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FIGURE 2. Zoea II in Morphology of the early larval stages of Lysmata lipkei Okuno & Fiedler, 2010 (Caridea: Lysmatidae): an invasive shrimp in the Western Atlantic
FIGURE 2. Zoea II of Lysmata lipkei Okuno & Fiedler, 2010. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod; L) fifth pereiopod; M) uropods and telson. (Scale: A–D, J–M = 0.2 mm; E, G–I = 0.1 mm; F = 0.05 mm).
FIGURE 1. Zoea I in Morphology of the early larval stages of Lysmata lipkei Okuno & Fiedler, 2010 (Caridea: Lysmatidae): an invasive shrimp in the Western Atlantic
FIGURE 1. Zoea I of Lysmata lipkei Okuno & Fiedler, 2010. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod; L) telson. (Scale: A–D, I–L = 0.2 mm; F–H = 0.1 mm; E = 0.05 mm).
Modeling of a chain of three plasma accelerator stages with the WarpX electromagnetic PIC code on GPUs
<p>This archive contains the data used for plots 1, 2, 3, 6 and 7 of the Physics of Plasma paper "Modeling of a chain of three plasma accelerator stages with the WarpX electromagnetic PIC code on GPUs" by J.-L. Vay et al (2021).</p> <p> </p> <p>To produce plots 1, 2 and 3, cd into the corresponding directory and run the python script.</p> <p> </p> <p>To produce plots 6 and 7, cd in the directory Figures_6_7 and run the script mkzplots.</p> <p> </p> <p>Simulations were performed on Summit (OLCF) with WarpX Version 19.10-2404-gafa3d4808ff0-dirty (code with slight modification from repo is given in archive warpx_source.tar.gz).</p> <p> </p> <p>Loaded Modules:</p> <p> 1) hsi/5.0.2.p5 3) lsf-tools/2.0 5) DefApps 7) spectrum-mpi/10.3.1.2-20200121 9) ccache/3.7.9 11) boost/1.66.0 13) hdf5/1.10.4 15) openblas/0.3.9-omp 17) nano/2.6.3</p> <p> 2) xalt/1.2.1 4) darshan-runtime/3.1.7 6) gcc/6.4.0 8) cuda/10.1.243 10) fftw/3.3.8 12) cmake/3.18.2 14) adios2/2.5.0 16) netlib-lapack/3.8.0 18) python/3.6.6-anaconda3-5.3.0</p>
Towards genetic modification of plant-parasitic nematodes: Delivery of macromolecules to male germlines and expression of exogenous mRNA in second stage juveniles
<p>Plant-parasitic nematodes are a current and future threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics. Forward genetics is largely restricted to studies of natural variation in populations, and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate progress in plant-parasitic nematology, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic "tool kit" in plant-parasitic nematodes. We characterise the gonads of male <em>Heterodera schachtii</em> and Meloidogyne hapla in the context of spermatogenesis. We test and optimise various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of <em>H. schachtii</em> juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, and, taken together, will expedite the development of genetic modification protocols for sedentary endoparasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.</p>
Arabidopsis ovule primordium stages 0-I to 2-II, wild-type Col_0, Ws-4 and botero (bot1-7) mutant
<p>This image resource describes the development of ovule primordia from stages 0-I to 2-I in 3D and at cellular resolution. The images were segmented using ImarisCell (BitplaneAG) and annotated as described in the associated manuscript Hernandez-Lagana et al. https://www.biorxiv.org/content/10.1101/2020.07.30.226670v3</p>
FIGURE 3. Alpheus formosus Gibbes, 1850 in First zoeal stage of the snapping shrimps Alpheus formosus Gibbes, 1850 and Alpheus malleator Dana, 1852 (Caridea: Alpheidae), with new characters to the genus
FIGURE 3. Alpheus formosus Gibbes, 1850 (B, C, G, H) and Alpheus malleator Dana, 1852 (A, D–F). Zoea I. Light microscopy (A), Scanning electron microscopy (B–H). A–F. Simple dorsal setae on the pleon (white arrows). G–H. Denticles (black arrows) and spines (black arrowheads) in the posterior margin of the telson. Scale bars: A. 100 µm; B–D, F–H. 10 µm; E. 20 µm.
