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4,480 results for “hybrid”
Engineering Fano-resonant hybrid metastructures with ultra-high sensing performances
<p>Here the data related to our recent work that uses metasurfaces designed on metamaterials to excite Fano resonances and Rabi Split analogue modes for sensing.</p> <p> </p> <p>In this repository the following data are available:</p> <ul> <li>The Reflectance, Transmittance and Absorbance (1-T-R) evaluated over all the diffraction angles (from 0° to 89°) for the proposed structure (ring + cross) and the other tested structures, available in the .mat file.</li> <li>The .m file to repeat all the simulations are available in main folder. The available Matlab codes allow reproducing numerical simulations using Reticolo (RCWA) as the main framework to do the computation.</li> <li>Use "getrefractiveindex.m" to interpolate refractive index on finest wavelength range. Please, note that according to the uploaded codes this function have to be in the same folder of the loaded refractive indices. </li> <li>You can use the function "textprogressbar.m" to get a progress bar in real time to know the status of the current simulation. Please, note that this function have to stay in the "/RETICOLO V8/reticolo_allege" folder. </li> <li>One of the available Matlab code allows displaying the electric and magnetic field evaluated in the structure section or on the top view. </li> <li>The sensing test performed for the reported structures using different surrounding medium, for this purpose it is possible to use the codes that allow studying the parameters variation, the incident angle variation or just a single run changing the refractive index of the surrounding medium. </li> </ul> <p>The proposed code works using the Reticolo main code. To download it please visit the following link <a href="https://www.lp2n.institutoptique.fr/light-complex-nanostructures">https://www.lp2n.institutoptique.fr/light-complex-nanostructures</a> or using Zenodo <a href="https://zenodo.org/record/5905381#.Y8rvbC9abpA">https://zenodo.org/record/5905381#.Y8rvbC9abpA</a></p> <p>Once Reticolo has been downloaded copy and paste its path in the proposed Matlab code for Fano resonances on ENZ cavities as reported in the example codes.</p> <p>In this repository you will find the refractive indices that have been used.</p>
Interspecific hybridization explains rapid gorget color divergence in Heliodoxa hummingbirds (Aves: Trochilidae)
Hybridization is a known source of morphological, functional, and communicative signal novelty in many organisms. Although diverse mechanisms of established novel ornamentation have been identified in natural populations, we lack an understanding of hybridization effects across levels of biological scales and upon phylogenies. Hummingbirds display diverse structural colors resulting from coherent light scattering by feather nanostructures. Given the complex relationship between feather nanostructures and the colors they produce, intermediate coloration does not necessarily imply intermediate nanostructures. Here, we characterize nanostructural, ecological, and genetic inputs in a distinctive Heliodoxa hummingbird from the foothills of eastern Peru. Genetically, this individual is closely allied with Heliodoxa branickii and H. gularis, but it is not identical to either when nuclear data are assessed. Elevated interspecific heterozygosity further suggests it is a hybrid backcross to H. branickii. Electron microscopy and spectrophotometry of this unique individual reveal key nanostructural differences underlying its distinct gorget color, confirmed by optical modeling. Phylogenetic comparative analysis suggests that the observed gorget coloration divergence from both parentals to this individual would take 6.6–10 My to evolve at the current rate within a single hummingbird lineage. These results emphasize the mosaic nature of hybridization and suggest that hybridization may contribute to the structural color diversity found across hummingbirds.
