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2,395 results for “Contrast”
Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species
The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the ITS region, frequently used in plant phylogenetics, is now recognised as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analysed datasets from the Saccharomyces Genome Resequencing Project, characterising rDNA sequence variation within multiple strains of the baker's yeast <i>Saccharomyces cerevisiae</i> and its nearest wild relative <i>Saccharomyces paradoxus</i> in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterisation of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intra-species phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridisation events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multi-locus rDNA systems.
Contrast solution properties and scan parameters influence the apparent diffusivity of computed tomography contrast agents in articular cartilage
<p>The inability to detect early degenerative changes to the articular cartilage surface that commonly precede bulk osteoarthritic degradation is an obstacle to early disease detection for research or clinical diagnosis. Leveraging a known artifact that blurs tissue boundaries in clinical arthrograms, contrast agent diffusivity can be derived from computed tomography arthrography (CTa) scans. We combined experimental and computational approaches to study protocol variations that may alter the CTa-derived apparent diffusivity. In experimental studies on bovine cartilage explants, we examined how contrast agent dilution and transport direction (absorption vs. desorption) influence the apparent diffusivity of untreated and enzymatically digested cartilage. Using multiphysics simulations, we examined mechanisms underlying experimental observations and the effects of image resolution, scan interval and early scan termination. The apparent diffusivity during absorption decreased with increasing contrast agent concentration by an amount similar to the increase induced by tissue digestion. Models indicated that osmotically induced fluid efflux strongly contributed to the concentration effect. Simulated changes to spatial resolution, scan spacing and total scan time all influenced the apparent diffusivity, indicating the importance of consistent protocols. With careful control of imaging protocols and interpretations guided by transport models, CTa-derived diffusivity offers promise as a biomarker for early degenerative changes.</p>
Contrasting molecular profiles of clownfishes and damselfishes-RPLC_positive_mode
<p>Lipidomics positive ionization mode acquired data samples</p>
Figure 2 from: Harbach RE, Dallimore T, Briscoe AG, Culverwell CL, Vaux AGC, Medlock JM (2017) Aedes nigrinus (Eckstein, 1918) (Diptera, Culicidae), a new country record for England, contrasted with Aedes sticticus (Meigen, 1838). ZooKeys 671: 119-130. https://doi.org/10.3897/zookeys.671.12477
Figure 2 - Doral aspects (pre-rotation sense) of the male genitalia of Ae. nigrinus (A) and Ae. sticticus (B), which are distinguished by the shape of the basal dorsomesal lobe (BDL).
Figure 1 from: Harbach RE, Dallimore T, Briscoe AG, Culverwell CL, Vaux AGC, Medlock JM (2017) Aedes nigrinus (Eckstein, 1918) (Diptera, Culicidae), a new country record for England, contrasted with Aedes sticticus (Meigen, 1838). ZooKeys 671: 119-130. https://doi.org/10.3897/zookeys.671.12477
Figure 1 - Proximal half of the right wing of female mosquitoes. A Ae. nigrinus, showing the presence of pale scaling on the costa, subcosta, remigium and anal vein B Ae. sticticus, showing the absence of pale scaling.
Figure 5 from: Espinasa L, Bonaroti N, Wong J, Pottin K, Queinnec E, Rétaux S (2017) Contrasting feeding habits of post-larval and adult Astyanax cavefish. Subterranean Biology 21: 1-17. https://doi.org/10.3897/subtbiol.21.11046
Figure 5 - Gut content of adult Pachón cave fish. A White, orange, and black "gunk" of undetermined origin B Hair-like filaments in stomach contents C Unidentified pigmented arthropod sclerites, possibly of surface insects or by-product of eating guano. D Mud E Fly F Beetle.
Figure 3 from: Espinasa L, Bonaroti N, Wong J, Pottin K, Queinnec E, Rétaux S (2017) Contrasting feeding habits of post-larval and adult Astyanax cavefish. Subterranean Biology 21: 1-17. https://doi.org/10.3897/subtbiol.21.11046
Figure 3 - Digestive system of an Astyanax fry. A A live specimen photographed in the Pachón cave. Note the healthy-looking appearance of this juvenile, the two parts of the inflated swim bladder, the almost completely degenerated eye, and the digestive system filled with food. Scale bar as in B. B Body, with the digestive system exposed C Stomach and intestine. Notice that the food content can be seen through the translucent walls. All fish studied were well fed and their guts were full of food.
Figure 1 from: Espinasa L, Bonaroti N, Wong J, Pottin K, Queinnec E, Rétaux S (2017) Contrasting feeding habits of post-larval and adult Astyanax cavefish. Subterranean Biology 21: 1-17. https://doi.org/10.3897/subtbiol.21.11046
Figure 1 - Pachón cave map (from NNS News, September 2003, p255.). Adult fish were found in the main pool (Right arrow). Adult fish and post-larval fish were found in small pools in a side gallery (Left arrow).
Figure 2 from: Espinasa L, Bonaroti N, Wong J, Pottin K, Queinnec E, Rétaux S (2017) Contrasting feeding habits of post-larval and adult Astyanax cavefish. Subterranean Biology 21: 1-17. https://doi.org/10.3897/subtbiol.21.11046
Figure 2 - Size and estimated age of the fry captured in the Pachón cave. A Live Pachón fry photographed in a small fish aquarium, in the cave B Size/age relationship for lab-raised Pachón individuals with a linear regression curve. Data were collected in Rétaux's lab from larvae, post-larvae and juvenile grown as described in Elipot et al. (2014), and which were fed twice a day with live Artemia, ad libitum C Photograph of a specimen swimming in the natural pool. Note the muddy/sandy substrate and the low water level D, E Photographs of live arthropod specimens cohabiting with Astyanax fry.
