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12,455 results for “Promoters”
Data from: SMAD4 promotes somatic-germline contact during murine oocyte growth
<p>Development of the mammalian oocyte requires physical contact with the surrounding granulosa cells of the follicle, which provide it with essential nutrients and regulatory signals. This contact is achieved through specialized filopodia, termed transzonal projections (TZPs), that extend from the granulosa cells to the oocyte surface. Transforming growth factor (TGFβ) family ligands produced by the oocyte increase the number of TZPs, but how they do so is unknown. Using an inducible Cre recombinase strategy together with expression of green fluorescent protein to verify Cre activity in individual granulosa cells, we examined the effect of depleting the canonical TGFβ mediator, SMAD4. We observed a 20-50% decrease in the total number of TZPs in SMAD4-depleted granulosa cell-oocyte complexes, and a 50% decrease in the number of newly generated TZPs when the granulosa cells were reaggregated with granulosa cell-free wild-type oocytes. Three-dimensional image analysis revealed that TZPs of SMAD4-depleted cells were also longer than controls and more frequently oriented towards the oocyte. Strikingly, the transmembrane proteins, N-cadherin and Notch2, were reduced by 50% in these cells. SMAD4 may thus modulate a network of cell adhesion proteins that stabilize the attachment of TZPs to the oocyte, thereby amplifying signalling between the two cell types.</p>
Data from: Salinity decline promotes growth and harmful blooms of a toxic alga by diverting carbon flow
<p>Global climate change intensifies the water cycle and makes freshest waters become fresher and vice‑versa. But how this change impacts phytoplankton in coastal, particularly harmful algal blooms (HABs), remains poorly understood. Here, we monitored a coastal bay for a decade and found a significant correlation between salinity decline and the increase of <em>Karenia mikimotoi</em> blooms. To examine the physiological linkage between salinity decreases and <em>K. mikimotoi</em> blooms, we compare chemical, physiological and multi-omic profiles of this species in laboratory cultures under high (33) and low (25) salinities. Under low salinity, photosynthetic efficiency and capacity as well as growth rate and cellular protein content were significantly higher than that under high salinity. More strikingly, the omics data show that low salinity activated the glyoxylate shunt to bypass the decarboxylation reaction in the tricarboxylic acid cycle, hence redirecting carbon from CO<sub>2</sub> release to biosynthesis. Furthermore, the enhanced glyoxylate cycle could promote hydrogen peroxide metabolism, consistent with the detected decrease in reactive oxygen species (ROS). These findings suggest that salinity declines can reprogram metabolism to enhance cell proliferation, thus promoting bloom formation in HAB species like <em>K. mikimotoi</em>, which has important ecological implications for future climate-driven salinity declines in the coastal ocean with respect to HAB outbreaks.</p>
RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing
<p>This dataset accompanies the study "RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing". The study introduces RepliChrom, a computational framework designed to predict enhancer–promoter interactions (EPIs) by leveraging multi-scale replication timing (RT) signals. This approach addresses the fundamental challenge of distinguishing gene targets regulated by distal enhancers from those activated by proximal transcriptional activity-a key problem in understanding the causal basis of complex diseases.</p> <p>Despite recent advances in high-throughput technologies such as Hi-C, ChIA-PET, and Hi-TrAC that allow genome-wide reconstruction of 3D chromatin architecture, the role of DNA replication timing in mediating these spatial interactions remains underexplored. RepliChrom fills this gap by using cell-type-specific RT profiles as predictive features for chromatin interaction inference.</p> <p>To support model development, training, and evaluation, we provide a comprehensive multi-omics dataset covering six human cell lines (K562, GM12878, HeLaS3, IMR90, NHEK, and HUVEC ), encompassing:</p> <p>Hi-C datasets: Processed chromatin interaction loops used to define positive and negative enhancer–promoter interaction pairs.