Postrelease exploration and stress tolerance of landlocked and anadromous Atlantic salmon and their hybrids
<p><strong>Background</strong></p> <p>We studied postrelease explorative behavior and stress tolerance of Landlocked and anadromous Atlantic salmon and their hybrids. For the research, we hybridized the Landlocked salmon of Lake Saimaa with a Baltic anadromous salmon from River Kymijoki, Southern Finland (strain originally from River Neva, Russia). These fish were hybridized in November 2017 and October 2018 in the Kainuu Fisheries Research Station, Paltamo, Kainuu, Finland (kfrs.fi).<br><br>In the data the fish are treated as four strains (column 'Strain'): <strong>1.</strong> Purebred Landlocked salmon (LLxLL), <strong>2. </strong>hybrids, where the maternal population was landlocked salmon (LLxBA), <strong>3. </strong>hybrids, where the maternal population was Baltic anadromous salmon (BAxLL) and <strong>4. </strong>purebred Baltic anadromous salmon (BAxBA).</p> <p><strong>Experiment 1. Post-release exploration</strong></p> <p>In experiment 1., consisting of two separate trials, we studied post-release exploration of the fish in four circular seminatural streams. (Datasets 'Exploration2018.csv' & 'Exploration2020.csv', see also 'Figure_1.jpg')</p> <p><strong>Experiment 2. Stress tolerance</strong></p> <p>In experiment 2. we studied the stress response and recovery of the fish (Dataset 'Stress_BernoulliData.csv', see also 'Figure_2.jpg').</p>
Complex hybridization between deeply diverged fish species in a disturbed ecosystem
<p>Over the past two decades, researchers have documented the extent of natural hybridization between closely related species using genomic tools. Many species across the tree of life show evidence of past hybridization with their evolutionary relatives. In some cases, this hybridization is complex – involving gene flow between more than two species. While hybridization is common over evolutionary timescales, some researchers have proposed that it may be even more common in contemporary populations where anthropogenic disturbance has modified a myriad of aspects of the environments in which organisms live and reproduce. Here, we develop a flexible tool for local ancestry inference in hybrids derived from three source populations and describe a complex, recent hybridization event between distantly related swordtail fish lineages (<em>Xiphophorus</em>) and its potential links to anthropogenic disturbance.</p>
Data for: Simulation and social network analysis provide insight into the acquisition of tool behavior in hybrid macaques
<p>The pathways through which primates acquire skills are a central focus of cultural evolution studies. The roles of social and genetic inheritance processes in skill acquisition are often confounded by environmental factors. Hybrid macaques from Koram Island, Thailand provide an opportunity to examine the roles of inheritance and social learning to skill acquisition within a single ecological setting. These hybrids are a cross between tool-using Burmese long-tailed (<em>Macaca</em> <em>fascicularis</em> <em>aurea</em>) and non-tool-using common long-tailed macaques (<em>Macaca</em> <em>fascicularis</em> <em>fascicularis</em>). This population provides an opportunity to explore the roles of social learning and inheritance processes while being able to exclude underlying ecological factors. Here, we investigate the roles of social learning and inheritance in tool use prevalence within this population using social network analysis and simulation. Agent-based modeling (ABM) is used to generate expectations for how social/asocial learning and inheritance structure the patterning in a social network. The results of the simulation show that various transmission mechanisms can be differentiated based on associations between individuals in a social network. The results provide an investigative framework for discussing tool-use transmission pathways in the Koram social network. By combining ABM, network analysis, and behavioral data from the field we can investigate the roles social learning and inheritance play in tool acquisition in wild primates. </p>
HETEAC – The Hybrid End-To-End Aerosol Classification model for EarthCARE: Look-Up Table (LUT) for aerosol mixtures
<p>The dataset contains the look-up table (LUT) of EarthCARE’s Hybrid End-To-End Aerosol Classification (HETEAC) model. The LUT contains optical and radiative parameters for four pure aerosol components (fine mode weakly absorbing, fine mode strongly absorbing, coarse mode spherical and coarse mode non-spherical) and their mixtures. In total, 314 aerosol mixtures are considered. The LUT returns the mixing state of an aerosol mixture based on the lidar ratio and the particle linear depolarization ratio at 355 nm. The mixing state is expressed in terms of relative volume contribution of the four pure aerosol components. Additionally, the LUT returns the effective radius, the asymmetry parameter, the single scattering albedo (at 355, 532, 550, 670, 865, 1064, 1650 and 2210 nm) and the Angstrom exponent (at 28 wavelength combinations) of the aerosol mixture. The lidar ratio and the particle linear depolarization ratio is also provided at 532, 550, 670, 865, 1064, 1650 and 2210 nm.</p> <p>The datafile contains two top-level groups: the HeaderData, which contains the header variables, and the ScienceData with the variables. The latter contains two groups, the AerosolComponents, which includes the aerosol-component-related optical and microphysical variables, and the LookUpTable, which contains the HETEAC LUT variables.</p> <p>The variables included in the datafile are listed below. For each variable, a full description is provided in the long_name attribute.</p> <ul> <li>HeaderData <ul> <li>angstrom_exponent_header</li> </ul> </li> <li>ScienceData <ul> <li>AerosolComponents <ul> <li>backscatter</li> <li>effective_radius</li> <li>extinction</li> <li>logarithmic_width</li> <li>mode_radius_number</li> <li>mode_radius_volume</li> <li>particle_linear_depolarization_ratio</li> <li>refractive_index_imaginary</li> <li>refractive_index_real</li> <li>scattering</li> </ul> </li> <li>LookUpTable <ul> <li>angstrom_exponent</li> <li>asymmetry_parameter</li> <li>effective_radius</li> <li>lidar_ratio</li> <li>particle_linear_depolarization_ratio</li> <li>relative_volume_contribution</li> <li>single_scattering_albedo</li> </ul> </li> <li>radiation_wavelength</li> </ul> </li> </ul> <p>Contact</p> <p>For any further clarifications or expression of interest with respect to the EarthCARE LUT, please contact Ulla Wandinger (ulla.wandinger@tropos.de) and/or Athena Augusta Floutsi (floutsi@tropos.de).</p> <ul> </ul>
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 % complete dataset, consisting of 4561 loci. Circles on the branch represent a local posterior probability support of 0.95 to 1.0. Abbreviations – AT – Atractaspidinae, CL – Cyclocoridae, EL – Elapidae, LM – Lamprophiinae, MC – Micrelapidae fam. nov., OG – outgroup, PD – Pseudaspidinae, PR – Prosymninae, PS – Psammophiinae, PX – Pseudoxyrhophiinae.
