acetylthiocholine and showed extremely low activity against butyrylthiocholine. Therefore, the <i>PChE</i> gene product was characterized as a propionylcholinesterase, a pseudocholinesterase. The rice PChE displayed lower sensitivity to the cholinesterase inhibitor, neostigmine bromide, than electric eel, maize, and rice AChEs. The recombinant PChE functions as a 171 kDa homotetramer. PChE was expressed during the later developmental stage, and it was found be localized in the extracellular spaces of the rice leaf tissue. These results suggest that the rice plant possesses PChE, which functions in the extracellular spaces at a later developmental stage. To the best of our knowledge, this study provides the first direct evidence and molecular characterization of <i>PChE</i> in plants.
DOI: 10.6084/m9.figshare.15090125.v3
title: Identification and molecular characterization of propionylcholinesterase, a novel pseudocholinesterase in rice

description: Cholinesterase is consisting of acetylcholinesterase (AChE) and pseudocholinesterase in vertebrates and invertebrates. <i>AChE</i> gene has been identified in several plant species, while pseudocholinesterase gene has not yet been found in any plant species. In this study, we report that the <i>AChE</i> gene paralog encodes propionylcholinesterase (PChE), a pseudocholinesterase in rice. <i>PChE</i> was found to be located adjacent to <i>AChE</i> (Os07g0586200) on rice chromosome 7 and designated as Os07g0586100. Phylogenetic tree analysis showed a close relationship between rice <i>AChE</i> and <i>PChE. PChE</i>-overexpressing rice had higher hydrolytic activity toward propionylthiocholine than acetylthiocholine and showed extremely low activity against butyrylthiocholine. Therefore, the <i>PChE</i> gene product was characterized as a propionylcholinesterase, a pseudocholinesterase. The rice PChE displayed lower sensitivity to the cholinesterase inhibitor, neostigmine bromide, than electric eel, maize, and rice AChEs. The recombinant PChE functions as a 171 kDa homotetramer. PChE was expressed during the later developmental stage, and it was found be localized in the extracellular spaces of the rice leaf tissue. These results suggest that the rice plant possesses PChE, which functions in the extracellular spaces at a later developmental stage. To the best of our knowledge, this study provides the first direct evidence and molecular characterization of <i>PChE</i> in plants.
DOI: 10.6084/m9.figshare.16437005.v2
title: Exogenous carbon source supplementation counteracts root and hypocotyl growth limitations under increased cotyledon shading, with glucose and sucrose differentially modulating growth curves

description: Plant growth is continuously modulated by endogenous and exogenous stimuli. By no means the only, but well described, signaling molecules produced in plants and distributed through the plant body to orchestrate efficient growth are photosynthates. Light is a potent exogenous stimulus that determines, first, the rate of photosynthesis, but also the rate of plant growth. Root meristem activity is reduced with direct illumination but enhanced with increased sugar levels. With reduced cotyledon illumination, the seedling increases hypocotyl elongation until adequate light exposure is again provided. If endogenous carbon sources are limited, this leads to a temporary inhibition of root growth. Experimental growth conditions include exogenous supplementation of sucrose or glucose in addition to culturing seedlings under light exposure in Petri dishes. We compared total root length and hypocotyl elongation of <i>Arabidopsis thaliana</i> wild type <i>Col-0</i> in response to illumination status and carbon source in the growth medium. Overall, sucrose supplementation promoted hypocotyl and root length to a greater extent than glucose supplementation. Glucose promoted root length compared to non-supplemented seedlings especially when cotyledon illumination was greatly reduced.
DOI: 10.6084/m9.figshare.15090125.v2
title: Identification and molecular characterization of propionylcholinesterase, a novel pseudocholinesterase in rice

