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12,455 results for “promoters”
Mutations in the telomerase reverse transcriptase promoter and PIK3CA gene are common events in penile squamous cell carcinoma of Italian and Ugandan patients
<p>Somatic mutations in the promoter region of TERT (TERTp) gene are highly frequent in penile carcinoma in Italian and Ugandan patients, predominantly in human papillomavirus (HPV) negative cancers (67.6%). TERTp and PIK3CA hotspot changes coexist in 15.8% of cases. The higher mutant allele frequencies (MAFs) of TERT -124A/-146A compared to PIK3CA E545K MAFs suggest an asynchronous mutation timing. The coexistence of TERTp and PIK3CA mutations may represent a novel co-actionable therapeutic target in penile carcinoma patients.</p>
Karuk ecological fire management practices promote elk habitat in Northern California
<p>After a century of fire suppression and accumulating fuel loads in North American forests, prescribed burns are increasingly used to prevent conditions leading to catastrophic megafire. There is widespread evidence that prescribed fire was used by Indigenous communities to manage natural and cultural resources tribes for thousands of years. Wildlife habitat is an example of an ecological response that was actively managed with prescribed burns by Indigenous American peoples and is an important factor in western U.S. forest management planning, restoration and climate resilience efforts. We analyzed the effects of modern prescribed burns informed by traditional ecological knowledge (TEK) on the predicted change in elk winter habitat in Karuk aboriginal territory in Northern California between 2013 and 2018 using species distribution and simultaneous autoregressive modeling techniques. Burn types most closely resembling Karuk traditional practices, specifically those incorporating multiple-year broadcast burns, had significant positive effects on elk winter habitat suitability. Conversely, concentrated burns focused solely on reducing fuel loads had significant negative effects on elk winter habitat suitability. However, areas where these fuel-reduction burns were combined with multiple years of broadcast burns featured the highest increases in habitat. Our results suggest that transitioning to prescribed burns that more closely follow Karuk TEK will promote elk habitat in the region. This would be best achieved through continuing to work closely with Indigenous representatives to plan and implement cultural fire prescriptions on a landscape-scale, a trend we posit would benefit environmental management efforts across the globe.</p>
Storytelling and its influence on the tourist promotion of the national sanctuary of Huayllay, Pasco Region-2021
<p><strong>Background:</strong> The objective of the study article was to determine the influence of Storytelling in the tourist promotion of the National Sanctuary of Huayllay</p> <p><strong>Methods:</strong> For which a quantitative approach study was used, pre-experimental design with a single control group, the study population consisted of 19 visitors to which (Pre test-post test).</p> <p><strong>Results:</strong> The information collected was processed through the statistical program spss, and then the Eta analysis was performed to determine the degree of influence between the variables of study. The result obtained was 0.677/0.795, which indicates that storytelling does influence the tourism promotion of the place. The importance of the study consists in the investigation of a new commercial communication tool known as storytelling, which appeals to the emotional factor, and which already represents a successful model in different countries of the world, since it has reached an extraordinary importance in the decision-making process of potential tourists and has turned out to be an excellent alternative for the promotion of tourist destinations.</p> <p><strong>Conclusion:</strong> The study was able to demonstrate that Storytelling can be used as a tool for tourism promotion not only at the level of the locality of the area of the study site, but also at the national level.</p> <p><strong>Background:</strong> The objective of the study article was to determine the influence of Storytelling in the tourist promotion of the National Sanctuary of Huayllay</p> <p><strong>Methods:</strong> For which a quantitative approach study was used, pre-experimental design with a single control group, the study population consisted of 19 visitors to which (Pre test-post test).</p> <p><strong>Results:</strong> The information collected was processed through the statistical program spss, and then the Eta analysis was performed to determine the degree of influence between the variables of study. The result obtained was 0.677/0.795, which indicates that storytelling does influence the tourism promotion of the place. The importance of the study consists in the investigation of a new commercial communication tool known as storytelling, which appeals to the emotional factor, and which already represents a successful model in different countries of the world, since it has reached an extraordinary importance in the decision-making process of potential tourists and has turned out to be an excellent alternative for the promotion of tourist destinations.</p> <p><strong>Conclusion:</strong> The study was able to demonstrate that Storytelling can be used as a tool for tourism promotion not only at the level of the locality of the area of the study site, but also at the national level.</p>
Promotion of Circum-Pacific Earthquakes on Plate Movement-data
