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This repository contains data generated in the wet lab need for characterization and validation of strain specific GEMs

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License: MIT ZENODO DOI Frontiers DOI

C_striatum_wetlab

This repository contains data generated in the wet lab needed for characterization and validation of strain specific GEMs

Folder structure

  • binary_growth_phenotypes contains data, code and analysis of binary growth phenotype experiments
  • growth_kinetics contains data, code and analysis of plate reader experiments for growth curves
  • supporting_experiments contains data, code and analysis of other experiments (OD-CFU, manual growth curves)

About Corynebacterium striatum

Corynebacterium striatum, a gram-positive and non-sporulating rod, has recently been discovered for its pathogenic properties. Even though it has been known since the early 20th cen- tury, C.striatum was often disregarded as a pathogen since it is part of the typical human skin microbiota1. Nevertheless, it was found that, especially in immunocompromised patients, C.striatum can be the source for diseases such as Chronic Obstructive Pulmonary Disease, also known as COPD or pneumonia2. Not only is C. striatum active within the respiratory tract, but it was also attributed to long-standing open wound infections3 and prolonged hospitalizations4.

How to cite

Famke Bäuerle, Gwendolyn O. Döbel, Laura Camus, Simon Heilbronner, and Andreas Dräger. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum. Front. Bioinform., oct 2023. doi:10.3389/fbinf.2023.1214074.

Conversion of jupyter notebooks

We can convert jupyter notebooks to other formats. Use this command to convert to a pdf that can be included in the thesis: jupyter nbconvert --to pdf plate_reader_curves.ipynb --output-dir '/Users/baeuerle/Organisation/Masterarbeit/thesis/files/jupyter_nb' --template=classic.tplx

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This repository contains data generated in the wet lab need for characterization and validation of strain specific GEMs

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