FIGURE 2. Alpheus malleator Dana, 1852. Zoea I. A in First zoeal stage of the snapping shrimps Alpheus formosus Gibbes, 1850 and Alpheus malleator Dana, 1852 (Caridea: Alpheidae), with new characters to the genus
FIGURE 2. Alpheus malleator Dana, 1852. Zoea I. A. Lateral view; B. Carapace; C. Left antennule; D. Left antenna; E. Left maxillule; F. Left maxilla; G. Left first maxilliped; H. Left second maxilliped; I. Left third maxilliped; J. Left first pereopod; K. Pleon, lateral view; L. Fourth somite of pleon, lateral view; M. Telson, dorsal view. Scale bars: A, L, K. 0.15mm; B–D, G–J, M. 0.07 mm; E, F. 0.04 mm.
FIGURE 1. Alpheus formosus Gibbes, 1850. Zoea I. A in First zoeal stage of the snapping shrimps Alpheus formosus Gibbes, 1850 and Alpheus malleator Dana, 1852 (Caridea: Alpheidae), with new characters to the genus
FIGURE 1. Alpheus formosus Gibbes, 1850. Zoea I. A. Lateral view; B. Carapace; C. Left antennule; D. Left antenna; E. Left maxillule; F. Left maxilla; G. Left first maxilliped; H. Left second maxilliped; I. Left third maxilliped; J. Left first pereopod; K. Pleon, lateral view; L. Third somite of pleon, lateral view; M. Telson, dorsal view. Scale bars: A, L, K. 0.15mm; B–D, G–J, M. 0.07 mm; E, F. 0.04 mm.
FIGURES 9–12 in Biology, immature stages, and systematics of snail-killing flies of the genus Colobaea (Diptera: Sciomyzidae), with overviews of aspects of the tribe Sciomyzini
FIGURES 9–12. Cephalopharyngeal skeletons: 9, Colobaea pectoralis (Zetterstedt), first-instar larva; 10, C. pectoralis, second-instar larva; 11, C. punctata (Lundbeck), second-instar larva; 12, C. deemingi Knutson & Bratt, second-instar larva. Abbreviations: DB, dorsal bridge; DC, dorsal cornu; HS, hypostomal sclerite; MH, mouthhook; PS, pharyngeal sclerite; VA, ventral arch; VC, ventral cornu. Measurement in mm.
Data from: Contact zone dynamics during early stages of speciation in a chorus frog (Pseudacris crucifer)
Characterizing the genetic and behavioural consequences of contact between previously geographically isolated lineages provides insights into the mechanisms underlying diversification and ultimately speciation. The spring peeper (Pseudacris crucifer) is a widespread Nearctic chorus frog with six divergent mitochondrial DNA (mtDNA) lineages, many of which came into secondary contact during the Holocene. We examined genetics, morphology, advertisement calls and female preference for two lineages that began diverging in allopatry in the Pliocene and now overlap in southwestern Ontario, Canada. We found non-coincident clines in mtDNA and nuclear DNA, mirroring directionality of premating isolation barriers. We also found divergence in a range of traits between these two lineages, displacement in male call attributes and female preference for calls of their natal lineage in sympatry. Hybrids were morphologically distinct from both parental lineages, but hybrid male calls were acoustically intermediate. Female hybrids showed asymmetrical preference for Eastern male calls. These results considered together provide evidence of either unidirectional hybridization or selection against hybrids, potentially implying reproductive character displacement. Our work demonstrates the utility of integrated, multi-character approaches to understanding the processes of divergence and the nature of speciation.