Figure 4 from: Espinasa L, Bonaroti N, Wong J, Pottin K, Queinnec E, Rétaux S (2017) Contrasting feeding habits of post-larval and adult Astyanax cavefish. Subterranean Biology 21: 1-17. https://doi.org/10.3897/subtbiol.21.11046
Figure 4 - Gut contents of Pachón cave fry. A–C Cladocera Water fleas. This species constituted by number the most encountered prey. On average, fry had in their guts 9.3 individuals of this species D Harpacticoida copepod. Arrow highlights the short antennae diagnostic of class Harpacticoida. This species constituted by number the second most encountered prey. On average, fry had in their guts 4.7 individuals of this species E–F Copepods. Arrow highlights the long antennae diagnostic of non-harpacticoida copepods G Ostracod. This and possibly two more species of ostracods were in their guts H Isopod. While only one specimen was eaten, due to its large size it constitutes a large stomach content by volume I Sclerites of arthropods, possibly of insects. Contrary to all of the above, they have pigment, suggesting that some may be surface insects. Some may be a by-product of eating guano from insectivorous bats.
Dual nematode infection in Brassica nigra affects shoot metabolome and aphid survival in distinct contrast to single-species infection
<p><strong><span>Abstract</span></strong></p> <p><span>Previous studies showed that aphid performance was compromised on <em>Brassica nigra</em> infected by root-lesion nematodes (<em>Pratylenchus penetrans</em>, Pp), but less, or positively influenced by root-knot nematode (<em>Meloidogyne</em> <em>spp</em>., Mi) infection. These experiments were on single-nematode infections, while naturally, roots are infected with several nematode species simultaneously.</span></p> <p><span>We performed greenhouse assays to assess the effects of single (Mi, Pp) and concurrent (MP)-nematode infections on aphid performance. Using targeted and untargeted profiling of leaf and phloem metabolomes, we examined how single- and concurrent-nematode infections affect shoots metabolomes, and elucidated the possible consequences on aphid performance. We found that the metabolic response towards double-infection is different from single-species infections. Moreover, Mi- and Pp-infections triggered discrete changes in <em>B. nigra</em> leaf and phloem metabolic profiles. Both Pp and MP-infections reduced aphid survival, suggesting that the biological effect could primarily be dominated by Pp-induced changes. This concurred with increased indole glucosinolates and hydroxycinnamic acid levels in the leaves, in particular the putative involvement of salicylic acid-2-O-β-D-glucoside. </span></p> <p><span>This study provides evidence that concurrent infection of different nematode species, as is common in natural environments, is associated with distinct changes in aboveground plant metabolomes, which may be linked to variations in the survival of an aboveground herbivore.<span> </span></span></p>
Fig. 6 in Contrasting phylogeographic patterns of intertidal mites (Acari, Oribatida) along the South African shoreline
Fig. 6 Graphs showing results of multivariate analyses performed on size-corrected data of four different Halozetes capensis populations; left side non-metric multidimensional scaling (NMDS), right side linear discriminant analysis (LDA)
Fig. 7 in Contrasting phylogeographic patterns of intertidal mites (Acari, Oribatida) along the South African shoreline
Fig. 7 Graphs showing results of multivariate analyses performed on size-corrected data of four different Schusteria ugraseni populations; left side non-metric multidimensional scaling (NMDS), right side linear discriminant analysis (LDA)
DAPI and Phase Contrast Images Dataset
<p>Data was acquired on an Olympus IX83 microscope using a 20x/0.4 Ph2 Objective.</p> <p>Kohler illimination was established before acquistion started.</p> <p>Sample consists of cultured HeLa Cells on #1.5 (170 um) coverslips, 12mm diameter.</p> <p> </p> <p>A single coverlsip was imaged in a 10x10 grid with no overlap (total: 100 images)</p> <p>Each image was acquired sequentially in</p> <ul> <li><strong>Phase Contrast</strong> (50ms exposure time, using a 535nm LED)</li> <li><strong>DAPI</strong> 100 ms exposure time</li> </ul>
Figures 2-5 in Great unexpected differences between two populations of the intertidal crab Neohelice granulata inhabiting close but contrasting habitats (Crustacea: Decapoda: Brachyura)
Figures 2-5. Neohelice granulata. Size frequency distributions of males and females in mudflats (2-3) and salt marshes (4-5) of San Antonio Oeste and Riacho San José.
Fig. 1 in Contrasting patterns of insecticide resistance and knockdown resistance (kdr) in Aedes aegypti populations from Jacarezinho (Brazil) after a Dengue Outbreak
Fig. 1. Location of Jacarezinho town (PR = Paraná state) in Brazil (A). Jacarezinho map shows the collection sites in the urban area used for the analysis of the Val1016Ile mutation in 2011 and 2012. Additionally, the main roads that cross Jacarezinho are presented (B).
Figure 5 in Body size variation in a lineage of spur-thighed tortoises (Testudo graeca whitei) contrasts with that expected from the species level
Figure 5. Von Bertalanffy growth curves describing Testudo graeca whitei growth by sex and range.
Dataset for "Electric-field-enhanced second-harmonic domain contrast and nonreciprocity in a van der Waals antiferromagnet"
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Continental Mapping Of African Sand Mining Shows Contrasting Links To Urban Development
<p>Continental African sand mining detection data used in '<strong>Continental Mapping Of African Sand Mining Shows Contrasting Links To Urban Development'</strong></p>
Aligned Cross-modal Integration and Regulatory Heterogeneity Characterization of Single-Cell Multiomic Data with Deep Contrastive Learning
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