<p>data S1. The steady-state deformation data supporting Figure 1(a).</p> <p>The first and second columns show the location of point (longitude and latitude). The third, fourth, and fifth columns show the displacement induced by 2011 Tohoku-Oki Mw 9.0 earthquake (east-west, north-south, and up-down components in m). The sixth, seventh, and eighth columns show the displacement induced by 2010 Chile Mw 8.8 earthquake (east-west, north-south, and up-down components in m).</p> <p>data S2. Expansion of normal direction in the East Pacific Rise supporting Figure 1(b).</p> <p>The first and second columns show the location of point (longitude and latitude). The third and fourth columns show the displacement induced by 2011 Tohoku-Oki Mw 9.0 earthquake (the angle from east and the magnitude of displacement vector in m). The fifth and sixth columns show the displacement induced by 2010 Chile Mw 8.8 earthquake (the angle from east and the magnitude of displacement vector in m).</p> <p>data S3. Steady-state strain field supporting Figure 1(c).</p> <p>The first and second columns show the location of point (longitude and latitude). The third, fourth and fifth columns show the strain changes induced by two earthquakes (east-west, north-south, and shear components).</p> <p>data S4. The co-seismic and post-seismic displacement data supporting Figure 2.</p> <p>The first and second columns show the location of point (longitude and latitude), and the third column show the epicenter distance. The co-seismic and post-seismic displacement induced by 2011 Tohoku-Oki Mw 9.0 earthquake in the fourth column to the ninth column at different times (0, 10yr, 100yr, 1000yr,10000yr, and infinity in m).</p>
The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest
<p>Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated Species Distribution Models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine-learning approach to compare models with and without gene flow between populations upon secondary contact after the Last Glacial Maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support the role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.</p>
Time to run: Late rather than early exercise training in mice promotes fat mass loss and reduces atherosclerosis development
<p>This dataset contains forward and reverse reads of 16S sequencing of the V3-V4 region of caecal bacteria. As indicated in the metadata file, mice are divided into three groups - SED (sedentary mice, E-SED for early sedentary and L-SED for late sedentary), E-RUN (early runners) and L-RUN (late runners). For more information about the groups, sequencing etc., consult the manuscript.</p>
The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural Taraxacum populations
<p>This data accompanies the pending publication "The cost of self-promotion: Ecological and demographic implications of the mentor effect in natural <em>Taraxacum </em>populations" by Lynn et al. The work is also published under Austin Lynn's PhD Dissertation, which is under embargo until 2022.</p>
ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA
<p>One-dimensional (1D) target search is a well-characterized phenomenon for many DNA-binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a conserved yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome-depleted region (NDR) at gene promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single-particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA-binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 μm2/s, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.</p>
Can immune gene silencing via dsRNA feeding promote pathogenic viruses to control the globally invasive Argentine ant?
<p><span>Pest control methods that can target pest species with limited environmental impacts are a conservation and economic priority. Species-specific pest control using RNA interference is a challenging but promising avenue in developing the next generation of pest management. We investigate the feasibility of manipulating a biological invader's immune system using double-stranded RNA (dsRNA) in order to increase susceptibility to naturally occurring pathogens. We used the invasive Argentine ant as a model, targeting the immunity-associated genes <em>Spaetzle</em> and <em>Dicer-1</em> with dsRNA. We show that feeding of <em>Spaetzle</em> dsRNA can result in partial target gene silencing for up to 28 days in the laboratory and five days in the field. <em>Dicer-1</em> dsRNA only resulted in partial gene knockdown after two days in the laboratory. Double-stranded RNA treatments were associated with significant gene expression disruptions across immune pathways in the laboratory and to a lower extent in the field. We observed occasional changes in viral loads in dsRNA-treated groups. However, immune pathways disruption did not result in consistent increase in microbial infections, nor did they alter ant abundance in the field. Our study explores the feasibility of lowering a pest's immunity as a control tool. We demonstate that it is possible to alter immune gene expression of pest species and pathogen loads, though in our system the affected pathogens did not appear to influence pest abundance. We provide advice on future directions for dsRNA-mediated immune disruption in pest species, including potential avenues to improve dsRNA delivery as well as the importance of the biology of the pest system and its pathogens.</span></p>
Data for "Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton"
