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Fig. 3 in Nutritional restriction triggers callose accumulation on the sieve plates of the funiculus of developing bean seeds
Fig. 3. Analysis of carbohydrate concentration in the bean fruits. The concentration of sucrose (A and D), glucose (B and E) and fructose (C and F), was determined in placenta (PL), funiculus (FUN), seed coat (SC) and cotyledon (COT) of seeds developed under normal conditions (full bar) for 23 (A–C) and 25 DAA (D–F); and seeds that were able or not to continue their development (gray and empty bars, respectively) in fruits detached from the plant at 20 DAA and analyzed 3 (A–C) and 5 (D–F) days after, respectively. Bars correspond to the analysis of five fruits from different plants ± SD. NS, not significant difference, *, ** and *** indicate significant difference at P <.05, 0.01 and 0.001, respectively, as indicated by ANOVA statistical analysis.
Fig. 5 in Nutritional restriction triggers callose accumulation on the sieve plates of the funiculus of developing bean seeds
Fig. 5. Analysis of sucrose distribution. Fruits incubated in sucrose [U-14C] were dissected (A), and the total incorporation in the placenta (PL), lower and upper funiculus (LF and UF, respectively), seed coat (SC) and cotyledon (C) sections was quantified (B). Full bars correspond to the analysis of fruits at 23 DAA developed under normal conditions. Gray bars indicate seeds that continued their development in fruits of the same age that were removed from the plant three days before the label experiment, and open bars indicate seed that did not continue their development in detached fruits. Bars correspond to the average of analysis of three biological replicates for placenta, funiculus and seed coat, and six for cotyledon ± SD. * and *** indicate significant differences at P <.05 and 0.001, respectively, as indicated by Kruskal–Wallis statistical analysis. Bar in panel A corresponds to 500 μm.
Fig. 7 in Nutritional restriction triggers callose accumulation on the sieve plates of the funiculus of developing bean seeds
Fig. 7. Quantification of the sieve plate thickness by callose immunodetection in the funiculus of developing seeds. Callose deposition in the funiculus of normally developed seeds of 23 and 25 DAA, and in seeds that continued (20 + 3 L and 20 + 5 L), or stopped their development (20 + 3S and 20 + 5S) after the fruits had been removed from the plant, was used to measure changes in the sieve plate thickness after 3 and 5 days following the detachment of the fruits from the plant. ** indicate significant differences at P ≤.01, according to Kruskal-Wallis and Dunn tests (n = 90 sieve plates per treatment).
Fig. 2 in Ultrastructure of somatic embryo development and plant propagation for Lachenalia montana
Fig. 2. The effect of MS medium salt concentrations, sucrose and PG on the germination of somatic embryos of L. montana. The results are expressed as the means with SE from five replicates per treatment. The data were recorded after 8 weeks of culture. Means ± SE followed by the same letter are not significantly different at the 5% level as determined by Duncan's multiple range test.
Fig. 4 in Ultrastructure of somatic embryo development and plant propagation for Lachenalia montana
Fig. 4. TEM analyses of different developmental stages of somatic embryos of L. montana. Formation of cell with large vacuole (V), mitochondria (M), nucleus (N) and nucleolus (NU) in globular embryos (Bar, 0.5 μm) (A). More vacuolated with cytoplasmic organelles in SM regions of pear-shaped (Bar, 0.5 μm) (B) and early torpedo-shaped (Bar, 0.5 μm) (C) embryos. Development of cytoplasmic components with nucleus (N), nucleolus (NU), Golgi apparatuses (GA), mitochondria (M) and chloroplasts (CP) in SM regions of torpedo (Bar, 0.5 μm and 0.2 μm) (D) and cotyledonary embryos (Bar, 0.5 μm) (E). Large intercellular spaces (IS) and thick cell wall (CW) in connective regions of SM and RM of cotyledonary embryos (Bar, 0.5 μm and 0.2 μm) (F). Development of thick IS and CW with cytoplasmic components of mitochondria, starch grains (SG) and plastids (PS) in RMs of torpedo (Bar, 0.2 μm) (G) and cotyledonary (Bar, 0.5 μm and 0.2 μm) (H) embryos.
