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3,484 results for “Plastic”
Genome-Wide Association Studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity
<p>Postembryonic primary root growth relies on meristems that harbour multipotent stem cells that produce new cells that will duplicate and provide all the different root cell types. <em>Arabidopsis thaliana</em> primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth. We used 639 accessions from nine different studies and performed different GWAS tests ranging from single studies and pairwise analysis with high correlation associations, analyzing the same number of accessions in different studies to using the daily data of the root growth kinetic of the same research. We found that primary root growth changes were associated with 41 genomic loci, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown of genes associated with two of these loci: a gene that participates in Trans-acting siRNAs (tasiRNAs) processing <em>Suppressor of Gene Silencing</em> (<em>SGS3</em>) and a gene with a Sterile Alpha Motif (SAM) confirmed their participation as repressors of primary root growth. As none has been shown to participate in this developmental process before, our GWAS analysis identified new genes that participate in primary root growth. Overall, our findings provide novel insights into the genomic basis of root development and further demonstrate the usefulness of GWAS meta-analyses in non-human species.</p>
Dataset for "A critical role for CaMKII in behavioral timescale synaptic plasticity in hippocampal CA1 pyramidal neurons"
<p>Dataset for "A critical role for CaMKII in behavioral timescale synaptic plasticity in hippocampal CA1 pyramidal neurons"</p>
Molecular and circuit determinants in the globus pallidus mediating control of cocaine-induced behavioral plasticity
<p>The globus pallidus external segment (GPe) acts as a gatekeeper of initial cocaine-induced behavioral plasticity. However, the molecular and circuit mechanisms of action by which it does so are unknown. Here we show that parvalbumin-positive cells in the GPe (GPe<sup>PV</sup>) control cocaine reward and sensitization by selectively modulating activity of dopamine (DA) cells projecting to the lateral shell of the nucleus accumbens (NAc). GPe<sup>PV </sup>cells are embedded in a closed-loop circuit controlled by indirect pathway neurons of the dorsomedial striatum (DMS<sup>D2</sup>), which in part receive DAergic innervation from collaterals of the ventral tegmental DA neurons projecting to the nucleus accumbens lateral shell (VTA<sup>DA</sup>®NAcLat). The GPe<sup>PV</sup> cells control these VTA<sup>DA</sup>®NAcLat cells indirectly via GABAergic neurons in the substantia nigra pars reticulata (SNr<sup>GABA</sup>). Cocaine modifies activity in each node in the loop, resulting in long-lasting changes in GPe<sup>PV</sup> and VTA<sup>DA</sup>®NAcLat cell activity, as well as DA levels in the DMS. The principal action of cocaine is likely in the DMS, and this cocaine-induced elevation of DA triggers a depression in the inhibition from DMS<sup>D2</sup> cells onto GPe<sup>PV</sup> neurons, increasing activity of GPe<sup>PV</sup> cells. Interestingly, the levels of spontaneous activity of GPe<sup>PV</sup> cells is more strongly related to the extent of reward and sensitization that animals experience in response to future administration of cocaine than the other cell types in the loop, indicating that the activity in GPe<sup>PV</sup> cells is a key predictor of future cocaine-induced behavioral responses. Single nucleus RNA-sequencing of GPe cells indicated that voltage-gated potassium channels <em>Kcnq3</em> and <em>Kcnq5</em> that control intrinsic excitability are downregulated in GPe<sup>PV</sup> cells following a single cocaine exposure, contributing to the elevation in GPe<sup>PV</sup> cell excitability. Acutely activating the heteromeric KCNQ3/5 channels using the small molecule carnosic acid, a key psychoactive component of rosemary extract, impaired cocaine reward and learning in a volitional cocaine administration task, indicating its potential as a therapeutic to counteract psychostimulant use disorder. Our findings illuminate the molecular and circuit mechanisms by which the GPe orchestrates brain-wide changes in response to cocaine that are required for reward, sensitization, and self-administration behaviors.</p>
Plasticity and the adaptive evolution of switchlike reaction norms under environmental change