<p>This publication contains 27 coral reef bacterioplankton metagenome-assembled genomes (MAGs) from the following paper: </p> <p>Cárdenas, A., Neave, M. J., Haroon, M. F., Pogoreutz, C., Rädecker, N., Wild, C., Gärdes, A., & Voolstra, C. R. (2018). Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton. <em>The ISME Journal</em>, <em>12</em>(1), 59–76. https://doi.org/10.1038/ismej.2017.142</p> <p> </p>
Livestock management promotes bush encroachment in savanna systems by altering plant-herbivore feedback
<p>This repository contains all code to reproduce the analysis in Koch et al. 2022 "Livestock management promotes bush encroachment in savanna systems by altering plant-herbivore feedback".</p> <p>We use a set of coupled differential equations to describe competition between shrubs and grasses, as well as plant biomass consumption via grazing and browsing. Grazers were assumed to receive a certain level of care from farmers, so that grazer densities emerge dynamically from the combined effect of vegetation abundance and farmer<br>support. Our main goal was to understand how critical transitions from grass-dominated to shrub-dominated system states were affected by the dynamic role of grazing.</p> <p>Our results show that bistability emerges for intermediate levels of farmer support due to positive feedback that arises from competition between shrubs and grasses and from herbivory. We furthermore demonstrate that disturbances, such as drought events, trigger abrupt transitions from the grass dominated to the shrub dominated state and that the system becomes more susceptible to disturbances with increasing farmer support.</p>
Dataset for "Applicability of Control Materials To Support Gene Promoter Characterization and Expression in Engineered Cells Using Digital PCR"
<p>This dataset constitutes the pre-processed data contained in the publication 'Applicability of Control Materials To Support Gene Promoter Characterization and Expression in Engineered Cells Using Digital PCR' Analytical Chemistry (2022) 94(14):5566-5574 (DOI: 10.1021/acs.analchem.1c05134).</p>
Subducting seafloor anomalies promote porphyry copper formation
<p>Source data used to interrogate relationships between subducting seafloor anomalies and porphyry copper deposits presented in:</p> <p>Mather, B., Müller, R.D., Alfonso, C.P., Wright, N.M., Seton, M. (In prep.) Subducting seafloor anomalies promote porphyry copper formation.</p> <p>Python notebooks and scripts can be found in the <a href="https://github.com/brmather/SeafloorAnomalies">GitHub repository</a>.</p>
Native plant diversity creates microbial legacies that either promote or suppress non-natives, depending on drought history
<p>High-diverse native plant communities resist non-native plants more strongly than low-diverse communities, in part through resource competition. Yet, the role of soil biota is largely unknown, although non-native plants interact with soil biota. Here, we tested the responses of non-native plants to soil conditioned by different native plant diversities. We applied well-watered and dry treatments in the conditioning and response phases to explore the effects of historical and contemporary environmental stresses. Historical water conditions determined the effects of native diversity via soil biota on responding non-natives grown in well-watered environments. Non-native growth decreased with native species richness for well-watered soil inocula but increased for dry soil inocula. However, non-native growth in dry environments did not depend on conditioning native species richness of soil inocula. We provide a new understanding of mechanisms behind diversity-invasibility relationships and demonstrate that temporal variation in environmental stress shapes relationships among native plant diversity, soil biota, and non-native plants.</p>
Data from: The biogeochemical boomerang: Site fidelity creates nutritional hotspots that may promote recurrent calving site reuse
<p>Animals interact with nutrient cycles by consuming and depositing nutrients, interactions that are studied in the separate fields of nutritional ecology and zoogeochemistry. Recent theoretical work has begun bridging these disciplines, highlighting that animal-driven nutrient recycling could be crucial in helping animals meet nutritional needs. When animals exhibit site fidelity, they consistently deposit nutrients, potentially improving vegetation quality. We investigated this potential feedback by analyzing changes in forage nitrogen stocks following simulated caribou calving. We found that forage nitrogen stocks increased after two weeks and remained elevated after one year, a change due to an increase in forage quality but not quantity. We thus highlight a positive zoogeochemical feedback whereby caribou deposit nutrients during calving that become bioavailable during lactation and provide evidence that site fidelity creates a biogeochemical boomerang in which animals deposit nutrients that can be reused at a later time.</p>
Dataset related to article: QUALITY ASSESSMENT OF THE MRI-RADIOMICS STUDIES FOR MGMT PROMOTER METHYLATION PREDICTION IN GLIOMA: A SYSTEMATIC REVIEW AND META-ANALYSIS
<p><strong><span>This table contains the raw data used to generate the heatmap illustrated in Fig 2. Each row of the table shows the distribution of the scores achieved by the studies for a domain. Colors from red to green denote progressive increase from minimum to maximum score obtainable for each domain.</span></strong></p>
Can developmental plasticity shape sexual competition and promote reproductive isolation?