Fig. 1 in Ultrastructure of somatic embryo development and plant propagation for Lachenalia montana
Fig. 1. In vitro plant regeneration from somatic embryos in cell suspension culture of L. montana: A. Production of FEC on solid MS medium plus 35 g L −1, 10 μM 2,4-D and 2 μM TDZ. B. Formation of white and soft embryo stages in MSL after 3 weeks of culture. C. Different developmental stages of somatic embryos on MSL medium plus 1 μM 2,4-D and 0.5 μM TDZ after 6 weeks of culture. D. Proliferation and germination of embryos on MSL containing 0.5 μM 2,4-D and 1 μM TDZ. E. Germination of SEs on MSL plus 1 μM 2,4-D and 2 μM TDZ. F. Germination of clustered SEs in solid MS medium containing 15 g L −1 sucrose and 10 μM PG. G. Germinated SEs on plant induction medium. H and I. Well-developed plantlets from plant induction medium. J. Acclimatized plants of L. montana in the greenhouse after 3 months.
Novel formulations for developing fresh hybrid cheese analogues utilizing fungal-fermented brewery side-stream flours
<p>Datasets corresponding to the main and supplementary material of the research article "<span>Novel formulations for developing fresh hybrid cheese analogues utilizing fungal-fermented brewery side-stream flours</span> ". This research paper was a result of a scientific project which was part of the European Union's HORIZON 2020 with the acronym SMARTPROTEIN. </p>
Species and plot characteristics for River restoration effects on dispersal and the development of riparian seed bank: Do poor seed banks limit restoration of boreal riparian zones?
<p>Vegetation composition in boreal streams in the standing vegetation and the seed bank, </p>
A comprehensive descriptive analysis : Assessing the guidance and counseling needs through cognitive and non-cognitive development of students in secondary level public schools
<p>This data has been collected from a secondary level public school in Karachi for a descriptive analysis . I</p> <p> </p>
Data from: Cell proliferation and migration during early development of a symbiotic scleractinian coral
In scleractinian reef-building corals, patterns of cell self-renewal, migration and death remain virtually unknown, limiting our understanding of cellular mechanisms underlying initiation of calcification, and ontogenesis of the endosymbiotic dinoflagellate relationship. In this study we pulse-labeled the coral Stylophora pistillata for 24 h with BrdU at four life stages (planula, early metamorphosis, primary polyp, and adult colony) to investigate coral and endosymbiont cell proliferation during development, while simultaneously recording TUNEL-positive, i.e. apoptotic, nuclei. In the primary polyp, the fate of BrdU-labeled cells was tracked during a 3 days chase. The pharynx and gastrodermis were identified as the most proliferative tissues in the developing polyp, and BrdU-labeled cells accumulated in the surface pseudostratified epithelium and the skeletogenic calicodermis during the chase, revealing cell migration to these epithelia. Surprisingly, the lowest cell turnover was recorded in the calicodermis at all stages, despite active, ongoing skeletal deposition. In dinoflagellate symbionts, DNA synthesis was systematically higher than in coral host gastrodermis, especially in planula and early metamorphosis. The symbiont to host cell ratio remained however constant, indicating successive post-mitotic control mechanisms by the host of its dinoflagellate density in early life stages, increasingly shifting to apoptosis in the growing primary polyp.
Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology
Minimally-invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping-by-sequencing approaches, which have been traditionally developed for high-quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex amplicon sequencing approach, to effectively genotype minimally-invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT-seq from a de novo restriction-site associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT-seq for the same individuals found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT-seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT-seq and RADseq datasets, as were inferred patterns of population structure. Overall, GT-seq can be effectively applied to low quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally-invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.