Data from: Signatures of natural selection between life cycle stages separated by metamorphosis in European eel
Background: Species showing complex life cycles provide excellent opportunities to study the genetic associations between life cycle stages, as selective pressures may differ before and after metamorphosis. The European eel presents a complex life cycle with two metamorphoses, a first metamorphosis from larvae into glass eels (juvenile stage) and a second metamorphosis into silver eels (adult stage). We tested the hypothesis that different genes and gene pathways will be under selection at different life stages when comparing the genetic associations between glass eels and silver eels. Results: We used two sets of markers to test for selection: first, we genotyped individuals using a panel of 80 coding-gene single nucleotide polymorphisms (SNPs) developed in American eel; second, we investigated selection at the genome level using a total of 153,423 RAD-sequencing generated SNPs widely distributed across the genome. Using the RAD approach, outlier tests identified a total of 2413 (1.57 %) potentially selected SNPs. Functional annotation analysis identified signal transduction pathways as the most over-represented group of genes, including MAPK/Erk signalling, calcium signalling and GnRH (gonadotropin-releasing hormone) signalling. Many of the over-represented pathways were related to growth, while others could result from the different conditions that eels inhabit during their life cycle. Conclusions: The observation of different genes and gene pathways under selection when comparing glass eels vs. silver eels supports the adaptive decoupling hypothesis for the benefits of metamorphosis. Partitioning the life cycle into discrete morphological phases may be overall beneficial since it allows the different life stages to respond independently to their unique selection pressures. This might translate into a more effective use of food and niche resources and/or performance of phase-specific tasks (e.g. feeding in the case of glass eels, migrating and reproducing in the case of silver eels).
Data from: Population structure in Atlantic cod in the eastern North Sea-Skagerrak-Kattegat: early life stage dispersal and adult migration
Background: In marine fish species, where pelagic egg and larvae drift with ocean currents, population structure has been suggested to be maintained by larval retention due to hydrographic structuring and by homing of adult fish to natal areas. Whilst natal homing of adults has been demonstrated for anadromous and coral reef fishes, there are few documented examples of philopatric migration in temperate marine fish species. Results: Here, we demonstrate temporally stable genetic differentiation among spawning populations of Atlantic cod (Gadus morhua L.), and present genetic and behavioural evidence for larval drift and philopatric migration in the eastern North Sea-Skagerrak-Kattegat area. We show that juvenile cod collected in the eastern Skagerrak and central Kattegat are genetically similar to cod from offshore spawning areas in the eastern North Sea. Genetic assignment of individual 2–5 year old fish indicates that cod residing at, or migrating towards, spawning areas in Kattegat and the North Sea display philopatric behaviours. Conclusions: Together these findings suggest a loop between spawning, larval drift and adult return-migrations to spawning areas and underlines that both oceanographic processes and migratory behaviour in the adult phase may be important for stock separation and integrity in marine temperate fishes such as Atlantic cod.
Data from: Seasonal differences in baseline innate immune function are better explained by environment than annual cycle stage in a year-round breeding tropical songbird
1. Seasonal variation in innate immunity is often attributed to either temporal environmental variation or to life history trade-offs that arise from specific annual cycle stages but decoupling them is difficult in natural populations. 2. Here, we effectively decouple seasonal environmental variation from annual cycle stage effects by exploiting cross-seasonal breeding and moult in the tropical Common Bulbul Pycnonotus barbatus. We test how annual cycle stage interacts with a key seasonal environmental variable, rainfall, to determine immunity at population and individual level. If immune challenge varies with precipitation, we might expect immune function to be higher in the wet season due to increased environmental productivity. If breeding or moult imposes resource constraints on birds, depending on or independent of precipitation, we might expect lower immune indices during breeding or moult. 3. We sampled blood from 818 birds in four annual cycle stage categories: breeding, moult, simultaneous breeding and moulting, or neither. We quantified indices of innate immunity (haptoglobin, nitric oxide (NOx) and ovotransferrin concentrations, and haemagglutination and haemolysis titres) over two annual cycles of wet and dry seasons. 4. Environment (but not annual cycle stage or interactions between both) explained variation in all immune indices, except NOx. NOx concentration differed between annual cycle stages but not between seasons. However, within the wet season, haptoglobin, NOx, ovotransferrin and haemolysis differed significantly between breeding and non-breeding females. Aside from some recorded inconsistences, population level results were largely similar to results within individuals that were measured repeatedly. Unexpectedly, most immune indices were higher in the dry season and during breeding. 5. Higher immune indices may be explained if fewer or poorer quality resources force birds to increase social contact, thereby exposing individuals to novel antigens and increased infection risk, independently of environmental productivity. Breeding birds may also show higher immunity if less immune-competent and/or infected females omit breeding. We conclude that seasonal environmental variation impacts immunity more directly in natural animal populations than via resource trade-offs. In addition, immune indices were more often variable within than among individuals, but some indices are characteristic of individuals, and so may offer selective advantages if heritable.