Superconductor-ferromagnet hybrids for non-reciprocal electronics and detectors
<p># Data for the manuscript "Superconductor-ferromagnet hybrids for non-reciprocal electronics and detectors", submitted to Superconductor Science and Technology, arXiv:2302.12732.</p> <p>This archive contains the data for all plots of numerical data in the manuscript.</p> <p>## Fig. 4 <br> Data of Fig. 4 in the WDX (Wolfram Data Exchange) format (unzip to extract the files). Contains critical exchange fields and critical thicknesses as functions of the temperature. Can be opened with Wolfram Mathematica with the command: Import[FileNameJoin[{NotebookDirectory[],"filename.wdx"}]]</p> <p>## Fig. 5<br> Data of Fig. 5 in the WDX (Wolfram Data Exchange) format (unzip to extract the files). Contains theoretically calculated I(V) curves and the rectification coefficient R of N/FI/S junctions. Can be opened with Wolfram Mathematica with the command Import[FileNameJoin[{NotebookDirectory[],"filename.wdx"}]].</p> <p>## Fig. 7a<br> Data of Fig. 7a in the ascii format. Contains G in uS as a function of B in mT and V in mV.</p> <p>## Fig. 7c<br> Data of Fig. 7c in the ascii format. Contains G in uS as a function of B in mT and V in mV.</p> <p>## Fig. 7e<br> Data of Fig. 7e in the ascii format. Contains G in uS as a function of B in mT and V in mV.</p> <p>The plots 7b, d, and f are taken from the plots a, c and e as indicated in the caption of the figure.</p> <p>## Fig. 8<br> Data of Fig. 8 in the ascii format. Contains G in uS as a function V in mV for several values of B in mT.</p> <p>## Fig. 8 inset<br> Data of Fig. 8 inset in the ascii format. Contains G_0/G_N as a function of B in mT. </p> <p>## Fig9a_b</p> <p>First raw Magnetic field values in T, first column voltage drop in V, <br> rest of the columns differential conductance in S</p> <p>## Fig9b_FIT</p> <p>First raw Magnetic field values in T, first column voltage drop in V, <br> rest of the columns differential conductance in S</p> <p>## Fig9c</p> <p>First raw Magnetic field values in T, first column voltage drop in V, <br> rest of the columns R (real number)</p> <p>## Fig9c inset</p> <p>First raw Magnetic field values in T, odd columns voltage drop in V, <br> even columns injected current in A</p> <p>## Fog9d</p> <p>Foist column magnetic field in T, second column conductance ration (real <br> number), sample name in the file name.</p> <p> ## Fig. 12<br> Data of Fig. 12 in the ascii format. Contains energy resolution as functions of temperature and tunnel resistance with current and voltage readout.</p> <p>## Fig. 13<br> Data of Fig. 13 in the ascii format. Contains energy resolution as functions of (a) exchange field, (b) polarization, (c) dynes, and (d) absorber volume with different amplifier noises.</p> <p>## Fig. 14<br> Data of Fig. 14 in the ascii format. Contains detector pulse current as functions of (a) temperature change (b) time with different detector parameters.</p> <p><br> ## Fig. 17<br> Data of Fig. 17 in the ascii format. Contains dIdV curves as function of the voltage for different THz illumination frequency and polarization.</p> <p>## Fig. 18<br> Data of Fig. 18 in the ascii format. Contains the current flowing throughout the junction as function time (arbitrary units) for ON and OFF illumination at 150 GHz for InPol and CrossPol polarization.</p> <p>## Fig. 21<br> Data of Fig. 21c in the ascii format. Contains the magnitude of readout line S43 as frequency.<br> Data of Fig. 21d in the ascii format. Contains the magnitude of iKID line S21 as frequency.</p>
Brain-inspired multimodal hybrid neural network for robot place recognition
<p>Brain-inspired multimodal hybrid neural network for robot place recognition</p>
Data from: Transgressive segregation in mating traits drives hybrid speciation
<p><span>Hybridization can instantaneously generate novel genetic variation, which can promote ecological speciation by creating novel adaptive phenotypes. However, it remains unclear how hybridization, creating novel mating phenotypes (e.g., mating season, genitalia shapes, sexual displays, mate preferences), affects speciation especially when the phenotypes do not confer adaptive advantages. Here, based on individual-based evolutionary simulations, we propose that transgressive segregation of mating traits can drive incipient hybrid speciation. Simulations demonstrated that incipient hybrid speciation occurred most frequently when the hybrid population received moderate continued immigration from parental lineages</span><span> causing </span><span>recurrent episodes of hybridization. Recurrent hybridization constantly generated genetic variation, which </span><span>promoted</span> <span>the rapid stochastic evolution of mating phenotypes</span><span> in a hybrid population.