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4,004 results for “In vivo”
Enzyme-like nanoparticle engineered-mesenchymal stem cell secreting HGF promotes visualized therapy for idiopathic pulmonary fibrosis in vivo
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Data from: In vivo functional phenotypes from a computational epistatic model of evolution
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Data from: In vitro to in vivo extrapolation from three-dimensional hiPSC-derived cardiac microtissues and physiologically based pharmacokinetic modeling to inform next-generation arrythmia risk assessment
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An in vivo microscopy dataset of immune cells for the characterization of apoptotic cell death
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Transcranial detection of amyloid-beta at single plaque resolution in vivo with large-field multifocal illumination fluorescence microscopy
<p>The abnormal deposition of beta-amyloid proteins in the brain is one of the major histopathological hallmarks of Alzheimer’s disease. Currently available intravital microscopy techniques can visualize plaques with high resolution, but are limited to a small field-of-view and with depth limitation. Here, we report the transcranial detection of amyloid-beta deposits at the whole brain scale with 20 mm resolution in APP/PS1 and arcAb mouse models of Alzheimer’s disease amyloidosis using a novel large-field multifocal illumination (LMI) fluorescence microscopy technique. High sensitive and specific detection of amyloid-beta deposits at single plaque level in APP/PS1 and arcAb mice was facilitated using luminescent conjugated oligothiophene HS-169. Immunohistochemical staining with HS-169, anti-Ab antibody 6E10, conformation antibodies OC (fibrillar) on brain tissue sections further showed that HS-169 resolved compact parenchymal and vessel-associated amyloid deposits. In conclusion, we demonstrate a new <em>in vivo </em>imaging platform for detection of amyloid-beta deposits at single plaque resolution in murine models of Alzheimer’s disease amyloidosis.</p>
Tandem Tag Assay Optimized for Semi-automated in vivo Autophagic Activity Measurement in Arabidopsis thaliana roots
<p>This is demo data set for AuTToFlux, the semi-automated assay for <em>in vivo</em> autophagic activity measurement in <em>Arabidopsis thaliana</em> roots.</p> <p>The protocol and software required for the assay are available here: <a href="https://github.com/jonasoh/AuTToFlux">https://github.com/jonasoh/AuTToFlux</a></p>
Sample data for analysis of period/frequency gradient and phase gradient in spreadouts, ex vivo models of somitogenesis
<p>Here are timelapse imaging (as .tif) of a dynamic Notch signaling reporter (i.e. LuVeLu) in spreadouts, ex vivo models of somitogenesis. Also here are the corresponding period and phase wavelet movies, generated using a wavelet analysis workflow developed by Gregor Mönke. These sample data are used to run an accompanying Python script, available at: <a href="https://github.com/PGLSanchez/EMBL_OscillationsAnalysis/tree/master/FrequencyPhase_GradientSlopeAnalysis">https://github.com/PGLSanchez/EMBL_OscillationsAnalysis/tree/master/FrequencyPhase_GradientSlopeAnalysis</a></p>
In-house 3-D printed aligners: effect of in vivo ageing on mechanical properties
<p>Dataset for all analyses in the paper.</p>
In vivo microbial coevolution favours host protection and plastic downregulation of immunity
<p>Microbiota can protect their hosts from infection. The short timescales in which microbes can evolve presents the possibility that 'protective microbes' can take-over from the immune system of longer-lived hosts in the coevolutionary race against pathogens. Here, we found that coevolution between a protective bacterium (<em>Enterococcus faecalis</em>) and a virulent pathogen (<em>Staphylococcus aureus</em>) within an animal population (<em>Caenorhabditis elegans</em>) resulted in more disease suppression than when the protective bacterium adapted to uninfected hosts. At the same time, more protective <em>E. faecalis </em>populations became costlier to harbour and altered the expression of 134 host genes. Many of these genes appear to be related to the mechanism of protection, reactive oxygen species production. Crucially, more protective <em>E. faecalis</em> populations downregulated a key immune gene, <em>sodh-1</em>, known to be effective against <em>S. aureus</em> infection. These results suggest that a microbial line of defence is favoured by microbial coevolution and may cause hosts to plastically divest of their own immunity.</p>
Labeling and tracking of immune cells in ex vivo human skin
<p>Example imaging datasets linked to the publication 'Labeling and tracking of immune cells in ex vivo human skin' (doi: 10.1038/s41596-020-00435-8).</p> <p>Additional information filenames:<br> - m = ex vivo murine skin<br> - h = ex vivo human skin<br> - mCD8= anti-murine CD8-AF594 nanobody staining (red)<br> - hCD8= anti-human CD8-AF594 nanobody staining (red)<br> - Hoechst= Hoechst 33342 staining (grey)<br> - CD1a= anti-hCD1a-AF488 staining (green)<br> - CD103= anti-hCD103-AF488 staining (green)<br> - SHG = second harmonic generation (cyan)</p> <p>Imaris x64 v9.2.0.</p>
Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells
<p>Single cell gene expression data for the paper "Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells" to appear in PLOS Pathogens.</p> <p>Package contains two single cell data sets, one consisting of single cells from PBMCs in three animals, and the other three tissues from one animal.</p> <p>The single-cells are grouped based on the SIV viral genes that they express.</p> <p> </p>
Dataset for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."
