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Identifying in vitro toxicity testing approaches for (novel) proteins in the context of food and feed risk assessment
<p>Annexes to EFSA external scientific report Identifying <em>in vitro</em> toxicity testing approaches for (novel) proteins in the context of food and feed risk assessment</p>
Data from: Do ecological niche models accurately identify climatic determinants of species ranges?
Defining species' niches is central to understanding their distributions and is thus fundamental to basic ecology and climate change projections. Ecological niche models (ENMs) are a key component of making accurate projections and include descriptions of the niche in terms of both response curves and rankings of variable importance. In this study, we evaluate Maxent's ranking of environmental variables based on their importance in delimiting species' range boundaries by asking whether these same variables also govern annual recruitment based on long-term demographic studies. We found that Maxent-based assessments of variable importance in setting range boundaries in the California tiger salamander (Ambystoma californiense; CTS) correlate very well with how important those variables are in governing ongoing recruitment of CTS at the population level. This strong correlation suggests that Maxent's ranking of variable importance captures biologically realistic assessments of factors governing population persistence. However, this result holds only when Maxent models are built using best-practice procedures and variables are ranked based on permutation importance. Our study highlights the need for building high-quality niche models and provides encouraging evidence that when such models are built, they can reflect important aspects of a species' ecology.
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: Combined transcriptome and metabolome analysis identifies defence responses in spider-mite infested pepper
<p>Plants regulate responses towards herbivory through fine-tuning of defence-related hormone production, expression of defence genes and production of secondary metabolites. Jasmonic acid (JA) plays a key role in plant-herbivorous arthropod interactions. To understand how pepper responds to herbivory, leaf transcriptomes and metabolomes of two genotypes different in their susceptibility to spider mites, were studied. Mites induced both JA and salicylic acid (SA) signalling. However, mite infestation and exogenous JA resulted in distinct transcriptome profiles. Compared with JA, mites induced less differentially expressed genes involved in metabolic processes (except for genes involved in the phenylpropanoid pathway) and lipid metabolic processes. Furthermore, pathogen-related defence responses including WRKY transcription factors, were stronger induced upon mite infestation, likely as result of induced SA signalling. Untargeted analysis of secondary metabolites confirmed that JA treatment induced larger changes in metabolism than spider-mite infestation, resulting in a higher terpenoid and flavonoid production. The more resistant genotype exhibited a larger increase in endogenous JA and volatile and non-volatile secondary metabolites upon infestation, which could explain its stronger defence. Reasoning that in JA-SA antagonizing crosstalk, SA-defences are prioritized over JA-defences, we hypothesize that lack of SA-mediated repression of JA-induced defences could result in gain-of-resistance towards spider mites in pepper.</p>
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: Identifying cryptic diversity with predictive phylogeography
Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.
Data from: Identifying demographic and environmental drivers of recruitment and population growth in a cavity nesting sea duck population
Traits with the greatest proportional effects on fitness are typically conserved (Stearns 1992), and traits with larger temporal variation frequently play a dominant role in population dynamics (Cooch et al. 2001). We examined recruitment patterns and population growth in Common Goldeneyes (Bucephala clangula; hereafter goldeneye), using Pradel mark-recapture models from a long-term nest box study (1997-2010). Our objectives were to estimate recruitment (f) and population growth (λ) relative to recruitment origin group (in-situ or unknown), investigate environmental and density dependent effects on these parameters, and evaluate potential immigration patterns. We detected group-specific differences for f (in-situ: 0.47± 0.13 SE, unknown: 0.31 ± 0.04), and the proportion of boxes occupied by goldeneyes the year prior to recruitment had a significant negative effect on recruitment for the in-situ group (β = -1.04; 85% CI -1.29, -0.78), and a positive effect for the unknown group (β = 0.45; 85% CI 0.30, 0.61). The negative box occupancy effect in the year prior to recruitment, when in-situ yearling goldeneyes prospect for potential nest sites, suggests that local nesting densities may limit recruitment of locally hatched females. We identified two competitive models for λ, which averaged 1.04 ± 0.03 and included interactions between recruitment origin group and a linear temporal trend, and the proportion of ducklings marked two years prior. By evaluating all levels of marking effort on λ, we determined that even if all hatched ducklings were marked in a given year, the resulting in-situ λ was consistently lower than all observed population-level λs during the study, indicating that individuals produced outside of study area nest boxes contributed to λ. Though female goldeneyes are considered highly philopatric, our results suggest that female natal and breeding dispersal may be more prevalent than previously thought, and the spatial scale at which these processes occur requires further investigation.