<p>Environmental factors such as dietary nutrients can shape the expression of developmentally plastic sexual traits in many species. However, while there has been extensive research into the developmental plasticity of sexual traits at the individual level, the broader consequences of this variation at the population scale remain poorly understood. Here, we asked whether plastic responses to the developmental environment can shape sexual competition and initiate reproductive isolation between populations. We reared neriid flies, <em>Telostylinus angusticollis</em>,<em> </em>on nutrient-rich and nutrient-poor larval diets, generating adult flies that differed in body size and secondary sexual trait expression. We then investigated sexual competition in experimental populations from each developmental environment, and tested for reproductive isolation between flies from mismatched environments. We found that, compared with poor-diet populations, rich-diet populations exhibited more frequent and escalated male-male combat and more frequent mating and mate-guarding. However, we found no evidence that sexual selection was affected by the developmental environment. Mismatched female-male pairs tended to take longer to mate and rich-diet females often rejected poor-diet males, but mismatched pairs were not less likely to mate within 1 hour or produce viable offspring. Our findings suggest that developmental plasticity could generate dramatic differences in sexual competition between populations, and could contribute to reproductive isolation.</p>
Biotic interactions promote local adaptation to soil in plants - Supplementary data
<p>Although different ecological factors shape adaptative evolution in natural habitats, we know little about how their interactions impact local adaptation. Here we used eight generations of experimental evolution with outcrossing <em>Brassica rapa</em> plants as a model system, in eight treatment groups that varied in soil type, herbivory (with/without aphids), and pollination mode (hand- or bumblebee-pollination), to study how biotic interactions affect local adaptation to soil. First, we show that several plant traits evolved in response to biotic interactions in a soil-specific way. Second, using a reciprocal transplant experiment, we demonstrate that significant local adaptation to soil-type evolved in the "number of open flowers", a trait used as a fitness proxy, but only in plants that evolved with herbivory and bee pollination. Whole genome re-sequencing of experimental lines revealed that biotic interactions caused a 10-fold increase in the number of SNPs across the genome with significant allele frequency change, and that alleles with opposite allele frequency change in different soil types (antagonistic pleiotropy) were most common in plants with an evolutionary history of herbivory and bee pollination. Our results demonstrate that the interaction with mutualists and antagonists can facilitate local adaptation to soil type through antagonistic pleiotropy. </p>
Figure 5 in Under pressure: maternal effects promote drought tolerance in progeny seed of Palmer amaranth (Amoronthus polmeri)
Figure 5. Shifts in distribution of base water potential of progeny seeds from two Amoronthus polmeri populations (California and Kansas) grown under contrasting maternal water conditions (continuous̜ ̜ ̹ water-deficit ̹ vs. well-watered). Seed germination was tested at two temperatures (20 and 30 C) under five water potentials. A hydrotime model, ̜ ̹ θ Equation 3, g w,t¼ Φ w ― H w,σ, was fit to estimate the median base water potentials, w (vertical dashed lines), and their respective standard deviations, σ, g tg bð50Þ wb bð50Þ wb to produce these probability density curves of normal distribution (see Table 1 for parameter estimates). Note that the area under the curve for base water potential values>0 indicates the proportion of seeds that have not germinated (i.e., dormancy level).
Figure 1 in Under pressure: maternal effects promote drought tolerance in progeny seed of Palmer amaranth (Amoronthus polmeri)
Figure 1. Plant height for Amoronthus polmeri populations (California and Kansas) grown under continuous water-deficit or well-watered irrigation conditions. Vertical lines on bars indicate SE.
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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.