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12,455 results for “Promoters”
Time-lapse photograph dataset: 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>Time-stamped photographs are provided in twelve directories by camera (twelve overlapping fields of view) and a manifest file with file SHA-1 sums is included.</p> <p>Metadata 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.</p>
Supplemental Figures S1-S8: Direct CD137 costimulation of CD8 T cells promotes retention and innate-like function within nascent atherogenic foci
<p>Supplemental Figures and Table S1-S8 for "Direct CD137 costimulation of CD8 T cells promotes retention and innate-like function within nascent atherogenic foci" H-00088-2019, to the American Journal of Physiology-Heart and Circulatory Physiology.</p>
Recruiting, Retaining, and Promoting for Careers at Transportation Agencies
<p>Corresponding data set for Tran-SET Project No. 17PPLSU07. Abstract of the final report is stated below for reference:</p> <p>"State transportation agencies currently face complex challenges in recruiting and retaining the workforce necessary to function effectively. The situation exacerbates due to the number of employees from different generations that have to coexist with varying values, expectations, and principles. These agencies are primarily comprised of two generational groups: the baby-boomers, who are approaching retirement and occupy many managerial positions; and the millennials, who are demonstrating their interest in technology and demanding dynamism in their careers. This multiplicity of interest represents a challenge for human resources (HR) in addressing workforce issues and providing the necessary means to recruit and retain qualified employees within a transportation agency. Therefore, the purpose of the study is to examine the practices in recruiting, training, and retaining qualified employees at state departments of transportation (DOTs) primarily from Region 6 DOTs of Arkansas, Louisiana, New Mexico, Oklahoma, and Texas. A comprehensive literature review, including journal articles, books, and District 6 DOT documents, reports, and training manuals provided the basis to discuss current practices in recruitment and retention with Region 6 DOT human resources (HR) staff. A total of nine HR professionals were interviewed for this study. These interviews identified the most difficult to fill positions as engineers and engineer technicians. These positions also have high turnover rates within DOTs. The primary difficulty in retaining and recruiting staff in these positions was ascribed to the wage differences between the public and the private sector. The results of the HR interviews were used to compile a questionnaire that was distributed to current DOT District 6 employees. A total of 1,109 employee surveys were collected and reviewed to develop a recommended list of best practices for recruiting and retaining DOT employees. The list of best practices includes increased social media presence, quantification of overall benefit packages, implementation of flexible work schedules and telecommuting, clarification and restructuring of the promotions and incentives process, and increased communication and feedback between staff and management."</p>
Serum response factor utilizes distinct promoter- and enhancer-based mechanisms to regulate cytoskeletal gene expression in macrophages.
<p>Cells of the monocyte/macrophage lineage play essential roles in tissue homeostasis and immune responses, but mechanisms underlying the coordinated expression of cytoskeletal genes required for specialized functions of these cells, such as directed migration and phagocytosis, remain unknown. Here, using genetic and genomic approaches, we provide evidence that serum response factor (SRF) regulates both general and cell type-restricted components of the cytoskeletal gene expression program in macrophages. Genome-wide location analysis of SRF in macrophages demonstrates enrichment of SRF binding at ubiquitously expressed target gene promoters, as expected, but also reveals that the majority of SRF binding sites associated with cell type-restricted target genes are at distal inter- and intragenic locations. Most of these distal SRF binding sites are established by the prior binding of the macrophage- and the B cell-specific transcription factor PU.1 and exhibit histone modifications characteristic of enhancers. Consistent with this, representative cytoskeletal target genes associated with these elements require both SRF and PU.1 for full expression. These findings suggest that SRF uses two distinct molecular strategies to regulate programs of cytoskeletal gene expression: a promoter-based strategy for ubiquitously expressed target genes and an enhancer-based strategy at target genes that exhibit cell type-restricted patterns of expression.</p>
