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Novel integrative modeling of molecules and morphology across evolutionary timescales
<p>Evolutionary models account for either population or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.</p>
Modified poly(L-lysine)-based structures as novel antimicrobials for diabetic foot infections, an in-vitro study.
<p><strong>Data used to generate Figures 2 to 7 </strong></p> <p>Figure 2. Bactericidal activity of poly-L-lysine polymers against <em>S. aureus</em> and <em>P. aeruginosa</em> laboratory strains compared to antibiotics.</p> <p>Figure 3. Bactericidal activity of poly-L-lysine polymers against <em>S. aureus</em> and <em>P. aeruginosa</em> laboratory strains.</p> <p>Figure 4. Comparative bactericidal activity of poly-L-lysine G3(16) copolymers series with hydrophobic amino acid isoleucine, tyrosine and phenylalanine.</p> <p>Figure 5. Comparison of Bactericidal activity of poly-L-lysine polymers, PLL<sub>160 </sub>and G2(8)PLL<sub>20</sub> against <em>S. aureus</em> clinical isolates from wound infections. </p> <p>Figure 6. Bactericidal activity of linear PLL<sub>160 </sub>against <em>S. aureus</em> and <em>P. aeruginosa </em>isolates from suspected diabetic foot infections.</p> <p>Figure 7. Investigation of PLL polymer-induced loss of biofilm viability by resazurin staining of 24 h biofilms.</p>
Figure 7–13 in Novel host records of some cassidine leaf beetles from Ecuador (Coleoptera: Chrysomelidae: Cassidinae)
Figure 7–13. Aslamidium and their Marantaceae hosts in Ecuador. 7) Aslamidium capense adult (Body length ca. 6mm). 8) Feeding damage of A. capense. 9) EETP technicians R. Troya and J. Cedeño under a mature Calathea lutea. 10) Calathea majestica (with author R.W. Flowers). 11) Local house with roof made of Calathea and Carludovica leaves. 12) Aslamidium semicirculare adults (Body length ca. 5 mm) feeding on young C. lutea leaf. 13) Underside of leaf of C. majestica damaged by beetle chewing.
Figure 14–16 in Novel host records of some cassidine leaf beetles from Ecuador (Coleoptera: Chrysomelidae: Cassidinae)
Figure 14–16. Demotispa elaeicola and its host, Elaeis guineensis (oil palm). 14) Adult (Body length ca. 5 mm) (photo by M. Haseeb). 15) Undamaged fruit. 16) Heavily damaged fruit.
Figure. 1–6. Spaethiella with their hosts. 1 in Novel host records of some cassidine leaf beetles from Ecuador (Coleoptera: Chrysomelidae: Cassidinae)
Figure. 1–6. Spaethiella with their hosts. 1) Spaethiella sp. 1 (Body length ca. 4mm), larvae and pupae on Heliconia latispatha. 2) Adult of Spaethiella sp. 1 with trenching feeding pattern. 3) Carludovica sp., host of Spaethiella sp. 2. 4) Spaethiella sp. 2, larva with bird's nest fecal case. 5) Spaethiella sp. 2, larvae and pupae, and window panes produced from trenching feeding pattern. 6) Spaethiella sp. 2, adult (Body length ca. 5mm).
Figure 1 in Novel Australian Polyzoinae (Styelidae, Tunicata)
Figure 1. (A) Polyandrocarpa colemani (QM G308755): left and right pallial wall showing gut and gonads. (B, C) Polyandrocarpa colligata (QM G308758): (B) colony surface; (C) gut loop. (D–H) Oculinaria australis (SAM E3267): (D) portion of colony; (E) inner pallial body wall on right showing gonads; (F) inner pallial body wall on left showing gut and gonads; (G, H) siphonal spines. In (G), the open base of the spine in the centre of the light micrograph is showing; in all the other spines, only the hollow centres of the pointed tips are in focus. Scale bars: 1.0 mm (A); 2.0 mm (B, D–F); 0.2 mm (C); 0.05 mm (G, H).
Figure 2 in Novel Australian Polyzoinae (Styelidae, Tunicata)
Figure 2. Stolonica styeliformis (QM G308759). (A) External view of zooids; (B) internal pallial body wall on right. Scale bars: 2 mm (A); 1.0 mm (B).
Figure 3 in Novel Australian Polyzoinae (Styelidae, Tunicata)
Figure 3. Stolonica vermiculata sp. nov. (QM G308756, holotype). (A) Colony surface; (B) ventral view of zooid showing rectum curving around branchial sac; (C) dorsal view of internal body wall of the zooid, branchial sac and the upper half of the zooid removed; (D) testis follicles; (E) larva. Scale bars: 0.2 mm (A); 0.4 mm (B, C); 0.1 mm (D, E).
