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Cellular Computing

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Free MIT / edX SynBio  course

Principles of Synthetic Biology
Learn how to engineer biological systems and program organisms to perform novel tasks.

http://bit.ly/1EgSTud
Learn how to engineer biological systems and program organisms to perform novel tasks.
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Cellular Computing

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Synthetic histone code

Fischle W, Mootz HD, Schwarzer D

"Chromatin is the universal template of genetic information in all eukaryotic cells. This complex of DNA and histone proteins not only packages and organizes genomes but also regulates gene expression. A multitude of posttranslational histone modifications and their combinations are thought to constitute a code for directing distinct structural and functional states of chromatin. Methods of protein chemistry, including protein semisynthesis, amber suppression technology, and cysteine bioconjugation, have enabled the generation of so-called designer chromatin containing histones in defined and homogeneous modification states. Several of these approaches have matured from proof-of-concept studies into efficient tools and technologies for studying the biochemistry of chromatin regulation and for interrogating the histone code. We summarize pioneering experiments and recent developments in this exciting field of chemical biology."

http://bit.ly/1N0AWms
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Cellular Computing

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Synthetic biology and biomimetic chemistry as converging technologies fostering a new generation of smart biosensors

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Viviana Scognamiglio , Amina Antonacci, Maya D. Lambreva, Simona C. Litescu, Giuseppina Rea

"Biosensors are powerful tunable systems able to switch between an ON/OFF status in response to an external stimulus. This extraordinary property could be engineered by adopting synthetic biology or biomimetic chemistry to obtain tailor-made biosensors having the desired requirements of robustness, sensitivity and detection range. Recent advances in both disciplines, in fact, allow to re-design the configuration of the sensing elements - either by modifying toggle switches and gene networks, or by producing synthetic entities mimicking key properties of natural molecules.

The present review considered the role of synthetic biology in sustaining biosensor technology, reporting examples from the literature and reflecting on the features that make it a useful tool for designing and constructing engineered biological systems for sensing application. Besides, a section dedicated to bioinspired synthetic molecules as powerful tools to enhance biosensor potential is reported, and treated as an extension of the concept of biomimetic chemistry, where organic synthesis is used to generate artificial molecules that mimic natural molecules. Thus, the design of synthetic molecules, such as aptamers, biomimetics, molecular imprinting polymers, peptide nucleic acids, and ribozymes were encompassed as “products” of biomimetic chemistry."

http://bit.ly/1J2bkF2
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Cellular Computing

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Bacteria Programmed to Develop Basic Computing Elements Like Sensors, Memory and Circuits

"The researchers at the Massachusetts Institute of Technology have successfully programmed the friendly bacteria inside our body to detect diseases like colon cancer and immune disorder- and treat them. They have unveiled sensors, circuits, and memory switches to be encoded in bacterium Bacteroides thetaiotaomicron, found in human gut system."

http://bit.ly/1LLTpl4
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Signal-to-noise ratio measures efficacy of biological computing devices and circuits

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Jacob Beal

"Engineering biological cells to perform computations has a broad range of important potential applications, including precision medical therapies, biosynthesis process control, and environmental sensing. Implementing predictable and effective computation, however, has been extremely difficult to date, due to a combination of poor composability of available parts and of insufficient characterization of parts and their interactions with the complex environment in which they operate. In this paper, the author argues that this situation can be improved by quantitative signal-to-noise analysis of the relationship between computational abstractions and the variation and uncertainty endemic in biological organisms. This analysis takes the form of a ΔSNRdB function for each computational device, which can be computed from measurements of a device’s input/output curve and expression noise. These functions can then be combined to predict how well a circuit will implement an intended computation, as well as evaluating the general suitability of biological devices for engineering computational circuits. Applying signal-to-noise analysis to current repressor libraries shows that no library is currently sufficient for general circuit engineering, but also indicates key targets to remedy this situation and vastly improve the range of computations that can be used effectively in the implementation of biological applications."

http://bit.ly/1J2qg4w
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Cellular Computing

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How do I construct busses, wires in a biological microprocessor

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http://bit.ly/1RtVmHQ
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Cellular Computing

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Why Researchers Want to Build Computers...Made of DNA

http://bit.ly/1NFIbNS
New research on DNA transformations from the University of East Anglia just might make nano-scale computing possible.
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Synthetic Quorum Sensing and Cell–Cell Communication in Gram-Positive Bacillus megaterium

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Nicholas Marchand and Cynthia H. Collins 

"The components of natural quorum-sensing (QS) systems can be used to engineer synthetic communication systems that regulate gene expression in response to chemical signals. We have used the machinery from the peptide-based agr QS system from Staphylococcus aureus to engineer a synthetic QS system in Bacillus megaterium to enable autoinduction of a target gene at high cell densities. Growth and gene expression from these synthetic QS cells were characterized in both complex and minimal media. We also split the signal production and sensing components between two strains of B. megaterium to produce sender and receiver cells and characterized the resulting communication in liquid media and on semisolid agar. The system described in this work represents the first synthetic QS and cell–cell communication system that has been engineered to function in a Gram-positive host, and it has the potential to enable the generation of dynamic gene regulatory networks in B. megaterium and other Gram-positive organisms."

http://bit.ly/1Pa6DrW
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Modulating protein activity using tethered ligands with mutually exclusive binding sites

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Alberto Schena, Rudolf Griss & Kai Johnsson

"The possibility to design proteins whose activities can be switched on and off by unrelated effector molecules would enable applications in various research areas, ranging from biosensing to synthetic biology. We describe here a general method to modulate the activity of a protein in response to the concentration of a specific effector. The approach is based on synthetic ligands that possess two mutually exclusive binding sites, one for the protein of interest and one for the effector. Tethering such a ligand to the protein of interest results in an intramolecular ligand–protein interaction that can be disrupted through the presence of the effector. Specifically, we introduce a luciferase controlled by another protein, a human carbonic anhydrase whose activity can be controlled by proteins or small molecules in vitro and on living cells, and novel fluorescent and bioluminescent biosensors."

 http://bit.ly/1RU8shG
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Thanks for the invitation. My work is basically about Synthetic Biology Informatics (biological computing, bioinformatic, Apple development - main language Swift and Objective- C)
Looking forward to the discussion.
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How are nature and computers related

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http://bit.ly/1IY6gA8
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How do I engineer a memory unit with biomolecules?

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http://bit.ly/1J8vJ5p
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