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Collective motions and specific effectors: a statistical mechanics perspective on biological regulation.

Giuliani A - BMC Genomics (2010)

Bottom Line: This will allow to both obtain a general frame of reference for rationalizing the burden of data coming from high throughput technologies and to derive effective operational views on biological systems.The network paradigm in which microscopic level elements (nodes) are each other related by functional links so giving rise to both global (entire network) and local (specific) behavior is a promising metaphor to try and develop a statistical mechanics inspired approach for biological systems.The need to complement the purely molecular view with mesoscopic approaches is evident in all the studied examples that in turn demonstrate the untenability of the simple ergodic approach dominant in molecular biology in which the data coming from huge ensemble of cells are considered as relative to a single 'average' cell.

View Article: PubMed Central - HTML - PubMed

Affiliation: Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma, Italy. alessandro.giuliani@iss.it

ABSTRACT

Background: The interaction of a multiplicity of scales in both time and space is a fundamental feature of biological systems. The complementation of macroscopic (entire organism) and microscopic (molecular biology) views with a mesoscopic level of analysis able to connect the different planes of investigation is urgently needed. This will allow to both obtain a general frame of reference for rationalizing the burden of data coming from high throughput technologies and to derive effective operational views on biological systems.

Results: The network paradigm in which microscopic level elements (nodes) are each other related by functional links so giving rise to both global (entire network) and local (specific) behavior is a promising metaphor to try and develop a statistical mechanics inspired approach for biological systems. Here we show the application of this paradigm to different systems going from yeast metabolism to murine macrophages response to immune stimulation.

Conclusions: The need to complement the purely molecular view with mesoscopic approaches is evident in all the studied examples that in turn demonstrate the untenability of the simple ergodic approach dominant in molecular biology in which the data coming from huge ensemble of cells are considered as relative to a single 'average' cell.

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The LPS stimulus processing pathway.
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Figure 5: The LPS stimulus processing pathway.

Mentions: In this case we were dealing with mutations affecting the so called innate immunity process, i.e. the response set for by organisms when invaded by a potentially pathogen biological entity (generally a bacterium). The defense response starts from very specialized cells called macrophages: the innate immune system utilizes pattern-recognition receptors (PRRs), proteins present on the cell membrane that are able to recognize and bind to pathogen associated molecules, such as lypopolisaccharides (LPS). LPS, which are located in the outer membrane of Gram-negative bacteria, after being recognized by the macrophage receptors, trigger a cascade of signaling events eventually leading to the digestion of the bacteria. Two effector proteins that are essential for the correct execution of the above process are called MyD88- and TRIF- (see Figure 5).


Collective motions and specific effectors: a statistical mechanics perspective on biological regulation.

Giuliani A - BMC Genomics (2010)

The LPS stimulus processing pathway.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2822530&req=5

Figure 5: The LPS stimulus processing pathway.
Mentions: In this case we were dealing with mutations affecting the so called innate immunity process, i.e. the response set for by organisms when invaded by a potentially pathogen biological entity (generally a bacterium). The defense response starts from very specialized cells called macrophages: the innate immune system utilizes pattern-recognition receptors (PRRs), proteins present on the cell membrane that are able to recognize and bind to pathogen associated molecules, such as lypopolisaccharides (LPS). LPS, which are located in the outer membrane of Gram-negative bacteria, after being recognized by the macrophage receptors, trigger a cascade of signaling events eventually leading to the digestion of the bacteria. Two effector proteins that are essential for the correct execution of the above process are called MyD88- and TRIF- (see Figure 5).

Bottom Line: This will allow to both obtain a general frame of reference for rationalizing the burden of data coming from high throughput technologies and to derive effective operational views on biological systems.The network paradigm in which microscopic level elements (nodes) are each other related by functional links so giving rise to both global (entire network) and local (specific) behavior is a promising metaphor to try and develop a statistical mechanics inspired approach for biological systems.The need to complement the purely molecular view with mesoscopic approaches is evident in all the studied examples that in turn demonstrate the untenability of the simple ergodic approach dominant in molecular biology in which the data coming from huge ensemble of cells are considered as relative to a single 'average' cell.

View Article: PubMed Central - HTML - PubMed

Affiliation: Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma, Italy. alessandro.giuliani@iss.it

ABSTRACT

Background: The interaction of a multiplicity of scales in both time and space is a fundamental feature of biological systems. The complementation of macroscopic (entire organism) and microscopic (molecular biology) views with a mesoscopic level of analysis able to connect the different planes of investigation is urgently needed. This will allow to both obtain a general frame of reference for rationalizing the burden of data coming from high throughput technologies and to derive effective operational views on biological systems.

Results: The network paradigm in which microscopic level elements (nodes) are each other related by functional links so giving rise to both global (entire network) and local (specific) behavior is a promising metaphor to try and develop a statistical mechanics inspired approach for biological systems. Here we show the application of this paradigm to different systems going from yeast metabolism to murine macrophages response to immune stimulation.

Conclusions: The need to complement the purely molecular view with mesoscopic approaches is evident in all the studied examples that in turn demonstrate the untenability of the simple ergodic approach dominant in molecular biology in which the data coming from huge ensemble of cells are considered as relative to a single 'average' cell.

Show MeSH