</span><span> The stochastic evolution continued until a novel mating phenotype came to dominate the hybrid population, which reproductively isolates the hybrid population from parental lineages. However, too </span><span>frequent hybridization rather hindered the evolution of reproductive isolation by inflating the variation of mating phenotypes to produce phenotypes allowing mating with parental lineages. Simulations also revealed conditions for long-term persistence of hybrid species after their incipient emergence. </span><span>Our results suggest that recurrent transgressive segregation of mating phenotypes can offer a plausible explanation for hybrid speciation and radiations that involved little adaptive ecological divergence.</span></p>
Mantis shrimp locomotion: coordination and variation of hybrid metachronal swimming
<p><span>Across countless marine invertebrates, coordination of closely spaced swimming appendages is key to producing diverse locomotory behaviors. Using a widespread mechanism termed hybrid metachronal propulsion, mantis shrimp swim by moving five paddle-like pleopods along their abdomen in a posterior to anterior sequence during the power stroke and a near-synchronous motion during the recovery stroke. Despite the ubiquity of this mechanism, it is not clear how hybrid metachronal swimmers coordinate and modify individual appendage movements to achieve a range of swimming capabilities. Using high-speed imaging, we measured pleopod kinematics of mantis shrimp (<em>Neogonodactylus</em> <em>bredini</em>) while they performed two swimming behaviors: burst swimming and taking off from the substrate. By tracking each of the five pleopods, we tested how stroke kinematics vary across swimming speeds and the two swimming behaviors. We found that mantis shrimp achieve faster swimming speeds through a combination of higher beat frequencies, smaller stroke durations, and partially via larger stroke angles. The five pleopods exhibit non-uniform kinematics that contribute to the coordination and forward propulsion of the whole system. Micro-hook structures (retinacula) connect each of the five pleopod pairs and differ in their attachment across pleopods – possibly contributing to passive kinematic control. We compare our findings in <em>N</em>. <em>bredini</em> to previous studies to identify commonalities across hybrid metachronal swimmers at high Reynolds numbers and centimeter scales. Through our large experimental dataset and by tracking each pleopod's movements, our study reveals key parameters by which mantis shrimp adjust and control their swimming, yielding diverse locomotor abilities.</span></p>
DataSet for "Hybrid Based on Phenazine Conjugated Microporous Polymer as a High-Performance Organic Electrode in Aqueous Electrolytes"
<p>All raw data were obtained directly by the instruments and were then elaborated by us using Origin and/or Excel. All the facilities used, except for the NMR measurements, are present in IMDEA Energy Institute <br> <br> </p>
Data from: Predictive links between petal color and pigment quantities in natural Penstemon hybrids
<p class="MsoNormal">Flowers have evolved remarkable diversity in petal color, in large part due to pollinator-mediated selection. This diversity arises from specialized metabolic pathways that generate conspicuous pigments. Despite the clear link between flower color and floral pigment production, studies determining predictive relationships between pigmentation and petal color are currently lacking. In this study, we analyze a dataset consisting of hundreds of natural <em>Penstemon</em> hybrids that exhibit variation in flower color, including blue, purple, pink, and red. For each individual hybrid, we measured anthocyanin pigment content and petal spectral reflectance. We found that floral pigment quantities are correlated with hue, chroma, and brightness as calculated from petal spectral reflectance data: hue is related to the relative amounts of delphinidin vs. pelargonidin pigmentation, whereas brightness and chroma are correlated with the total anthocyanin pigmentation. We used a partial least squares regression approach to identify predictive relationships between pigment production and petal reflectance. We find that pigment quantity data provide robust predictions of petal reflectance, confirming a pervasive assumption that differences in pigmentation should predictably influence flower color. Moreover, we find that reflectance data enables accurate inferences of pigment quantities, where the full reflectance spectra provide much more accurate inference of pigment quantities than spectral attributes (brightness, chroma, and hue). Our predictive framework provides readily interpretable model coefficients relating spectral attributes of petal reflectance to underlying pigment quantities. These relationships represent key links between genetic changes affecting anthocyanin production and ecological functions of petal coloration.</p>