SmartLife smart clothing gamification to promote energy-related behaviours among adolescents
<p>Inactivity and high sedentary behavior among adolescents are main societal problems. Unhealthy lifestyles place a large burden on society and promoting healthy lifestyles is thus key for health, wellness and economic prosperity. These non-communicable diseases and unhealthy lifestyles furthermore occur more often among lower socio-economic groups, which indicates a need for healthy lifestyle promotion programs to help reduce health inequalities and improve social inclusion. The SmartLife project aims to create a mobile game that requires lower body movement, and is personalized by physiological feedback measured by smart textiles. Personalization via smart textiles can present a game challenge achievable for the current fitness level of the player and can adjust this based on activity levels during game play. This approach can improve current exergames to achieve a higher level of intensity in physical activity, needed to create a health impact, and can do so considering what is achievable for the person and hence reduce drop-out and injury risks.</p>
Dopamine signaling in the dorsomedial striatum promotes compulsive behavior -- Western Blot Supplement
<p>Compulsive behavior is a defining feature of disorders such as substance use disorders. Current evidence suggests that corticostriatal circuits control the expression of established compulsions, but little is known about the mechanisms regulating the development of compulsions. We hypothesized that dopamine, a critical modulator of striatal synaptic plasticity, could control alterations in corticostriatal circuits leading to the development of compulsions (defined here as continued reward seeking in the face of punishment). We used dual-site fiber photometry to measure dopamine axon activity in the dorsomedial striatum (DMS) and the dorsolateral striatum (DLS) as compulsions emerged. Individual variability in the speed with which compulsions emerged was predicted by DMS dopamine axon activity. Amplifying this dopamine signal accelerated animals’ transitions to compulsion, whereas inhibition delayed it. In contrast, amplifying DLS dopamine signaling had no effect on the emergence of compulsions. These results establish DMS dopamine signaling as a key controller of the development of compulsive reward seeking.</p>
ERL-118550 Data: Rebates and Grid Decarbonization from the Inflation Reduction Act Promote Equitable Adoption of Energy Efficiency Retrofits
<p>The authors have self-reported an issue in how they used RSMeans 2019 City Cost Index (CCI) data to adjust for regional cost differences. The publicly available webpage stated these data could be used to “adjust for cost differences when compared to the national average, show cost differences between cities, compare cost differences between quarters of the same year, or adjust costs to Canadian cities.” However, the RSMeans Data and Engineering Department later clarified that these values “were intended to show how much CCI values changed for each city at the start of 2019 compared to the values in our 2019 book.” Nevertheless, our capital cost estimates closely align with several peer-reviewed studies and publicly available data sources. Based on our review, we do not believe our method significantly affected the study’s overall findings or conclusions. Further discussion is provided in the manuscript’s Limitations section and Appendix S5 of the Supplementary Materials.</p> <p>Peer-reviewed article available here: https://iopscience.iop.org/article/10.1088/1748-9326/adb765</p> <p>Article DOI: 10.1088/1748-9326/adb765</p>
Research Data for "Promoting effect of interfacial hole accumulation on photoelectrochemical water oxidation in BiVO4 and Mo doped BiVO4"
<p>This dataset supports the Figures and Tables for the publication "Promoting effect of interfacial hole accumulation on photoelectrochemical water oxidation in BiVO4 and Mo doped BiVO4" published in Advanced Powder Materials under <a href="https://doi.org/10.1016/j.apmate.2024.100234" rel="noreferrer">https://doi.org/10.1016/j.apmate.2024.100234</a></p>
P300 promotes acetylation of H3K18 during osteogenesis of hAD-MCSs
Open the record for dataset details and reuse information.
Promoting Indonesian Batik as a Symbol of National Identity: A Bibliometric Approach
Open the record for dataset details and reuse information.
Data related to "Lysosomal damage triggers a p38 MAPK-dependent phosphorylation cascade to promote lysophagy via the small heat shock protein HSP27."