</p> <p>ChIA-PET datasets: Interaction data anchored around transcription factor binding, including POLR2A and CTCF, used for model validation across different interaction types.</p> <p>Hi-TrAC datasets: Targeted chromatin accessibility-derived interaction data, offering complementary validation of the model on alternate platforms.</p> <p>Replication Timing (RT) data: Processed RT signal profiles for each cell line, used to extract multi-scale temporal features as inputs for RepliChrom.</p> <p>These datasets enable reproducibility of the model training process and serve as benchmark resources for future research into DNA replication–mediated regulation of 3D genome architecture.</p> <p><strong>Included Files</strong></p> <p>Hi-C_datasets.zip (2.23 MB): Processed Hi-C interaction pairs for six cell types.</p> <p>ChIA-PET_datasets.zip (818.18 KB): CTCF and POLR2A ChIA-PET interactions across multiple lines.</p> <p>Hi-TrAC_datasets.zip (196 bytes): Hi-TrAC-based chromatin interaction training datasets across multiple lines.</p> <p>Cellline_RT_data.zip (86.17 MB): Replication timing signal data across multiple human cell types for multi-scale replication timing feature extraction.</p> <p><strong>Usage</strong><br>All datasets are intended for academic, non-commercial use. The provided files can be directly used to reproduce the training and evaluation of RepliChrom, and may also support broader applications in enhancer–promoter modeling, replication-timing analysis, and 3D genomics studies. For detailed usage instructions and code implementation, please refer to the GitHub repository: https://github.com/DaoFuying/RepliChrom</p>
HaHB4 promoter mutants GUS histochemistry assays
<p>CORRECTION</p> <p>Manavella PA, Dezar CA, Ariel FD, Chan RL. Two ABREs, two redundant root-specific and one W-box cis-acting elements are functional in the sunflower HAHB4 promoter. Plant Physiol Biochem. 2008 Oct;46(10):860-7. doi: 10.1016/j.plaphy.2008.05.003.</p> <p>During the assembly of Figure 3, the root picture in panel D was accidentally and unintentionally duplicated in panel H. The authors reviewed the original photographs and prepared a corrected version that contains the correct images. The authors apologize for this mistake. The figure legend and main text remain unaltered. This correction does not affect any of the conclusions of this paper.</p> <p>This dataset includes the original photographs of GUS staining of all Arabidopsis transgenic plants shown in Figure 3.</p>
Data from: Earthworms promote crop growth by enhancing the connections among soil microbial communities
<p>Earthworms benefit plant growth and play a vital role in shaping soil microbial communities. However, how earthworms modify the soil microorganisms and thus affect plant growth is still unclear. Although fertilizers alter the assembly of microbial communities, further investigations are required to test the effect of fertilizer type on the relationship between earthworms, soil microbial communities, and plants. We evaluated the role of earthworms in soil microorganisms and maize plant growth characteristics under organic or chemical fertilizers in field and greenhouse experiments. We explored the relationships between earthworms, soil microbial community, and plant growth under different fertilizer types. We found that the presence of earthworms promoted plant growth, increased the amount of plant root exudates, and enhanced the connections between rhizosphere bacterial, fungal, and protist communities. Both earthworms and fertilizer application significantly changed the structure of soil bacterial, fungal, and protist communities. The complexity of the soil microbial community network increased under organic, compared to chemical fertilizer application. The greenhouse experiment showed that the effect of earthworms on plant growth was weakened when maize plants were grown in sterilized soil under organic or chemical fertilizers.</p> <p><em>Synthesis and applications:</em> Our study provides solid evidence that earthworms largely depend on soil microorganisms for their effects on plants under the application of different fertilizer conditions. This may provide new insights into reducing the amounts of fertilizer used by enhancing the role of earthworms and soil microorganisms.</p>
How do fine root traits of fast-growing trees promote soil organic carbon stabilization?