description: Cholinesterase is consisting of acetylcholinesterase (AChE) and pseudocholinesterase in vertebrates and invertebrates. <i>AChE</i> gene has been identified in several plant species, while pseudocholinesterase gene has not yet been found in any plant species. In this study, we report that the <i>AChE</i> gene paralog encodes propionylcholinesterase (PChE), a pseudocholinesterase in rice. <i>PChE</i> was found to be located adjacent to <i>AChE</i> (Os07g0586200) on rice chromosome 7 and designated as Os07g0586100. Phylogenetic tree analysis showed a close relationship between rice <i>AChE</i> and <i>PChE. PChE</i>-overexpressing rice had higher hydrolytic activity toward propionylthiocholine than acetylthiocholine and showed extremely low activity against butyrylthiocholine. Therefore, the <i>PChE</i> gene product was characterized as a propionylcholinesterase, a pseudocholinesterase. The rice PChE displayed lower sensitivity to the cholinesterase inhibitor, neostigmine bromide, than electric eel, maize, and rice AChEs. The recombinant PChE functions as a 171 kDa homotetramer. PChE was expressed during the later developmental stage, and it was found be localized in the extracellular spaces of the rice leaf tissue. These results suggest that the rice plant possesses PChE, which functions in the extracellular spaces at a later developmental stage. To the best of our knowledge, this study provides the first direct evidence and molecular characterization of <i>PChE</i> in plants.
DOI: 10.6084/m9.figshare.15161666.v2
title: Exploring the role of soil types on defense and fitness traits of silverleaf nightshade (<i>Solanum elaeagnifolium</i>), a worldwide invasive species through a field survey in the native range

description: Silverleaf nightshade (<i>Solanum elaeagnifolium</i>) is a highly successful invasive weed that has caused agricultural losses both in its home and invaded ranges. Surveying 50 sub-populations over 36,000 km<sup>2</sup> in its native range in South Texas, we investigated the interactions among soil type, population size, plant height, herbivory, and plant defenses in its home range with the expectation that populations growing in the plant’s preferred sandier soils would host larger colonies of healthier and better defended plants. At each sampling location, on randomly selected plants, we measured height, insect herbivore damage, and presence, and density of internode spines. Soil type was determined using the NRCS Web Soil Survey and primarily grouped into sand, clay, or urban. Our results show a tradeoff between growth and defense with larger colonies and taller plants in clay soils, but smaller colonies of shorter, spinier plants in sandy soils. We also observed decreased herbivory in urban soils, further confirming the plant’s ability to survive and even be strengthened by highly disturbed conditions. This study is a starting point for a better understanding of silverleaf nightshade’s ecology in its home range and complicates the assumption that it thrives best in sandy soils.
DOI: 10.6084/m9.figshare.17114141
title: Role of mTOR pathway in modulation of radiation induced bystander effects

description: Radiation-induced bystander effect (RIBE) is considered as an important consequence of radiation exposure. Based on the type of effect induced, it has important implications in radiation therapy. mTOR pathway, a key regulator of cell survival, plays an important role in radiation-induced damages. However, the role of mTOR signaling in the modulation of RIBE is still unclear. We evaluated the role of mTOR pathway in RIBE and its relationship with the radiation response of target cells. Direct and bystander effects were evaluated by using clonogenic and MTT assay in five different cell lines. Expression of mTOR pathway proteins in directly targeted and bystander cells was studied using western blotting. Among five different cell lines naïve HT1080 and A549 cells exhibited proliferative bystander effect induced by conditioned media and irradiated conditioned media, while no effect was observed in other cell lines. Everolimus significantly abolished the proliferative bystander effect induced in naïve cells. These results suggested that the mTOR pathway plays an important role in RIBEs. These effects are cell type-specific and depending on the radiosensitivity of the target cells, therapeutic benefits of radiation may be modulated by treatment with mTOR inhibitors.
DOI: 10.6084/m9.figshare.17114141.v2
title: Role of mTOR pathway in modulation of radiation induced bystander effects