<p>Data used to generate figures, as well as all uncropped blots. Article abstract: "Maintenance of lysosomal integrity is essential for cell viability. Upon injury, lysosomes may be targeted for degradation via a selective form of autophagy known as lysophagy. The engulfment of a damaged lysosome by an autophagosome is mediated by the recruitment of adaptor proteins, including SQSTM1/p62. p62 promotes lysophagy via the formation of phase separated condensates in a mechanism that is regulated by the heat shock protein HSP27. Here, we demonstrate a direct interaction between HSP27 and p62. We used structural modeling to predict the binding interface between HSP27 and p62 and identify several disease-associated mutations that map to this interface. We used proteomics to identify post-translational modifications of HSP27 that regulate HSP27 recruitment to stressed lysosomes, finding robust phosphorylation at several serine residues. Next, we characterized the upstream signaling mechanism leading to HSP27 phosphorylation, and found that p38 MAPK and its effector kinase MK2 are activated upon lysosomal damage by the kinase mTOR and the production of intracellular reactive oxygen species (ROS). Increased ROS activates p38 MAPK, which in turn allows MK2-dependent phosphorylation of HSP27. Depletion of HSP27 or the inhibition of HSP27 phosphorylation alters the dynamics of p62 condensates on stressed lysosomes, significantly inhibiting p62-dependent lysophagy. Thus, we define a novel lysosomal quality control mechanism in which lysosomal injury triggers a p38 MAPK/MK2 signaling cascade promoting p62-dependent lysophagy. Further, this signaling cascade is activated by many cellular stressors, including oxidative and heat stress, suggesting that other forms of selective autophagy may be regulated by p38 MAPK/MK2/HSP27." </p>
Animal-APdb: a comprehensive animal alternative promoter database
<p>Alternative promoter (AP) events, as a major pre-transcriptional mechanism, can initiate different transcription start sites to generate distinct mRNA isoforms and regulate their expression. At present, hundreds of thousands of APs have been identified across human tissues, and a considerable number of APs have been demonstrated to be associated with complex traits and diseases. Recent researches have also proven important effects of APs on animals. However, the landscape of APs in animals has not been fully recognized.</p> <p>In this study, 102,349 AP profiles from 23,137 samples across 12 species were systematically characterized. We further identified tissue-specific APs and investigated trait-related promoters among various species. In addition, we analyzed the associations between APs and enhancer RNAs (eRNA)/transcription factors (TF) as a means of identifying potential regulatory factors. Integrating these findings, we finally developed Animal-APdb, a database for the searching, browsing and downloading of information related to Animal APs.</p> <p>Animal-APdb is expected to serve as a valuable resource for exploring the functions and mechanisms of APs in animals. Animal-APdb is available at <a href="http://gong_lab.hzau.edu.cn/Animal_AP#!/" target="_blank" rel="noopener">http://gong_lab.hzau.edu.cn/Animal_AP#!/</a>.</p>
Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1
<p>1. spaSPT data for endogenously tagging HaloTag-YY1 in mESCs (clones YN11 and YN31).</p> <p>2. spaSPT data for HaloTag-YY1 in CTCF- (clone CD1) or RAD21- (clone RD35) depleted mESCs.</p> <p>3. sptSPT data for stably expressing HaloTag-YY1 in clone PBYN2 and YY1-HaloTag in clone PBYC3.</p> <p> </p> <div> </div>
Parental population range expansion before secondary contact promotes heterosis
<p>Population genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that have undergone post-glacial range expansion. Here we show that explicitly accounting for historical parental isolation followed by range expansion prior to secondary contact is fundamental for explaining genetic and fitness patterns in these hybrid zones. Specifically, ancestral population expansion can result in allele surfing where neutral or slightly deleterious mutations drift to high frequency at the expansion front. If these surfed deleterious alleles are recessive, they can contribute to substantial heterosis in hybrids produced at secondary contact, counteracting negative effects of Bateson-Dobzhansky-Muller incompatibilities (BDMIs) hence weakening reproductive isolation. When BDMIs are linked to such recessive deleterious alleles the fitness benefit of introgression at these loci can facilitate introgression at the BDMIs. The extent to which this occurs depends on the strength of selection against the linked deleterious alleles and the distribution of recombination across the chromosome. Finally, surfing of neutral loci can alter the expected pattern of population ancestry, thus accounting for historical population expansion is necessary to develop accurate null genomic models of secondary-contact hybrid zones.</p>
