Journal: Cell

Article Title: A white-box machine learning approach for revealing antibiotic mechanisms of action

doi: 10.1016/j.cell.2019.04.016

Figure Lengend Snippet: Key Resources Table

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Eschehchia coli K-12 MG1655 ATCC ATCC 700926 Chemicals, Peptides, and Recombinant Proteins 6-Mercaptopurine Sigma-Aldrich Cat# 852678-1G-A; CAS: 6112-76-1 13 C-Glucose Cambridge Isotope Laboratories, Inc. Cat# CLM-1396-1; CAS: 110187-42-3 Adenine Sigma-Aldrich Cat# A8626-5G; CAS: 73-24-5 Ampicillin Sigma-Aldrich Cat# A9518-5G; CAS: 69-52-3 Ciprofloxacin Sigma-Aldrich Cat# 17850-25G-F; CAS: 85721-33-1 Cytosine Sigma-Aldrich Cat# C3506-1G; CAS: 71-30-7 Gentamicin Sigma-Aldrich Cat# G1914-5G; CAS: 1405-41-0 Glutamine Sigma-Aldrich Cat# G8540-25G; CAS: 56-85-9 Guanine Sigma-Aldrich Cat# G11950-10G; CAS: 73-40-5 MOPS EZ Rich Defined Medium Kit Teknova Cat# M2105 MOPS Minimal Media Kit Teknova Cat# M2106 Phenotype Microarray 1 MicroPlate Biolog ( Bochner, 2009 ) Cat# 12111 Phenotype Microarray 2 MicroPlate Biolog ( Bochner, 2009 ) Cat# 12112 Phenotype Microarray 3 MicroPlate Biolog ( Bochner, 2009 ) Cat# 12121 Phenotype Microarray 4 MicroPlate Biolog ( Bochner, 2009 ) Cat# 12131 Phosphoribosyl pyrophosphate Sigma-Aldrich Cat# P8296-100MG; CAS: 108321-05-7 Thymine Sigma-Aldrich Cat# T0376-100G; CAS: 65-71-4 Trimethoprim Sigma-Aldrich Cat# T7883-5G; CAS: 738-70-5 Uracil Sigma-Aldrich Cat# U0750-100G; CAS: 66-22-8 Oligonucleotides See Table S9 This paper Software and Algorithms MATLAB 2018a Mathworks https://www.mathworks.com/ COBRA Toolbox v. 2.0 ( Schellenberger et al., 2011 ) https://opencobra.github.io/cobratoolbox/ Gurobi Optimizer v. 6.0.4 Gurobi Optimization http://www.gurobi.com/ optGpSampler ( Megchelenbrink et al., 2014 ) http://cs.ru.nl/~wmegchel/optGpSampler/ Spyder IDE v. 3.3.0 Spyder Project Contributors https://www.spyderide.org/ scikit-learn v. 0.17.0 ( Pedregosa et al., 2011 ) https://scikitlearn.org/ Ecocyc v. 22.0 ( Keseler et al., 2017 ) https://ecocyc.org/ Prism v. 8.0.2 GraphPad https://www.graphpad.com/ AB SCIEX MultiQuant v. 3.0.1 SCIEX https://sciex.com/products/software/multiquant-software Amelia II v. 1.7.4 ( Honaker et al., 2011 ) https://cran.r-project.org/web/packages/Amelia/index.html LMGene v. 3.3 ( Lu et al., 2008 ) http://www.bioconductor.org/packages/release/bioc/html/LMGene.html Open in a separate window Key Resources Table A white-box machine learning approach is developed for antibiotics research.

Techniques: Virus, Recombinant, Microarray, Software, Combined Bisulfite Restriction Analysis Assay

Journal: Microbial Cell Factories

Article Title: Low-mutation-rate, reduced-genome Escherichia coli : an improved host for faithful maintenance of engineered genetic constructs

doi: 10.1186/1475-2859-11-11

Figure Lengend Snippet: Doubling times of strains used in the study . Doubling times were measured in MOPS minimal medium at 37°C in microtiter plates (see methods). Error bars represent 95% confidence intervals for the average of 14 independent measurements. ANOVA revealed a significance of p < 0.005. Pairwise t-tests were conducted for each strain compared to the MDS42 strain, none of the strains showed a significant difference.

Article Snippet: Growth measurements were made in MOPS minimal defined medium (Scarab Genomics, Madison, Wisconsin, USA).

Techniques: