Characterizing preferred motif choices and distance impacts.
Ontology highlight
ABSTRACT:
SUBMITTER: Cao J
PROVIDER: S-EPMC6467417 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundSolanum aethiopicum L. is a nutrient dense African indigenous vegetable. However, advancement of its improved varieties that can increase productivity, household income, and food security has not been prioritized. Further still, studies on some of the crops that have been worked have indicated that it is not a guarantee that the improved varieties will be accepted by the end users and therefore there is need to identify and profile what genotypes are of interest to farmers and their preferred traits through inclusive participatory evaluations.MethodologyFarmer participatory evaluations were conducted to profile farmers' traits of interest and preferred genotypes. A total of 24 genotypes were established in three replications in 6 farms in 3 districts; Wakiso, Mukono, and Luwero as these are the major producing districts of the vegetable in Uganda. A total of 177 sex-disaggregated farmers were engaged in scoring the genotypes for pest, disease and drought tolerance, general appeal, leaf yield, leaf texture, and seed yield for best 10 genotypes under each variable.ResultsNon-significant differences in trait (p > 0.05) and genotype preferences (p > 0.05) were obtained between men and women. The most desired farmer traits were seed and leaf yield, followed by pest and disease resistance. The overall preferred genotype in terms of disease and pest resistance, leaf yield, leaf texture, and seed yield were E12 followed by E11.ConclusionGender does not seem to influence farmer choices for the S. aethiopicum, Shum group, indicating an opportunity for single variety prototype advancement by breeders and dissemination by seed companies.
| S-EPMC8042716 | biostudies-literature
Project description:The structural principles that govern interactions between l- and d-peptides are not well understood. Among natural proteins, coiled-coil assemblies formed between or among α-helices are the most regular feature of tertiary and quaternary structures. We recently reported the first high-resolution structures for heterochiral coiled-coil dimers, which represent a starting point for understanding associations of l- and d-polypeptides. These structures were an unexpected outcome from crystallization of a racemic peptide corresponding to the transmembrane domain of the influenza A M2 protein (M2-TM). The reported structures raised the possibility that heterochiral coiled-coil dimers prefer an 11-residue (hendecad) sequence repeat, in contrast to the 7-residue (heptad) sequence repeat that is dominant among natural coiled coils. To gain insight on sequence repeat preferences of heterochiral coiled-coils, we have examined three M2-TM variants containing substitutions intended to minimize steric clashes between side chains at the coiled-coil interface. In each of the three new crystal structures, we observed heterochiral coiled-coil associations that closely match a hendecad sequence motif, which strengthens the conclusion that this motif is intrinsic to the pairing of α-helices with opposite handedness. In each case, the presence of a hendecad motif was established by comparing the observed helical frequency to that of an ideal hendecad. This comparison revealed that decreasing the size of the amino acid side chain at positions that project toward the superhelical axis produces tighter packing, as determined by the size of the coiled-coil radius. These results provide a basis for future design of heterochiral coiled-coil pairings.
| S-EPMC6500429 | biostudies-literature
Project description:Social distancing during a pandemic might be influenced by different attitudes: people may decide to reduce the risk and protect themselves from viral contagion, or they can opt to maintain their habits and be more exposed to the infection. To better understand the underlying motivating attitudes, we asked participants to indicate in an online platform the interpersonal distance from different social targets with professional/social behaviors considered more or less exposed to the virus. We selected five different social targets: a cohabitant, a friend working in a hospital, a friend landed from an international flight, a friend who is back from a cycling ride, or a stranger. In order to measure the realistic and the symbolic perceived threat, we administered the Brief 10-item COVID-19 threat scale. Moreover, in order to measure the risk attitude in different domains, the participants were also asked to fill in the Domain-Specific Risk-Taking DOSPERT scale. Results reveal a general preference for an increased distance from a stranger and the friends who are considered to be more exposed to the virus: the friend working in a hospital or landed from an international flight. Moreover, the interpersonal distance from friends is influenced by the perception of Realistic Threat measured through the Integrated Covid Threat Scale and the Health/Safety Risk Perception/Assumption as measured by the DOSPERT scale. Our results show the flexible and context-dependent nature of our representation of other people: as the social categories are not unchangeable fixed entities, the bodily (e.g., spatial) attitudes towards them are an object of continuous attunement.
| S-EPMC8660879 | biostudies-literature
Project description:N6-methyladenosine is the most prominent RNA modification in mammals. Here, we study mouse skin embryogenesis to tackle m6A's functions and physiological importance. We first landscape the m6A modifications on skin epithelial progenitor mRNAs. Contrasting with in vivo ribosomal profiling, we unearth a correlation between m6A modification in coding sequences and enhanced translation, particularly of key morphogenetic signaling pathways. Tapping physiological relevance, we show that m6A loss profoundly alters these cues and perturbs cellular fate choices and tissue architecture in all skin lineages. By single-cell transcriptomics and bioinformatics, both signaling and canonical translation pathways show significant downregulation after m6A loss. Interestingly, however, many highly m6A-modified mRNAs are markedly upregulated upon m6A loss, and they encode RNA-methylation, RNA-processing and RNA-metabolism factors. Together, our findings suggest that m6A functions to enhance translation of key morphogenetic regulators, while also destabilizing sentinel mRNAs that are primed to activate rescue pathways when m6A levels drop.