description: Radiation-induced bystander effect (RIBE) is considered as an important consequence of radiation exposure. Based on the type of effect induced, it has important implications in radiation therapy. mTOR pathway, a key regulator of cell survival, plays an important role in radiation-induced damages. However, the role of mTOR signaling in the modulation of RIBE is still unclear. We evaluated the role of mTOR pathway in RIBE and its relationship with the radiation response of target cells. Direct and bystander effects were evaluated by using clonogenic and MTT assay in five different cell lines. Expression of mTOR pathway proteins in directly targeted and bystander cells was studied using western blotting. Among five different cell lines naïve HT1080 and A549 cells exhibited proliferative bystander effect induced by conditioned media and irradiated conditioned media, while no effect was observed in other cell lines. Everolimus significantly abolished the proliferative bystander effect induced in naïve cells. These results suggested that the mTOR pathway plays an important role in RIBEs. These effects are cell type-specific and depending on the radiosensitivity of the target cells, therapeutic benefits of radiation may be modulated by treatment with mTOR inhibitors.
DOI: 10.6084/m9.figshare.16888449
title: Radio-protective efficacy of <i>Gymnema sylvestre</i> on <i>Pangasius sutchi against</i> gamma (<sup>60</sup>Co) irradiation

description: Freshwater fish <i>Pangasius sutchi</i> was used in this study as a vertebrate model. We evaluated the induction of certain antioxidant enzymes in various vital organs. The radioprotective efficacy of <i>Gymnema sylvestre</i> leaves extract (GS) [25<b> </b>mg/kg Body Weight (B.W)] and its bioactive compound Gymnemagenin (GG) [0.3<b> </b>mg/kg B.W] was compared with Amifostine (Ami), the only radioprotector clinically approved by the US-FDA [Ami- 83.3<b> </b>mg/kg B.W] against different doses of gamma radiation – <sup>60</sup>Co (Lethal Dose: LD<sub>30</sub>-9.2<b> </b>Gy, LD<sub>50</sub>-10.2<b> </b>Gy and LD<sub>70</sub>-11.4<b> </b>Gy). This study was done via stress marker enzymes, cell cycle analysis (CCA) and DNA damage assay prediction with molecular docking, which are reported here for the first time. The results indicate an elevated LPO level and decreased level of CAT, SOD and GSH due to oxidative stress initiation by <sup>60</sup>Co Ionizing Radiation (IR) on 4th day and slightly reduced on 32nd day while the reverse observed when the fishes were pretreated with Ami, GS and GG. Similarly, CCA and dead/live cells counts were conducted with pretreatment of Ami, GS and GG against <sup>60</sup>Co IR dose (LD<sub>50</sub>-10.2<b> </b>Gy). In CCA, G0/G1 phase was observed to be the highest in Ami and lowest in GG, against <sup>60</sup>Co IR doses 10.2<b> </b>Gy which was 51.76<b> </b>±<b> </b>7.55. The dead cells range observed in pretreated group of Ami, GS and GG was lowest in Ami and highest in GG and live cells (highest in Ami and lowest in GG) as compared to <sup>60</sup>Co IR group (86.43<b> </b>±<b> </b>3.42 and 8.77<b> </b>±<b> </b>5.95). Thus, antioxidant profile improvement by oxidative stress reduction and gradual progression of different phases of cell cycle except the apoptotic phase along with the live cells counts indicates that the radio-protective efficacy of GS is similar to Ami. Predictive assessment was carried out by docking of Ami, various components of GS with p53, NF-κβ cells and Rad51 proteins structures responsible for CCA, apoptosis and repair mechanism. These structural proteins were docked with other structural proteins like USP7, TNF-α and partner and localizer of BRCA2 associated (PALB2/BRCA2) complex which made us perform these systemic efforts to find the functional activity of these known radio-protectants.
DOI: 10.6084/m9.figshare.16888449.v1
title: Radio-protective efficacy of <i>Gymnema sylvestre</i> on <i>Pangasius sutchi against</i> gamma (<sup>60</sup>Co) irradiation