Data from: Identifying fishing grounds from vessel tracks: model-based inference for small scale fisheries
Recent technological developments facilitate the collection of location data from fishing vessels at an increasing rate. The development of low-cost electronic systems allows tracking of small-scale fishing vessels, a sector of fishing fleets typically characterised by many, relatively small vessels. The imminent production of large spatial datasets for this previously data-poor sector, creates a challenge in terms of data analysis. Several methods have been used to infer the spatial distribution of fishing activities from positional data. Here, we compare five approaches using either vessel speed, or speed and turning angle, to infer fishing activity in the Scottish inshore fleet. We assess the performance of each approach using observational records of true vessel activity. Although results are similar across methods, a trip-based Gaussian mixture model provides the best overall performance and highest computational efficiency for our use-case, allowing accurate estimation of the spatial distribution of active fishing (97% of true area captured). When vessel movement data can be validated, we recommend assessing the performance of different methods. These results illustrate the feasibility of designing a monitoring system to efficiently generate information on fishing grounds, fishing intensity, or monitoring of compliance to regulations at a nationwide scale in near-real time.
FIGURE 14 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 14. First feeding in the Albemarle turtle leech. Shown are three pre-juvenile individuals collected soon after taking their first blood meal on a turtle host. Their teguments are still transparent and the body shape is cylindroid. A, 5.0 mm (PM-11a) on Chelydra serpentina. B, 8.3 mm (PM-26) on Chrysemys floridana. C, 7.8 mm (PM-24a) on Kinosternum odoratus. Specimen A was collected within hours of first feeding and already had diluted blood in its crop. The intermediate rows of tubercles on the a2 annulus were discernible but do not show up in this image. In specimen B the tip of its lengthy proboscis protrudes from the apical mouth. The darkened rectum indicates some digestion of blood had already occurred. This correlates with the faintly pigmented tegument of this specimen. In specimen C the crooked proboscis and compact salivary glands are visibly well developed at this stage. Scale bars: 0.5 mm.
FIGURE 10 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 10. Accessory 'eyes' as shown here are strongly expressed in about one-third of the Albemarle turtle leeches. Shown are close-ups of the head regions of two individuals. A, C, dorsal and ventral views, respectively, of specimen (PM-15a). B, dorsal view of extended specimen (PM-14b). Such heavily pigmented individuals typically display paramedial stripes on dorsum (pd) and on venter (vs), respectively. Scale bar: 1.0 mm.
FIGURE 12 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 12. This scheme summarises appearance of key tubercles during development of the Albemarle turtle leech. Depicted are dorsal views of a mid-body segment, comprised of three annuli a1, a2 and a3, respectively. A, pre-feeding embryo (5–7 mm). B, post-feeding juvenile (10–15 mm). C, heavily tuberculated adult (20–40 mm). The intermediate tubercles (ti) arise first on the a2 annulus, and remain most prominent throughout life. Soon thereafter, tubercles arise in medial position (tm) on the a2 annulus, and in paramedial position (tp) on the a3 annulus. The indicated tubercles constitute a flattened 'W' configuration on each segment (red dashes), a taxonomically useful character specific to this species at virtually all stages of its life cycle. Together these respective tubercles constitute five longitudinal rows on the dorsum (see also Fig. 15A, B).
FIGURE 13 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 13. Early development of the Albemarle turtle leech. Shown are unfed, unpigmented embryos of varying ages depicting progressive changes in foregut and crop caeca. A, 4.4 mm (PM-15e), ventral view. B, 4.8 mm (PM-6b), dorsal view. C, 6.0 mm (PM-15h), ventral view. In specimen A the cuticle (cu) separated from the anterior part of the body during preservation. The proboscis (p) is already relatively long and penetrates through the brain (b). The relative length of the proboscis is corroborated by the long cuticle lining the proboscis sheath (cup) emerging from the mouth. Scale bars: 0.5 mm.
