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Table 4 Designs for expression profiling of Y. pestis

From: Comparative transcriptomics in Yersinia pestis: a global view of environmental modulation of gene expression

Environmental perturbation

Description

Reference (s)

Stimulon analysis

  

   Temperature shift

 

[8, 9]

Vegetative growth temperatures

Shift from 26°C to 37°C for 3 hr

 

Heat shock

Shift from 37°C to 45°C for 10 min

 

Cold shock

Shift from 37°C to 10°C for 1 hr

 

   Osmotic stress

 

[10]

High osmolarity

Treatment with 0.5 M sorbitol for 20 min

 

High salinity

Treatment with 0.5 M NaCl for 20 min

 

   Oxidative stress

Treatment with 1 mM H2O2 for 30 min at 26°C

 

   Mild acid stress

Shift from pH7.2 to pH 5.5 for 10 min

 

   Low Mg2+

Growth under 10 μM Mg2+

[15]

   Iron starvation

Treatment with 100 μM of 2, 2'-dipyridyl for 30 min

[11]

26°C

26°C cell cultures

 

37°C

37°C cell cultures

 

   Minimal versus rich medium

TMH versus BHI medium

 

Exponential phase

Growth to an A620 nm of approximately 0.8

 

Stationary phase

Growth to an A620 nm of approximately 2.0

 

   Growth phase

Exponential versus stationary phase

 

Minimum medium

Growth in TMH medium

 

Rich medium

Growth in BHI medium

 

   Antibiotics treatment

10× MIC concentration of antibiotics for 30 min

 

Streptomycin

37°C cell cultures

[12]

chloramphenicol

37°C cell cultures

 

Tetracycline

37°C cell cultures

 

Antibacterial peptide

26°C cell cultures

 

Regulon analysis

  

   PhoP regulon

phoP mutant versus Wide-type (WT) strain

 

pH5.5

Growth at pH5.5

 

Low Mg2+

Growth under 10 μM Mg2+

[15]

   Fur regulon

fur mutant versus WT strain

[11]

26°C

26°C cell cultures with addition of 40 μM of FeCl3 for 30 min

 

37°C

37°C cell cultures with addition of 40 μM of FeCl3 for 30 min

 

   OxyR regulon

oxyR mutant versus WT strain upon exposure to 1 mM H2O2 for 30 min at 26°C

 

   OmpR regulon

ompR mutant versus WT strain

 

High osmolarity

Upon exposure to 0.5 M sorbitol for 20 min

 

High salinity

Upon exposure to 0.5 M NaCl for 20 min

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