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22,597 results for “Regulation”
Evaluation of aquaculture regulations' adaptiveness to low trophic aquaculture (LTA) in selected countries and regions of the Atlantic.
<p>Assessments of documents relevant for LTA according to 15 adaptiveness criteria. Scores are assigned on the scale between -2 and 2. In total 22 documents are analyzed (5 for Galicia, Spain; 2 for Schleswig-Holstein, Germany; 8 for Scotland; 6 for Norway, 1 for South Africa and). General analysis is done for Brazilian aquaculture legislation. The data consists of an Excel file with scores and 6 pdf files with explanation of each score.</p>
Data from: The roles of growth regulation and appendage patterning genes in the morphogenesis of treehopper pronota
<p>Treehoppers of the insect family Membracidae have evolved enlarged and elaborate pronotal structures, which is hypothesized to involve co-opted expression of genes that are shared with the wings. Here, we investigate the similarity between the pronotum and wings in relation to growth. We show that the ontogenetic allometry of the pronotum is similar to that of wings in Membracidae, but not the outgroup. Using transcriptomics, we find genes related to protein synthesis and translation are mutually upregulated. These genes are implicated in the eIF2, eIF4/p70S6K, and mTOR pathways, and have known roles in regulating cell growth and proliferation. We show that species-specific differential growth patterning of the pronotum begins as early as the third instar. This finding suggests that co-option of appendage patterning genes must occur before the metamorphic molt. We propose that a network related to growth and size determination is the more likely mechanism shared with wings. However, regulators upstream of the shared genes in the pronotum and wings need to be elucidated to substantiate whether co-option has occurred. Finally, we<span> believe it will be helpful to distinguish the mechanisms leading to pronotal size from those regulating pronotal shape as we make sense of this spectacular evolutionary innovation. </span></p>
MRI data for "Stress-inducible phosphoprotein 1 (HOP/STI1/STIP1) regulates the spreading, aggregation, and toxicity of α-synuclein in vivo"
<p>Repository for magnetic resonance imaging data from the project titled "Stress-inducible phosphoprotein 1 (HOP/STI1/STIP1) regulates the spreading, aggregation, and toxicity of α-synuclein in vivo"</p> <p>Contains the pre-processed ex vivo T1-weighted images (Bruker 7T; 70 micron isotropic voxel resolution) for WT mice, M83 homozygous, and M83 homozygous mice with one copy of the TPR transgene. Full subject list can be viewed with the prado_MRI_M83dTPR_subjectlist_final.csv file.</p> <p>Whole brain region segmentations are available for these mice. These labels were generated using the MAGeT-Brain segementation pipleine (https://github.com/CobraLab/MAGeTbrain) and using a modified/merged version of the Allen brain atlas. The full list of regions included can be found in the file named Allen_brain_mapping_final.csv.</p> <p>See readme.txt file for more information</p>
Data from: Active regulation of ultraviolet light exposure overrides thermal preference behaviour in eastern fence lizards
<p>1. Over a century of ecophysiological studies on lizards have perpetuated the assumption that basking and shuttling movements between sun and shade function solely for temperature regulation. However, these behaviors also modulate exposure to ultraviolet (UV) wavelengths that are essential for maintaining physiological homeostasis as well as ensuring proper growth and development and enhancing long-term fitness.</p> <p>2. An alternative hypothesis is that lizards also actively regulate their UV exposure. In this scenario, UV needs may even override temperature needs (or vice versa), generating asymmetries in the ability of a lizard to regulate both conditions equally. We test this hypothesis using field and laboratory data collected on adult <em>Sceloporus undulatus</em>.</p> <p>3. We found that <em>S. undulatus</em> actively regulate UV exposure and prioritize UV over temperature, favoring body temperatures much higher than preferred values to sustain preferred UV exposure. In stark contrast, temperature had no reciprocal impact on UV regulation behavior. Our field data support these patterns, suggesting that lizards may even seek out hotter environments despite thermal costs to enhance UV exposure.</p> <p>4. We conclude that <em>S. undulatus</em> actively regulate for UV as well as temperature. Unfortunately, outside of zoos and private hobbyists, appreciation of the importance of UV for ectotherm survival and reproductive success has been minimal. Addressing this deficit will therefore be vital to improve our understanding of the factors shaping the evolution of ectotherm photoregulation behavior in nature.</p>