FIGURE 7 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 7. Variation of the dorsal stripe and tubercles in the Albemarle turtle leech. A, interrupted dorsal stripe (PM-15a). B, continuous dorsal stripe (PM-15c). C, no discernible dorsal stripe (PM-12). The primary tubercles, ti and tm on the a2 annulus, and tp on the a3 annulus, together with their bilateral counterparts, constitute a flattened letter 'W'. This configuration is specific for the Albemarle turtle leech. Furthermore, in this species the intermediate tubercles (ti) are invariably the most prominent. Dorsal views. A, B, LED light; C, incandescent light. Scale bar: 10 mm.
FIGURE 8 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 8. Cartouche-like rectangular shields are the basis of the interrupted stripe in the Albemarle turtle leech (see also Fig. 6A, B). A, in this preserved, post-fed juvenile (PM-17f, 7.8 mm) the dorsal stripe is continuous along most of the dorsal midline, but is obfuscated at intervals by the opacity of the respective shields. B, the cellular nature of these shields is shown in a slightly earlier stage of development. In this specimen (PM-24a, 7.8 mm) consecutive shields 3 and 4 are comprised of aggregations of white cells localised mid-dorsally at segments XV/XVI (wp3) and XVIII/XIX (wp4), respectively. A, reflected LED light; B, transmitted LED light. Scale bars: A, 1.0 mm; B, 0.3 mm.
FIGURE 9 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 9. The eyes of the Albemarle turtle leech develop remarkably early in the embryo, long before any other pigment is discernible. Shown are the eyes of an early embryo (4.5 mm, PM-9) at different magnifications. A, head region showing one apparent pair of contiguous eyes. B, C, higher magnifications reveal the eyes are actually compound, each comprised of a smaller anterior and larger posterior eye. Scale bars: A, B, 0.1 mm; C, 20 μm.
FIGURE 6 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 6. Taxonomic features of the Albemarle turtle leech can vary considerably under different conditions of lighting and preservation. Shown is a recently fed, late juvenile specimen (PM-20) from Virginia Beach, VA, photographed as follows. A, in life, under natural light. B, same individual relaxed and preserved in 5 % formalin, under LED light. C, same preserved individual, under ultraviolet light. Scale bar: 2.0 mm.
FIGURE 5 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 5. Scheme of the reproductive systems of the Albemarle turtle leech, based on dissection of specimen PM-12 from Pasquotank County, NC. A, dorsal view. B, lateral view. Distance between segmental ganglia is approximately 2.0 mm.
FIGURE 4 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 4. Scheme of the proboscis complex of the Albemarle turtle leech, based on dissection of specimen PM-1b from Tyrrell County, NC. A, dorsal view, with proboscis inset separately for clarity. B, lateral view. The long tapering proboscis (blue), with a proximal crook and termination of its tip beyond the brain, is specific for this species. Proboscis is approximately 10 mm long.
FIGURE 3 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 3. Archetypal specimen of the Albemarle turtle leech on which the external description of this species is based. Collected at edge of swamp, Stephens Ridge, Gum Neck, Tyrrell County, NC (PM-14d). A, dorsal view. B, ventral view of same specimen. Scale bar: 5.0 mm.
FIGURE 11 in Description and taxonomic analysis of a tuberculated turtle leech from the Outer Banks, North Carolina, USA, provisionally identified as Placobdella multilineata Moore, 1953 (Hirudinea: Glossiphoniidae)
FIGURE 11. The last three body segments (XXV–XXVII) of the Albemarle turtle leech constitute the peduncle. A, specimen (PM-21a) showing typical configuration of pre-anal tubercles (pt1–pt3), a characteristic of this species. B, atypical specimen (PM-1a) with a distinctive narrowing of the peduncle as fixed during extension of the body. C, D, under ultraviolet light. C, fluorescence restricted to margins of this specimen (PM-14b). D, fluorescence primarily confined to tips of the pre-anal tubercles in this specimen (PM-14d). Scale bar: 1.0 mm.
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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.