Difference between revisions of "PMID:11435407"

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(→‎Materials and Methods Used)
(Table edited by Azweifel via TableEdit)
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*abolished utilization of xylose as a C source
 
*abolished utilization of xylose as a C source
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*absent cellular respiration using xylose
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*no growth on xylose
 
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Metabolic Activity
 
Metabolic Activity
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*abolished utilization of maltose as a C source
 
*abolished utilization of maltose as a C source
−
*absent cellular respiration using maltose
+
*no growth on maltose
 
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Metabolic Activity
 
Metabolic Activity
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*abolished utilization of maltotriose as a C source
 
*abolished utilization of maltotriose as a C source
−
*absent cellular respiration using maltotriose
+
*no growth on maltotriose
 
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Metabolic Activity
 
Metabolic Activity
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*abolished utilization of L-arginine as a N source
 
*abolished utilization of L-arginine as a N source
−
 
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*no growth on L-arginine
 
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Metabolic Activity
 
Metabolic Activity
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*abolished utilization of ornithine as a N source
 
*abolished utilization of ornithine as a N source
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*no growth on ornithine
 
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Metabolic Activity
 
Metabolic Activity
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Figure 2  
 
Figure 2  
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''Escherichia coli''
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NCBI:83333
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 +
EP0005
 +
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 +
''malF3089::Tn10''
 +
|
 +
*abolished utilization of maltose as a C source
 +
*no growth on maltose
 +
|
 +
Metabolic Activity
 +
|
 +
Biolog phenotype microarray
 +
|
 +
Biochemical Assay
 +
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 +
Figure 3
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|-
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 +
''Escherichia coli''
 +
|
 +
NCBI:83333
 +
|
 +
EP0005
 +
|
 +
''malF3089::Tn10''
 +
|
 +
*abolished utilization of maltotriose as a C source
 +
*no growth on maltotriose
 +
|
 +
Metabolic Activity
 +
|
 +
Biolog phenotype microarray
 +
|
 +
Biochemical Assay
 +
|
 +
Figure 3
 +
|-
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 +
''Escherichia coli''
 +
|
 +
NCBI:83333
 +
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 +
EP0007
 +
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 +
del-''cya1400::kan''
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 +
*abolished utilization of secondary carbon sources
 +
*no growth on secondary C sources
 +
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 +
Metabolic Activity
 +
|
 +
Biolog phenotype microarray
 +
|
 +
Biochemical Assay
 +
|
 +
Figure 4- see for a list 
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|-
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''Escherichia coli''
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 +
NCBI:83333
 +
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 +
EP0012
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''fruR::Tn5''
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 +
*increased utilization of some C sources
 +
*decreased utilization of some C sources
 +
|
 +
Metabolic Activity
 +
|
 +
Biolog phenotype microarray
 +
|
 +
Biochemical Assay
 +
|
 +
Figure 5- see for a list 
 +
|-
 +
|
 +
''Escherichia coli''
 +
|
 +
NCBI:83333
 +
|
 +
EP0007
 +
|
 +
del-''cya1400::kan''
 +
|
 +
*abolished utilization of pyruvate
 +
*no growth on pyruvate
 +
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 +
Metabolic Activity
 +
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 +
Biolog phenotype microarray
 +
|
 +
Biochemical Assay
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|
 +
Figure 4- as a result, this strain gave negative results on the EN, EPS, and EA arrays
  
 
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Revision as of 14:08, 29 April 2011

Citation

Bochner, BR, Gadzinski, P and Panomitros, E (2001) Phenotype microarrays for high-throughput phenotypic testing and assay of gene function.Genome Res. 11:1246-55

Abstract

The bacterium Escherichia coli is used as a model cellular system to test and validate a new technology called Phenotype MicroArrays (PMs). PM technology is a high-throughput technology for simultaneous testing of a large number of cellular phenotypes. It consists of preconfigured well arrays in which each well tests a different cellular phenotype and an automated instrument that continuously monitors and records the response of the cells in all wells of the arrays. For example, nearly 700 phenotypes of E. coli can be assayed by merely pipetting a cell suspension into seven microplate arrays. PMs can be used to directly assay the effects of genetic changes on cells, especially gene knock-outs. Here, we provide data on phenotypic analysis of six strains and show that we can detect expected phenotypes as well as, in some cases, unexpected phenotypes.

Links

PubMed Online version:10.1101/gr.186501

Keywords

Escherichia coli; Gene Deletion; Cellular Respiration; Phenomics; Mutation; Oligonucleotide Array Sequence Analysis; Phenotype; Phenotype Microarray

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Main Points of the Paper

Please summarize the main points of the paper.

Materials and Methods Used

  • Phenotype Microarrays
    • ES- measuring carbon catabolism
    • EN- measuring nitrogen catabolism
    • EPS- measuring phosphate and sulfur catabolism
    • EA- measuring auxotrophy (growth stimulation by nutrients)
    • ES1, 2, and 3- measuring alterations in sensitivity or resistance to toxic chemicals
  • OmniLog instrument
    • read and record the color change
  • Color CCD camera
    • provide quantitative and kinetic information about the response of the cells

Phenotype Annotations

See Help:AnnotationTable for details on how to edit this table.
<protect>

Species Taxon ID Strain Gene (if known) OMP Phenotype Details Evidence Notes

Escherichia coli

fb753

xylA

  • abolished utilization of xylose as a C source
  • no growth on xylose

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 2

Escherichia coli

fb753

xylA

  • abolished utilization of maltose as a C source
  • no growth on maltose

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 2

Escherichia coli

fb753

xylA

  • abolished utilization of maltotriose as a C source
  • no growth on maltotriose

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 2

Escherichia coli

NCBI:83333

EP014

ynjB::Tn10

  • abolished utilization of L-arginine as a N source
  • no growth on L-arginine

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 2

Escherichia coli

NCBI:83333

EP014

ynjB::Tn10

  • abolished utilization of ornithine as a N source
  • no growth on ornithine

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 2

Escherichia coli

NCBI:83333

EP0005

malF3089::Tn10

  • abolished utilization of maltose as a C source
  • no growth on maltose

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 3

Escherichia coli

NCBI:83333

EP0005

malF3089::Tn10

  • abolished utilization of maltotriose as a C source
  • no growth on maltotriose

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 3

Escherichia coli

NCBI:83333

EP0007

del-cya1400::kan

  • abolished utilization of secondary carbon sources
  • no growth on secondary C sources

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 4- see for a list

Escherichia coli

NCBI:83333

EP0012

fruR::Tn5

  • increased utilization of some C sources
  • decreased utilization of some C sources

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 5- see for a list

Escherichia coli

NCBI:83333

EP0007

del-cya1400::kan

  • abolished utilization of pyruvate
  • no growth on pyruvate

Metabolic Activity

Biolog phenotype microarray

Biochemical Assay

Figure 4- as a result, this strain gave negative results on the EN, EPS, and EA arrays

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</protect>

Notes

References

See Help:References for how to manage references in omp dev.

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