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The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
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The work done by a thermodynamic system depends not only on the initial and final states but also on the intermediate states—that is, on the path. Like work, when heat is added to a thermodynamic system, it undergoes a change of state, and the state attained depends on the path from the initial state to the final state. Consider an ideal gas cylinder fitted with a piston. When the cylinder is heated at a constant temperature, the gas molecules absorb energy and expand slowly in a...
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The expansion of alcohol in a thermometer is one of many commonly encountered examples of thermal expansion, which is the change in size or volume of a given system as its temperature changes. The most visible example is the expansion of hot air. When air is heated, it expands and becomes less dense than the surrounding air, which then exerts an upward force on the hot air to, for example, make steam and smoke rise, and hot air balloons float. The same behavior happens in all liquids and gases,...
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Expanding a binomial expression such as (a + b)n results in a predictable sequence of terms that can be systematically derived using Pascal’s Triangle. This triangular array of numbers plays a central role in understanding and computing the coefficients of binomial expansions.Pascal’s Triangle is constructed such that each row corresponds to the coefficients of a binomial raised to a power. The topmost row, known as the zeroth row, corresponds to (a + b)0, and each successive row...
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Masonry walls are subject to slight expansion and contraction due to variations in temperature and moisture. Thermal movement in masonry is relatively straightforward to measure and plan for. On the other hand, moisture movement poses more of a challenge. New clay masonry units typically absorb water and expand over time under normal environmental conditions. Conversely, new concrete masonry units tend to shrink as they lose the excess moisture acquired during their production process.
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San Francisco's Golden Gate Bridge is exposed to temperatures ranging from -15 °C to 40 °C. At its coldest, the main span of the bridge is 1275 m long. Assuming that the bridge is made entirely of steel, what is the change in its length between these temperatures?
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SMILE: a novel procedure for subcellular module identification with localisation expansion.

Lixin Cheng1, Pengfei Liu1, Kwong-Sak Leung2

  • 1Department of Computer Science & Engineering, Chinese University of Hong Kong, Ma Liu Shui, Hong Kong.

IET Systems Biology
|March 14, 2018
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This study introduces SMILE, a new method to identify protein functional modules by considering subcellular localization. SMILE enhances module discovery by integrating protein location, revealing more biologically relevant protein complexes and pathways.

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Area of Science:

  • Computational biology
  • Systems biology
  • Bioinformatics

Background:

  • Protein-protein interaction (PPI) networks are crucial for understanding biological pathways.
  • Subcellular localization is vital for protein function but often overlooked in PPI module identification.
  • Existing methods may miss functionally diverse modules by not considering cellular compartments.

Purpose of the Study:

  • To propose a novel computational procedure, Subcellular Module Identification with Localisation Expansion (SMILE).
  • To identify super modules by integrating information from subcellular compartments.
  • To improve the functional diversity and biological relevance of identified protein modules.

Main Methods:

  • Developed the SMILE procedure to identify super modules from compartmentalized PPI networks.
  • Applied SMILE to compartmentalised PPI and InWeb_InBioMap datasets.
  • Compared SMILE-identified super modules with those from global PPI networks.

Main Results:

  • SMILE successfully identified super modules comprising several subcellular modules.
  • Super modules identified by SMILE demonstrated greater functional diversity.
  • These super modules showed stronger associations with known protein complexes and biological pathways compared to global PPI network modules.

Conclusions:

  • Subcellular localization is a key feature for identifying functional modules in PPI networks.
  • Integrating subcellular localization significantly enhances the detection of biologically meaningful results.
  • The SMILE method provides valuable guidance for more accurate protein module discovery.