<p>Phenotypic plasticity is often posited as an avenue for adaptation to environmental change, whereby environmental influences on phenotypes could shift trait expression toward new optimal values. Conversely, plastic trait expression may inhibit adaptation to environmental change by reducing selective pressure on ill-adapted traits. While plastic responses are often assumed to be linear, non-linear phenotype-environment relationships are common, especially in thermally-sensitive traits. Here we examine non-linear plasticity in a trait with great ecological and evolutionary significance: sexual phenotype in species with environmental sex determination (ESD). In species with ESD development switches between male and female at an environmental threshold (the inflection point). The inflection point is a key trait for adaptive responses to changing environments and should evolve toward the new optimum in order to maintain evolutionarily stable sex ratios. We used an individual-based theoretical model to investigate how two forms of plasticity in the ESD reaction norm – the non-linear slope of the reaction norm and a linear shift in the inflection point – influence the evolution of the inflection point under climate warming. We found that steeper reaction norm slopes (high non-linear plasticity) promoted evolution toward new optimal phenotypes (higher inflection points). In contrast, increased linear plasticity in the inflection point (shift) hindered adaptive evolution. Additionally, populations in moderate warming scenarios showed greater adaptive evolution of the inflection point compared with extreme warming scenarios, suggesting that the proximity of existing phenotypes to new optimal phenotypes influences evolutionary outcomes. Unexpectedly, we found greater population persistence under high climate variability, due to the increased production of rare-sex individuals in unusually cold years. Our results demonstrate that different forms of phenotypic plasticity have crucially different effects on adaptive evolution. Plasticity that prevented sex ratio bias hindered the evolution of the inflection point, while plasticity that exacerbated sex ratio bias promoted adaptation to environmental change. </p>
Fig. 6. S491A in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 6. S491A mutation increases the rigidity of the active pocket when it binds the pinyl cation. RMSD values of the active site residues between WT and S491A in complex with the pinyl cation (a), terpinyl cation (b) and thujyl cation (c) are compared.
Fig. 5 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 5. The effect of the S491A mutation. Chromatograms in a, b and c show the GC-MS analysis of terpene production for S491A, F482A/S491A, and F482I/S491A, respectively. The x-axis is the retention time and the y-axis is the relative abundance of each species. The numbers in each peak correspond to α-pinene (1), sabinene (2) and limonene (3). d shows the overall activity and the percentage of sabinene within total products produced by F482A, F482A/S491A, F482I and F482I/S491A. The asterisk indicates P <0.05.
Fig. 4 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 4. Conformational differences in the pinyl cation in WT and F482Y as demonstrated by molecular dynamics simulation. The structures of WT and F482Y are superimposed. Results after 0, 1 and 2 ns of simulation are shown in a, d and c, respectively. Carbon in WT is colored in yellow and carbon in F482Y is colored in green. Oxygen is colored in red. Nitrogen is colored in blue. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 2. Converting pinene synthase to sabinene synthase by mutations on 482 position. Chromatograms in a, b, c, d and e show the GC-MS analysis of terpene products for WT, F482A, F482I, F482V and F482T, respectively. The x-axis is the retention time and the y-axis is the relative abundance of each species. The numbers in each peak correspond to α-pinene (1), sabinene (2) and limonene (3).
Fig. 3 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 3. Hybrid quadrupole-orbitrap GC-MS/MS. a shows the chromatogram of terpene products of F482L. The elution peak corresponding to sabinene is labeled. The mass spectrum of the product eluted at 9.29 min from a is shown in b. The mass spectrum of the standard sabinene is shown in c.
Fig. 1. a in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 1. a, The proposed reaction mechanism for the synthesis of limonene, pinene and sabinene. b, The structural model of pinene synthase docked with the terpinyl (left), pinyl (middle) and thujyl (right) cations. Carbocations are colored in magenta (terpinyl), wheat (pinyl) and cyan (thujyl). Other atoms are colored according to their types (red: oxygen; yellow: carbon; blue: nitrogen; orange: phosphorus; green: magnesium). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 7 in Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism
Fig. 7. The RMSD profiles of the region with high (RMSD H) and low (RMSD L) mobility from the simulation of WT (a), S491A (b) and F482/S491A (c) in complex with the pinyl cation.
Fig. 4 in Comparing essential oils from Australia's 'Victorian Christmas Bush' (Prostanthera lasianthos Labill., Lamiaceae) to closely allied new species: Phenotypic plasticity and taxonomic variability
Fig. 4. The PCA scores plot with individual clusters of chemical profiles highlighted. Clustering shows consistent patterns against taxa or chemotype: LL = P. lasianthos subsp. lasianthos; LS = P. lasianthos subsp. subcoriaceae; Eu = P. eungella; BM = P. sp. Bald Mountain; MK = P. sp. Mount Kaputar; PL= P. sp. Point Lookout; SG = P. sp. Schofields Gap; WG = P. sp. Wollomombi Gorge.
