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7,327 results for “Pathway”
Aggregating statistically correlated metabolic pathways into groups to improve pathway prediction outcomes
<p>We included files used in <a href="https://github.com/hallamlab/chap">hallamlab/chap</a></p>
Berberine protects against sepsis-related acute lung injury in rats via the upregulation of the PPAR - Υ signaling pathway, with amelioration at the cellular level - A functional, immune-histological and biochemical study
<p>Aim: To assess the therapeutic effects of berberine in experimentally induced lung sepsis. Examining its effects on selected cytokines, gene and protein expression and the histopathological findings.</p> <p>Results: Berberine significantly reduced the wet/dry lung ratio, the BALF protein, cell, and neutrophils percentage & the BALF cytokines levels. In addition, pretreatment with berberine decreases the myeloperoxidase and MDA levels and decreases gene expression of NFKB, MCP -1 and the ICAM - 1 by RT - PCR analysis. Thus, suggesting an antioxidant and anti-inflammatory mode of the action. Western blot analysis revealed increased PPAR – Υ expression in the berberine pretreated group compared to the CLP group. Histopathological examination revealed improved histopathological parameters, in the berberine pretreated group, compared to the CLP group.</p> <p>Conclusion: Berberine improves the outcome in sepsis via antioxidant and anti-inflammatory effects, modulation of cytokine levels, upregulation of PPAR - Υ protein expression, and histopathological amelioration.</p>
Juvenile hormone pathway in honey bee larvae: a source of possible signal molecules for the reproductive behavior of Varroa destructor
<p>The parasitic mite <i>Varroa destructor </i>devastates honey bee (<i>Apis mellifera</i>) colonies around the world. Entering a brood cell shortly before capping, the <i>Varroa</i> mother feeds on the honey bee larvae. The hormones 20-hydroxyecdysone (20E) and juvenile hormone (JH), acquired from the host, have been considered to play a key role in initiating <i>Varroa</i>'s reproductive cycle. This study focuses on differential expression of the genes involved in the biosynthesis of JH and ecdysone at 6 time points during the first 30 hours after cell capping in both drone and worker larvae of <i>A. mellifera</i>. This time frame, covering the conclusion of the honey bee brood cell invasion and the start of <i>Varroa</i>'s ovogenesis, is critical to the successful initiation of a reproductive cycle. Our findings support a later activation of the ecdysteroid cascade in honey bee drones compared to worker larvae, which could account for the increased egg production of <i>Varroa</i> in <i>A. mellifera</i> drones. The JH pathway was generally downregulated confirming its activity is antagonistic to the ecdysteroid pathway during the larva development. Nevertheless, the genes involved in JH synthesis revealed an increased expression in drones. The upregulation of <i>jhamt</i> gene involved in methyl farnesoate (MF) synthesis came into attention since the MF is not only a precursor of JH but it is also an insect pheromone in its own right as well as JH-like hormone in Acari. This could indicate a possible kairomone effect of MF for attracting the mites into the drone brood cells, along with its potential involvement in ovogenesis after the cell capping, stimulating <i>Varroa</i>'s initiation of egg laying.</p>
Comprehensive result data for a pathway for the German energy sector compatible with a 1.5°C carbon budget
<p>This data set covers the results of an energy scenario for Germany within a 1.5°C carbon budget. It represents all relevant results from an energ system modelling excersise, coupling two complementary models.</p> <p>The data set consists of two excel files</p> <ul> <li>Comprehensive results of the energy balance based Energy System Model (ESM) for the heat, transport and power sectors for Germany, disaggregated by consumption sectors (residential, service & commerce, industry, transport)</li> <li>Comprehensive results of the linear optimization energy system model REMix for power, heat and sector coupling</li> </ul> <p>Methodology, models and scenario assumption are detailed in:</p> <p>Simon, S., Xiao, M., Harpprecht, C., Pregger, T., Gardian, H., & Sasanpour, S. (submitted). A pathway for the German energy sector compatible with a 1.5°C carbon budget. <em>Sustainability</em>.</p>
Data from: Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway
<p>Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of sex determination and sex chromosomes. Here we sequenced the genome of the Common Lumpfish (<i>Cyclopterus lumpus</i> Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70K SNP array and tissue-specific expression data. The chromosome-level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb, a scaffold N50 of 23.86 Mb, and genome annotation predicted 21,480 protein-coding genes. Genome wide association analysis located a highly sex-associated region on chromosome 13, suggesting that anti-Müllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13 support a proto-XX/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of <i>AMH</i> in the Lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One <i>AMH</i> copy showed similarity to <i>AMH/AMHY</i> in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of <i>AMH</i> in Lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits Lumpfish conservation management and aquaculture.</p>
Data from: Different evolutionary pathways lead to incomplete convergence of elongate body shapes in carnivoran mammals
<p><span>Although convergence is often recognized as a ubiquitous feature across the Tree of Life, whether the underlying traits also exhibit similar evolutionary pathways towards convergent forms puzzles biologists. In carnivoran mammals, "elongate," "slender," and "long" are often used to describe and even to categorize mustelids (martens, polecats, and weasels), herpestids (mongooses), viverrids (civets and genets), and other carnivorans together. But just how similar these carnivorans are and whether there is convergence in the morphological component that contribute to elongation has never been assessed. Here, I found that these qualitatively-described elongate carnivorans exhibited incomplete convergence towards elongate bodies compared to other terrestrial carnivorans. In contrast, the morphological components underlying body shape variation do not exhibit convergence despite evidence that these components are more elongate in elongate carnivorans compared to non-elongate carnivorans. Furthermore, these components also exhibited shorter but different phylogenetic half-lives towards more elongate adaptive peaks, indicating that different selective pressures can create multiple pathways to elongation. Incorporating the fossil record will facilitate further investigation of whether body elongation evolved adaptively or if it is simply a retained ancestral trait. </span></p>
Long-term shifts in the functional diversity of abandoned wet meadows – Impacts of historical disturbance and successional pathways
<p>Investigating the direction of changes in functional diversity involving successional pathways and historical disturbances may be a promising tool for predictions of the effectiveness of the semi-natural meadows conservation, with great emphasis on formulation of more cost-effective restoration strategies. The goal of this research was to assess the differences in long-term shifts in the functional diversity of plant species in semi-natural wet meadows unmanaged for the last 40 years, under the influence of different successional pathways and historical disturbances. Using ordination techniques, linear mixed-effect models, a set of plant functional traits and parameters of functional diversity, we assessed the importance of habitat filtering, competition and niche partitioning in shaping community assembly changes over time. The most dramatic shifts in functional diversity were found in the <i>Carex acutiformis </i>successional pathway after topsoil removal, where colonization by successional inhibitors was the main driver causing decreases in functional dispersion and divergence. This was expressed as a decrease in the importance of habitat filtering and replacement of specialized species by competitors with heavier seeds and higher specific leaf area. Regarding the <i>C. cespitosa</i> and <i>Salix cinerea </i>pathways, the magnitudes of shifts in functional diversity were milder and differed less between the historical topsoil removal and mowing treatments, thereby maintaining a large role for niche partitioning in shaping the vegetation structure. The results of our study highlight the importance of tussock sedges and shrubs as effective buffers against the biotic homogenization of meadows driven by the simplification of functional composition, even from a long-term perspective.</p>
Synergistic phase separation of two pathways promotes integrin clustering and nascent adhesion formation