Data from: An island endemic born out of hybridization between introduced lineages
<p>Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human-mediated movement of individuals, either through translocation of individuals within their range or the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural versus human-mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographic patterns. Studies combining genetic data with archeological, linguistic, and historical evidence have confirmed prehistoric examples of human-mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (<em>Colinus virginianus</em>) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human-mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent introduced lineages.</p>
Figure 2 in Multiple resistance to primary pests of grain sorghum hybrids: Spodoptera frugiperda (Lepidoptera: Noctuidae), Diatraea saccharalis (Lepidoptera: Crambidae), and Diceraeus melacanthus (Hemiptera: Pentatomidae)
Figure 2 Dendrogram of cluster analysis based on the Euclidean distance and grouping by UPGMA regarding scores of damage by Spodoptera frugiperda larvae on grain sorghum hybrids at 7 and 14 days after infestation.
Figure 5 in Multiple resistance to primary pests of grain sorghum hybrids: Spodoptera frugiperda (Lepidoptera: Noctuidae), Diatraea saccharalis (Lepidoptera: Crambidae), and Diceraeus melacanthus (Hemiptera: Pentatomidae)
Figure 5 Scores of injury on sorghum plants caused by S. frugiperda (a); D. saccharalis (b); and D. melacanthus (c).
Figure 1 in Multiple resistance to primary pests of grain sorghum hybrids: Spodoptera frugiperda (Lepidoptera: Noctuidae), Diatraea saccharalis (Lepidoptera: Crambidae), and Diceraeus melacanthus (Hemiptera: Pentatomidae)
Figure 1 Green-belly stink bug injury based on the damage rating scale adapted by Roza-Gomes et al. (2011) (0-4) to maize injury.
Data for First-Order Quantum Phase Transition in the Hybrid Metal-Mott Insulator Transition Metal Dichalcogenide 4Hb-TaS2
<p>Data to reproduce the main text figures of the paper "First-Order Quantum Phase Transition in the Hybrid<br> Metal-Mott Insulator Transition Metal Dichalcogenide 4Hb-TaS2" are provided. They are either in the *.txt format or *.fig (matlab figure) format. The *.txt files contain the relevant header information.</p>
Genotype, phenotype and linkage data for Mimulus parishii x M. cardinalis hybrid incompatibility study
<p>The evolution of genomic incompatibilities causing postzygotic barriers to hybridization is a key step in species divergence. Incompatibilities take two general forms – structural divergence between chromosomes leading to severe hybrid sterility in F<sub>1</sub> hybrids and epistatic interactions between genes causing reduced fitness of hybrid gametes or zygotes (Dobzhansky-Muller incompatibilities). Despite substantial recent progress in understanding the molecular mechanisms and evolutionary origins of both types of incompatibility, how each behaves across multiple generations of hybridization remains relatively unexplored. Here, we use genetic mapping in F<sub>2</sub> and RIL hybrid populations between the phenotypically divergent but naturally hybridizing monkeyflowers <em>Mimulus cardinalis</em> and <em>M. parishii</em> to characterize the genetic basis of hybrid incompatibility and examine its changing effects over multiple generations of experimental hybridization. In F<sub>2</sub>s, we found severe hybrid pollen inviability (< 50% reduction vs. parental genotypes) and pseudolinkage caused by a reciprocal translocation between Chromosomes 6 and 7 in the parental species. RILs retained excess heterozygosity around the translocation breakpoints, which caused substantial pollen inviability when interstitial crossovers had not created compatible heterokaryotypic configurations. Strong transmission ratio distortion and inter-chromosomal linkage disequilibrium in both F<sub>2</sub>s and RILs identified a novel two-locus genic incompatibility causing sex-independent gametophytic (haploid) lethality. The latter interaction eliminated three of the expected nine F<sub>2</sub> genotypic classes via F<sub>1</sub> gamete loss without detectable effects on the pollen number or viability of F<sub>2</sub> double heterozygotes. Along with the mapping of numerous milder incompatibilities, these key findings illuminate the complex genetics of plant hybrid breakdown and are an important step toward understanding the genomic consequences of natural hybridization in this model system.</p>