Figure 1 in Novel trophobiotic interactions in lantern bugs (Insecta: Auchenorrhyncha: Fulgoridae)
Figure 1. Trophobiotic interactions of lantern bugs (Fulgoridae) with insects and snails. (a) Lantern bug, Enchophora sanguinea, with two simultaneous moth guests (small Platynota sp. and larger Elaeognatha argyritis); (b) Enchophora sanguinea tended by cockroach, Eurycotis sp. 1; (c) Enchophora sanguinea with a trophobiotic snail, Euglandina aurantiaca, and kleptotrophobiotic ant, Camponotus sp. n.; (d) snail, E. aurantiaca, catching a droplet of honeydew (red arrow) ejected by Enchophora sanguinea; (e) moth, Euclystis proba, waiting for a stream of honeydew; (f) snail, Euglandina aurantiaca, with lantern bug Phrictus quinquepartitus; (g) moth, Elaeognatha argyritis tapping Enchophora sanguinea with its antennae, which elicits immediate honeydew production; (h) lantern bug E. sanguinea squirting honeydew—this photograph shows a single droplet exposed multiple times with a stroboscopic flash.
Novel Genomic Regions linked to Ascochyta blight Resistance in two differentially resistant cultivars of chickpea
<p><em>Ascochyta</em> blight (AB) caused by the fungal pathogen <em>Ascochyta rabiei</em> is a devastating foliar disease of chickpea (<em>Cicer arietinum</em> L.). Genotyping-by-sequencing (GBS) has been used in the current study for the identification of AB associated quantitative trait loci (QTLs) and their gene(s). We evaluated genotyping-by-sequencing (GBS)-based approach for mapping QTLs associated with AB resistance in chickpea using two recombinant inbred lines populations (AB<sub>3279</sub> and AB<sub>482</sub>) derived from two crosses ILC 1929 X ILC 3279 and ILC 1929 X ILC 482, under six different environments. In total, twenty-one different genomic regions were identified on linkage groups CalG02 and CalG04 pertaining to AB resistance in both populations AB<sub>3279</sub> and AB<sub>482</sub>. Four genomic regions were detected on CalG02 in the population AB<sub>3279</sub> and nine major genomic regions were associated with AB resistance on CaLG04, five out of them were common to both resistant parents ‘ILC3279’ and ‘ILC482’, and eight minor genomic regions with two out of them common between both populations. These regions contain 1,118 SNPs significantly associated (p ≤ 0.001) with AB resistance. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, with most important genes belonging to resistance gene families including Leucine-Rich Repeat (LRR), and transcription factors families. Our results may refer to the flowering-associated gene GIGANTEA as a possible key factor in AB resistance in chickpea. The results have narrowed the AB resistance associated regions on the chickpea physical map and the associated markers will help in breeding programs for chickpea improvement.</p>
Diagnostic accuracy of a novel enzyme‑linked immunoassay for the detection of IgG and IgG4 against Strongyloides stercoralis based on the recombinant antigens NIE/SsIR.
<p>Background: The diagnosis of strongyloidiasis is challenging. Serological tests are acknowledged to have high sensitivity, but issues due to cross-reactions with other parasites, native parasite antigen supply and intrinsic test variability do occur. Assays based on recombinant antigens could represent an improvement. The aim of this study was to assess the sensitivity and specificity of two novel immunoglobulin (Ig)G and IgG4 enzyme-linked immunosorbent assays (ELISAs) based on the recombinant antigens NIE/SsIR for the diagnosis of strongyloidiasis.</p> <p>Methods: This was a retrospective diagnostic accuracy study. We included serum samples collected from immigrants from strongyloidiasis endemic areas for whom there was a matched result for Strongyloides stercoralis on agar plate culture and/or PCR assay, or a positive microscopy for S. stercoralis larvae. For the included samples, results were also available from an in-house indirect fluorescent antibody test (IFAT) and a commercial (Bordier ELISA; Bordier Affinity Products SA) ELISA. We excluded: (i) samples with insufficient serum volume; (ii) samples from patients treated with ivermectin in the previous 6 months; and (iii) sera from patients for whom only routine coproparasitology was performed after formol–ether concentration, if negative for S. stercoralis larvae. The performance of the novel assays was assessed against: (i) a primary reference standard, with samples classified as negative/positive on the basis of the results of fecal tests; (ii) a composite reference standard (CRS), which also considered patients to be positive who had concordant positive results for the IFAT and Bordier ELISA or with a single “high titer” positive result for the IFAT or Bordier ELISA. Samples with a single positive test, either for the IFAT or Bordier ELISA, at low titer, were considered to be “indeterminate,” and analyses were carried out with and without their inclusion.