Data from: Early development of vocal interaction rules in a duetting songbird
Exchange of vocal signals is an important aspect of animal communication. Although birdsong is the premier model for understanding vocal development, the development of vocal interaction rules in birds and possible parallels to humans have been little studied. Many tropical songbirds engage in complex engage in vocal interactions in the form of duets between mated pairs. In some species duets show precise temporal coordination and follow rules (duet codes) governing which song type one bird uses to reply to each of the song types of its mate. We determined whether these duetting rules are acquired during early development in canebrake wrens. Results show that juveniles acquire a duet code by singing with a mated pair of adults and that juveniles gradually increase their fidelity to the code over time. Additionally, we found that juveniles exhibit poorer temporal coordination than adults and improve their coordination as time progresses. Human turn-taking, an analogous rule to temporal coordination, is learned during early development. We report that the ontogeny of vocal interaction rules in songbirds is analogous to that of human conversation rules.
Data from: Evaluation of the psychometric properties of the Brazilian version of the Oral Health Literacy Assessment in Spanish and development of a shortened form of the instrument
Objective: The objective of this study was to investigate the psychometric properties of the Oral Health Literacy Assessment in Spanish (OHLA-S) for the Brazilian-Portuguese language using robust analysis and with the results disclose possibilities to develop a shorter and more valid instrument. Methods: OHLA-S is an oral health literacy instrument comprising a word recognition section and a comprehension section. It consists of 24 dental words. It was translated into the Brazilian-Portuguese language (OHLA-B) and its psychometric properties were evaluated in a random sample of 250 adults aged 20–59 years. To assess the dimensionality and factor structure were tested by means of Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA). Reliability was assessed using two indicators: Cronbach's alpha and McDonald's Omega. Results: EFA and CFA demonstrated that the OHLA-B with 24 items did not present an adequate adjustment of the model, compromising its validity. In addition, reliability values at 0.50 for Cronbach's alpha and 0.67 for McDonald's omega were below the minimum acceptable rate of 0.70. As no support was found for the original structure, we decided to proceed with the withdrawal of individual items and successive reanalysis of the model until the indicators were adjusted in a shorter instrument. A new structure with 15 items produced an instrument with two dimensions and a better goodness of fit than the original instrument. The Alpha and Omega reliability index values increased to 0.83 and 0.80, respectively, and all scores were better in the OLHA-B with 15 items than in the instrument with 24 items. Conclusion: OLHA-B with the original structure composed by 24 items did not show acceptable construct validity. The shorter version with 15 items showed more promising results for assessing oral health literacy levels in the Brazilian population.
Data from: Identifying patterns of non-communicable diseases in developed eastern coastal China: a longitudinal study of electronic health records from 12 public hospitals
Objective: Few studies have examined the spectrum and trends of non-communicable diseases (NCDs) in inpatients in eastern coastal China, which is transforming from an industrial economy to a service-oriented economy and is the most economically developed region in the country. This study aimed to dynamically elucidate the spectrum and characteristics of severe NCDs in eastern coastal China by analysing patients' longitudinal electronic health records (EHRs). Setting: To monitor the spectrum of NCDs dynamically, we extracted the EHR data from 12 general tertiary hospitals in eastern coastal China from 2003 to 2014. The rankings of and trends in the proportions of different NCDs presented by inpatients in different gender and age groups were calculated and analysed. Participants: We obtained a total sample of 1,907,484 inpatients with NCDs from 2003 to 2014, 50.05% of whom were male and 81.53% were aged 50 years or older. Results: There was an increase in the number of total NCD inpatients in eastern coastal China from 2003 to 2014. However, the proportion of chronic respiratory diseases and cancer inpatients decreased over the 12-year period. Compared with men, women displayed a significant increase in the proportion of mental and behavioural disorders (P<0.001) over time. Additionally, digestive diseases and sensory organ diseases significantly decreased among men, but not women. The older group accounted for a larger and growing proportion of the NCD inpatients, and the most common conditions in this group were cerebral infarctions, coronary heart disease and hypertension. In addition, the proportion of 21- to 50-year-old inpatients with diabetes, blood diseases or endocrine diseases skyrocketed from 2003 to 2014 (P<0.001). Conclusions: The burden of inpatients' NCDs increased rapidly, particularly among women and younger people. The NCD spectrum observed in eastern coastal China is a good source of evidence for developing prevention guides for regions experiencing transition.