Single-molecule Fluorescent In Situ Hybridization (smFISH) for RNA detection in the fungal pathogen Candida albicans dataset
<p><strong>This dataset is connected to the protocol article titled:</strong></p> <p>Single-molecule Fluorescent <em>In Situ</em> Hybridization (smFISH) for RNA detection in the fungal pathogen <em>Candida albicans</em></p> <p><strong>Abstract:</strong></p> <p><em>Candida albicans</em> is the most prevalent human fungal pathogen. Its pathogenicity is linked to the ability of <em>C. albicans</em> to reversibly change morphology and to grow as yeast, pseudohyphal or hyphal cells in response to environmental stimuli. Understanding the molecular regulation controlling those morphological switches remains a challenge that, if solved, could help fight <em>C. albicans</em> infections.</p> <p>While numerous studies investigated gene expression changes occurring during <em>C. albicans</em> morphological switches using bulk approaches (e.g., RNA sequencing), here we describe a single-cell and single-molecule RNA imaging and analysis protocol to measure absolute mRNA counts in morphologically intact cells. To detect endogenous mRNAs in single fixed cells, we optimized a single molecule fluorescent <em>in situ</em> hybridization (smFISH) protocol for <em>C. albicans</em>, which allows one to quantify the differential expression of mRNAs in yeast, pseudohyphae or hyphal cells. We quantified the expression of two mRNAs, cell cycle-controlled mRNA (<em>CLB2)</em> and a transcription regulator (<em>EFG1</em>), which show differential expression in the different morphological cell types and in different nutrient conditions. In this protocol we described in detail the major steps of this approach: growth and fixation, hybridization, imaging, cell-segmentation and mRNA spot analysis. Raw data is provided with the protocol to favour reproducibility. This approach could benefit the molecular characterization of <em>C. albicans</em> and other filamentous fungi, pathogenic or non-pathogenic.</p> <p><strong>Data description:</strong></p> <p>This dataset consists of a FISH experiment spanning two different mRNAs, EFG1 and CLB2, and two different nutrient condition, being SPIDER37 and TSB37 in Candida albicans. For culturing, the C. albicans wildtype strain SC5314 was inoculated at 30 degrees overnight (~15 hours) in 10 mL of TSB medium in a 30 degree (celsius) shaking incubator. Next, samples were diluted to a density of 10^5 cells/ mL and inoculated for 6 hours in either 30 mL TSB medium or Spider medium at 37 degrees in falcon tubes on an orbital microplate shaker. Then, samples were fixated by adding PFA to a final concentration of 4% to the medium. For hybridization, both mRNAs were hybridized independently by specific DNA oligo labelled with a Quasar670 dye to enable the visualisation of single mRNA molecules. As both genes are labelled by the same dye, these oligos were not co-applied to the same sample but to independent samples.</p> <p><strong>Microscopy</strong></p> <p>For smFISH imaging we use an Olympus BX-63 epifluorescence microscope equipped with Ultrasonic stage and UPlanApo 100x 1.35NA oil-immersion objective (Olympus). Lumencore SOLA FISH light source, a Hamamatsu ORCA-Fusion sCMOS camera (6.5 µm-pixel size) mounted using U-CMT C-Mount Adapter, and zero-pixel shift filter sets: F36-500 DAPI HC Brightline Bandpass Filter, F36-502 FITC HC BrightLine Filter, F36-542 Cy3 HC BrightLine Filter, and F36-523 Cy5 HC BrightLine Filter. Images are acquired across 61-81 optical sections (depending on the sample thickness) with a z-step size of 0.2 μm. The CellSens software (Olympus) is used for instrument control and image acquisition. For the DAPI channel 10-50 ms of exposure was used. Whilst, for the CY5 channel, used imaging the FISH probes, 750 ms was applied. </p> <p> </p>
ScienceDex guides
Understand access before you commit
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.