| S-EPMC7535931 | biostudies-literature
Project description:While visual size preferences regarding still objects have been investigated and linked to the "canonical size" effect-where preferred on-screen size was significantly related to objects' real-world size-the visual size preferences related to moving images of natural scenes has not been researched. In this study, we measured the preferred size of moving images of natural scenes and short duration and investigated the effect of viewing distance on size preferences. Our results showed that the preferred size varied strongly depending on content, and we found moving images' canonical size effect. The preferred size in images of scenery was significantly larger than in images of persons, and there was a positive correlation between the preferred size and the real-world physical size of the main subjects in the images. When the viewing distance was doubled, the preferred size increased about 10% as a ratio to screen size-in contrast to the findings of a previous study. While the rationale for these findings is not yet clear, our analysis suggests that neither the motion component in the images nor the nature of their background area are contributing factors. We suggest that environment, viewing distance, and screen size may contribute to this effect.
| S-EPMC7409065 | biostudies-literature
Project description:RNA structural motifs are recurrent structural elements occurring in RNA molecules. RNA structural motif recognition aims to find RNA substructures that are similar to a query motif, and it is important for RNA structure analysis and RNA function prediction. In view of this, we propose a new method known as RNA Structural Motif Recognition based on Least-Squares distance (LS-RSMR) to effectively recognize RNA structural motifs. A test set consisting of five types of RNA structural motifs occurring in Escherichia coli ribosomal RNA is compiled by us. Experiments are conducted for recognizing these five types of motifs. The experimental results fully reveal the superiority of the proposed LS-RSMR compared with four other state-of-the-art methods.
| S-EPMC3753925 | biostudies-literature
Project description:Backgrounds The COVID-19 pandemic has resulted in not only significant mortalities in Vietnam but has had an impact on its economy. Previous studies have highlighted how the pandemic has had a marginal impact on Vietnamese healthcare workers working at the frontlines. To date, there have been several other studies examining the impact of COVID-19 on intentions to transition between jobs among healthcare professionals, but this has yet to be explored amongst Vietnamese healthcare workers. Methods To achieve the study’s objectives an online cross-sectional study was conducted between September to November 2021. Snowball sampling methodology was adopted for the recruitment of participants. The questionnaire that was used for this study comprised of the following sections: (a) socio-demographic information; (b) impact of COVID-19 on work; (c) risk of exposure to COVID-19; (d) career choices/intentions to change job, and (e) motivation at work. Results There were 5727 completed the entire survey. 17.2% of the respondents have had increased job satisfaction, 26.4% reported increased motivation to work, and 40.9% reported decreased motivation to work. Whilst there were changes in the daily work intensity and the level of work-related stress, more than 60% of respondents we sampled did not intend to switch careers. Demographic variables like gender, whether one was a student or an existing healthcare worker, and income related to work motivation. The community’s stigma was a negative factor that declined intrinsic motivation as well as decreased work retention. Conclusions Our study is instrumental in identifying the impact of COVID-19 on career choices amongst Vietnamese healthcare workers. The factors identified have clear implications for policymaking. Supplementary Information The online version contains supplementary material available at 10.1186/s12909-023-04328-8.
| S-EPMC10215048 | biostudies-literature
Project description:G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions.
| S-EPMC3753619 | biostudies-literature
Project description:Social scientists and community advocates have expressed concerns that many social and cultural impacts important to citizens are given insufficient weight by decision makers in public policy decision-making. In two large cross-sectional surveys, we examined public perceptions of a range of social, cultural, health, economic, and environmental impacts. Findings suggest that valued impacts are perceived through an initial lens that highlights both tangibility (how difficult it is to understand, observe, and make changes to an impact) and scope (how broadly an impact applies). Valued impacts thought to be less tangible and narrower in scope were perceived to have less support by both decision makers and the public. Nearly every valued impact was perceived to have more support from the public than from decision makers, with the exception of three economic considerations (revenues, profits, and costs). The results also demonstrate that many valued impacts do not fit neatly into the single-category distinctions typically used as part of impact assessments and cost-benefit analyses. We provide recommendations for practitioners and suggest ways that these results can foster improvements to the quality and defensibility of risk and impact assessments.
| S-EPMC8214679 | biostudies-literature
Project description:Supplementary feeding of wildlife is widespread, being undertaken by more than half of households in many countries. However, the impact that these supplemental resources have is unclear, with impacts largely considered to be restricted to urban ecosystems. We reveal the pervasiveness of supplementary foodstuffs in the diet of a wild bird using metabarcoding of blue tit (Cyanistes caeruleus) faeces collected in early spring from a 220 km transect in Scotland with a large urbanization gradient. Supplementary foodstuffs were present in the majority of samples, with peanut (Arachis hypogaea) the single commonest (either natural or supplementary) dietary item. Consumption rates exhibited a distance decay from human habitation but remained high at several hundred metres from the nearest household and continued to our study limit of 1.4 km distant. Supplementary food consumption was associated with a near quadrupling of blue tit breeding density and a 5-day advancement of breeding phenology. We show that woodland bird species using supplementary food have increasing UK population trends, while species that do not, and/or are outcompeted by blue tits, are likely to be declining. We suggest that the impacts of supplementary feeding are larger and more spatially extensive than currently appreciated and could be disrupting population and ecosystem dynamics.
| S-EPMC8150026 | biostudies-literature