<p><span><span><span><span><span><span><span><span><span><span><span>Integrin adhesion complexes (IACs) are integrin-based plasma membrane-associated compartments where cells sense environmental cues. The physical mechanisms and molecular interactions that mediate initial IAC formation are unclear. We found that both p130Cas ("Cas") and Focal adhesion kinase ("FAK") undergo liquid-liquid phase separation <i>in vitro</i>under physiologic conditions. Cas- and FAK- driven phase separation is sufficient to reconstitute kindlin-dependent integrin clustering <i>in vitro </i>with recombinant mammalian proteins. <i>In vitro</i> condensates and IACs in mouse embryonic fibroblasts (MEFs) exhibit similar sensitivities to environmental perturbations including changes in temperature and pH. Furthermore, mutations that inhibit or enhance phase separation <i>in vitro</i> reduce or increase the number of IACs in MEFs, respectively. Finally, we find that the Cas and FAK pathways act synergistically to promote phase separation, integrin clustering, IAC formation and partitioning of key components <i>in vitro</i> and in cells. We propose that Cas- and FAK- driven phase separation provides an intracellular trigger for integrin clustering and nascent IAC formation.</span></span></span></span></span></span></span></span></span></span></span></p>
Supplementary material 1 from: Strokov AS, Potashnikov VY (2022) Environmental tradeoffs of agricultural growth in Russian regions and possible sustainable pathways for 2030. Russian Journal of Economics 8(1): 60-80. https://doi.org/10.32609/j.ruje.8.78331
Maps of main environmental indicators of Russian regional agricultural development
Supplementary material 2 from: Strokov AS, Potashnikov VY (2022) Environmental tradeoffs of agricultural growth in Russian regions and possible sustainable pathways for 2030. Russian Journal of Economics 8(1): 60-80. https://doi.org/10.32609/j.ruje.8.78331
The dataset on agricultural waste, nitrogen concentration, and GHG emissions in Russian regions
Pathways, form drag, and turbulence in a simulated ocean flowing through through an ice melange: datasets
<p>Data associated with Hughes (2022). <em>J. Geophys. Res. </em><a href="https://doi.org/10.1029/2021JC018228">doi:10.1029/2021JC018228</a></p> <p>This archive contains</p> <ol> <li>Output from all model simulations together with a summary csv file. Full details in <strong>melange_flow_simulations_readme.pdf</strong></li> <li>A directory (<strong>icebergs.zip</strong>) containing the scripts necessary to reproduce model outputs described in the paper.</li> </ol> <p> </p>
Epigenetic regulation of autonomous pathway mediates polymorphism of flowering time in Arabidopsis
<p><span>Plant flowering time is affected by endogenous and exogenous factors, but its polymorphism among different populations of a species has not been fully explained yet. Here, 27 <em>Arabidopsis thaliana</em> populations were used to </span><span>determine</span><span> how autonomous pathway gene methylation affects flowering differences </span><span>by</span><span> regulating gene expression patterns. DNA methylation analysis, qPCR and transgenic verification</span> <span>showed that polymorphism in the flowering time among the <em>Arabidopsis</em> populations ranged from 19 to 55 days was significantly correlated with methylation of the coding regions of six upstream genes in the autonomous pathway</span><span>,</span><span> <em>FVE</em>, <em>FY</em>, <em>FLD</em>, <em>PEP</em>, <em>HDA5</em> and <em>PPR</em> <em>39-1</em> and</span><span> their </span><span>relative expression levels</span> <span>(P < 0.05). Expression of selected <em>FVE</em> and <em>FVE(CS) </em>separately</span> <span>through codon degeneracy substitution of cytosine led to earlier flowering of transgenic plants by 8 days and 25 days, respectively. An accurate determination of </span><span>methylated sites</span><span> of <em>FVE</em> and <em>FVE(CS)</em> among those transgenic plants and recipient Col-0 verified the close relationship between their methylation number, expression and the flowering times. Our findings firstly suggest that the methylation variation of those six key upstream transcription factors regulates</span><span> the</span><span> gene expression level of </span><span>the</span><span> autonomous pathway, leading to phenotypic differences in flowering time of Arabidopsis. </span><span>The</span><span> <em>FVE(CS)</em></span><span> and <em>FVE</em> genes in transgenic plants tend to be hypermethylated, and this could be a protective mechanism for plants. However, modification of gene sequence through codon degeneracy substitution to reduce cytosine can avoid hypermethylated transferred-genes in transgenic plants. It may be possible to partially regulate the flowering of plants by modified trans-epigenetic technology.</span></p>
Supplementary Spreadsheet S1. Canonical pathway using IPA analysis
<p>Supplementary Spreadsheet S1. Canonical pathway using IPA analysis</p>
Fig. 7. A proposed pathway for compound 3 in Cytotoxic sesquiterpene lactones from Campuloclinium macrocephalum (=Eupatorium macrocephalum)
Fig. 7. A proposed pathway for compound 3.