<p>Soil represents a larger reservoir of soil organic carbon (SOC) than terrestrial vegetation, offering a great potential for reducing the widespread adverse consequences of climate change. In forests and tree plantations, fine roots significantly impact SOC stabilization through their functional traits. However, it is not obvious which fine root traits between those related to chemistry (easily decomposable or recalcitrant), to architecture or morphology are the most conducive to SOC stabilization in phylogenetically related fast-growing trees. We assessed the effects of root functional traits on SOC storage and stabilization by studying <span>five hybrid poplar clones </span><span>(<em>Populus </em>spp.)</span><span> </span><span>with different root traits in plantations located in New Liskeard, ON, Canada</span>. We collected <span>soil cores at depths of 0-20, 20-40 and 40-60 cm, and determined bulk soil organic carbon, </span><span>particulate organic carbon (> 53 μm, POC) and mineral-associated organic carbon (< 53 μm, MAOC) fractions and fine root (< 2 mm diameter) traits.</span><span> We found that r</span>oot length density (RLD) was the best predictor of increased SOC stocks and MAOC among all root traits. Soil organic C stocks and MAOC were also positively correlated with root traits indicative of low chemical recalcitrance (i.e. high N and soluble compounds concentrations and low lignin/N). Such easily decomposed root matter could be readily consumed by soil microorganisms and promote adsorption of microbial by-products onto mineral surfaces. Thus, root traits that increase the soil volume explored by fine roots and are associated with easily decomposed organic compounds play a key role in SOC accumulation and persistence.</p>
Research data for: Patchy energy landscapes promote stability of small groups of active particles
<p>Research data supporting the pubblication "Patchy energy landscapes promote stability of small groups of active particles"</p>
The unsteady shock boundary layer interaction in a compressor cascade - Part 3: Mechanisms of shock oscillation - Promotional video 2
<p>Second promotional video with animation of mechanisms of shock oscillation for the ASME Turbo Expo 2024 open access publication with identifier GT2024-128197 and title "The unsteady shock boundary layer interaction in a compressor cascade - Part 3: Mechanisms of shock oscillation."</p>
Ungulate herbivores promote beta diversity and drive stochastic plant community assembly by selective defoliation and trampling: From a four-year simulation experiment
<p>Ungulate herbivores shape grassland plant communities at multiple scales, ultimately affecting ecosystem function. However, ungulates have complex effects on grasslands, including defoliation, trampling, excreta return, and their interactions. Moreover, the effects of ungulate density on grasslands are regulated by these three mechanisms. Nevertheless, how these three mechanisms affect biodiversity at multiple scales and community assembly remains poorly understood.</p> <p>Here, we conducted a 4-year novel field experiment to disentangle the effects of defoliation, trampling, and excreta return by ungulates on plant community assembly in a temperate grassland in Inner Mongolia, China. This experiment set two different scenarios: moderate ungulate density (Moderate, characterised by selective defoliation and moderate trampling) and high ungulate density (Intense, characterised by non-selective defoliation and heavy trampling), including different combinations of defoliation, trampling, and excreta return in each scenario.</p> <p>We found that defoliation and trampling increased stochasticity in community assembly and promoted alpha and beta diversity under both scenarios. Specifically, defoliation promoted the coexistence of species with multiple resource acquisition strategies (higher functional trait diversity) by reducing interspecific competition; trampling tended to facilitate random species colonisation. Conversely, excreta return favoured grasses, promoting deterministic assembly and impacting species coexistence. Notably, selective defoliation in the moderate scenario led to a dominance of stochastic processes during community assembly, whereas non-selective defoliation still did not change the dominance of deterministic processes. Further, communities subject to selective defoliation were insensitive to changes in soil properties caused by trampling and excreta return, maintaining a high-level beta diversity and the stochastic of community assembly.</p> <p><em>Synthesis:</em></p> <p>Our study provides important insights into the mechanisms by which ungulate herbivores influence plant community assembly, suggesting that defoliation and trampling have the potential to drive stochastic processes, while excreta return plays the opposite role. Our study also suggests that selective foraging by ungulates acts as stronger stochastic forces during community assembly compared to non-selective defoliation. These results imply that considering ungulate feeding preferences and foraging behaviour in grassland management will help prevent biodiversity loss and biotic homogenisation.</p>
Microplastics promote the invasiveness of invasive alien species under fluctuating water regime
