Biology subjects

Braisted, J.

Publications and source records attributed to Braisted, J..

4 recordsLinked to original sources

bioRxiv2026

CalFluxTools: An R package for analysis of high-throughput calcium oscillation screening data

Whole plate detection of calcium flux signals using fluorescence is a powerful technology for monitoring oscillatory activity of excitable cells in a high throughput fashion that sees broad applications in neurotoxicity and cardiotoxicity research. However, analysis of calcium oscillation profiles can output more than 60 peak kinetic parameters, which makes manual data analysis challenging. We have created the CalFluxTools R package, an automated pipeline for parsing plate data for 384 well plates, generating quality control metrics and plots, and performing data analysis, including T-tests, Z-score analysis, and machine learning prediction of compound toxicity values. CalFluxTools requires a plate map and experimental manifest that includes parameter filtration specifications, as well as data in the ".statall" format. CalFluxTools runs in less than a minute on a Macbook Pro with a 2.6 GHz 6-Core Intel Core i7 processor.

bioinformatics↗

bioRxiv2022

Enhancing the Fitness of Embryoid Bodies and Organoids by Chemical Cytoprotection

Embryoid bodies (EBs) and self-organizing organoids derived from human pluripotent stem cells (hPSCs) recapitulate tissue development in a dish and hold great promise for disease modeling and drug development. However, current protocols are hampered by cellular stress and apoptosis during cell aggregation, resulting in variability and impaired cell differentiation. Here, we demonstrate that EBs and various organoid models (e.g., brain, gut, and kidney) can be optimized by using the CEPT small molecule cocktail, a polypharmacology approach that ensures cytoprotection and cell survival. Application of CEPT (chroman 1, emricasan, polyamines, trans-ISRIB) for just 24 hours during cell aggregation has long-lasting consequences affecting morphogenesis, gene expression, and cellular differentiation. Various qualification methods confirmed that CEPT treatment consistently improved EB and organoid fitness as compared to the widely used ROCK inhibitor Y-27632. Collectively, we discovered that stress-free cell aggregation and superior cell survival in the presence of CEPT are critical quality control determinants that establish a robust foundation for bioengineering complex tissue and organ models.

developmental biology↗

bioRxiv2022

RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites

RaMP-DB 2.0 is a web interface, API, relational database and R package designed for straightforward and comprehensive functional interpretation of metabolomic and multi-omic data. Since its first release in 2018, RaMP-DB 2.0 has been upgraded with an expanded breadth and depth of functional and chemical annotation. Content from the source databases (Reactome, HMDB, and Wikipathways) has been updated, and new data types related to metabolite annotations have been incorporated. Structural information incorporated in RaMP-DB 2.0 includes SMILES strings, InChIs, InChIKeys. Chemical classes have been sourced from ClassyFire and LIPID MAPS. Accordingly, the RaMP-DB 2.0 R package has been updated and supports queries on pathways, common reactions, ontologies, chemical classes, and chemical structures. Additionally, RaMP-DB 2.0 now supports enrichment analyses on pathways and chemical classes. Our process for integrating annotations across resources has also been upgraded to lessen the burden of harmonization, thereby supporting more frequent updates. The code used to build all components of RaMP-DB 2.0 is freely available on GitHub at https://github.com/ncats/ramp-db and https://github.com/ncats/RaMP-Backend.

bioinformatics↗

bioRxiv2020

Robotic High-Throughput Biomanufacturing and Functional Differentiation of Human Pluripotent Stem Cells

Efficient translation of human induced pluripotent stem cells (hiPSCs) depends on implementing scalable cell manufacturing strategies that ensure optimal self-renewal and functional differentiation. Currently, manual culture of hiPSCs is highly variable and labor-intensive posing significant challenges for high-throughput applications. Here, we established a robotic platform and automated all essential steps of hiPSC culture and differentiation under chemically defined conditions. This streamlined approach allowed rapid and standardized manufacturing of billions of hiPSCs that can be produced in parallel from up to 90 different patient-and disease-specific cell lines. Moreover, we established automated multi-lineage differentiation to generate primary embryonic germ layers and more mature phenotypes such as neurons, cardiomyocytes, and hepatocytes. To validate our approach, we carefully compared robotic and manual cell culture and performed molecular and functional cell characterizations (e.g. bulk culture and single-cell transcriptomics, mass cytometry, metabolism, electrophysiology, Zika virus experiments) in order to benchmark industrial-scale cell culture operations towards building an integrated platform for efficient cell manufacturing for disease modeling, drug screening, and cell therapy. Combining stem cell-based models and non-stop robotic cell culture may become a powerful strategy to increase scientific rigor and productivity, which are particularly important during public health emergencies (e.g. opioid crisis, COVID-19 pandemic).

bioengineering↗