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4,004 results for “In vivo”
Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup
<p>Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a Line Weaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when single-copy plasmid-borne, shown to be impervious to Gyrase inhibition. Next, we estimate the fraction of time in locked states and number of transcription events prior to locking, which we validate by measurements under Gyrase inhibition. Replacing the gene of interest by one with slower transcription rate decreases the fraction of time in locked states due to PSB. Finally, we combine data from both constructs to infer a range of possible transcription initiation locking kinetics in a chromosomal location, obtainable by tuning the transcription rate. We validate with measurements of transcription activity at different induction levels. This strategy for dissecting transcription initiation locking kinetics due to PSB can contribute to resolve the transcriptional programs of E. coli and in the engineering of synthetic genetic circuits.</p>
In vivo transcriptome of Lactobacillus acidophilus and colonization impact on murine host intestinal gene expression
<p><i>Lactobacillus acidophilus </i>NCFM is a probiotic strain commonly used in dairy products and dietary supplements. Post-genome <i>in vitro </i>studies of NCFM thus far have linked potential key genotypes to its probiotic-relevant attributes including gut survival, prebiotic utilization, host interactions and immunomodulatory activities. To corroborate and extend beyond previous <i>in vivo and</i> <i>in vitro </i>functional studies, we employed a dual RNA-seq transcriptomic approach to identify genes potentially driving the gut fitness and activities of <i>L. acidophilus </i>NCFM<i> in vivo</i>, and in parallel, examine the ileal transcriptional response of its murine hosts during monocolonization. Spatial expression profiling of NCFM from the ileum through the colon revealed a set of 134 core genes that were consistently overexpressed during gut transit. These <i>in vivo </i>core genes are predominantly involved in the metabolism of carbohydrates, amino acids and nucleotides, along with mucus-binding proteins and adhesion factors, confirming their functionally important roles in nutrient acquisition and gut retention. Functional characterization of the highly expressed major S-layer encoding gene established its indispensable role as a cell shape determinant and maintenance of cell surface integrity, essential for viability and probiotic attributes. Host colonization by <i>L. acidophilus</i> resulted in significant down-regulation of several pro-inflammatory cytokines and tight junction proteins. Genes related to redox signaling, mucin glycosylation and circadian rhythm modulation were induced, suggesting impacts on intestinal development and immune functions. Metagenomic analysis of NCFM populations post-colonization demonstrated the genomic stability of <i>L. acidophilus </i>as a gut transient and further established its safety as a probiotic and biotherapeutic delivery platform.</p>
Nonresonant Raman spectroscopy of isolated human retina samples complying with laser safety regulations for in vivo measurements
<p>Raman raw data for the paper "Nonresonant Raman spectroscopy of isolated human retina samples complying with laser safety regulations for in vivo measurements"</p> <ul> <li>two sets of unprocessed Raman spectra recorded under restricted conditions as seen in Figure 5(b)</li> <li>each spectrum was recorded at 785 nm with 1 mW laser power and 10 s integration time</li> </ul>
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo
<p>Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine. We hypothesised that plasmid properties would be the primary determinants of plasmid spread and that bacterial strain identity would also contribute. We found clinical Escherichia coli strains natively associated with ESBL-plasmids conjugated to three distinct E. coli strains and one Salmonella enterica serovar Typhimurium strain. Final transconjugant frequencies varied across plasmid, donor, and recipient combinations, with qualitative consistency when comparing transfer in vitro and in vivo in mice. In both environments, transconjugant frequencies for these natural strains and plasmids covaried with the presence/absence of transfer genes on ESBL-plasmids and were affected by plasmid incompatibility. By moving ESBL-plasmids out of their native hosts, we showed that donor and recipient strains also modulated transconjugant frequencies. This suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.</p>
Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"
<p>Phase-contrast CT of BDL rats liver-8 week</p>
Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"
<p>Phase-contrast CT of BDL rats liver-6 week</p>
Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"
<p>Phase-contrast CT of BDL rats liver-control group</p>
Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"
<p>Phase-contrast CT of BDL rats liver-4 week</p>
Data from: Morphological, cellular and molecular evidences of chromosome random elimination in vivo upon haploid induction in maize
The mechanism of maternal in vivo haploid induction is not fully understood. In this study, the young embryos were identified by morphology, cytology and simple sequence repeat (SSR) markers at different developmental stages in the cross HZ514 (sweet corn) × HZI1 (inducer). The results indicated that the low seed setting rate was determined by the inducer pollen during the process of fertilization. The mosaic endosperm kernels and the different percentages of aneuploidy, mixploidy, lagged chromosome, micronuclei, chromosomal bridge and ring chromosome were found in the cross; 7.37% of the haploid embryos carried chromosome segments from HZI1. About 1% twin seedlings resulted from the cross and were analyzed by cytology and SSR markers. Four pairs of twin seedlings had different chromosome numbers (2n = 20 and 2n = 10–20) and there were some chromosome fragments from HZI1. Aneuploidy, mixploidy and the abnormal chromosomes occurred in the in vivo haploid induction by HZI1, which is the cytological basis for haploid induction and indicates that the inducer's chromosomes are prone to be lost during mitotic and meiotic divisions. Morphological, cellular and molecular evidences reveal that complete or partial chromosome elimination from inducer HZI1 controls the maize in vivo haploid induction.
Data from: Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus
Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of male sexual characteristics in the female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one of the most clearcut ecological examples of anthropogenically induced ED in aquatic ecosystems. To identify the underpinning mechanisms of imposex for this 'nonmodel' species, we combined Roche 454 pyrosequencing with custom oligoarray fabrication inexpensively to both generate gene models and identify those responding to chronic tributyltin (TBT) treatment. The results supported the involvement of steroid, neuroendocrine peptide hormone dysfunction and retinoid mechanisms, but suggested additionally the involvement of putative peroxisome proliferator–activated receptor (PPAR) pathways. Application of rosiglitazone, a well-known vertebrate PPARγ ligand, to dogwhelks induced imposex in the absence of TBT. Thus, while TBT-induced imposex is linked to the induction of many genes and has a complex phenotype, it is likely also to be driven by PPAR-responsive pathways, hitherto not described in invertebrates. Our findings provide further evidence for a common signalling pathway between invertebrate and vertebrate species that has previously been overlooked in the study of endocrine disruption.
Data from: Quantifying the effect of gape and morphology on bite force: biomechanical modeling and in vivo measurements in bats
Maximum bite force is an important metric of feeding performance that defines the dietary ecology of many vertebrates. In mammals, theoretical analyses and empirical studies suggest a trade-off between maximum bite force and gape at behavioural and evolutionary scales; in vivo bite force is expected to decrease at wide gapes, and cranial morphologies that enable high mechanical advantage are thought to have a lower ability to generate high bite forces at wide gapes, and vice versa. However, very few studies have confirmed these relationships in free-ranging mammals. This study uses an ecologically diverse sample of bats to document the variation in bite force with respect to gape angle, and applies three-dimensional models of the feeding apparatus to identify the major morphological and biomechanical predictors of the gape-bite force relationship. In vivo and model data corroborated that bite force decreases significantly at wide gapes across species, but there is substantial intraspecific variation in the data obtained from live bats. Results from biomechanical models, analysed within a phylogenetic framework, revealed that species with larger temporalis muscles, higher temporalis stretch factors and high mechanical advantages experience a steeper reduction in bite force with increasing gape. These trends are illustrated by short-faced durophagous frugivores. The results from this study suggest that gape-mediated changes in bite force can be explained both by behavioural effects and cranial morphology, and that these links are relevant for functional analyses of mammal dietary ecology.