<p>Microplastic pollution and alien plant invasions are two important threats to terrestrial ecosystems. Microplastics (MPs) alter the physical and chemical characteristics of soil, potentially affecting the performance of alien plants. However, previous studies have overlooked the impact of weather on invasive plants in areas polluted by MPs. With the global increase in extreme rainfall events, it is imperative to redefine the correlation between MPs and invasive plants. Here, we conducted an experiment in a climate chamber to examine the effects of MPs on the growth and development of both native and invasive alien plants under a constant and fluctuating water regime (FWR). The FWR simulated extreme water pulses during the 2016-2020 growing seasons in Wuhan, China. Our results indicated that biomass accumulation and roots development were influenced by water conditions and MPs pollution in both invasive and native species. The extent of the effects varied between the two groups of plant species. FWR promoted plant growth and fine root development in invasive plants but reduced the maximum quantum efficiency of photosystem II (<em>F</em><em><sub>v</sub></em><em>/F</em><em><sub>m</sub></em>) and nonphotochemical quenching (<em>NPQ</em>) indices of native plants. Moreover, FWR attenuated the negative effects of polybutylene succinate (PBS, degradable MPs) on biomass and root characteristics (length, surface area, and tips). FWR compensates for the negative impacts of MPs on the total and belowground biomass of the invasive species <em>Paspalum dilatatum</em> and <em>Sphagneticola trilobata</em>, but not on the native species. Consequently, invasive species showed better performance than native species in the fine-root development of biomass growth and chlorophyll fluorescence under the combined effects of MPs and FWR.</p> <p><em>Synthesis and Applications</em>. Our findings suggest that MPs pollution enhances the competitiveness of invasive alien species over the native species when exposed to pronounced dry-wet water cycle conditions, potentially affecting the composition and biodiversity of the ecosystems. Thus, controlling MPs pollution should be a part of the management strategy to conserve biodiversity and ecosystems.</p>
Fig. 3 in Skin extract from Rhamdia quelen (Siluriformes: Heptapteridae) does not promote stress in conspecifics
Fig. 3. Locomotion displayed by Rhamdia quelen. Symbols
Figure 2 in Plant growth promoting bacteria drive food security
Figure 2. Screening steps to obtain efficient bioinoculants.
Figure 1 in Plant growth promoting bacteria drive food security
Figure 1. Mode of actions of PGPB.
Promoting responsible business conduct due diligence in public procurement: Cutting edge insights from academics, practitioners and policy makers
<p>On the 30<sup> </sup>May 2024 Sapiens Network, through our Early Stage Researcher Laura Treviño-Lozano and the OECD Centre for Responsible Business Conduct hosted an online about the link between responsible business conduct (RBC) due diligence and public procurement. The aim was to encourage debate about the ways in which RBC due diligence can be operationalised to prevent and address various adverse impacts that derive from public procurement. A topic that has been little explored so far and already a reality established in the adopted EU Corporate Sustainability Due Diligence Directive.</p> <p>Moderated by Lena Diesing (OECD), Sarah Reso (OECD) started the discussion with a presentation on the OECD’s research on the implications of RBC due diligence regulation on public procurement. Next, Laura Treviño-Lozano (Sapiens network) presented an open access <a title="https://url.uk.m.mimecastprotect.com/s/BOsTCGvj1hZPJAzukUTp5?domain=journals.sagepub.com" href="https://url.uk.m.mimecastprotect.com/s/BOsTCGvj1hZPJAzukUTp5?domain=journals.sagepub.com" target="_blank" rel="noopener">research paper</a>, co-authored with Ezgi Uysal (Sapiens Network), on establishing RBC due diligence as a contract performance condition under the EU Procurement Directive. Their presentations followed a roundtable discussion by experts and practitioners Zsofia Kerecsen (European Commission), Roberto Caranta (Sapiens Network), Carla Canal (Barcelona City Council) and Sophie Derksen (International Responsible Business Conduct Unit at the Ministry of Foreign Affairs in the Netherlands) on the importance, challenges and opportunities to integrate RBC due diligence in public procurement.</p> <p>This webinar is ideal for students, policymakers, and procurement practitioners aiming to learn from research and practice insights on responsible business conduct due diligence and public procurement.</p>
CD4+ T cells re-wire granuloma cellularity and regulatory networks, promoting immunomodulation following Mtb reinfection
<p>Here we include the necessary .ipynb, .h5ad, and .rds (used for cell-cell interaction analyses) files used in our work: "Immunomodulatory re-wiring of granuloma cellularity and regulatory networks by CD4 T cells following Mtb reinfection"</p>
Rewarding Fitness Tracking – The Communication and Promotion of Health Insurers' Bonus Programs and the Use of Self-Tracking Data
<p>The data set offers additional information for the study on "Rewarding Fitness Tracking – The Communication and Promotion of Health Insurers’ Bonus Programs and the Usage of Self-Monitored Data", to be submitted at HCII 2018.</p> <p>The data set includes the full lists of German and Australian Health Insurers investigated, including a link to their apps.</p> <p>This study aims at giving an overview on the current status quo of health insurances that investigate self-tracking opportunities and possible rewards for customers that share their fitness and health activities. We are interested in how insurers promote their health and well-being programs (intended program goals) and motivate customers to live healthier (incentives). We introduce research in progress while firstly focusing on the countries Germany and Australia. We discuss the current situation of health insurance clients’ data use, data security issues as well as long-term health benefits regarding those programs based on recent research on self-tracking activities. The research questions are: </p> <ol> <li>Which health insurers offer options for client to self-track health and fitness data?</li> <li>How do insurers communicate about the programs?</li> <li>How do those insurers communicate about data security?</li> </ol>
How do developers promote OSS?