Data from: Maternal and paternal contributions to pathogen resistance dependent on development stage in a whitefish (Salmonidae)
1. It is often assumed that maternal and paternal contributions to offspring phenotype change over the lifetime of an individual. However, studies on parental effects typically suffer from the problems that heritabilities and maternal environmental effects are difficult to separate, and that both may depend on environmental factors and developmental stage 2. In order to experimentally disentangle maternal from paternal contributions and the likely effects of developmental stage from ecological effects, we sampled a natural population of the whitefish Coregonus palaea, used gametes for full-factorial in vitro fertilizations, raised over 10,000 of the resulting offspring singly at controlled conditions, and exposed them at different points during embryonic development to one of two strains of Pseudomonas fluorescens that differed in their virulence characteristics (only one caused mortality, while both delayed hatching and reduced growth) 3. Vulnerability to infection increased markedly over embryo development. This change coincided with a distinct shift in the importance of maternal to additive genetic effects on survival. Timing of exposure also affected the variance components for hatching time and larval length, but in a less consistent direction than the variance components for mortality. No significant genetic variation was found for any reaction norms across time points of exposure, indicating a uniformity among genotypes in how susceptibility changed over development. Phenotypes were also typically correlated across time points, which could constrain the evolution of the reaction norms 4. Our experiment demonstrates that the relative maternal and paternal contributions to susceptibility to an infection, and hence the evolutionary potential to respond to pathogen-induced selection, depends not only on the kind of pathogenic stress but also on the timing of the challenge.
Data from: Development of 15 nuclear EST microsatellite markers for the palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae)
Premise of the study: Nuclear microsatellite markers were developed for population genetic analysis of the threatened palaeoendemic conifer Pherosphaera hookeriana W. Archer (Podocarpaceae). Methods and Results: Fifteen variable loci were identified showing 1 to 13 alleles per population with seven loci displaying over four alleles in all populations and the average number of alleles per locus ranging from 4.8 to 5.93 per population. The observed heterozygosity per locus varied from 0.00 to 0.91 and overall heterozygosity was markedly consistent between populations (from 0.54 to 0.57). All loci also amplified in the endangered congener P. fitzgeraldii but only five of the loci had more than one allele. Conclusions: These 15 loci are the first microsatellite markers developed in the genus Pherosphaera. These loci will be useful for investigating the species' extant genetic diversity and structure, the impact of past environmental change and the significance of asexual reproduction.
Data from: Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Background: Life history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related European Radix species. Results: Snails of the genus Radix occupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural selection driven speciation based on ecological niche differentiation. We then inferred phylogenetic relationships among the four Radix species based on whole mt-genomes plus 23 nuclear loci. Three different tests to infer selection and changes in amino acid properties yielded a total of 134 genes with signatures of positive selection. The majority of these genes belonged to the functional gene ontology categories "reproduction" and "genitalia" with an overrepresentation of the functions "development" and "growth rate". Conclusions: We show here that Radix species divergence may be primarily enforced by selection on life history traits such as (larval-) development and growth rate. We thus hypothesise that life history differences may confer advantages under the according climate regimes, e.g., species occupying warmer and dryer habitats might have a fitness advantage with fast developing susceptible life stages, which are more tolerant to habitat desiccation.
Data from: Regulation of thermal acclimation varies between generations of the short-lived mosquitofish (Gambusia holbrooki) that developed in different environmental conditions
1. Environmental variability and perturbations can influence population persistence. It is therefore important to understand whether and how animals can compensate for environmental variability, and thereby increase resilience of natural populations. Evolutionary theory predicts that in fluctuating environments selection should favour developmental modifiers that reduce phenotypic expression of genetic variation. The expected result is that phenotypes are buffered from environmental variation across generations. 2. Our aim was to determine whether phenotypes of mosquitofish (Gambusia holbrooki) remain stable across generations in which individuals were born into different thermal environments. We predicted that the spring generation (cool environment) would acclimate by increasing the concentration of regulatory transcription factor mRNA and activities of rate-limiting enzymes (hierarchical regulation) to compensate for the negative thermodynamic effects of lower temperatures on metabolic and locomotor performance. In contrast, the summer-born generation (warm environment) would show less capacity for acclimation and hierarchical regulation. 4. We show that fish from both generations acclimated, but that there were significant differences in the phenotypic consequences of acclimation. The overall result was that sprint performance, metabolic scope, and the activities of cyctochrome c oxidase and lactate dehydrogenase were buffered from environmental change, and did not differ between spring and summer fish at their natural water temperatures of 15oC and 25oC, respectively. However, there were differences between generations in sustained swimming performance and citrate synthase activity. 5. We used metabolic control analysis to show that modes of regulation of metabolic scope and locomotor performance differed between generations. Spring fish showed primarily hierarchical regulation, but regulation in summer fish relied to a lesser extent on rate-limiting enzymes and transcription factors. 6. We suggest that developmental modifiers are favoured in fluctuating environments to maximise phenotypic fitness of each generation. We show that the interaction between developmental and reversible acclimation can render physiological performance of a natural population independent from climate variation.