<p>Plasmid sequences for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."</p>
Accumulation of 3-aminopropylphosphonate in the ex vivo brain observed by phosphorus-31 nuclear magnetic resonance
<p>This dataset contains primary data for DOI: 10.1002/nbm.4721</p><p>NMR in Biomedicine. 2022; 35(8):e4721</p><p>Title: Accumulation of 3-aminopropylphosphonate in the ex vivo brain observed by phosphorus-31 nuclear magnetic resonance</p><p>Authors: David Shaul, Benjamin Grieb, Naama Lev-Cohain, Jacob Sosna, J. Moshe Gomori, Rachel Katz-Brull</p><p> </p><p>These primary datasets contain data presented in the above publication and consist of 31P-NMR spectra. </p><p> </p><p>Please consult the Archive Guide.</p>
Data from: Illuminating T cell-dendritic cell interactions in vivo by FlAsHing antigens
<p>Delineating the complex network of interactions between antigen-specific T cells and antigen presenting cells (APCs) is crucial for effective precision therapies against cancer, chronic infections, and autoimmunity. However, the existing arsenal for examining antigen-specific T cell interactions is restricted to a select few antigen-T cell receptor pairs, with limited in situ utility. This lack of versatility is largely due to the disruptive effects of reagents on the immune synapse, which hinder real-time monitoring of antigen-specific interactions. To address this limitation, we have developed a novel and versatile immune monitoring strategy by adding a short cysteine-rich tag to antigenic peptides that emits fluorescence upon binding to thiol-reactive biarsenical hairpin compounds. Our findings demonstrate the specificity and durability of the novel antigen-targeting probes during dynamic immune monitoring in vitro and in vivo. This strategy opens new avenues for biological validation of T-cell receptors with newly identified epitopes by revealing the behavior of previously unrecognized antigen-receptor pairs, expanding our understanding of T cell responses.</p>
Dataset of "Optical Signatures of Thermal Damage on ex-vivo Brain, Lung and Heart Tissues using Time-Domain Diffuse Optical Spectroscopy"
<p>Dataset for the article entitled "Optical Signatures of Thermal Damage on ex-vivo Brain, Lung and Heart Tissues using Time-Domain Diffuse Optical Spectroscopy" </p> <p> </p> <p>Abstract:</p> <p> </p> <p>Thermal Therapies treat tumors by means of heat, greatly reducing pain, post-operation complications, and cost as compared to traditional methods. Yet, effective tools to avoid under- or over-treatment are mostly needed, to guide surgeons in laparoscopic interventions.<br>In this work, we investigated the temperature-dependent optical signatures of ex-vivo calf brain, lung, and heart tissues, based on the reduced scattering and absorption coefficients in the near-infrared spectral range (657 to 1107 nm). These spectra were measured by time domain diffuse optics, applying a step-like spatially homogeneous thermal treatment at 43 °C, 60 °C, and 80 °C.<br>We found three main increases in scattering spectra, possibly due to the denaturation of collagen, myosin, and proteins secondary structure.<br>After 75 °C, we found the rise of two new peaks at 770 and 830 nm in the absorption spectra due to the formation of a new chromophore, possibly related to hemoglobin or myoglobin.<br>This research marks a significant step forward in controlling thermal therapies with diffuse optical techniques by identifying several key markers of thermal damage. This could enhance the ability to monitor and adjust treatment in real-time, promising improved outcomes in tumor therapy.</p> <p> </p> <p> </p> <p>Authors:</p> <p>ALESSANDRO BOSSI , LEONARDO BIANCHI , PAOLA SACCOMANDI , AND ANTONIO PIFFERI<br>Politecnico di Milano</p> <p> </p> <p> </p> <p><a href="https://opg.optica.org/boe/fulltext.cfm?uri=boe-15-4-2481&id=548108" target="_blank" rel="noopener">Link to the article</a></p>
Multi-level in vivo selection of the biocontrol agent Akanthomyces muscarius, virulence, growth, sporulation, and variant data