description: Freshwater fish <i>Pangasius sutchi</i> was used in this study as a vertebrate model. We evaluated the induction of certain antioxidant enzymes in various vital organs. The radioprotective efficacy of <i>Gymnema sylvestre</i> leaves extract (GS) [25<b> </b>mg/kg Body Weight (B.W)] and its bioactive compound Gymnemagenin (GG) [0.3<b> </b>mg/kg B.W] was compared with Amifostine (Ami), the only radioprotector clinically approved by the US-FDA [Ami- 83.3<b> </b>mg/kg B.W] against different doses of gamma radiation – <sup>60</sup>Co (Lethal Dose: LD<sub>30</sub>-9.2<b> </b>Gy, LD<sub>50</sub>-10.2<b> </b>Gy and LD<sub>70</sub>-11.4<b> </b>Gy). This study was done via stress marker enzymes, cell cycle analysis (CCA) and DNA damage assay prediction with molecular docking, which are reported here for the first time. The results indicate an elevated LPO level and decreased level of CAT, SOD and GSH due to oxidative stress initiation by <sup>60</sup>Co Ionizing Radiation (IR) on 4th day and slightly reduced on 32nd day while the reverse observed when the fishes were pretreated with Ami, GS and GG. Similarly, CCA and dead/live cells counts were conducted with pretreatment of Ami, GS and GG against <sup>60</sup>Co IR dose (LD<sub>50</sub>-10.2<b> </b>Gy). In CCA, G0/G1 phase was observed to be the highest in Ami and lowest in GG, against <sup>60</sup>Co IR doses 10.2<b> </b>Gy which was 51.76<b> </b>±<b> </b>7.55. The dead cells range observed in pretreated group of Ami, GS and GG was lowest in Ami and highest in GG and live cells (highest in Ami and lowest in GG) as compared to <sup>60</sup>Co IR group (86.43<b> </b>±<b> </b>3.42 and 8.77<b> </b>±<b> </b>5.95). Thus, antioxidant profile improvement by oxidative stress reduction and gradual progression of different phases of cell cycle except the apoptotic phase along with the live cells counts indicates that the radio-protective efficacy of GS is similar to Ami. Predictive assessment was carried out by docking of Ami, various components of GS with p53, NF-κβ cells and Rad51 proteins structures responsible for CCA, apoptosis and repair mechanism. These structural proteins were docked with other structural proteins like USP7, TNF-α and partner and localizer of BRCA2 associated (PALB2/BRCA2) complex which made us perform these systemic efforts to find the functional activity of these known radio-protectants.
DOI: 10.5281/zenodo.5914129
title: Phylogenetic placement of Pseudoneobacillus sp. JJ-79 within Bacillaceae family

description: This repository contains phylogenetic trees (and associated sequence data) inferred to assess the phylogenetic placement of <em>Pseudoneobacillus</em> sp. JJ-79 (tax id: 2880968) within 512 type strains representative of the <em>Bacillaceae</em> family. Three phylogenetic trees were inferred, each from a multi-gene dataset (as described at http://giphy.pasteur.fr/PhyloM/Bacillaceae): <strong>BM1</strong>: 87 conserved genes (Wu et al. 2013, Gupta et al. 2020, Patel and Gupta 2020), <strong>BM2</strong>: major subunits of the DNA Gyrase (<em>GyrA</em> and <em>GyrB</em>) and RNA polymerase (<em>RpoB</em> and <em>RpoC</em>; Patel and Gupta 2020), <strong>BM3</strong>: DNA helicase II and DNA polymerase I (<em>UvrD</em> and <em>PolA</em>; Patel and Gupta 2020). For each dataset <strong>BM<em>i</em></strong> (<em>i</em> = 1, 2, 3), four files are available: <code>BM<em>i</em>.faa </code> the concatenation of the filtered multiple sequence alignments (FASTA format); <code>BM<em>i</em>.nwk </code> a maximum likelihood phylogenetic tree inferred from <code>BM<em>i</em>.faa</code> (NEWICK format); <code>BM<em>i</em>.pdf </code> a graphical representation of the phylogenetic tree (PDF format); <code>BM<em>i</em>.seq.tar.gz </code> for each gene name, three FASTA files are available in this tar.gz archive: initial sequences (*.faa), multiple sequence alignment (*.afa), filtered multiple sequence alignment (*.ffa). In complement, the multiple sequence alignments of 11 loci are available in the archive <code>CSI.tar.gz</code>. Each of these loci shares a conservative signature indel (CSI) that is indicative of the closely related <em>Neobacillus</em> genus (see Table 4 —Niacini clade— in Patel and Gupta 2020): <em>fliF</em>, flagellar M-ring protein FliF; <em>rplX</em>, 50S ribosomal protein L24; <em>prmA</em>, 50S ribosomal protein L11 methyltransferase; <em>hisH</em>, imidazole glycerol phosphate synthase subunit HisH; <em>hisZ</em>, ATP phosphoribosyltransferase regulatory subunit; <em>mdoB</em>, LTA synthase family protein; <em>topA</em>, type I DNA topoisomerase; <em>pncB</em>, nicotinate phosphoribosyltransferase; <em>thiD</em>, phosphomethylpyrimidine kinase; <em>recJ</em>, single-stranded-DNA-specific exonuclease RecJ; <em>dxs</em>, 1-deoxy-D-xylulose-5-phosphate synthase.
DOI: 10.5281/zenodo.5576020
title: Phylogenetic placement of Pseudoneobacillus sp. JJ-79 within Bacillaceae family

