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Gerd Moe-Behrens
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Mammalian designer cells:
Engineering principles and biomedical applications 

by
Xie M, Fussenegger M

"Biotechnology is a widely interdisciplinary field focusing on the use of living cells or organisms to solve established problems in medicine, food production and agriculture. Synthetic biology, the science of engineering complex biological systems that do not exist in nature, continues to provide the biotechnology industry with tools, technologies and intellectual property leading to improved cellular performance. One key aspect of synthetic biology is the engineering of deliberately reprogrammed designer cells whose behavior can be controlled over time and space. This review discusses the most commonly used techniques to engineer mammalian designer cells; while control elements acting on the transcriptional and translational levels of target gene expression determine the kinetic and dynamic profiles, coupling them to a variety of extracellular stimuli permits their remote control with user-defined trigger signals. Designer mammalian cells with novel or improved biological functions not only directly improve the production efficiency during biopharmaceutical manufacturing but also open the door for cell-based treatment strategies in molecular and translational medicine. In the future, the rational combination of multiple sets of designer cells could permit the construction and regulation of higher-order systems with increased complexity, thereby enabling the molecular reprogramming of tissues, organisms or even populations with highest precision."


http://1.usa.gov/1HLkS6h
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Gerd Moe-Behrens
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Natural Computing

System theory inspired thinking has led to the identification of ideas behind data processing in nature, but also in machines, such as silicon computers.

"This idea based thinking led to three distinct, but inter-related approaches, termed natural computing: computing inspired by nature, computer models of nature, and computing with natural materials [14]" (see the figure)

Data processing in nature
Focusing on information flow can help us to understand better how cells and organisms work [15]. Data processing can be found in nature all down to the atomic and molecular level. Examples are DNA information storage, and the histone code [16]. Moreover, cells have the potential to compute, both intra cellular (e.g. transcription networks) and during cell to cell communication [17]. Higher order cell systems such as the immune and the endocrine system, the homeostasis system, and the nerve system can be described as computational systems. The most powerful biological computer we know is the human brain [18].

Computing inspired by nature
General systems theory is an important fundament for computer science [1]. Interesting work has be done, as discussed above, by the Biological Computer Laboratory led by Heinz Foerster [8] [9].

In practical terms, nature inspired to programming paradigms such as cellular automata, artificial neural networks, evolutionary algorithms, evolutionary biology, genetic programming, swarm intelligence, artificial immune systems, membrane computing and amorphous computing [14] [19]. The common aim of all these concepts is solving complex problems.

Computer models of nature
The aim of the simulation and emulation of nature in computers is to test biological theories, and provide models that can be used to facilitate biological discovery. Moreover, these models can potentially be used for computer aided design of artificial biological systems.

Systems biology provides theoretical tools to model complex interactions in biological systems [12]. Design principles of biological circuits have been translated into mathematical models. These design models find their practical application in synthetic biology in general, and cellular computer especially. The different areas of natural computing clearly influence each other.

A breakthrough in the modeling and synthesis of natural patterns and structures was the recognition that nature is fractal [14]. A fractal is a group of shapes that describes irregular and fragmented patterns in nature, different from Euclidean geometric forms [20].

Other mathematical systems, as cellular automata, are both inspired by nature and can be used to modulate nature in silico, as some biological processes occur, or can be simulated, by them such as shell growth and patterns, neurons and fibroblast interaction [ 21] [ 22].

Another computational model of nature is the Lindenmayer-system (or L-system), which is used to model the growth process of plant development [23]. A major step towards the creation of artificial life was recently achieved by Karr et al [24]. This group reports a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. This model provides new insight into the in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. Moreover, model predictions led to experiments which identified previously undetected kinetic parameters and biological functions.

Computing with natural materials
Engineering ideas behind silicon computers can be applied to engineering with natural materials in order to gain control over biological systems. This concept started to emerge in the 1960s when Sugita published ground breaking theoretical work where he performed a functional analysis of chemical systems in vivo using a logical circuit equivalent [ 25] [ 26]. He discussed the idea of a molecular automaton, the molecular biological interpretation of the self-reproducing automata theory, and the chemico-physical interpretation of information in biological systems [ 27] [ 28]. Sugita made analogies between an enzymatic cascade and logic, values and concentrations, and interactions and circuit wires.

The emerging field of synthetic biology has contributed with novel engineering concepts for biological systems [29] [30]. The development of standardized biological parts has been a major task in synthetic biology, which led among other things to the open MIT Registry of Standard Biological Parts, and the BIOFAB DNA tool kit [30] [31] [32]. Another engineering principle, abstraction hierarchy, deals with the question of how standardized parts build a complex system. Systems (systemics) are another important engineering paradigm dealing with complexity [9] [33]. A system is a set of interacting or independent components forming an integrated whole. Common characteristics of a system are: components, behaviors and interconnectivity. Systems have a structure defined by components. Systems behavior involves input, processing and output of data. Behavior can be described with terms such as self-organizing, dynamic, static, chaotic, strange attractor, adaptive. Systems have interconnectivity. This means that the parts of the system have functional as well as structural relationships between each other. This kind of thinking represents a move form molecular to modular biology [34]. The challenge is to define the hierarchical abstraction for such a modular system for biocomputers, and finally actually build such a system.

