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4 results for “synthetic consortia”
Synthetic microbial consortia with programmable ecological interactions
<p>1. Central to the composition, structure and function of any microbial community is the complex species interaction web. But understanding the overwhelming complexity of ecological interaction webs has been challenging, owing at least partly to the lack of efficient tools for disentangling species interactions in natural or artificial microbial communities.</p> <p>2. In this study, we developed a microbial experimental system which allows for rapidly generating microbial consortia with programmable ecological interactions. We engineered the model organism Escherichia coli to construct metabolism- and quorum sensing-based modules. The two engineered modules were used to create synthetic microbial consortia of synergy, competition and exploitation.</p> <p>3. We showed that each of synthetic microbial consortia displayed the unique mode of population dynamics under certain initial inoculation conditions. We also demonstrated that the transitions between exploitation and the types of competition or synergy based on the same paired strains were plausible by tuning the two engineered modules. We lastly derived mathematical models to quantitatively capture the experimentally observed population dynamics of these synthetic microbial consortia.</p> <p>4. This approach offers a fresh angle to engineering microbial systems for experimentally testing ecological questions with a much greater control and manipulation.</p>
Synthetic microbial consortia with programmable ecological interactions
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FASTA 16s gene sequencing files for Control points for design of taxonomic composition in synthetic human gut consortia
<p>FASTA file output from Illumina MiSeq. Processed tally files (reads / species used to calculate relative abundances) are available in the other Zenodo repository listed in the key resources table, under ~ BC###/rawData/tallyfile.xlsx</p>
Code and processed data - Control points for design of taxonomic composition in synthetic human gut consortia
<p>Code, optical density data, and sequencing tally files (relative abundance from 16S sequencing of defined communities) for <strong>Control points for design of taxonomic composition in synthetic human gut consortia. </strong>Files are organized by experiment with a readme file contained within the .zip file. "Setup" folders have information about expeirmental design, "rawData" folders have optical density and tallyfiles, "analysis" folders have scripts used to analyze data and generate models. </p>
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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.