Matlab Tutorial: Bacterial gene expression
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چکیده
From how a single cell develops into a multicellular organism to how bacteria decide to go about their diet, single cells interpret the information encoded in their DNA and in their surrounding media in order to make life-changing decisions. Cellular decision making is ubiquitous in biology. As an example, most animals have the same set of genes encoded in their DNA. However, what sets them apart is when, where and how each cell decided to produce those genes. In this Matlab tutorial we will explore simple cellular decisions in the context of the bacterium E. coli. We will propose a theoretical model to describe these decisions and use Matlab to generate falsifiable predictions that can be tested experimentally by quantifying the fluorescence intensity of several E. coli strains we will provide. We will obtain this data using fluorescence microscopy and invoke Matlab once again to analyze our microscopy images. The result will be a full cycle of the theory/experiment interplay where we go from theoretical prediction to experimental validation on our quest to test our predictive understanding of cellular decision making. Information about these decisions flows through the so-called “central dogma of molecular biology”, shown diagrammatically in Figure 1. Here, genes are encoded on the DNA. When a gene is turned “on” it is copied by the RNA polymerase molecular machine in a process deemed transcription. Both the DNA and mRNA molecules encode information in the familiar language of ATCGs for DNA and AUCGs for mRNA. The mRNA molecule is then translated by the ribosome molecular machine into a protein made out of amino acids. Gene expression can be regulated along any of the steps of this central dogma. For the purposes of this short tutorial we will focus on regulation at the level of transcription.
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تاریخ انتشار 2014