A breakthrough paper was published in 1994 by Leonard Adleman [35]. For the first time a biocomputer, based on DNA, was built. This system was able to solve a complex, combinatorial mathematical problem, the directed Hamiltonian path problem. This problem is in principle similar to the following: Imagine you wish to visit 7 cities connected by a set of roads. How can you do this by stopping in each city only once? The solution of this problem, a directed graph was encoded in molecules of DNA. Standard protocols and enzymes were used to perform the “operations” of the computation. Other papers using DNA computing for solving mathematical problems followed [36]. Adelman's paper basically kick started the field of biological computers (reviewed in [17] [18] [37] [38] [39])."
http://bit.ly/YI13bF
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Gerd Moe-Behrens
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Scientists develop atomic-scale hardware to implement natural computing

by
Lisa Zyga 

"Despite the many great achievements of computers, no man-made computer can learn from its environment, adapt to its surroundings, spontaneously self-organize, and solve complex problems that require these abilities as well as a biological brain. These abilities arise from the fact that the brain is a complex system capable of emergent behavior, meaning that the system involves interactions between many units resulting in macroscale behavior that cannot be attributed to any individual unit.
Unfortunately, conventional fabrication methods used for today's computers cannot be used to realize complex systems to their full potential due to scaling limits—the methods simply cannot make small enough interconnected units.
Now in a new paper published in Nanotechnology, researchers at UCLA and the National Institute for Materials Science in Japan have developed a method to fabricate a self-organized complex device called an atomic switch network that is in many ways similar to a brain or other natural or cognitive computing device.
"Complex phenomena and self-organization—though ubiquitous in nature, social behavior, and the economy—have never been successfully used in conventional computers for prediction and modelling," James Gimzewski, Chemistry Professor at UCLA, told Phys.org. "The device we have created is capable of rapidly generating self-organization in a small chip with high speed. Furthermore, it bypasses the issue of exponential machine complexity required as a function of problem complexity as in today's computers. Our first steps form the basis for a new type of computation that is urgently needed in our ever increasingly connected world."...."

 http://bit.ly/1LhoH19
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Gerd Moe-Behrens
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Self-replication of DNA rings

 http://bit.ly/1S1BYQ0
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Gerd Moe-Behrens
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In vivo programmed gene expression based on artificial quorum networks

by
Chu T et al

"Quorum sensing system, as a well-functioned population-dependent gene switch, has been widely applied in many gene circuits in synthetic biology. In our work, an efficient cell density-controlled expression system (QS) was established via engineering Vibrio fischeri luxI-luxR quorum sensing system. In order to achieve in vivo programmed gene expression, a synthetic binary regulation circuit (araQS) was constructed by assembling multiple genetic components including quorum quenching protein AiiA and arabinose promoter ParaBAD into the QS system. In vitro expression assay verified that the araQS system was only initiated in the absence of arabinose in the medium at high cell density. In vivo expression assay confirmed that the araQS system presented an in vivo-triggered and cell density-dependent expression pattern. Furthermore, the araQS system was demonstrated to function well in different bacteria, indicating a wide range of bacterial hosts for use. To explore its potential applications in vivo, the araQS system was used to control the production of a heterologous protective antigen in an attenuated Edwardsiella tarda, which successfully evoked efficient immune protection in fish model. This work suggested that the araQS system could program bacterial expression in vivo and might have potential uses, including, but not limited to, bacterial vector vaccine."

 http://bit.ly/1S1xWqY
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Gerd Moe-Behrens
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Free on Flipboard curated by me

THE BIOLOGICAL MICROPROCESSOR

Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts....

http://bit.ly/1c0f22D
By Gerd Moe-Behrens | Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts....
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Gerd Moe-Behrens
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BioCoder Spring 2015

Bioinformatics for Aspiring Synthetic Biologists

by

Edgar Andrés Ochoa Cruz, Sayane Shome, Pablo Cárdenas, Maaruthy Yelleswarapu, Jitendra Kumar Gupta, Eugenio Maria Battaglia, Alioune Ngom, Pedro L. Fernandes, and Gerd Moe-Behrens​

"For a synthetic biologist or biohacker to be able to hack, design, create, and engi- neer biological systems, the ability to work with biological data is essential. Basic bioinformatics skills will be required in order to read, interpret, write, and gener- ate files containing DNA, RNA, protein, and other biological information. In this article, we will show the path you need to follow to implement a biological func- tion using online data. As a case study, we are using Imperial College’s 2014 iGEM project, which focused on the optimization of bacterial cellulose production for use in water filtration."