An organizing feature of bumble bee life history: worker emergence promotes queen reproduction and survival in young nests
<p>Bumble bee queens initiate nests solitarily and transition to living socially once they successfully rear their first cohort of offspring. Bumble bees are disproportionately important for early season pollination, and many populations are experiencing dramatic declines. In this system, the onset of the social stage is critical for nest survival, yet the mechanisms that facilitate this transition remain understudied. Further, the majority of conservation efforts targets the social stage of the bumble bee life cycle and do not address the solitary founding stage. We experimentally manipulated the timing of worker emergence in young nests of bumble bee (Bombus impatiens) queens to determine whether and how queen fecundity and survival are impacted by the emergence of workers in the nest. We found that queens with workers added to the nest exhibit increased ovary activation, accelerated egg laying, elevated juvenile hormone (JH) titres and also lower mortality relative to solitary queens. We also show that JH is more strongly impacted by the social environment than associated with queen reproductive state, suggesting that this key regulator of insect reproduction has expanded its function in bumble bees to also influence social organization. We further demonstrate that these effects are independent of queen social history, suggesting that this underlying mechanism promoting queen fecundity is reversible and short lived. Synchronization between queen reproductive status and emergence of workers in the nest may ultimately increase the likelihood of early nesting success in social systems with solitary nest founding. Given that bumble bee workers regulate queen physiology as we have demonstrated, the timing of worker emergence in the nest likely impacts queen fitness, colony developmental trajectories and ultimately nesting success. Collectively, our findings underline the importance of conservation interventions for bumble bees that support the early nesting period and facilitate the production and maintenance of workers in young nests.</p>
Data from: A test of genomic modularity among life-history adaptations promoting speciation with gene flow
Speciation with gene flow may require adaptive divergence of multiple traits to generate strong ecologically based reproductive isolation. Extensive negative pleiotropy or physical linkage of genes in the wrong phase affecting these diverging traits may therefore hinder speciation, while genetic independence or "modularity" among phenotypic traits may reduce constraints and facilitate divergence. Here, we test whether the genetics underlying two components of diapause life history, initial diapause intensity and diapause termination timing, constrain differentiation between sympatric hawthorn and apple-infesting host races of the fly Rhagoletis pomonella through analysis of 10,256 SNPs measured via genotyping-by-sequencing (GBS). Loci genetically associated with diapause termination timing were mainly observed for SNPs mapping to chromosomes 1–3 in the genome, most notably for SNPs displaying higher levels of linkage disequilibrium (LD), likely due to inversions. In contrast, selection on initial diapause intensity affected loci on all five major chromosomes of the genome, specifically those showing low levels of LD. This lack of overlap in genetically associated loci suggests that the two diapause phenotypes are largely modular. On chromosome 2, however, intermediate level LD loci and a subgroup of high LD loci displayed significant negative relationships between initial diapause intensity and diapause termination time. These gene regions on chromosome 2 therefore affected both traits, while most regions were largely independent. Moreover, loci associated with both measured traits also tended to exhibit highly divergent allele frequencies between the host races. Thus, the presence of nonoverlapping genetic modules likely facilitates simultaneous, adaptive divergence for the measured life-history components.