Fig. 3 in Comparing essential oils from Australia's 'Victorian Christmas Bush' (Prostanthera lasianthos Labill., Lamiaceae) to closely allied new species: Phenotypic plasticity and taxonomic variability
Fig. 3. PCA Analysis of essential oils from taxa currently circumscribed as P. lasianthos or P. eungella. LL = P. lasianthos subsp. lasianthos; LS = P. lasianthos subsp. subcoriaceae; Eu = P. eungella; BM = P. sp. Bald Mountain; MK = P. sp. Mount Kaputar; PL= P. sp. Point Lookout; SG = P. sp. Schofields Gap; WG = P. sp. Wollomombi Gorge. A) The PCA scores plot, conveying the pronounced grouping of essential oil profiles according to the presence and absence (or trace amount) of 1,8-cineole. B) The loading plot, showing principle components that influenced chemometric clusters. See Fig. 4 for a clearer clustering pattern of individual taxa.
Fig. 2 in Comparing essential oils from Australia's 'Victorian Christmas Bush' (Prostanthera lasianthos Labill., Lamiaceae) to closely allied new species: Phenotypic plasticity and taxonomic variability
Fig. 2. Row fusion dendrogram -: LL = P. lasianthos subsp. lasianthos; LS = P. lasianthos subsp. subcoriaceae; Eu = P. eungella; BM = P. sp. Bald Mountain; MK = P. sp. Mount Kaputar; PL= P. sp. Point Lookout; SG = P. sp. Schofields Gap; WG = P. sp. Wollomombi Gorge.
Data and Code for: Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America
<p>This submission contains all the code and data necessary for reproducing 1) the dataset, 2) the main results, and 3) all supplemental analyses appearing in the manuscript titled: <em>Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America</em> (Ramirez-Parada, Park, Record, Davis, Ellison, and Mazer, 2023). A preprint of this manuscript can be accessed at: https://doi.org/10.21203/rs.3.rs-3131821/v1.</p> <p> </p> <p>Extracting the compressed file will generate a folder titled "Project folder", containing sub-folders named "Data" and "R code". In order for the code to work, users need to preserve the folder structure of the code and data, as the R Markdown files in the "R code" folder have relative file paths that read and write data within the "Data" folder. Moving either would require re-writing the filepaths across Rmds for the code to run.</p> <p><br> To replicate the results, the following R Markdowns must be run in sequence (once they have been run, the Rmds for supplemental analyses can be used in any order):</p> <p><br> <em>"1. Subsetting Dataset.Rmd"</em></p> <p>This file processes a specimen dataset of ca. 2.3 million specimens that we assembled for this project (publicly available on Dryad: <a href="https://doi.org/10.25349/D9WP6S">https://doi.org/10.25349/D9WP6S</a>), filtering out duplicates, specimens out of the spatial scope of the PRISM data used for all analyses, and subsetting to only those species represented by a minimum of 300 specimens. This filtering yields a dataset of 1,038,047 specimens in flower across 1,605 species.</p> <p>For an in-depth description of the starting dataset, please refer to the "READ ME.txt" file within the "Project folder", and visit its corresponding Dryad repository (linked above).</p> <p><br> <em>"2. Main Analysis - Estimating S_space, S_time, and S_diff.Rmd"</em></p> <p>This file uses the subset dataset produced by the previous Rmd to fit the varying-intercepts, varying-slopes model that produced the estimates of apparent plasticity and apparent adaptation underlying all main analyses. This Rmd exports a dataset of species-specific estimates of S<sub>space</sub>, S<sub>time</sub>, and S<sub>space</sub> - S<sub>time</sub> that is used to recreate Figures 2, 3, and 4 of the main text in the next step. This is the most time consuming R Markdown file to run, as each MCMC chain used to fit the model in Stan must be run on a dedicated processor (limiting the usefulness of parallel computation). Fitting the model using 3 MCMC chains, 1000 iterations for warmup, and 4000 iterations for sampling, took approximately 24 hours using an Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz processor. </p> <p> </p> <p><em>"3. Main Analysis - Figures 2, 3, and 4.Rmd"</em></p> <p>Finally, this Rmd uses the dataset of species-specific estimates to conduct all analyses underlying Figures 2, 3, and 4, recreating each of these figures.</p> <p><strong><em>For detailed descriptions of all materials (code and data) and instructions for using them, please refer to the "READ ME.txt" file within "Project folder". </em></strong></p> <p> </p>
A hybrid chemical-biological approach can upcycle mixed plastic waste with reduced cost and carbon footprint