ETV6 represses Tumor Necrosis Factor During Stress Hematopoiesis to Regulate Mouse Stem Cell Function
<p>At the root of the blood system lies a heterogenous population of hematopoietic stem and progenitor cells (HSPCs), which reside in the bone marrow (BM) and give rise to diverse blood lineages. Maintaining this pool of self-renewing HSPCs is critical to uphold hematopoiesis during period of stress such as bleeding or infection<sup>1</sup>. ETS Variant Transcription Factor 6 (ETV6) is a transcriptional repressor that is highly expressed in HSPCs<sup>2</sup> where it is essential for development and maintenance of the adult hematopoiesis <sup>3</sup>. In 2015, our group<sup>4</sup> and others<sup>5-7</sup> identified germline pathogenic <em>ETV6</em> variants in families with predisposition to B-acute lymphoblastic leukemia (B-ALL) and thrombocytopenia, defining a new genetic syndrome known as Thrombocytopenia 5 (T5). Subsequently, we performed targeted germline <em>ETV6 </em>sequencing of remission blood samples from over 4,000 children with B-ALL and identified germline <em>ETV6</em> variants in ~1% of cases<sup>7</sup>. <em>In vitro</em> studies revealed that ETV6 variant proteins exhibit impaired repressor activity, reduced DNA binding, and aberrant subcellular localization<sup>4,5,7,8</sup>. Overall, these studies indicated that T5-associated germline <em>ETV6</em> variants negatively impact the repressor activity of ETV6. In support of this notion, transcriptional profiling of peripheral blood cells from T5 patients has revealed upregulation of interferon response genes<sup>9</sup>. Nevertheless, little remains known about the mechanisms by which ETV6 regulates the HSPC compartment and how T5-associated <em>ETV6</em> variants contribute to disease.</p> <p> </p> <p>To address these questions, we used CRISPR-Cas9 gene editing to generate a novel mouse model harboring a pathogenic heterozygous germline <em>Etv6 </em>variant, R355X, the murine equivalent to the human T5-associated variant R359X<sup>10</sup>. Through the comprehensive study of this model, we describe a novel role for ETV6 during aging and regenerative hematopoiesis and show that the heterozygous <em>Etv6</em><sup>R355X</sup> variant impairs HSC function <em>in vitro</em> and <em>in vivo</em>. Using genomic approaches to interrogate mouse and human HSCs, we identify new ETV6 targets, including the gene encoding Tumor Necrosis Factor (TNF) and genes involved in TNF signaling. Further, we show increased TNF production and cell cycling in <em>Etv6<sup>R355X/+</sup></em> mouse HSPCs post-BM transplantation. Finally, we demonstrate that genetic ablation of <em>Tnf</em> restores the long-term potential of <em>Etv6<sup>R355X/+</sup></em> cells in serial replating assays <em>in vitro</em>. Together, these findings provide novel insights into the pathways regulated by ETV6 and demonstrate how a pathogenic variant impacts ETV6 function in the context of hematopoietic stress.</p> <p>All bulk RNAseq, Cut&Run, ATACseq, and Hi-C data has been submitted to in the Gene Expression Omnibus (accession number GSE213597) and Sequence Read Archive (BioProject number PRJNA880871). Due to the journal’s limitation on submitted supplementary data as an Excel file, all post-analysis supplemental data files are deposited in Dryad data repository to be made available with this manuscript.</p>
Transcriptional regulation underlying the temperature response of embryonic development rate in the winter moth
<p>Climate change will strongly affect the developmental timing of insects, as their development rate largely depends on ambient temperature. However, we know little about the genetic mechanisms underlying the temperature sensitivity of embryonic development in insects. We investigated embryonic development rate in the winter moth (<em>Operophtera brumata</em>), a species with egg dormancy that has been under selection due to climate change. We used RNAseq to investigate which genes are involved in the regulation of winter moth embryonic development rate in response to temperature. Over the course of development, we sampled eggs before and after an experimental change in ambient temperature, including two early development weeks when the temperature sensitivity of eggs is low and two late development weeks when temperature sensitivity is high. We found temperature-responsive genes that responded in a similar way across development, as well as genes with a temperature response specific to a particular development week. Moreover, we identified genes whose temperature effect size changed around the switch in temperature sensitivity of development rate. Interesting candidate genes for regulating the temperature sensitivity of egg development rate included genes involved in histone modification, hormonal signalling, nervous system development, and circadian clock genes. In conclusion, the diverse sets of temperature-responsive genes we found here indicate that there are many potential targets of selection to change the temperature sensitivity of embryonic development rate. Identifying for which of these genes there is genetic variation in wild insect populations will give insight into their adaptive potential in the face of climate change.</p>