Data from: Feeding sites promoting wildlife-related tourism might highly expose the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) to parasite transmission. DOI: 10.1038/s41598-021-95166-5
<p>An increasing number of studies have found that the implementation of feeding sites for wildlife-related tourism can affect animal health, behaviour and reproduction. Feeding sites can favour high densities, home range overlap, greater sedentary behaviour and increased interspecific contacts, all of which might promote parasite transmission. In the Yunnan snub-nosed monkey (Rhinopithecus bieti), human interventions via provisioning monkeys at specific feeding sites have led to the sub-structuring of a group into genetically differentiated sub-groups. The fed subgroup is located near human hamlets and interacts with domesticated animals. Using high-throughput sequencing, we investigated Entamoeba species diversity in a local host assemblage strongly influenced by provisioning for wildlife-related tourism. We identified 13 Entamoeba species or lineages in faeces of Yunnan snub-nosed monkeys, humans and domesticated animals (including pigs, cattle, and domestic chicken). In Yunnan snub-nosed monkeys, Entamoeba prevalence and OTU richness were higher in the fed than in the wild subgroup. Entamoeba polecki was found in monkeys, pigs and humans, suggesting that this parasite might circulates between the wild and domestic components of this local social–ecological system. The highest proportion of faeces positive for Entamoeba in monkeys geographically coincided with the presence of livestock and humans. These elements suggest that feeding sites might indirectly play a role on parasite transmission in the Yunnan snub-nosed monkey. The implementation of such sites should carefully consider the risk of creating hotspots of disease transmission, which should be prevented by maintaining a buffer zone between monkeys and livestock/humans. Regular screenings for pathogens in fed subgroup are necessary to monitor transmission risk in order to balance the economic development of human communities dependent on wildlife-related tourism, and the conservation of the endangered Yunnan snub-nosed monkey.</p>
Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
<p>The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules—well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using <i>C. elegans</i> germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of <i>eggd-1</i> and <i>eggd-2</i> results in separation of P granules from the nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.</p>
Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation
<p>This is the code and dataset for the article entitled "Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation," in the journal Ecology and Evolution.</p> <ul> <li>Competition for resources often contributes strongly to defining an organism's ecological niche. Endogenous biological rhythms are important adaptations to the temporal dimension of niches, but how other organisms influence such temporal niches have not been much studied, and the role of competition in particular has been even less examined. We investigated how interspecific and intraspecific competition for resources shape an organism's activity rhythms.</li> <li>To do this, we simulated communities of one or two species in an agent-based model. Individuals in the simulation move according to a circadian activity rhythm and compete for limited resources. Probability of reproduction is proportional to an individual's success in obtaining resources. Offspring may have variance in rhythm parameters, which allow for the population to evolve over time.</li> <li>We demonstrate that when organisms are arrhythmic, one species will always be competitively excluded from the environment, but the existence of activity rhythms allows niche differentiation and indefinite coexistence of the two species. Two species which are initially active at the same phase will differentiate their phase angle of entrainment over time to avoid each other. When only one species is present in an environment, competition within the species strongly selects for niche expansion through arrhythmicity, but the addition of an interspecific competitor facilitates evolution of increased rhythmic amplitude when combined with additional adaptations for temporal specialization. Finally, if individuals preferentially mate with others who are active at similar times of day, then disruptive selection by intraspecific competition can split one population into two reproductively isolated groups separated in activity time.</li> <li>These simulations suggest that biological rhythms are an effective method to temporally differentiate ecological niches, and that competition is an important ecological pressure promoting the evolution of rhythms and sleep. This is the first study to use ecological modeling to examine biological rhythms.</li> </ul>
FGF-2-dependent signaling activated in aged human skeletal muscle promotes intramuscular adipogenesis
<p><span><span><span><span><span><span><span><span><span><span><span>Aged skeletal muscle is markedly affected by fatty muscle infiltration and strategies to reduce the occurrence of intramuscular adipocytes are urgently needed. Here, we show that fibroblast growth factor-2 (FGF-2) not only stimulates muscle growth, but also promotes intramuscular adipogenesis. Using multiple screening assays upstream and downstream of microRNA (miR)-29a signaling, we located the secreted protein and adipogenic inhibitor SPARC to an FGF-2 signaling pathway that is conserved between skeletal muscle cells from mice and humans and that is activated in skeletal muscle of aged mice and humans. FGF-2 induces the miR-29a/SPARC axis through transcriptional activation of FRA-1, which binds and activates an evolutionary conserved AP-1 site element proximal in the miR-29a promoter. Genetic deletions in muscle cells and AAV-mediated overexpression of FGF-2 or SPARC in mouse skeletal muscle revealed that this axis regulates differentiation of fibro/adipogenic progenitors <i>in vitro</i> and intramuscular adipose tissue (IMAT) formation <i>in vivo</i>. Skeletal muscle from human donors aged > 75 years versus < 55 years showed activation of FGF-2-dependent signaling and increased IMAT. Thus, our data highlights a disparate role of FGF-2 in adult skeletal muscle and reveals a novel pathway to combat fat accumulation in aged human skeletal muscle.</span></span></span></span></span></span></span></span></span></span></span></p>
ScienceDex guides
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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.