Data from: In vivo tracking of dendritic cell using MRI reporter gene, ferritin
The noninvasive imaging of dendritic cells (DCs) migrated into lymph nodes (LNs) can provide helpful information on designing DCs-based immunotherapeutic strategies. This study is to investigate the influence of transduction of human ferritin heavy chain (FTH) and green fluorescence protein (GFP) genes on inherent properties of DCs, and the feasibility of FTH as a magnetic resonance imaging (MRI) reporter gene to track DCs migration into LNs. FTH-DCs were established by the introduction of FTH and GFP genes into the DC cell line (DC2.4) using lentivirus. The changes in the rate of MRI signal decay (R2*) resulting from FTH transduction were analyzed in cell phantoms as well as popliteal LN of mice after subcutaneous injection of those cells into hind limb foot pad by using a multiple gradient echo sequence on a 9.4 T MR scanner. The transduction of FTH and GFP did not influence the proliferation and migration abilities of DCs. The expression of co-stimulatory molecules (CD40, CD80 and CD86) in FTH-DCs was similar to that of DCs. FTH-DCs exhibited increased iron storage capacity, and displayed a significantly higher transverse relaxation rate (R2*) as compared to DCs in phantom. LNs with FTH-DCs exhibited negative contrast, leading to a high R2* in both in vivo and ex vivo T2*-weighted images compared to DCs. On histological analysis FTH-DCs migrated to the subcapsular sinus and the T cell zone of LN, where they highly expressed CD25 to bind and stimulate T cells. Our study addresses the feasibility of FTH as an MRI reporter gene to track DCs migration into LNs without alteration of their inherent properties. This study suggests that FTH-based MRI could be a useful technique to longitudinally monitor DCs and evaluate the therapeutic efficacy of DC-based vaccines.
Data associated with Cell Reports publication: Dura-Bernal, Griffith, et al. 2023, "Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics" (2/4)
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data for the following Cell Reports publication: <a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6">https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6</a></p><p>The source code for the associated A1 model and data analysis can be found here: <a href="https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data">https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data</a>.</p><p>All zip files should unzipped into a parent folder called /data inside the Github repository above.</p><p><strong>Important:</strong> Due to the Zenodo size limit, this dataset is split among 4 Zenodo uploads. This is upload <strong>2 out of 4</strong>. The other 3 uploads can be found at: </p><p>Upload 1/4: <a href="http://doi.org/10.5281/zenodo.10066993">http://doi.org/10.5281/zenodo.10066993</a> (https://zenodo.org/uploads/10066993)</p><p>Upload 3/4: <a href="http://doi.org/10.5281/zenodo.10071726">http://doi.org/10.5281/zenodo.10071726</a> (https://zenodo.org/uploads/10071726)</p><p>Upload 4/4: <a href="http://doi.org/10.5281/zenodo.10072277">http://doi.org/10.5281/zenodo.10072277</a> (https://zenodo.org/uploads/10072277)</p><p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
Data associated with Cell Reports publication: Dura-Bernal, Griffith, et al. 2023, "Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics" (3/4)
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data for the following Cell Reports publication: <a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6">https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6</a></p><p>The source code for the associated A1 model and data analysis can be found here: <a href="https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data">https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data</a>.</p><p>All zip files should unzipped into a parent folder called /data inside the Github repository above.</p><p><strong>Important:</strong> Due to the Zenodo size limit, this dataset is split among 4 Zenodo uploads. This is upload <strong>3 out of 4</strong>. The other 3 uploads can be found at: </p><p>Upload 1/4: <a href="http://doi.org/10.5281/zenodo.10066993">http://doi.org/10.5281/zenodo.10066993</a> (https://zenodo.org/uploads/10066993)</p><p>Upload 2/4: <a href="http://doi.org/10.5281/zenodo.10069553">http://doi.org/10.5281/zenodo.10069553</a> (https://zenodo.org/uploads/10069553)</p><p>Upload 4/4: <a href="http://doi.org/10.5281/zenodo.10072277">http://doi.org/10.5281/zenodo.10072277</a> (https://zenodo.org/uploads/10072277)</p><p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
