What do colony patterns mean a biologist s view
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What do colony patterns mean? - A biologist’s view. 1. The colony as an organized, differentiated structure with a complex morphogenesis, even laboratory E. coli . 2. Patterns that reflect the formation of adaptive structures: genetic analysis.

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What do colony patterns mean a biologist s view

What do colony patterns mean? - A biologist’s view

1. The colony as an organized, differentiated structure with a complex morphogenesis, even laboratory E. coli.

2. Patterns that reflect the formation of adaptive structures: genetic analysis.

3. A pattern that reflects the operation of adaptive systems under defined conditions: environmental analysis and modeling (Proteus mirabilis).

4. The dense-branching morphology of B. subtilis colonies under nutritional restriction: a problem for modeling.

James A. Shapiro, University of Chicago



Initiation of e coli colony development
Initiation of E. coli colony development




Patterns that reflect the formation of adaptive structures e coli
Patterns that reflect the formation of adaptive structures: E. coli

Budrene EO, Berg HC. Dynamics of formation of symmetrical patterns by chemotactic bacteria.

Nature. 1995 376(6535):49-53.


Patterns that reflect the formation of adaptive structures b subtilis
Patterns that reflect the formation of adaptive structures: B. subtilis

Fruiting Body Formation by Bacillus subtilis Steven S. Branda1†, José Eduardo González-Pastor2†, Sigal Ben-Yehuda2, Richard Losick2 and Roberto Kolter. Proc. Nat. Acad. Sci. USA, 98: 11621-11626


Patterns that reflect the formation of adaptive structures genetic analysis
Patterns that reflect the formation of adaptive structures: genetic analysis

Esteban Lombardía, Adrián J. Rovetto, Ana L. Arabolaza, and Roberto R. Grau. A LuxS-Dependent Cell-to-Cell Language Regulates Social Behavior and Development in Bacillus subtilis. Journal of Bacteriology, June 2006, p. 4442-4452, Vol. 188


A pattern that reflects the operation of adaptive systems under defined conditions: Proteus mirabilis. Where modeling matters most.

Synchronous inoculation Asynchronous inoculation (1 hr)


Proteus crew
Proteus under defined conditions: Crew

L-R: Todd Dupont, Mitsugu Matsushita, Bruce Ayati, Oliver Rauprich, JAS, Sergei Esipov & Sune Danø


Different cell types in proteus swarming
Different cell types in Proteus swarming under defined conditions:



Dependence of swarming velocity on amino acid not glucose concentration above a threshold
Dependence of swarming velocity on amino acid, not glucose concentration (above a threshold)

Sune Danø


Robust periodicity in proteus swarming
Robust Periodicity in concentration (above a threshold)Proteus Swarming

Rauprich O, Matsushita M, Weijer K, Siegert F, Esipov S, Shapiro JA. 1996. Periodic phenomena in Proteusmirabilis swarm colony development. J. Bacteriol. 178:6525-38



Interlocking cell cycles
Interlocking Cell Cycles acids)

Esipov, S. and J.A.Shapiro. 1998. Kinetic model of Proteus mirabilis swarm colony development. J. Math. Biol. 36, 249-268.


Kinetic equations

Swarmer cell density acids)

Diffusivity

Spatially Resolved Kinetics

Kinetic Equations

Esipov, S. and J.A.Shapiro. 1998. Kinetic model of Proteus mirabilis swarm colony development. J. Math. Biol. 36, 249-268.


Robust periodicity requires age dependent dedifferentiation
Robust periodicity requires age-dependent dedifferentiation acids)

Bruce P. Ayati. Modeling the role of the cell cycle in regulating Proteus mirabilis swarm-colony development. Applied Mathematics Letters 20 (2007) 913–918


Experimental examination of proteus dedifferentiation
Experimental examination of acids)Proteus dedifferentiation

A. Liew & JAS


The dense-branching morphology of acids)B. subtilis colonies under nutritional restriction: a problem ripe for modeling.

Fujikawa H, and Matsushita M. 1989. Fractal growth of Bacillussubtilis on agar plates. J. Phys. Soc. Japan 58:3875-78


Amino acid dependent branching at different temperatures
Amino acid-dependent branching at different temperatures acids)

Julkowska D, Obuchowski M, Holland IB, Séror SJ. 2004. Branched swarming patterns on a synthetic medium formed by wild-type Bacillus subtilis strain 3610: detection of different cellular morphologies and constellations of cells as the complex architecture develops. Microbiology 150:1839-49.



Observations and hypotheses for modeling b subtilis dbm
Observations and hypotheses for modeling tip of each dendriteB. subtilis DBM

Observations:

  • Amino acids necessary (I.B. Holland, personal communication)

  • DBM limited to a special region of the nutritional-mobility space

  • DBM characterized by branches that do not grow in width

  • Tip-splitting occurs when branches separated by a critical distance

  • Increased cell activity in a limited zone at the tip of each dendrite

    Hypotheses:

  • Tip expansion requires active cell movement inside front

  • Cell movement occurs only above a threshold amino acid level

  • Cell movement is the major sink for amino acid consumption

  • Glucose-based growth is not nutritionally limited


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