<p>Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. Theoretically, selection across different spatial scales, i.e. between- and within-hosts, shapes these trade-offs. However, trade-offs are also dependent on parasite biology. Despite their applied importance the evolution of virulence in fungal parasites is poorly understood: virulence can be unstable in culture and commonly fails to increase in simple passage experiments. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, <em>Akanthomyces muscarius</em>. Starting with a genetically diverse stock we selected for speed of kill, parasite yield, or infectivity by manipulating competition within and between hosts and between populations of hosts over 7 rounds of infection. We characterized ancestral and evolved lineages by whole genome sequencing and by measuring virulence, growth rate, sporulation, and fitness. While several lineages showed increases in virulence, we saw none of the trade-offs commonly found in obligately-killing parasites. Phenotypically similar lineages within treatments often shared multiple single-nucleotide variants, indicating strong convergent evolution. The most dramatic phenotypic changes were in the timing of sporulation and spore production <em>in vitro. </em>We found that early sporulation led to reduced competitive fitness but could increase the yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with the strongest between-population competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Multi-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits - virulence and spore production - that are often in conflict in other parasites.</p>
Data from: Self-amplifying RNA generated with the modified nucleotides 5-methylcytidine and 5-methyluridine mediate strong expression and immunogenicity in vivo
<p>When utilized in therapeutic applications, synthetic self-amplifying RNA can lead to higher and more sustained expression than standard messenger RNA. This feature is particularly important for gene replacement therapy applications where prolonged expression could reduce the dose and frequency of treatments. The inclusion of modified nucleotides in synthetic non-amplifying mRNA has been shown to increase RNA stability, reduce immune activation and enhance gene expression. Preclinical and clinical studies with self-amplifying RNA (saRNA) have so far exclusively relied on RNA containing the canonical nucleotides adenosine, cytidine, guanosine and uridine. For the first time, we show that non-canonical nucleotides, such as m5C and m5U, are sufficiently compatible with a replicon derived from Venezuelan equine encephalitis alphavirus mediating protein translation <em>in vitro</em>, while those containing m1ψ in place of uridine show no detectable expression. When administered <em>in vivo</em>, saRNA generated with m5C or m5U mediate sustained gene expression of the luciferase reporter gene with those incorporating m5U appearing to lead to more prolonged expression. Finally, distinct antigen-specific humoral and cellular immune responses were induced by modified saRNA encoding the model antigen ovalbumin. The use of modified nucleotides with saRNA-based platforms could enhance their potential to be used effectively in a variety of applications.</p>
Raman spectra from "Discrimination of immune cell activation using Raman micro-spectroscopy in an in-vitro & ex-vivo model"
<p>The uploaded files are data from Chaudhary et al, 2021 (Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Discrimination of immune cell activation using Raman micro-spectroscopy in an in-vitro & ex-vivo model, https://doi.org/10.1016/j.saa.2020.119118).</p> <p>There are two files in .mat format. In one (Preprocessed.mat) the data has been completely pre-processed according to the methods described in the paper.</p> <p>In the second (Unpreprocessed.mat) the data has been calibrated using the methods described in the paper, but has not received further pre-processing.</p> <p>Within both files there are datasets for the spectral measurement from each cell (‘spectra’), together with the treatment which was applied to each sample (‘treatment’) and the wavenumber at which the spectral measurements were made (‘wavenumber’).</p>
Dataset published in the article: "Electrospun poly(L-lactide-co-DL-lactide) nanofibrous scaffold as substrate for ex vivo limbal epithelial cell cultivation"
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Dynamic combinatorial optimization of in vitro and in vivo heparin antidotes
<p>This folder contains selected molecular dynamics simulations movies for the paper " Dynamic combinatorial optimization of <em>in vitro</em> and <em>in vivo</em> heparin antidotes"</p>
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.