FIGURE 3 in The first zoeal stage of the yellow land crab Johngarthia lagostoma (Milne Edwards 1837) (Decapoda: Brachyura: Gecarcinidae)
FIGURE 3. Johngarthia lagostoma (Milne Edwards, 1837), Zoea I. (A) complete larva, lateral view; (B) 1. antennule; 2. antenna; (C) maxillule; (D) maxilla; (E) first maxilliped; (F) second maxilliped; (G) pleon, dorsal view and (H) detail of a single mid-dorsal seta on first pleonite; (I) pair of posterolateral setae; (J- K) Telson and telson detail of furca, with a minute dorsal spine. Scale bars: A. 0.5 mm; B– F. 0.05 mm; G. 0.1 mm; H–I: 2 0.02 mm; J. 0.5 mm; K. 0.02 mm
FIGURE 2 in The first zoeal stage of the yellow land crab Johngarthia lagostoma (Milne Edwards 1837) (Decapoda: Brachyura: Gecarcinidae)
FIGURE 2. Johngarthia lagostoma (Milne Edwards, 1837), Zoea I. (A) antennule; (B) antenna; (C) maxillule; (D) maxilla; (E) first maxilliped; (F) second maxilliped; (G) pleon, dorsal view, (H) telson and telson detail of furca. Scale bars: 0.1 mm
FIGURE 1 in The first zoeal stage of the yellow land crab Johngarthia lagostoma (Milne Edwards 1837) (Decapoda: Brachyura: Gecarcinidae)
FIGURE 1. Johngarthia lagostoma (Milne Edwards, 1837), Zoea I. (A) complete larva, lateral view; (B) same, frontal view. Scale bar: a = 0.1 mm
Data from: Timing manipulations reveal the lack of a causal link across timing of annual-cycle stages in a long-distance migrant
Organisms need to time their annual-cycle stages, like breeding and migration, to occur at the right time of the year. Climate change has shifted the timing of annual-cycle stages at different rates, thereby tightening or lifting time constraints of these annual-cycle stages, a rarely studied consequence of climate change. The degree to which these constraints are affected by climate change depends on whether consecutive stages are causally linked (I) or whether the timing of each stage is independent of other stages (II). Under (I), a change in timing in one stage has knock-on timing effects on subsequent stages, whereas under (II) a shift in the timing of one stage affects the degree of overlap with previous and subsequent stages. For testing this we combined field manipulations, captivity measurements and geolocation data. We advanced and delayed hatching dates in pied flycatchers (Ficedula hypoleuca) and measured how the timing of subsequent stages (male moult and migration) were affected. There was no causal effect of manipulated hatching dates on the onset of moult and departure to Africa. Thus, advancing hatching dates reduced the male moult-breeding overlap with no effect on the moult-migration interval. Interestingly, the wintering location of delayed males was more westwards, suggesting that delaying the termination of breeding carries-over to winter location. Because we found no causal linkage of the timing of annual-cycle stages, climate change can shift these stages at different rates, with the risk that the time available for some become so short that this will have major fitness consequences.