description: This repository contains phylogenetic trees (and associated sequence data) inferred to assess the phylogenetic placement of <em>Pseudoneobacillus</em> sp. JJ-79 (tax id: 2880968) within 512 type strains representative of the <em>Bacillaceae</em> family. Three phylogenetic trees were inferred, each from a multi-gene dataset (as described at http://giphy.pasteur.fr/PhyloM/Bacillaceae): <strong>BM1</strong>: 87 conserved genes (Wu et al. 2013, Gupta et al. 2020, Patel and Gupta 2020), <strong>BM2</strong>: major subunits of the DNA Gyrase (<em>GyrA</em> and <em>GyrB</em>) and RNA polymerase (<em>RpoB</em> and <em>RpoC</em>; Patel and Gupta 2020), <strong>BM3</strong>: DNA helicase II and DNA polymerase I (<em>UvrD</em> and <em>PolA</em>; Patel and Gupta 2020). For each dataset <strong>BM<em>i</em></strong> (<em>i</em> = 1, 2, 3), four files are available: <code>BM<em>i</em>.faa </code> the concatenation of the filtered multiple sequence alignments (FASTA format); <code>BM<em>i</em>.nwk </code> a maximum likelihood phylogenetic tree inferred from <code>BM<em>i</em>.faa</code> (NEWICK format); <code>BM<em>i</em>.pdf </code> a graphical representation of the phylogenetic tree (PDF format); <code>BM<em>i</em>.seq.tar.gz </code> for each gene name, three FASTA files are available in this tar.gz archive: initial sequences (*.faa), multiple sequence alignment (*.afa), filtered multiple sequence alignment (*.ffa). In complement, the multiple sequence alignments of 11 loci are available in the archive <code>CSI.tar.gz</code>. Each of these loci shares a conservative signature indel (CSI) that is indicative of the closely related <em>Neobacillus</em> genus (see Table 4 —Niacini clade— in Patel and Gupta 2020): <em>fliF</em>, flagellar M-ring protein FliF; <em>rplX</em>, 50S ribosomal protein L24; <em>prmA</em>, 50S ribosomal protein L11 methyltransferase; <em>hisH</em>, imidazole glycerol phosphate synthase subunit HisH; <em>hisZ</em>, ATP phosphoribosyltransferase regulatory subunit; <em>mdoB</em>, LTA synthase family protein; <em>topA</em>, type I DNA topoisomerase; <em>pncB</em>, nicotinate phosphoribosyltransferase; <em>thiD</em>, phosphomethylpyrimidine kinase; <em>recJ</em>, single-stranded-DNA-specific exonuclease RecJ; <em>dxs</em>, 1-deoxy-D-xylulose-5-phosphate synthase.