Data from: Development of a PCR-RFLP assay to identify Drosophila melanogaster among field-collected larvae
The fruit fly Drosophila melanogaster is a model organism to study several aspects of metazoan biology. Most of the work has been conducted in adult fruit flies, including laboratory and field-derived specimens, but Drosophila melanogaster larvae recently became a valuable model to better understand animal physiology, development or host-microbe interactions. While adult flies can be easily assigned to a given Drosophila species based on morphological characteristics, such visual identification is more intricate at the larval stage. This could explain the limited number of studies focusing on larvae, especially field-derived samples. Here, we developed a Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assay that discriminates D. melanogaster from other ecologically relevant Drosophila species at the larval stage. The method, which targets the cytochrome oxidase I (COI) gene, was validated using laboratory-derived larvae from seven D. melanogaster populations originating from different geographic areas as well as six Drosophila species. We further validated this PCR-RFLP assay in a natural context, by identifying wild larvae collected in two locations in France. Notably, among all PCR-RFLP profiles that matched the D. melanogaster species, 100% were correctly identified, as confirmed by COI sequencing. In summary, our work provides a rapid, simple and accurate molecular tool to identify D. melanogaster from field-collected larvae.
Data from: Coffee berry borer (Hypothenemus hampei) (Coleoptera: Curculionidae) development across an elevational gradient on Hawai'i Island: applying laboratory degree-day predictions to natural field populations
Coffee berry borer (CBB, Hypothenemus hampei) (Coleoptera: Curculionidae: Scolytinae) is the most destructive pest of coffee worldwide. Information on CBB development times can be used to predict the initiation of new infestation cycles early in the coffee-growing season and thus inform the timing of insecticide applications. While laboratory estimates of CBB development under constant conditions exist, they have not been applied under the heterogeneous environmental conditions that characterize many coffee-growing regions. We measured CBB development times and abundance in commercial coffee farms across an elevational gradient on Hawai'i Island and applied thermal accumulation models from previous laboratory studies to test their fit to field data. Artificial lures were used to infest coffee berries at five farms ranging in elevation from 279-792 m, and weather variables were monitored at macro (farm-level) and micro (branch-level) scales. CBB development was followed in the field from the time of initial berry infestation by the founding female through the development of F1 mature adults. Mean development time from egg to adult across all sites was 38.5 ± 3.46 days, while the mean time required for the completion of a full life cycle (from time of infestation to presence of mature F1 females) was 50.9 ± 3.35 days. Development time increased with increasing elevation and decreasing temperature. Using macro-scale temperature data and two different estimates for the lower temperature threshold (14.9°C and 13.9°C), we estimated a mean requirement of 332 ± 14 degree-days and 386 ± 16 degree-days, respectively, from the time of berry infestation to the initiation of a new reproductive cycle in mature coffee berries. Similar estimates were obtained using micro-scale temperature data, indicating that macro-scale temperature monitoring is sufficient for life-cycle prediction. We also present a model relating elevation to number of CBB generations per month. Our findings suggest that CBB development times from laboratory studies are generally applicable to field conditions on Hawai'i Island and can be used as a decision support tool to improve IPM strategies for this worldwide pest of coffee.
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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.