Data associated with Cell Reports publication: Dura-Bernal, Griffith, et al. 2023, "Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics" (1/4)
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data for the following Cell Reports publication: <a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6">https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6</a></p><p>The source code for the associated A1 model and data analysis can be found here: <a href="https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data">https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data</a>.</p><p>All zip files should unzipped into a parent folder called /data inside the Github repository above.</p><p><strong>Important:</strong> Due to the Zenodo size limit, this dataset is split among 4 Zenodo uploads. This is upload <strong>1 out of 4</strong>. The other 3 uploads can be found at: </p><p>Upload 2/4: <a href="http://doi.org/10.5281/zenodo.10069553">http://doi.org/10.5281/zenodo.10069553</a> (https://zenodo.org/uploads/10069553)</p><p>Upload 3/4: <a href="http://doi.org/10.5281/zenodo.10071726">http://doi.org/10.5281/zenodo.10071726</a> (https://zenodo.org/uploads/10071726)</p><p>Upload 4/4: <a href="http://doi.org/10.5281/zenodo.10072277">http://doi.org/10.5281/zenodo.10072277</a> (https://zenodo.org/uploads/10072277)</p><p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
Data and code from "Nanoporous graphene-based thin-film microelectrodes for in vivo high-resolution neural recording and stimulation"
<p>Data and code for reproducing the main results of the paper "Nanoporous graphene-based thin-film microelectrodes for in vivo high-resolution neural recording and stimulation".</p>
Cardiac structure discontinuities revealed by ex-vivo microstructural characterization. A focus on the basal inferoseptal left ventricle region
<p>Data and materials regarding the submission of the paper. See Data Avaibility section and https://github.com/valeryozenne/Cardiac-Structure-Database for more information and code.</p>
Transcriptomic and spatial datasets of human ex vivo right atrial tissue in ischemic heart disease and heart failure
<p>This dataset contains raw counts and processed data and annotations for our transcriptomic and spatial dissection of human ex vivo right atrial tissue in ischemic heart disease and heart failure.</p> <p> </p> <p>snRNA.zip contains the snRNA-seq dataset for heart right atrial appendade and pericardial fluid.</p> <p>VISIUM.zip contains the Visium spatial transcriptomics data</p> <p>Molecular cartography.zip contains the Resolve Biosciences molecular cartography spatial transcriptomics data</p>
Fam134c and Fam134b shape axonal endoplasmic reticulum architecture in vivo
<p>Endoplasmic reticulum (ER) remodeling is vital for cellular organization. ER-phagy, a selective autophagy targeting ER, plays an important role in maintaining ER morphology and function. The FAM134 protein family, including FAM134A, FAM134B, and FAM134C, mediates ER-phagy. While FAM134B mutations are linked to hereditary sensory and autonomic neuropathy in humans, the physiological role of the other FAM134 proteins remains unknown. To address this, we investigated the roles of FAM134 proteins using single and combined knockouts (KOs) in mice. Single KO in young mice showed no major phenotypes, but combined <em>Fam134b</em> and <em>Fam134c</em> deletion (<em>Fam134b/c<sup>dKO</sup>)</em> led to rapid neuromuscular and somatosensory degeneration, resulting in premature death. <em>Fam134b/c<sup>dKO</sup></em> mice show rapid loss of motor and sensory axons in the peripheral nervous system. Long axons from <em>Fam134b/c<sup>dKO</sup></em> mice exhibited expanded tubular ER with a transverse ladder-like appearance, whereas no obvious abnormalities were observed in cortical ER. Our study unveils critical roles of FAM134C and FAM134B in the formation of tubular ER network in axons of both motor and sensory neurons.</p>
Salivary levels of eluents during InvisalignTM treatment with attachments: an in vivo preliminary investigation
<p>Dataset for all analyses.<br><br>Dataset initially made available to editor and peer-reviewers during the peer review phase. After acceptance, the dataset will be made openly available to all without any restrictions.</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.