Systems microscopy for the non-expert

Introduction

The modeling of a biological system needs input from the real life situation and it has to be in the shape of quantitative data, numbers that can be fed into mathematical models. A wealth of parallel technical advances in the past two decades has increased the possibility to make system-wide quantifications of biomolecules, their interactions and dynamics. Mathematical models evolve when challenged with new rounds of experimental data in a cyclical fashion. This reiterative wet-dry cycle is a distinguishing feature of systems biology. Methodology generally used for systems biology analysis does not permit analysis over time and provides information based on populations. Systems microscopy is a new and growing approach facilitating systems biology analysis of living, individual cells over time, an approach that has been made possible by recent developments of microscopy technology.

Systems biology

Since around a decade ago, the full sequence of the DNA that make up the human genome is known and publically accessible and has paved the way for cell-wide analytical methodologies. Since then, large amounts of information about the organization of the genome and the functions of its subcomponents and their products has been gathered. It is however increasingly evident that even the most detailed knowledge about a set of subcomponents or modules in isolation will not by default give predictive power as to what functions these will produce when combined in complex systems such as a cell or an organ.

To identify disease causing genes and their malformed or misexpressed gene products (RNA or proteins), present-day biomedicine is well equipped to do. If we however wish to gain a systems level understanding of how a disease state can emerge from organismal imbalances, we need to be able to build models of systems that allow for the prediction of parameters that impact state.  In a report outlining future directions in research, the European Science Foundation formulates the same notion in this way; 'Given the extremely complex behavior of such multilevel networks of interactions, intuitive approaches are ineffective. It requires quantitative and predictive mathematical modeling that helps the biologist to decide what the most informative experiments are' (R. van Driel & H Westerhoff, 2007). Thee billion DNA base pairs may encode the blueprint of a human being, but in no way is it intuitive how this string of As, Cs, Gs and Ts translates into cellular and, indeed, organismal function.

 

Closing in on individuals in 4D—systems microscopy

When extracting information about systems based on the average of populations —be it people, cells or molecular complexes— information about subpopulations may be masked. In fact, the average may be true on population level only, never on the level of the individual. In some cases this is intuitive; you would never expect to actually meet a family with 1.5 children even though this is the estimated average fertility rate for European women. When analyzing complex systems, your intuition may not help you decide whether an average represents only itself or is valid for every entity in the population. Methods to access information on the level of the individual are needed to resolve this issue.

Modern microscopy not only allows the analysis of individual, live cells, but their behavior can also be tracked over time and in the three spatial dimensions. The development of new tools, booth computational and biochemical, have also widened the range of questions that can be asked and have improved the output of quantitative data. For instance, the half-life of molecular complexes can be estimated in their natural environment, the dynamics of whole cells or subcellular structures can be quantified.

A closer analysis of individuals naturally slows down the cohort analysis. Microscopy has therefore previously been connected with low-throughput rather than the high-throughput desired to feed mathematical models with global data (representative of a system as a whole). Methods for automation and for parallel analysis of large numbers of cells have improved throughput rates so that microscopy now offers approaches that can fill in important gaps in the systems biology analysis of living cells. This growing technology platform makes the interrogation of complex cellular networks that enable cell growth, division and migration possible.

Seventh Framework Programme

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