Logic Gates - Emma Garren
Contents
Logic Gates in Synthetic Biology
Background: Logic Gates and Truth Tables
A logic gate, the building block for digital circuits, is a computing unit that performs a logical operation on one or more inputs and produces a single output. Gates are identified by their function, and each type of logic gate can be represented with a distinctive symbol. The input(s) are represented with short line segments to the left of the shape, and the output is represented by a short line segment to the right of the shape. A small circle on the right indicates that the output of the logical operation is inverted. A double line on the left represents that the function is "exclusive."
AND gate. | OR gate. | NOT gate.
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</center> A truth table is a useful way to describe the behavior or function of a logic gate. A "1" is used for "true" or a positive input, and a "0" is used for "false" or a negative input. Click here to see the most common logic gates and their truth tables. Logic gates can be combined to perform more complex functions. The design below will Logic Gates in Synthetic BiologyEngineering Principles
Challenges from the cellular environment: Synthetic biology research is hindered by the inability to predict the functions of even simple devices and modules within the cellular environment. Some of the confounding factors are gene expression noise, mutation, cell death, undefined and changing extracellular environments, and interactions with the cellular context (Adrianantoandro et al., 2006). Significance of modularity... High level of modularity in the regulatory elements of eukaryotic systems (Heinemann and Panke, 2006) - allows for integration of more and more signals into determining a single output or cellular function. Biomolecular Logic Gates: In VitroIn vitro studies have been used to design combinations of molecules that have emergent properties related to information processing--molecular computing devices. Both the inputs and outputs consist of molecular species, with the output being a biologically active molecule. The extent to which these devices will be used with the cellular context is unclear--however, they are bound to inspire new directions for research in synthetic biology, and have potential applications in biochemical sensing, pathway engineering, and medical diagnosis and treatment. Computing with EnzymesBaron et al. Ribozyme-Based Logic GatesStojanovic and Stephanovic Synthetic Signaling ProteinsDueber et al. - engineering synthetic signaling proteins with ultrasensitive input/output control. DNA Self-AssemblyYan et al. Seelig et. al. DNA-Based Logic GatesFrezza et al. Yoshida and Yokobayashi Miyoshi et al. OtherAn autonomous molecular computer for logical control of gene expression. (Benenson et al., 2004) This paper describes an in vitro system that recognizes a specific combination of mRNA levels as its inputs, and performs a logical operation that results in the production of a molecule that can affect gene expression. Because the mRNA levels have been designed to mimic a simplistic version of gene expression modeling cancer, and the output is a drug-like ssDNA with known anticancer activity, the molecular computer is analogous to "a computational version of 'diagnosis'" (424). Cellular Logic Gates: In VivoVarious types of molecular logic gates allow for the design of synthetic gene circuits... Modularity... Oscillators and Bistable SwitchesElowitz and Leibler Collins - toggle switch Environmental Signal IntegrationModular AND gate Artificial Cellular Communication NetworksQuorum-sensing as input for logical operation Circuits engineered in the context of multicellular systems... Two different cell types in a bacterial population (Basu et al. 2004 and 2005, described in "Designing biological systems" review paper) Logic Gates in Mammalian CellsFusseneger Applications and Future DirectionsSynthetic gene circuits - use multiple simple input-output logic systems to design and build more complex circuits. Medical applications - Cancer treatment - Increase specificity with which bacteria can sense an environment by combining multiple environmental inputs in logic gates. Autonomous biomolecular computing devices - use for molecular-level diagnostics and treatment References
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