Supplementary material 3 from: Sirbu C, Miu IV, Gavrilidis AA, Gradinaru SR, Niculae IM, Preda C, Oprea A, Urziceanu M, Camen-Comanescu P, Nagoda E, Sirbu IM, Memedemin D, Anastasiu P (2022) Distribution and pathways of introduction of invasive alien plant species in Romania. NeoBiota 75: 1-21. https://doi.org/10.3897/neobiota.75.84684
Appendix S3. Publications used to compile distribution of alien plant species in Romania.
Supplementary material 1 from: Sirbu C, Miu IV, Gavrilidis AA, Gradinaru SR, Niculae IM, Preda C, Oprea A, Urziceanu M, Camen-Comanescu P, Nagoda E, Sirbu IM, Memedemin D, Anastasiu P (2022) Distribution and pathways of introduction of invasive alien plant species in Romania. NeoBiota 75: 1-21. https://doi.org/10.3897/neobiota.75.84684
Appendix S1. List of invasive and potentially invasive alien plant species in Romania
Raw allelic matrix and supplementary materials: Origin and dispersion pathways of guava in the Galapagos Islands inferred through genetics and historical records
<p>Guava (<i>Psidium guajava</i>) is an aggressive invasive plant in the Galapagos Islands. Determining its provenance and genetic diversity could explain its adaptability and spread, and how this relates to past human activities. With this purpose, we analyzed 11 SSR markers in guava individuals from Isabela, Santa Cruz, San Cristobal and Floreana islands in the Galapagos, as well as from mainland Ecuador. The mainland guava population appeared genetically differentiated from the Galapagos populations, with higher genetic diversity levels found in the former. We consistently found that the Central Highlands region of mainland Ecuador is one of the most likely origins of the Galapagos populations. Moreover, the guavas from Isabela and Floreana show a potential genetic input from southern mainland Ecuador, while the population from San Cristobal would be linked to the coastal mainland regions. Interestingly, the proposed origins for the Galapagos guava coincide with the first human settlings of the archipelago. Through Approximate Bayesian Computation, we propose a model where San Cristobal was the first island to be colonized by guava from the mainland, then it would have spread to Floreana and finally to Santa Cruz; Isabela would have been seeded from Floreana. An independent trajectory could also have contributed in the invasion of Floreana and Isabela. The pathway shown in our model agrees with the human colonization history of the different islands in the Galapagos. Our model, in conjunction with the clustering patterns of the individuals (based on genetic distances), suggests that guava introduction history in the Galapagos archipelago was driven by either a single event or a series of introduction events in rapid succession. We thus show that genetic analyses supported by historical sources can be used to track the arrival and spread of invasive species in novel habitats and the potential role of human activities in such processes.</p>
ALKBH5 promotes tumour proliferation, migration, and invasion by regulating the lncRNA MIR210HG/Mir-206/WEE1 signalling pathway in glioma
<p>GRAPH</p>
Figure 5 from: Wetzel F, Despot Belmonte K, Bingham H, Underwood E, Hoffmann A, Häuser C, Mikolajczyk P, Vohland K (2017) 4th European Biodiversity Observation Network (EU BON) Stakeholder Roundtable: Pathways to sustainability for EU BONs network of collaborators and technical infrastructure. Research Ideas and Outcomes 3: e11875. https://doi.org/10.3897/rio.3.e11875
Figure 5 - Group 2 discussion: Strategies, Business Plan and EU BON sustainability (Credits: F. Wetzel)
Figure 4 from: Wetzel F, Despot Belmonte K, Bingham H, Underwood E, Hoffmann A, Häuser C, Mikolajczyk P, Vohland K (2017) 4th European Biodiversity Observation Network (EU BON) Stakeholder Roundtable: Pathways to sustainability for EU BONs network of collaborators and technical infrastructure. Research Ideas and Outcomes 3: e11875. https://doi.org/10.3897/rio.3.e11875
Figure 4 - Visualisation of Lepidoptera density occurences: World Map (darker colors indicate a higher number of occurrences) and Lepidoptera occurences chart bar per year, exemplified with the country data of Germany (EU BON European Biodiversity Portal, beta version 11/2016).
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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.