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opencc-by-4.0Sep 2018View details →

Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from Arabidopsis thaliana

Mass spectrometry raw data files for the determination of the molecular weight of the intact proteins. López-Castillo LM, Jiménez-Sandoval P, Baruch-Torres N, Trasviña-Arenas CH, Díaz-Quezada C, Lara-González S, Winkler R and Brieba LG (2016) Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from Arabidopsis thaliana. Front. Plant Sci. 7:1817. doi: 10.3389/fpls.2016.01817

Top-down photographs of Columbia-0 Arabidopsis thaliana vegetative growth under 16-hour days

Photograph with Raspberry Pi camera v1. Six overlapping fields of view (07 to 12). Two photos per hour from 11:30 UTC to 0300 UTC. (Photographed at 5-minute intervals -- this is a subset of the data.) Manifest file with checksums for the 2712 photos included.

Top-down time-lapse photograph dataset: Columbia-0 Arabidopsis thaliana vegetative growth under 8-hour days #2

Top-down time-lapse photograph dataset: Columbia-0 Arabidopsis thaliana vegetative growth under 8-hour days #1

Photographed with Raspberry Pi camera v1. Twelve overlapping fields of view (01 to 12). Two photos per hour from ZT 0030 to ZT 0800 (9 AM to 4:30 PM local time). Photographs were taken at 5-minute intervals -- this is a subset of the data. Manifest file with checksums for the 6181 photos (JPEG files) included. First timepoint photo was not captured for fov-04. An extra photo was captured right at dawn (8:30 AM) for both fov-04 and fov-06 and is included. Additional metadata will be deposited in a separate Zenodo record.

Top-down time-lapse photograph dataset: Landsberg erecta Arabidopsis thaliana vegetative growth under 8-hour days

Photographed with Raspberry Pi camera v1. Twelve overlapping fields of view (01 to 12). Two photos per hour from ZT 0030 to ZT 0800 (15:00 to 22:30 UTC). Photographs were taken at 5-minute intervals -- this is a subset of the data. Manifest file with checksums for the 5004 photos (JPEG files) included.

opencc-by-4.0Dec 2023View details →

Characterization of DNA methylation reader proteins of Arabidopsis thaliana

Genomic regions of interest from the study "Characterization of DNA methylation reader proteins of Arabidopsis thaliana".

opencc-by-4.0Nov 2024View details →

Computed tomography (CT) was used to study the interaction of NMs with the plant cell tissue in vivo using Zeiss Xradia 510 system on Arabidopsis thaliana leaf. T

This work was supported by the National Research Facility for Lab X-ray CT (NXCT) at the µ-VIS X-ray Imaging Centre, University of Southampton, through EPSRC grant EP/T02593X.

opencc-zeroDec 2017View details →

Data from: Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

Seed plants vary tremendously in size and morphology. However, variation and covariation between plant traits may at least in part be governed by universal biophysical laws and biological constants. Metabolic Scaling Theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near constant allometric scaling exponents across species. However, observed variation in scaling exponents questions the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST correlated with relative growth rate, seed production and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings support a core MST prediction and suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology, and begin to link adaptive variation in allometric scaling to specific genes.

opencc-zeroDec 2018View details →

Data from: Heterosis is common and inbreeding depression absent in natural populations of Arabidopsis thaliana

The importance of genetic drift in shaping patterns of adaptive genetic variation in nature is poorly known. Genetic drift should drive partially recessive deleterious mutations to high frequency, and inter‐population crosses may therefore exhibit heterosis (increased fitness relative to intra‐population crosses). Low genetic diversity and greater genetic distance between populations should increase the magnitude of heterosis. Moreover, drift and selection should remove strongly deleterious recessive alleles from individual populations, resulting in reduced inbreeding depression. To estimate heterosis, we crossed 90 independent line pairs of Arabidopsis thaliana from 15 pairs of natural populations sampled across Fennoscandia, and crossed an additional 41 line pairs from a subset of 4 of these populations to estimate inbreeding depression. We measured lifetime fitness of crosses relative to parents in a large outdoor common garden (8448 plants in total) in central Sweden. To examine the effects of genetic diversity and genetic distance on heterosis, we genotyped parental lines for 869 SNPs. Overall, genetic variation within populations was low (median expected heterozygosity = 0.02), and genetic differentiation was high (median FST = 0.82). Crosses between 10 of 15 population pairs exhibited significant heterosis, with magnitudes of heterosis as high as 117%. We found no significant inbreeding depression, suggesting that the observed heterosis is due to fixation of mildly deleterious alleles within populations. Widespread and substantial heterosis indicates an important role for drift in shaping genetic variation, but there was no significant relationship between fitness of crosses relative to parents and genetic diversity or genetic distance between populations.

opencc-by-4.0Jul 2021View details →

ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic

Raw data linked to the research article "ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic"

opencc-zeroNov 2022View details →

Data for: Parental environmental effects are common and strong, but unpredictable, in Arabidopsis thaliana

The phenotypes of plants can be influenced by the environmental conditions experienced by their parents. However, there is still much uncertainty about how common and how predictable such parental environmental effects really are. We carried out a comprehensive experimental test for parental effects, subjecting plants of multiple Arabidopsis thaliana genotypes to 24 different biotic or abiotic stresses, or combinations thereof, and comparing their offspring phenotypes in a common environment. The majority of environmental stresses caused significant parental effects, with ‑35% to +38% changes in offspring fitness. The expression of parental effects was strongly genotype-dependent, and multiple environmental stresses often acted non-additively when combined. The direction and magnitude of parental effects were unrelated to the direct effects on the parents: some environmental stresses did not affect the parents but caused substantial effects on offspring, while for others the situation was reversed. Our study demonstrates that parental environmental effects are common and often strong in A. thaliana, but they are genotype-dependent, act non-additively, and are difficult to predict. We should thus be cautious with generalizing from simple studies with single plant genotypes and/or only few individual environmental stresses. A thorough and general understanding of parental effects requires large multi-factorial experiments.

opencc-by-4.0May 2023View details →

Integrated Study on the natural variation in Arabidopsis thaliana responses to alkaline salinity

Supplementary Datasets of the doctoral thesis entitled "Integrated Study on the natural variation in Arabidopsis thaliana responses to alkaline salinity", comprising genomic and transcriptomic data from growth, nutritional and gene enrichment analyses of natural populations of A. thaliana in response to neutral and alkaline salinity treatments.

opencc-by-4.0Apr 2023View details →

PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid

Harvest yields depend on the plant's ability to fix carbon and deal with changing environmental conditions. Especially during seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals through metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from Arabidopsis thaliana is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, almost 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated. In the simulations, PLAFP does bind to the plasma membrane independent of the PA concentration, and it adopts a binding pose, where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequently, PA does insert into PLAFP's beta-sandwich and multiple amino acids besides W41 and R82 are identified that drive the insertion. Fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids could allow modulating the signaling sensitivity to the climate the plant is supposed to grow in.