<p>Hudson Silva Borges and Marco Tulio Valente. How do Developers Promote Open Source Projects?. Submitted to <em>IEEE Software</em>, pages 1-9, 2018.</p>
MADFORWATER: WP3: Adaptation of technologies for efficient water management and treated wastewater reuse in agriculture: Task3.1: Reduction of crop water requirement and tools for irrigation management with treated WW: Subtask 3.1.1: Plant Growth Promotion (PGP) bacteria to enhance crop resistance to water stress and salinity: Subset2
<p>This dataset contains the data underlying the following publication: Hassen W, Neifar M, Cherif H, Najjari A, Chouchane H, Driouich RC, Salah A, Naili F, Mosbah A, Souissi Y, Raddadi N, Ouzari HI, Fava F and Cherif A (2018) Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation. Front. Microbiol. 9:34. doi: 10.3389/fmicb.2018.00034</p>
Photomicrographs: transverse sections of GUS-stained apices for AGO7 promoter analysis
<p>These photomicrographs of histological sections of stained tissue support a paper by Hoyer et al. (2019): <a href="https://doi.org/10.1002/pld3.102">https://doi.org/10.1002/pld3.102</a></p> <p>Many additional photomicrographs from this and related experiments were taken by JSH, EEH, M. Hassert, and H. Fowler. Email j.s.hoyer@wustl.edu if you have questions or would like to examine this additional data.</p> <p> </p> <p>Methods text:</p> <p>Histological GUS assays were essentially as described (Bomblies 2002, Chitwood et al. 2009, Strader et al. 2011). Seedlings were collected into ice-cold 90% acetone, incubated at -20 °C for 20 minutes and then room temperature for another 20 minutes. Seedlings were washed twice (5 minutes each) with staining buffer (100 mM sodium phosphate [pH 7], 20% methanol, 0.1% Triton X-100, 1.5 mM ferri- and ferrocyanide).</p> <p>Staining buffer with 0.5 mg/mL 5-bromo-4-chloro-3-indolyl-beta-d-glucuronic acid (X-Gluc) was vacuum-infiltrated into seedlings on ice for two rounds of 15 minutes each. Samples were then incubated at 37 °C for 20 hours, taken through an ethanol/histoclear series, and infiltrated with Paraplast Plus at 60 °C, before embedding (Bomblies 2002). Tissue sections (10 µm thickness) were mounted on Probe-On Plus slides (Thermo Fisher), deparaffinized with histoclear, and coverslipped. Sections were viewed and photographed with a Leica DM750 microscope and ICC50 HD camera.</p>
Scans of leaves dissected in phyllotactic order: complementation of ago7 mutant A. thaliana plants with truncated promoter transgenes
<p>This transgenic complementation experiment is described in a paper by Hoyer et al. (2019): <a href="https://doi.org/10.1002/pld3.102">https://doi.org/10.1002/pld3.102</a></p> <p>Adaxial (ad) and abaxial (ab) surfaces of rosettes were photographed in between removal of leaves, to enable checking that leaves were removed in the correct phyllotactic order.<strong> </strong>A manifest file with file SHA-1 sums is included.</p> <p>Metadata and LeafJ measurements have been made available separately, to facilitate updates -- see <a href="https://github.com/jshoyer/raspi-photo-and-leaf-scan-metadata">https://github.com/jshoyer/raspi-photo-and-leaf-scan-metadata</a>, archived as <a href="https://doi.org/10.5281/zenodo.1340636">https://doi.org/10.5281/zenodo.1340636</a></p> <p>Seed was plated and growth started on 2016-08-26. Leaves were dissected and scanned 33 and 35 days post-stratification (2016-09-28 and 30).</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.