cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5517425
title: Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts

description: Gnaiger E (2021) Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8. doi:10.26124/mitofit:2021-0008 - https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA All respirometric data that were used for meta-analysis are obtained from the original publications, were converted to SI units, and are available here as a basis for bioenergetic cluster analysis.
description: This work was partially funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 859770, NextGen-O2k project.
description: {"references": ["Gnaiger E (2021) Bioenergetic cluster analysis \u2013 mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8. doi:10.26124/mitofit:2021-0008 - https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA", "Greco M, Villani G, Mazzucchelli F, Bresolin N, Papa S, Attardi G (2003) Marked aging-related decline in efficiency of oxidative phosphorylation in human skin fibroblasts. FASEB J 17:1706-8.", "H\u00fctter E, Renner K, Pfister G, St\u00f6ckl P, Jansen-D\u00fcrr P, Gnaiger E (2004) Senescence-associated changes in respiration and oxidative phosphorylation in primary human fibroblasts. Biochem J 380:919-28.", "Y\u00e9pez VA, Kremer LS, Iuso A, Gusic M, Kopajtich R, Ko\u0148a\u0159\u00edkov\u00e1 E, Nadel A, Wachutka L, Prokisch H, Gagneur J (2018) OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer. PLOS ONE 13:e0199938. https:// doi.org/10.1371/journal.pone.0199938", "Zdrazilova L, Hanskova H, Gnaiger E (2021) Comparable respiratory activity in attached and suspended fibroblasts. MitoFit Preprints 2021.7. doi:10.26124/mitofit:2021-0007"]}
DOI: 10.6084/m9.figshare.12851807
title: Functional characterization of the Glyoxalase-I (<i>PdGLX1</i>) gene family in date palm under abiotic stresses

description: Methylglyoxal (MG), a cytotoxic oxygenated short aldehyde, is a by-product of various metabolic reactions in plants, including glycolysis. The basal level of MG in plants is low, whereby it acts as an essential signaling molecule regulating multiple cellular processes. However, hyperaccumulation of MG under stress conditions is detrimental for plants as it inhibits multiple developmental processes, including seed germination, photosynthesis, and root growth. The evolutionarily conserved glyoxalase system is critical for MG detoxification, and it comprises of two-enzymes, the glyoxalase-I and glyoxalase-II. Here, we report the functional characterization of six putative glyoxalase-I genes from date palm (<i>Phoenix dactylifera</i> L.) (<i>PdGLX1</i>), by studying their gene expression under various environmental stress conditions and investigating their function in bacteria (<i>Escherichia coli</i>) and yeast (<i>Saccharomyces cerevisiae</i>) mutant cells. The putative <i>PdGLX1</i> genes were initially identified using computational methods and cloned using molecular tools. The <i>PdGLX1</i> gene expression analysis using quantitative PCR (qPCR) revealed differential expression under various stress conditions such as salinity, oxidative stress, and exogenous MG stress in a tissue-specific manner. Further, <i>in vivo</i> functional characterization indicated that overexpression of the putative <i>PdGLX1</i> genes in <i>E. coli</i> enhanced their growth and MG detoxification ability. The putative <i>PdGLX1</i> genes were also able to complement the loss-of-function MG hypersensitive GLO1 (YML004C) yeast mutants and promote growth by enhancing MG detoxification and reducing the accumulation of reactive oxygen species (ROS) under stress conditions as indicated by flow cytometry. These findings denote the potential importance of <i>PdGLX1</i> genes in MG detoxification under stress conditions in the date palm.
DOI: 10.6084/m9.figshare.12949622.v1
title: Overexpression of Arabidopsis <i>ICE1</i> enhances yield and multiple abiotic stress tolerance in indica rice