Large effect loci mediate rapid adaptation of salmon body size after river regulation
<p>Understanding the potential of natural populations to adapt to altered environments is becoming increasingly relevant in evolutionary research. Currently, our understanding of adaptation to human alteration of the environment is hampered by lack of knowledge on the genetic basis of traits, lack of time series, and little or no information on changes in optimal trait values. Here we used time series data spanning nearly a century to investigate how body mass of Atlantic salmon (<em>Salmo salar</em>) adapts to river regulation. We found that the change in body mass followed the change in waterflow, both decreasing to ~1/3 of their original values. Allele frequency changes at two loci in the regions of <em>vgll3</em> and <em>six6 </em>predicted more than 80% of the observed body mass reduction. Modelling the adaptive dynamics revealed that the population mean lagged behind its optimum before catching up ~6 salmon generations after the initial waterflow reduction. Our results demonstrate rapid adaptation mediated by large effect loci and provide insight into the temporal dynamics of evolutionary rescue following human disturbance.</p>
Figure 1 in Laboratory evaluation of Beauveria bassiana, some plant oils and insect growth regulators against two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae)
Figure 1. Infection caused by Beauveria bassiana on Tetranychus urticae, (a, b) dead female mites due to mycosis, (c) dead mite in control.
Genes regulated by CARTp/GPR160 in the dorsal horn of the spinal cord
<p><span>Analysis of the dorsal horn spinal cord (DH-SC) after an intrathecal injection of CARTp or CARTp with a neutralizing GPR160 antibody after 1hr. Results provide insight into genes regulated by CARTp/GPR160-induced behavioral hypersensitivities in the DH-SC.</span></p>
R code for: Following regulation, imidacloprid persists and flupyradifurone increases in non-target wildlife
<p>After regulation of pesticides, determination of their persistence in the environment is an important indicator of effectiveness of these measures. We quantified concentrations of two types of systemic insecticides: neonicotinoids (imidacloprid, acetamiprid, clothianidin, thiacloprid, and thiamethoxam) and butenolides (flupyradifurone), in off-crop non-target media of hummingbird cloacal fluid, honey bee (<em>Apis mellifera</em>) nectar and honey, and wildflowers before and after regulation of imidacloprid on highbush blueberries in Canada in April 2021. We found that mean total pesticide load increased in hummingbird cloacal fluid, nectar, and flower samples following imidacloprid regulation. On average, we did not find evidence of a decrease in imidacloprid concentrations after regulation. However, there were some decreases, some increases and other cases with no changes in imidacloprid levels depending on the specific media, time point of sampling and site type. At the same time, we found an overall increase in flupyradifurone, acetamiprid, thiamethoxam and thiacloprid, but no change in clothianidin concentrations. In particular, flupyradifurone concentrations observed in biota sampled near to agricultural areas increased by 2-fold in honey bee nectar, 7-fold in hummingbird cloacal fluid, and 8-fold in flowers after the 2021 imidacloprid regulation. The highest residue detected in this study was flupyradifurone at 665 ng/mL (PPB) in honey bee nectar. Mean total pesticide loads were highest in honey samples (84 ± 10 PPB) followed by nectar (56 ± 7 PPB), then hummingbird cloacal fluid (1.8 ± 0.5 PPB), and least, flowers (0.51 ± 0.06 PPB). Our results highlight that limited regulation of imidacloprid does not immediately reduce residue concentrations while other systemic insecticides, possibly replacement compounds, concurrently increase in wildlife.</p>
Data set for "A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides"
<p>Data associated with Sebastianelli L, Kaur H, Chen Z, Krishnamurthy R, Mansy SS (2024) A magnesium binding site and the anomeric effect regulate the abiotic redox chemistry of nicotinamide nucleotides. Chem Eur J. 30, e202400411. DOI: 10.1002/chem.202400411 [<a href="https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/chem.202400411">link</a>]</p>
Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly
<p>The intricate mechanisms shaping plant diversity and community composition are the cornerstone of ecological understanding. Yet, the role of mycorrhizal symbiosis, the fundamental partnership between fungi and plant roots, in influencing community composition has often been underestimated. Here, we use extensive species survey data from 1,315 terrestrial ecosystem sites to elucidate the influence of mycorrhizal symbiosis on plant phylogenetic diversity and its implications for community assembly processes. Our findings demonstrate that increasing mycorrhizal symbiotic potential leads to greater phylogenetic dispersion within plant communities. Furthermore, we unveil a distinct dichotomy in the assembly processes governed by mycorrhizal status. Mycorrhizal species predominantly influence deterministic processes, suggesting a role in niche-based community assembly. Conversely, non-mycorrhizal species exert a stronger influence on stochastic processes, highlighting the importance of random events in shaping community structure. These results underscore the crucial but often hidden role of mycorrhizal symbiosis in driving plant community diversity and assembly. This study provides valuable insights into the complex mechanisms shaping ecological communities and the way for more informed conservation and management practices that acknowledge the complex interplay between symbiosis and ecological community dynamics.</p>
Raw data to: Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule
<p>Initial configuration (PDB) and TIGER2hPE ensemble of all four simulations (R1-4) reported in this study in DCD trajectory format:</p> <ol> <li>AcuA + AcsA + Acetyl-CoA</li> <li>Acua + AcsA + Acetyl-CoA (AcuA:K549 deprotonated)</li> <li>AcuA + AcsA + CoA + AcP (Acetyl-Phosphate)</li> <li>AcuA + AcsA + Desulfo-CoA</li> </ol> <p> </p>
Reverse social contagion as a mechanism for regulating mass behaviors in highly integrated social systems
<h1>Reverse social contagion as a mechanism for regulating mass behaviors in highly integrated social systems</h1> <p>This repository houses supporting data for “Reverse social contagion as a mechanism for regulating mass behaviors in highly integrated social systems”. It contains three archives consisting of multiple files storing inter-individual interactions, trajectory data for multiple colonies of desert harvester ants (Pogonomyrmex californicus), and the code necessary to reproduce the study results. The behavioral data sets were obtained from 30s videos filmed at 15fps. </p> <h2>Description of the data and file structure</h2> <h3>Supplementary_Archive_1.zip</h3> <p>This collection of CSV files contains the antennal contact interactions among individual workers from colonies. Each file name represents the colony code and the data contained in each file belongs to a single colony. Each file contains three columns: The first (1) column represents the tag of an individual observed, the second (2) column represents the tag of the individual it interacted with, and the third (3) column represents the frame of the video at which the interaction occurred.</p> <h3>Supplementary_Archive_2.zip</h3> <p>This group of mdf files contains the trajectory data for each individual of a harvester ant colony. The files were generated using the ImageJ plugin MTrackJ. Each file contains the data of one colony and the filename represents the code of said colony. The data contained in this file is organized in rows and columns. The first row indicates the MTrackJ software version used to generate the file. The second row indicates the displaying preferences for the MTrackJ software. The third and fourth rows indicate the number of assemblies and clusters, respectively. However, this can be safely ignored as the colony was treated as a whole. The rows starting with ‘Track’ indicate the tag of the individual observed followed by its identifying number “Track 1” belongs to individual 1, “Track 2” belongs to individual 2, “Track 3 to individual 3, and so forth. The lines that start with ‘Point’ after each ‘Track’ represent the point in space in the video for each individual in a given frame. The second column after ‘Point’ simply refers to the point ID in the frame “e.g. Point 1”. The third and fourth columns represent the ‘x’ and ‘y’ coordinates in the video frame. The fourth, fifth, and sixth columns represent the dimensions of an image stack. In this case, the fourth and sixth columns are fixed to 1 and the fifth column represents the frame at which the point is taken. Each point is captured in 5-frame increments.</p> <h2>Code/Software</h2> <h3>Supplementary_Archive_3.zip</h3> <p>This archive contains the code necessary to reproduce the results of the study in the form of a Mathematica notebook. It also contains a folder with the trajectory data for each individual of a harvester ant colony, in a simplified format from that available in Supplementary_Archive_2.zip. Each CSV file in this folder corresponds to a different colony. It has four columns, respectively representing the identifying number of the individual observed, the frame number at which the observation, and the ‘x’ and ‘y’ coordinates, in that order. Finally, a XLSX file contains the number of individuals in each colony (first column), the metabolic rate of the colony (second column), and the identifying number of the colony (third column; numbers followed by the letter 's' correspond to size-reduced colonies). </p>