Data from: Blood-stage parasitaemia and age determine Plasmodium falciparum and P. vivax gametocytaemia in Papua New Guinea
A better understanding of human-to-mosquito transmission is crucial to control malaria. In order to assess factors associated with gametocyte carriage, 2083 samples were collected in a cross-sectional survey in Papua New Guinea. Plasmodium species were detected by light microscopy and qPCR and gametocytes by detection of pfs25 and pvs25 mRNA transcripts by reverse-transcriptase PCR (qRT-PCR). The parasite prevalence by PCR was 18.5% for Plasmodium falciparum and 13.0% for P. vivax. 52.5% of all infections were submicroscopic. Gametocytes were detected in 60% of P. falciparum-positive and 51% of P. vivax-positive samples. Each 10-fold increase in parasite density led to a 1.8-fold and 3.3-fold increase in the odds of carrying P. falciparum and P. vivax gametocytes. Thus the proportion of gametocyte positive and gametocyte densities was highest in young children carrying high asexual parasite densities and in symptomatic individuals. Dilution series of gametocytes allowed absolute quantification of gametocyte densities by qRT-PCR and showed that pvs25 expression is 10-20 fold lower than pfs25 expression. Between 2006 and 2010 parasite prevalence in the study site has decreased by half. 90% of the remaining infections were asymptomatic and likely constitute an important reservoir of transmission. However, mean gametocyte densities were low (approx. 1-2 gametocyte/μL) and it remains to be determined to what extent low-density gametocyte positive individuals are infective to mosquitos.
Data from: Dauer life stage of Caenorhabditis elegans induces elevated levels of defense against the parasite Serratia marcescens
Host-parasite research often focuses on a single host life stage, yet different life stages may exhibit different defenses. The nematode Caenorhabditis elegans has an alternate dispersal life stage, dauer. Despite dauer's importance in nature, we know little of how it responds to parasites. Previous research indicates that non-dauer C. elegans prefer to consume the virulent bacterial parasite, Serratia marcescens, when given a choice between the parasite and benign Escherichia coli. Here, we compared the preferences of dauer individuals from six strains of C. elegans to the preferences of other life stages. We found that dauer individuals exhibited reduced preference for S. marcescens, and dauers from some strains preferred E. coli to S. marcescens. In addition to testing food preference, a mechanism of parasite avoidance, we also measured host mortality rates after direct parasite exposure to determine if life stage also altered host survival. Overall, dauer individuals exhibited reduced mortality rates. However, dauer versus non-dauer larvae mortality rates also varied significantly by host strain. Collectively, we found evidence of dauer-induced parasite avoidance and reduced mortality in the presence of a parasite, but these effects were strain-specific. These results demonstrate the importance of host life stage and genotype when assessing infection dynamics.
Data from: Impacts of ocean acidification on sea urchin growth across the juvenile to mature adult life-stage transition is mitigated by warming
Understanding how growth trajectories of calcifying invertebrates are affected by changing climate requires acclimation experiments that follow development across life history transitions. In a long-term acclimation study, the effects of increased acidification and temperature on survival and growth of the tropical sea urchin Tripneustes gratilla from the early juvenile (5 mm test diameter- TD) through the developmental transition to the mature adult (60 mm TD) were investigated. Juveniles were reared in a combination of three temperature and three pH/pCO2 treatments, including treatments commensurate with global change projections. Elevated temperature and pCO2/pH both affected growth, but there was no interaction between these factors. The urchins grew more slowly at pH 7.6, but not at pH 7.8. Slow growth may be influenced by the inability to compensate coelomic fluid acid-base balance at pH 7.6. Growth was faster at +3 and +6 °C compared to that in ambient temperature. Acidification and warming had strong and interactive effects on reproductive potential. Warming increased the gonad index, but acidification decreased it. At pH 7.6 there were virtually no gonads in any urchins regardless of temperature. The T. gratilla were larger at maturity under combined near-future warming and acidification scenarios (+3 °C/pH 7.8). Although the juveniles grew and survived in near-future warming and acidification conditions, chronic exposure to these stressors from an early stage altered allocation to somatic and gonad growth. In the absence of phenotypic adjustment, the interactive effects of warming and acidification on the benthic life phases of sea urchins may compromise reproductive fitness and population maintenance as global climatic change unfolds.
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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.