description: ICE1 (Inducer of CBF Expression 1), a MYC-type bHLH transcription factor, is a regulator of cold tolerance in Arabidopsis. Indica rice, which occupies the major rice cultivated area, is highly sensitive to cold stress. Hence in this study, Arabidopsis <i>ICE1</i> (<i>AtICE1</i>) was overexpressed in indica rice to analyze its role in reproductive stage cold and other abiotic stress tolerance to indica rice. <i>AtICE1</i> was overexpressed by using stress inducible <i>AtRD29A</i> promoter in mega rice cv. MTU1010. Under cold stress conditions, <i>AtICE1</i> overexpression lines showed lower accumulation of MDA and H<sub>2</sub>O<sub>2</sub>, higher membrane stability, and thus higher seedling survival rate than the WT plants. Expression levels of <i>OsDREB1A, OsMYB3R2</i>, and <i>OsTPP1</i> were significantly higher in transgenics as compared with WT under cold stress conditions. <i>AtICE1</i> transgenic rice plants produced 44–60% higher grain yield as compared with WT plants under control conditions in three independent experiments. Of the three <i>AtICE1</i> overexpression lines, two lines produced significantly higher grain yield as compared with WT plants after recovery from cold, salt and drought stresses. <i>AtICE1</i> overexpression lines showed significantly higher stomatal density and conductance under non-stress conditions. qRT-PCR analysis showed that expression levels of stomatal pathway genes viz., <i>OsSPCH1, OsSPCH2, OsSCR1, OsSCRM1, OsSCRM2</i> and <i>OsMUTE</i> were significantly higher in <i>AtICE1</i> transgenics as compared with WT plants. The components of water use viz., stomatal conductance, photosynthesis, and instantaneous WUE were higher in transgenics as compared with WT plants. The results showed that <i>AtICE1</i> confers multiple stress tolerance to indica rice, and the role of <i>ICE1</i> in stress tolerance and stomatal development is conserved across species.
DOI: 10.6084/m9.figshare.12851789
title: Stable expression of bacterial transporter ArsB attached to SNARE molecule enhances arsenic accumulation in <i>Arabidopsis</i>

description: Acute and chronic arsenic (As) toxicity is a global health issue affecting millions of people, which leads to inactivation of over 200 enzymes, particularly those involved in cellular energy pathways and DNA synthesis and repair. The fern <i>Pteris vittata</i> acts as a hyperaccumulator of As and may be useful for phytoremediation to reduce disposal risks by utilizing metal-enriched plant biomass in energy and metal recovery. However, these ferns grow in limited environments and its transplantation and transport can be challenging. Therefore, we generated a transgenic <i>Arabidopsis</i> plant as a seed plant model, capable of accumulating As in their vacuole lumen. This was achieved by transforming the As-resistant bacterial As transporter, ArsB, via fusion with a organelle-targeting signal to the vacuolar membrane, N-ethyl-maleimide-sensitive factor attachment protein receptors (SNAREs) protein, VAMP711. In this study, we developed the iVenus assay as a method for detecting whether the N- or C-terminus of a membrane protein is located on the cytoplasmic or exoplasmic side, and from the result of the iVenus assay, we generated the transgenic plant introduced N-terminal end of ArsB with VAMP711, localized to the central vacuolar membrane to accumulate As in the shoot and differentiation zone of root.
DOI: 10.6084/m9.figshare.12851807.v2
title: Functional characterization of the Glyoxalase-I (<i>PdGLX1</i>) gene family in date palm under abiotic stresses

description: Methylglyoxal (MG), a cytotoxic oxygenated short aldehyde, is a by-product of various metabolic reactions in plants, including glycolysis. The basal level of MG in plants is low, whereby it acts as an essential signaling molecule regulating multiple cellular processes. However, hyperaccumulation of MG under stress conditions is detrimental for plants as it inhibits multiple developmental processes, including seed germination, photosynthesis, and root growth. The evolutionarily conserved glyoxalase system is critical for MG detoxification, and it comprises of two-enzymes, the glyoxalase-I and glyoxalase-II. Here, we report the functional characterization of six putative glyoxalase-I genes from date palm (<i>Phoenix dactylifera</i> L.) (<i>PdGLX1</i>), by studying their gene expression under various environmental stress conditions and investigating their function in bacteria (<i>Escherichia coli</i>) and yeast (<i>Saccharomyces cerevisiae</i>) mutant cells. The putative <i>PdGLX1</i> genes were initially identified using computational methods and cloned using molecular tools. The <i>PdGLX1</i> gene expression analysis using quantitative PCR (qPCR) revealed differential expression under various stress conditions such as salinity, oxidative stress, and exogenous MG stress in a tissue-specific manner. Further, <i>in vivo</i> functional characterization indicated that overexpression of the putative <i>PdGLX1</i> genes in <i>E. coli</i> enhanced their growth and MG detoxification ability. The putative <i>PdGLX1</i> genes were also able to complement the loss-of-function MG hypersensitive GLO1 (YML004C) yeast mutants and promote growth by enhancing MG detoxification and reducing the accumulation of reactive oxygen species (ROS) under stress conditions as indicated by flow cytometry. These findings denote the potential importance of <i>PdGLX1</i> genes in MG detoxification under stress conditions in the date palm.
DOI: 10.6084/m9.figshare.12851807.v1
title: Functional characterization of the Glyoxalase-I (<i>PdGLX1</i>) gene family in date palm under abiotic stresses

