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36 results for “tripartite”
Data from: Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription
<p>One of the widely used applications of the popular Cre-loxP method for targeted recombination is the permanent activation of marker genes, such as reporter genes or antibiotic resistance genes, by excision of a preceding transcriptional stop signal. The STOP cassette consists of three identical SV40-derived poly(A) signal repeats and is flanked by two loxP sites. We found that in addition to complete loxP-mediated recombination, limiting levels of the Cre recombinase also cause incomplete recombination of the STOP cassette. Partial recombination leads to the loss of only one or two of the three identical poly(A) repeats with recombination breakpoints always precisely matching the end/start of each poly(A) signal repeat without any relevant similarity to the canonical or known cryptic loxP sequences, suggesting that this type of Cre-mediated recombination is loxP-independent. Incomplete deletion of the STOP cassette results in partial read-through transcription, explaining at least some of the variability often observed in marker gene expression from an otherwise identical locus.</p>
The free-breathing motion-corrected phase sensitive inversion recovery sequence provides improved myocardial fibrosis evaluation while significantly shortening acquisition time upon comparison to conventional gradient echo sequences: a tripartite comparison of phase-sensitive inversion recovery sequences.
<p>This article includes original research performed at a US Academic Center related to comparison of three separate Phase-Sensitive Inversion Recovery (PSIR) pulse sequences (Breath-hold Single-Shot SFFP, Breath-hold TurboFLASH, and Free-breathing Motion-Corrected SSFP) evaluating the ability of each PSIR sequence to demonstrate myocardial hyperenhancement. All three PSIR sequences were performed as a part of a cardiac MRI performed on a patient clinically referred for cardiac MRI with and without contrast. A total of 28 patients were examined with the three PSIR sequences. All three PSIR sequences were performed in the short axis 10 – 25 minutes after intravenous injection of a Gadolinium-based contrast agent. </p> <p>Evaluation of the PSIR sequences ability to detect myocardial late gadolinium enhancement (LGE) was performed by a retrospective review by two blinded, experienced cardiovascular imagers. The review was a qualitative inspection that included grading by a 5-point Likert scale for the sequence’s ability to resist motion artifact, image resolution, ability to visualize hyperenhancement, and overall satisfaction. The number of myocardial segments demonstrating LGE was also quantitated, and the acquisition time of each PSIR sequence was performed.</p> <p>To our knowledge this is the first study that compares the 3 available PSIR LGE sequences with a specific attention to acquisition time (TA). Given our initial study resulted in the conclusion that the motion-corrected SSFP PSIR sequence was superior the the TurboFLASH Gradient Echo PSIR sequence in regards to evaluator grading and acquisition time efficiency.</p>
Data from: 'ILSM': A package to analyze the interconnection structure of tripartite interaction networks
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Data from: Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription
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Data from: Multitrophic assembly influences β-diversity across a tripartite system of flowering plants, bees, and bee-gut microbiomes
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Sequencing data and normalized counts for tripartite RNAseq of Drosophila, Wolbachia, and SINV virus
<p><span><i>Wolbachia</i> is a maternally transmitted bacterium that manipulates arthropod and nematode biology in myriad ways. The <i>Wolbachia</i> strain colonizing <i>Drosophila melanogaster</i> creates sperm-egg incompatibilities and protects its host against RNA viruses, making it a promising tool for vector control. Despite successful trials using <i>Wolbachia</i>-transfected mosquitoes for Dengue control, knowledge of how <i>Wolbachia</i> and viruses jointly affect insect biology remains limited. Using the <i>Drosophila melanogaster </i>model, transcriptomics and gene expression network analyses revealed pathways with altered expression and splicing due to <i>Wolbachia</i> colonization and virus infection. Included are metabolic pathways previously unknown to be important for <i>Wolbachia</i>-host interactions. Additionally, <i>Wolbachia</i>-colonized flies exhibit a dampened transcriptomic response to virus infection, consistent with early blocking of virus replication. Finally, using <i>Drosophila</i> genetics, we show <i>Wolbachia</i> and expression of nucleotide metabolism genes have interactive effects on virus replication. Understanding the mechanisms of pathogen blocking will contribute to the effective development of <i>Wolbachia</i>-mediated vector control programs.</span></p>
Tripartite quantum Rabi model with trapped Rydberg ions data
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Molecular dynamics simulations of the tripartite interface (Syt1_C2B—SNARE—Cpx Complex)
<p>Synaptic transmission is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon an action potential. Critical to this process are the neuronal SNAREs (Soluble N-ethylmaleimide sensitive factor Attachment protein REceptor), the Ca2+-sensor synaptotagmin, the activator/regulator complexin, and other factors. Here we present the data for molecular dynamics simulations of the tripartite interface bewteen these proteins. </p>
Tripartite International Research for the Elimination of Trachoma
ClinicalTrials.gov study NCT01202331. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria and mycorrhizal fungi
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Tripartite symbioses regulate plant-soil feedback in alder
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Molecular dynamics simulations of the tripartite interface (Syt1_C2B—SNARE—Cpx Complex)
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Data from: Heritability of symbiont density reveals distinct regulatory mechanisms in a tripartite symbiosis
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Sequencing data and normalized counts for tripartite RNAseq of Drosophila, Wolbachia, and SINV virus
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Data from: Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction
Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities, bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here, we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage, SBW25φ2, and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions.
Supplementary material: Fundamental watersheds and altitudinal tripartition of the mountain cloud forests from Northwestern Argentina (Yungas)
<p>Vegetation zonation along the slopes of a mountain, from low to high altitude, is a well-known pattern in landscape ecology. A similar picture is also described in the field of freshwater ecology. Rivers and streams show different types of habitats between upland and downland site locations. We studied both segmentations of altitudinal gradient in a subtropical hotspot of biodiversity, namely the mountainous rainforest <span>of Yungas from Northwestern Argentina. We assessed the agreement between vegetation stratification (</span>fog grasslands, cloud montane forest and low montane rainforest<span>) and the tripartition of assemblages of mayflies (an ancient group of aquatic insects). The products we offer here accompany the paper of Biotropica entitled </span><em>The inter-forest line could be the master key to track biocoenotic effects of climate change in a subtropical forest</em>.</p> <p>We established a pair of altitudinal cutoffs in each of the watersheds from Argentinean Yungas. They correspond to the upper and lower limits of the middle layer, and they were obtained through an optimization task. The objective function was to maximize the overlap between the extent of such a middle layer and the area classified as cloud montane forest. The upper limit approaches to the treeline, whereas the lower limit is expected to fit the inter-forest line. Interestingly enough, assemblages of aquatic insects can be ordinated along altitudinal transects, but the main distinction occurs at either side of the hypothetical inter-forest line rather than the treeline. This finding is consistent throughout the study area. Map of the three altitudinal floors, as well as the different watersheds, are available as raster files. </p>
Data from: Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction
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Supplementary material: Fundamental watersheds and altitudinal tripartition of the mountain cloud forests from Northwestern Argentina (Yungas)
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Yeast Lachancea Kluyveri uses tripartite mechanism for haploid specific gene repression [RNA-seq]
GEO Series GSE221890. Lachancea kluyveri. 9 samples. Type: Expression profiling by high throughput sequencing.
Comparative Transcriptional Profiling of the Axolotl Limb Identifies a Tripartite Regeneration-Specific Gene Program
GEO Series GSE36451. Ambystoma mexicanum. 80 samples. Type: Expression profiling by array.
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.