FIG. 2 in Does the removal of non-photosynthetic sections lead to a down-regulation of photosynthesis in mosses? A first experiment
FIG. 2. — Comparisons of the sample- (A-C) and mass- (D-F) based CO2 assimilation rates of green and brown moss sections, and the sum of these two sections (sample-based plots) and the changes through time for three moss species. Shown are the mean values ± standard errors (smaller than the symbol in some cases) of different sections determined at different time points, starting at a few minutes after separation. Sample-based plots are expressed as the CO2 exchange per sample to allow a direct comparison of intact and separated sections. Gray solid and dashed lines show the mean values of intact shoots (values shown to the right), ± standard errors. Asterisks indicate significant differences in assimilation rates between intact shoots and the sum of the separated sections (paired t-test, p<0.05, n = 4). And the capital and lowercase letters indicate significant differences among time points (p<0.05).
FIG. 1 in Does the removal of non-photosynthetic sections lead to a down-regulation of photosynthesis in mosses? A first experiment
FIG. 1. — Shoots of the three moss species used for the "brown-section-removal" experiment, collected on the eastern slope of Gongga Mountain. A, Actinothuidium hookeri (Mitt.) Broth.; B, Pleuroziopsis ruthenica (Weinm.) Kindb. ex E. Britton; C, Pogonatum nudiusculum Mitt. The red arrows indicate the points where the brown and green sections were separated.
Data from: Live-cell analysis of IMPDH protein levels during yeast colony growth provides insights into the regulation of GTP synthesis
<p>Here we present real-time, live-cell analysis of accumulation of the Imd2 isoform of IMPDH in <em>Saccharomyces cervisiae</em> yeast cells forming a monolayer colony in a microfluidic device over a 50-hour time course. We observe two distinct phases of increased Imd2 accumulation: a guanine-insensitive phase early in outgrowth and a guanine-sensitive phase later, when cells become crowded. We show that the IMPDH inhibitor mycophenolic acid enhances both phases of increase. Deletion of a transcription attenuator upstream of the mRNA start site that decreases Imd2 mRNA synthesis in the presence of high GTP increases the baseline level of Imd2 protein ten-fold and abolishes guanine-sensitive but not guanine-insensitive induction. Our results suggest that at least two mechanisms of yeast Imd2 regulation exist, the known GTP-dependent attenuation of RNA polymerase II elongation and a GTP concentration-independent pathway that may be controlled by cell growth state.</p>
Identification and characterization of ATOH7-regulated target genes and pathways in human neuroretinal development
<p>The files presented here represent the original data collected during the study presented in the Cells (MDPI) publication "Identification and characterization of ATOH7-regulated target genes and pathways in human neuroretinal development" (<a href="https://doi.org/10.3390/cells13131142">https://doi.org/10.3390/cells13131142</a>). The data include:</p> <ul> <li>scRNA sequencing data (matrix, features and barcodes)</li> <li>RNA sequencing data (fastq)</li> <li>CUT&RUN sequencing data (raw data: fastq; coverage: bigWig)</li> <li>RNA sequencing alignments, with custom built reference (RNA_alignments)</li> </ul>
Figure 1 in Growth regulators and their reflection on different hop genotypes cultivated under in vitro conditions
Figure 1. Explants of a hop genotype, grown in different culture media (yellow, blue and pink). Each medium provided different development behavior for the number of nodal segments. The larger the number of nodal segments, the more new plants will be obtained.
Figure 2 in Growth regulators and their reflection on different hop genotypes cultivated under in vitro conditions
Figure 2. Estimates of the direct and indirect effects of the variables root length (RL), shoot height (SH) and number of shoots (NS) on the variable number of nodal segments (NNS) (main variable).
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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.