description: Methylglyoxal (MG), a cytotoxic oxygenated short aldehyde, is a by-product of various metabolic reactions in plants, including glycolysis. The basal level of MG in plants is low, whereby it acts as an essential signaling molecule regulating multiple cellular processes. However, hyperaccumulation of MG under stress conditions is detrimental for plants as it inhibits multiple developmental processes, including seed germination, photosynthesis, and root growth. The evolutionarily conserved glyoxalase system is critical for MG detoxification, and it comprises of two-enzymes, the glyoxalase-I and glyoxalase-II. Here, we report the functional characterization of six putative glyoxalase-I genes from date palm (<i>Phoenix dactylifera</i> L.) (<i>PdGLX1</i>), by studying their gene expression under various environmental stress conditions and investigating their function in bacteria (<i>Escherichia coli</i>) and yeast (<i>Saccharomyces cerevisiae</i>) mutant cells. The putative <i>PdGLX1</i> genes were initially identified using computational methods and cloned using molecular tools. The <i>PdGLX1</i> gene expression analysis using quantitative PCR (qPCR) revealed differential expression under various stress conditions such as salinity, oxidative stress, and exogenous MG stress in a tissue-specific manner. Further, <i>in vivo</i> functional characterization indicated that overexpression of the putative <i>PdGLX1</i> genes in <i>E. coli</i> enhanced their growth and MG detoxification ability. The putative <i>PdGLX1</i> genes were also able to complement the loss-of-function MG hypersensitive GLO1 (YML004C) yeast mutants and promote growth by enhancing MG detoxification and reducing the accumulation of reactive oxygen species (ROS) under stress conditions as indicated by flow cytometry. These findings denote the potential importance of <i>PdGLX1</i> genes in MG detoxification under stress conditions in the date palm.
DOI: 10.6084/m9.figshare.12851789.v3
title: Stable expression of bacterial transporter ArsB attached to SNARE molecule enhances arsenic accumulation in <i>Arabidopsis</i>

description: Acute and chronic arsenic (As) toxicity is a global health issue affecting millions of people, which leads to inactivation of over 200 enzymes, particularly those involved in cellular energy pathways and DNA synthesis and repair. The fern <i>Pteris vittata</i> acts as a hyperaccumulator of As and may be useful for phytoremediation to reduce disposal risks by utilizing metal-enriched plant biomass in energy and metal recovery. However, these ferns grow in limited environments and its transplantation and transport can be challenging. Therefore, we generated a transgenic <i>Arabidopsis</i> plant as a seed plant model, capable of accumulating As in their vacuole lumen. This was achieved by transforming the As-resistant bacterial As transporter, ArsB, via fusion with a organelle-targeting signal to the vacuolar membrane, N-ethyl-maleimide-sensitive factor attachment protein receptors (SNAREs) protein, VAMP711. In this study, we developed the iVenus assay as a method for detecting whether the N- or C-terminus of a membrane protein is located on the cytoplasmic or exoplasmic side, and from the result of the iVenus assay, we generated the transgenic plant introduced N-terminal end of ArsB with VAMP711, localized to the central vacuolar membrane to accumulate As in the shoot and differentiation zone of root.
DOI: 10.6084/m9.figshare.12851789.v2
title: Stable expression of bacterial transporter ArsB attached to SNARE molecule enhances arsenic accumulation in <i>Arabidopsis</i>

description: Acute and chronic arsenic (As) toxicity is a global health issue affecting millions of people, which leads to inactivation of over 200 enzymes, particularly those involved in cellular energy pathways and DNA synthesis and repair. The fern <i>Pteris vittata</i> acts as a hyperaccumulator of As and may be useful for phytoremediation to reduce disposal risks by utilizing metal-enriched plant biomass in energy and metal recovery. However, these ferns grow in limited environments and its transplantation and transport can be challenging. Therefore, we generated a transgenic <i>Arabidopsis</i> plant as a seed plant model, capable of accumulating As in their vacuole lumen. This was achieved by transforming the As-resistant bacterial As transporter, ArsB, via fusion with a organelle-targeting signal to the vacuolar membrane, N-ethyl-maleimide-sensitive factor attachment protein receptors (SNAREs) protein, VAMP711. In this study, we developed the iVenus assay as a method for detecting whether the N- or C-terminus of a membrane protein is located on the cytoplasmic or exoplasmic side, and from the result of the iVenus assay, we generated the transgenic plant introduced N-terminal end of ArsB with VAMP711, localized to the central vacuolar membrane to accumulate As in the shoot and differentiation zone of root.
DOI: 10.6084/m9.figshare.12949622
title: Overexpression of Arabidopsis <i>ICE1</i> enhances yield and multiple abiotic stress tolerance in indica rice

description: ICE1 (Inducer of CBF Expression 1), a MYC-type bHLH transcription factor, is a regulator of cold tolerance in Arabidopsis. Indica rice, which occupies the major rice cultivated area, is highly sensitive to cold stress. Hence in this study, Arabidopsis <i>ICE1</i> (<i>AtICE1</i>) was overexpressed in indica rice to analyze its role in reproductive stage cold and other abiotic stress tolerance to indica rice. <i>AtICE1</i> was overexpressed by using stress inducible <i>AtRD29A</i> promoter in mega rice cv. MTU1010. Under cold stress conditions, <i>AtICE1</i> overexpression lines showed lower accumulation of MDA and H<sub>2</sub>O<sub>2</sub>, higher membrane stability, and thus higher seedling survival rate than the WT plants. Expression levels of <i>OsDREB1A, OsMYB3R2</i>, and <i>OsTPP1</i> were significantly higher in transgenics as compared with WT under cold stress conditions. <i>AtICE1</i> transgenic rice plants produced 44–60% higher grain yield as compared with WT plants under control conditions in three independent experiments. Of the three <i>AtICE1</i> overexpression lines, two lines produced significantly higher grain yield as compared with WT plants after recovery from cold, salt and drought stresses. <i>AtICE1</i> overexpression lines showed significantly higher stomatal density and conductance under non-stress conditions. qRT-PCR analysis showed that expression levels of stomatal pathway genes viz., <i>OsSPCH1, OsSPCH2, OsSCR1, OsSCRM1, OsSCRM2</i> and <i>OsMUTE</i> were significantly higher in <i>AtICE1</i> transgenics as compared with WT plants. The components of water use viz., stomatal conductance, photosynthesis, and instantaneous WUE were higher in transgenics as compared with WT plants. The results showed that <i>AtICE1</i> confers multiple stress tolerance to indica rice, and the role of <i>ICE1</i> in stress tolerance and stomatal development is conserved across species.
DOI: 10.6084/m9.figshare.12673133.v1
title: Research Data: An adjustment methodology of linear finite element models for frequency response functions correlation improvement

description: Supporting research data for paper
DOI: 10.6084/m9.figshare.15052601
title: Characterization of a novel stimulus-induced glial calcium wave in <i>Drosophila</i> larval peripheral segmental nerves and its role in PKG-modulated thermoprotection

description: Insects, as poikilotherms, have adaptations to deal with wide ranges in temperature fluctuation. Allelic variations in the <i>foraging</i> gene that encodes a cGMP dependent protein kinase, were discovered to have effects on behavior in <i>Drosophila</i> by Dr. Marla Sokolowski in 1980. This single gene has many pleiotropic effects and influences feeding behavior, metabolic storage, learning and memory and has been shown to affect stress tolerance. PKG regulation affects motoneuronal thermotolerance in <i>Drosophila</i> larvae as well as adults. While the focus of thermotolerance studies has been on the modulation of neuronal function, other cell types have been overlooked. Because glia are vital to neuronal function and survival, we wanted to determine if glia play a role in thermotolerance as well. In our investigation, we discovered a novel calcium wave at the larval NMJ and set out to characterize the wave’s dynamics and the potential mechanism underlying the wave prior to determining what effect, if any, PKG modulation has on the thermotolerance of glia cells. Using pharmacology, we determined that calcium buffering mechanisms of the mitochondria and endoplasmic reticulum play a role in the propagation of our novel glial calcium wave. By coupling pharmacology with genetic manipulation using RNA interference (RNAi), we found that PKG modulation in glia alters thermoprotection of function as well as glial calcium wave dynamics.
DOI: 10.6084/m9.figshare.15052601.v1
title: Characterization of a novel stimulus-induced glial calcium wave in <i>Drosophila</i> larval peripheral segmental nerves and its role in PKG-modulated thermoprotection

