Additional file 1 of Practical application of a Bayesian network approach to poultry epigenetics and stress

Additional file 1. Arcs and their corresponding probabilities of being part of a high scoring network.List of arcs identified between differentially methylated regions and with the stress condition, with their corresponding probabilities of being part of a high scoring network. The first column (“arc”) is an arbiratry numbering for the arc;the second column (“from”) represents the parent node for each arc (arcs from); the third column (“to”) represents the child node for each arc (arcs to); the third column (“Average.Probablity”) represents the average probability value for each arc of being part of a high scoring network

SYNBIOCHEM - Combinatorial plasmid libraries for material monomer production in Escherichia coli.

Combinatorial plasmid libraries for material monomer production in Escherichia coli. - Design of Experiments: To investigate the production of material monomer targets in E. coli, combinatorial plasmid libraries (carrying genes for enzyme steps in target biosynthetic pathways) were designed using a D-optimal design of experiments (DoE) approach. Varied factors include plasmid copy number (ColE1, p15a, BBR1 or SC101 origins of replication), promoter strength (Ptrc or PlacUV5 promoters), candidate gene selection, and sequential ordering of genes/promoters within the plasmid. Library sizes were selected in the range of 2-48 plasmids, depending on the number of factors and combinatorial space. The pdf file contains schematic illustrations of the plasmid libraries (Figures D1-18) along with DNA sequences of the PCR primers (Table D1) and bridging oligosaccharides (Table D2) required for LCR assembly of the libraries

SYNBIOCHEM Design-Build-Test-Learn pipeline

Quantified titers and peak values measured through different rounds of the SYNBIOCHEM Design-Build-Test-Learn (DBTL) pipeline for microbial production of fine chemicals. The pipeline was applied for the production of flavonoids and alkaloids in Escherichia coli. The flavonoids data contains cinnamate and (2S)-pinocembrin measurements for combinatorial libraries for: a) DBT round 1; b) DBT round 2; c) Chassis selection; d) Media screening; e) Optimization. The alkaloids data provides (S)-reticuline and (S)-scoulerine measurements for a combinatorial library corresponding to one DBTL round