<p>Derived from renewable feedstocks, such as biomass, polylactic acid (PLA) is considered a more environmentally-friendly plastic than conventional petroleum-based polyethylene terephthalate (PET). However, PLA must still be recycled and its growing popularity and mixture with PET plastics at the disposal stage poses a cross-contamination threat in existing recycling facilities and results in low-value and low-quality recycled products. Hybrid upcycling has been proposed as a promising sustainable solution for mixed plastic waste; but its techno-economic and lifecycle environmental performance remain understudied. Here we propose a hybrid upcycling approach using a biocompatible ionic liquid (IL) to first chemically depolymerize plastics, then convert the depolymerized stream via biological upgrading with no extra separation. We show that over 95% of mixed PET/PLA was depolymerized into their respective monomers, which then served as the sole carbon source for the growth of <i>Pseudomonas putida</i>, enabling the conversion of the depolymerized plastics into biodegradable polyhydroxyalkanoates (PHA). In comparison to conventional commercial PHA, the estimated optimal production cost and carbon footprint are reduced by 62% and 29%, respectively.</p>
Rupture Jumping and Seismic Complexity in Models of Earthquake Cycles for Fault Stepovers with Off-Fault Plasticity
<p>Fault stepovers are prime examples of geometric complexity in natural fault zones which may affect seismic hazard by determining whether an earthquake rupture continues propagating, or abruptly stops. However, the long-term pattern of seismicity near fault stepovers and underlying mechanisms of rupture jumping in the context of earthquake cycles are rarely studied. Leveraging a hybrid numerical scheme combining the finite element and the spectral boundary integral methods, FEBE, we carry out fully dynamic simulations of Sequences of Earthquakes and Aseismic Slip (SEAS) for both compressive and tensile stepovers, with off-fault plasticity. We consider a rate-and-state friction law for the fault friction, and pressure sensitive Drucker-Prager plasticity for the off-fault bulk response. We observe that the accumulation of plastic deformation, an indication of off-fault damage, is significantly different in the two cases with more plastic deformation projected in the overlapping region for the tensile stepover. The seismic pattern for a tensile stepover is more complex than for a compressive stepover, and incorporating plasticity also increases complexity, relative to the elastic case. A tensile stepover with off-fault plasticity shows rupture segmentation, temporal clustering, and frequent rupture jumping from one fault to another. These results shed light on possible mechanisms of rupture jumping in fault stepovers as well as the long-term evolution of the fault zone.</p>
Diversity, plasticity and asynchrony of actuarial and reproductive senescence in the Collembola Folsomia candida (Willem, 1902)
<p>This spreadsheet contains the data that has been analysed in the paper entitled </p><p> Diversity, plasticity and asynchrony of actuarial and reproductive senescence in the Collembola Folsomia candida (Willem, 1902)</p><p>Thomas Tully Original Research, Front. Ecol. Evol. - Behavioral and Evolutionary Ecology </p><p>10.3389/fevo.2023.1112045<br> </p><p>220 isolated individuals of the Collembola Folsomia candida have been raised and followed until their death. The Collembola belong to 11 clonal lineages grouped into two distinct clades (A and B, see "Clones" sheet). Half of the Collembola have been raised in an environment where food was provided ad libitum (high food, "+"), while for the other half, food was available only one day per week (low food "-").</p><p>We report the age of death in the "Lifespan" sheet, together with the Collembola size at death, and their lifetime reproductive success.</p><p>We report the clutch size (number of eggs) of each clutch laid by each individual in the "Reproduction" sheet. For each clutch we have the Collembola size and for some of the clutches the mean egg size and proportion of sterile eggs. </p><p>In the "Egg_size" sheet we put all the egg size measurements that have been made (one line per egg measured). </p><p>In the "Cumulative_Fecundity" sheet, we have the age, fecundity and cumulative fecundity for each laying event and also for the individual death ("clutch number=0 for death). </p>
The Patency Period of the New Plastic Anti-reflux Biliary Stent
ClinicalTrials.gov study NCT01142921. IPD Sharing: NO. Countries: 1. Publications: 1.
Virtual Reality in Plastic Surgery: Pain Control and Augmented Satisfaction
ClinicalTrials.gov study NCT03914937. IPD Sharing: NO. Countries: 1. Publications: 0.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.