description: Insects, as poikilotherms, have adaptations to deal with wide ranges in temperature fluctuation. Allelic variations in the <i>foraging</i> gene that encodes a cGMP dependent protein kinase, were discovered to have effects on behavior in <i>Drosophila</i> by Dr. Marla Sokolowski in 1980. This single gene has many pleiotropic effects and influences feeding behavior, metabolic storage, learning and memory and has been shown to affect stress tolerance. PKG regulation affects motoneuronal thermotolerance in <i>Drosophila</i> larvae as well as adults. While the focus of thermotolerance studies has been on the modulation of neuronal function, other cell types have been overlooked. Because glia are vital to neuronal function and survival, we wanted to determine if glia play a role in thermotolerance as well. In our investigation, we discovered a novel calcium wave at the larval NMJ and set out to characterize the wave’s dynamics and the potential mechanism underlying the wave prior to determining what effect, if any, PKG modulation has on the thermotolerance of glia cells. Using pharmacology, we determined that calcium buffering mechanisms of the mitochondria and endoplasmic reticulum play a role in the propagation of our novel glial calcium wave. By coupling pharmacology with genetic manipulation using RNA interference (RNAi), we found that PKG modulation in glia alters thermoprotection of function as well as glial calcium wave dynamics.
DOI: 10.6084/m9.figshare.14192507.v2
title: A quick and versatile protocol for the 3D visualization of transgene expression across the whole body of larval <i>Drosophila</i>

description: Larval <i>Drosophila</i> are used as a genetically accessible study case in many areas of biological research. Here we report a fast, robust and user-friendly procedure for the whole-body multi-fluorescence imaging of <i>Drosophila</i> larvae; the protocol has been optimized specifically for larvae by systematically tackling the pitfalls associated with clearing this small but cuticularized organism. Tests on various fluorescent proteins reveal that the recently introduced monomeric infrared fluorescent protein (mIFP) is particularly suitable for our approach. This approach comprises an effective, low-cost clearing protocol with minimal handling time and reduced toxicity in the reagents employed. It combines a success rate high enough to allow for small-scale screening approaches and a resolution sufficient for cellular-level analyses with light sheet and confocal microscopy. Given that publications and database documentations typically specify expression patterns of transgenic driver lines only within a given organ system of interest, the present procedure should be versatile enough to extend such documentation systematically to the whole body. As examples, the expression patterns of transgenic driver lines covering the majority of neurons, or subsets of chemosensory, central brain or motor neurons, are documented in the context of whole larval body volumes (using nsyb-Gal4, IR76b-Gal4, APL-Gal4 and mushroom body Kenyon cells, or OK371-Gal4, respectively). Notably, the presented protocol allows for triple-color fluorescence imaging with near-infrared, red and yellow fluorescent proteins.
DOI: 10.6084/m9.figshare.15002214
title: Fly seizure EEG: field potential activity in the <i>Drosophila</i> brain

description: Hypersynchronous neural activity is a characteristic feature of seizures. Although many <i>Drosophila</i> mutants of epilepsy-related genes display clear behavioral spasms and motor unit hyperexcitability, field potential measurements of aberrant hypersynchronous activity across brain regions during seizures have yet to be described. Here, we report a straightforward method to observe local field potentials (LFPs) from the <i>Drosophila</i> brain to monitor ensemble neural activity during seizures in behaving tethered flies. High frequency stimulation across the brain reliably triggers a stereotypic sequence of electroconvulsive seizure (ECS) spike discharges readily detectable in the dorsal longitudinal muscle (DLM) and coupled with behavioral spasms. During seizure episodes, the LFP signal displayed characteristic large-amplitude oscillations with a stereotypic temporal correlation to DLM flight muscle spiking. ECS-related LFP events were clearly distinct from rest- and flight-associated LFP patterns. We further characterized the LFP activity during different types of seizures originating from genetic and pharmacological manipulations. In the ‘bang-sensitive’ sodium channel mutant <i>bangsenseless</i> (<i>bss</i>), the LFP pattern was prolonged, and the temporal correlation between LFP oscillations and DLM discharges was altered. Following administration of the pro-convulsant GABA<sub>A</sub> blocker picrotoxin, we uncovered a qualitatively different LFP activity pattern, which consisted of a slow (1-Hz), repetitive, waveform, closely coupled with DLM bursting and behavioral spasms. Our approach to record brain LFPs presents an initial framework for electrophysiological analysis of the complex brain-wide activity patterns in the large collection of <i>Drosophila</i> excitability mutants.