</p> <p>Results: When assessed against the primary reference standard, the sensitivities of the IgG and IgG4 ELISAs were 92% (95% confidence interval [CI]: 88–97%) and 81% (95% CI: 74–87%), respectively, and the specificities were 91% (95% CI: 88–95%) and 94% (95% CI: 91–97%), respectively. When tested against the CRS, the IgG ELISA performed best, with 78% sensitivity (95% CI: 72–83%) and 98% specificity (95% CI: 96–100%), when a cut-off of 0.675 was applied and the indeterminate samples were excluded from the analysis.</p> <p>Conclusion: The NIE-SsIR IgG ELISA demonstrated better accuracy than the IgG4 assay and was deemed promising particularly for serosurveys in endemic areas.</p>
Visual Tracking of Entire Bumblebee Colonies Using Novel Pipeline Finds No Evidence of Gut-Brain Axis (Replicates 1, 2)
<p>This archive contains raw data processed from video files taken of bumblebee colonies during replicates 1 and 2 of a study on the effect of the gut microbiome on social behaviour. Files ending with "_raw.csv" contain data on read tags, while ones ending with "_noID.csv" contain data on potential tags. Files are named as follows: R[replicate number][Baseline/Data][Day]R[recording session][HiveID][VideoID]</p>
The widespread trade in stingless beehives may introduce them into novel places and could threaten species
<p>Dataset used in <strong>The widespread trade in stingless beehives may introduce them into novel places and could threaten species </strong>published in <em>Journal of Applied Ecology</em> (<a href="https://doi.org/10.1111/1365-2664.14108">https://doi.org/10.1111/1365-2664.14108</a>).</p>
Fig. 8 in Re-description of Thysanozoon nigropapillosum (Polycladida: Pseudocerotidae) from the South China Sea, with observations on a novel pre-copulatory structure, sexual behaviour and diet
Fig. 8. Multi-rayed star-like spicules of colonial tunicates Didemnum sp. in food pellets of Thysanozoon nigropapillosum (Hyman, 1959).
Fig. 6 in Re-description of Thysanozoon nigropapillosum (Polycladida: Pseudocerotidae) from the South China Sea, with observations on a novel pre-copulatory structure, sexual behaviour and diet
Fig. 6. Longitudinal section of Thysanozoon nigropapillosum (Hyman, 1959). A, pharynx and main intestine; B, food pellet remains inside the main intestine. fp, food pellet; mi, main intestine; ph, pharynx.
Fig. 9 in Re-description of Thysanozoon nigropapillosum (Polycladida: Pseudocerotidae) from the South China Sea, with observations on a novel pre-copulatory structure, sexual behaviour and diet
Fig. 9. Thysanozoon nigropapillosum (Hyman, 1959): copulation observed at Longdong bay, northeast coast of Taiwan, 25 July 2011. A, Dermal impregnation for unilateral insemination; B, One individual (right), with the paired penis stretched, gripping its partner (left) at the outermost margin. (spermatophore is indicated by an arrow)
Fig. 7 in Re-description of Thysanozoon nigropapillosum (Polycladida: Pseudocerotidae) from the South China Sea, with observations on a novel pre-copulatory structure, sexual behaviour and diet
Fig. 7. Thysanozoon nigropapillosum (Hyman, 1959) A, with colonial tunicates (indicated by arrows), found at Longdong Bay, Northeast Coast of Taiwan, 28 August 2008; B, regurgitated food pellet (indicated by arrowhead). Chuanfanshr, Kenting, southern Taiwan, 9 February 2006.
Fig. 4 in Re-description of Thysanozoon nigropapillosum (Polycladida: Pseudocerotidae) from the South China Sea, with observations on a novel pre-copulatory structure, sexual behaviour and diet
Fig. 4. Thysanozoon nigropapillosum (Hyman, 1959): rhabdites on epidermis (indicated by arrows). A, B, on the tips of papillae; C, distributed on the inner surface of the male atrium; D, distributed on the female pore.
Fig. 5 in Re-description of Thysanozoon nigropapillosum (Polycladida: Pseudocerotidae) from the South China Sea, with observations on a novel pre-copulatory structure, sexual behaviour and diet
Fig. 5. Distribution of Thysanozoon nigropapillosum (Hyman, 1959) A, around Taiwan; B, type locality (hollow square), and the probably distribution of Newman et al. (2003) collection (filled triangles), the distribution of Gosliner et al. (1996) collection (filled circles) in Indo-west Pacific.
Fig. 3 in Re-description of Thysanozoon nigropapillosum (Polycladida: Pseudocerotidae) from the South China Sea, with observations on a novel pre-copulatory structure, sexual behaviour and diet
Fig. 3. Diagrammatic representation of the reproductive anatomy of Thysanozoon nigropapillosum (Hyman, 1959). A, male. e, ejaculatory duct; in, intestine; ma, male pore; pr, prostate gland; se, seminal vesicle; sp, sperm; st, stylet; v, vas deferens. B, female. c, cement gland; f, female pore; mi, main intestine; p, pharynx; v, vagina.
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.