free download can be found here:
http://oreil.ly/WfVCzh
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Gerd Moe-Behrens
owner

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Single Cell Genetic Amplifier

by
Drew Endy

"Time Lapse Movie by Jerome Bonnet et al. (Stanford) showing brightfield (left), control signal change over time (middle) and gate output (right) in individual cells operating a transcriptor-based genetic amplifier. "

http://bit.ly/1GLzr7l


ref to 
Amplifying Genetic Logic Gates
http://bit.ly/1Fhukgv
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Gerd Moe-Behrens
owner

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Boosting riboswitch efficiency by RNA amplification

by
Masoumeh Emadpour, Daniel Karcher and Ralph Bock

"Riboswitches are RNA sensors that regulate gene expression in response to binding of small molecules. Although they conceptually represent simple on/off switches and, therefore, hold great promise for biotechnology and future synthetic biology applications, the induction of gene expression by natural riboswitches after ligand addition or removal is often only moderate and, consequently, the achievable expression levels are not very high. Here, we have designed an RNA amplification-based system that strongly improves the efficiency of riboswitches. We have successfully implemented the method in a biological system for which currently no efficient endogenous tools for inducible (trans)gene expression are available: the chloroplasts of higher plants. We further show that an HIV antigen whose constitutive expression from the chloroplast genome is deleterious to the plant can be inducibly expressed under the control of the RNA amplification-enhanced riboswitch (RAmpER) without causing a mutant phenotype, demonstrating the potential of the method for the production of proteins and metabolites that are toxic to the host cell."

 http://bit.ly/1bPDRP7
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Gerd Moe-Behrens
owner

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RNA that activates transcription

by
Nicole Rusk

"Synthetic small RNA transcriptional activators can regulate gene transcription in Escherichia coli.

'Learn from nature and copy what it does' is one of the guiding principles in the laboratory of Julius Lucks at Cornell University, but in their recent work, the researchers developed a strategy that seemingly expands what nature has to offer.

“We want to leverage our ability to model and measure RNA structures to make gene networks,” says Lucks. His team focuses on transcriptional control, and they aim to have RNA inputs control RNA outputs without involving proteins such as transcription factors. “The big conceptual advantage of RNA over proteins is that you can do design,” explains Lucks. “We know a lot more about RNA folding than we do about protein folding.”

The strategy of the Lucks team has been to observe RNA design principles in nature, characterize their structure and then apply these designs to the engineering of genetic circuits. The limitation is that whereas nature very efficiently uses small RNAs to repress transcription, there are to date no known instances of small RNAs alone activating transcription. “But,” says Lucks, “if you want to build networks, you need to turn things on as well as off.”

Melissa Takahashi, a graduate student in the lab, first focused on characterizing the function of a natural RNA transcriptional repressor mechanism: a special sequence upstream of a gene's coding region that can form RNA structures that allow or prevent progression of the RNA polymerase. These structures are switchable: in one case transcription is stopped by a transcriptional terminator RNA hairpin, and in the other case transcription is allowed by an antiterminator sequence that sequesters the terminator and prevents the formation of the blocking hairpin. Takahashi looked at the structural transitions needed in order to undergo the switch from active to inactive transcription; she then came up with a strategy to invert this repression mechanism into one that activates transcription by adding yet another layer of structural transitions using a small transcription activating RNA (STAR)...."

http://bit.ly/1OZAWTi

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Creating small transcription activating RNAs

by
James Chappell, Melissa K Takahashi & Julius B Lucks

"We expanded the mechanistic capability of small RNAs by creating an entirely synthetic mode of regulation: small transcription activating RNAs (STARs). Using two strategies, we engineered synthetic STAR regulators to disrupt the formation of an intrinsic transcription terminator placed upstream of a gene in Escherichia coli. This resulted in a group of four highly orthogonal STARs that had up to 94-fold activation. By systematically modifying sequence features of this group, we derived design principles for STAR function, which we then used to forward engineer a STAR that targets a terminator found in the Escherichia coli genome. Finally, we showed that STARs could be combined in tandem to create previously unattainable RNA-only transcriptional logic gates. STARs provide a new mechanism of regulation that will expand our ability to use small RNAs to construct synthetic gene networks that precisely control gene expression."
http://bit.ly/1HjhZW7
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Gerd Moe-Behrens
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Mammalian synthetic biology: emerging medical applications

by
Zoltán Kis , Hugo Sant'Ana Pereira , Takayuki Homma , Ryan M. Pedrigi , Rob Krams

"In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON–OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes."

http://bit.ly/1CU8GN0
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Gerd Moe-Behrens
owner

Discussion  - 
 
GPCR-Based Chemical Biosensors for Medium-Chain Fatty Acids

by
Kuntal Mukherjee, Souryadeep Bhattacharyya and Pamela Peralta-Yahya 

"A key limitation to engineering microbes for chemical production is a reliance on low-throughput chromatography-based screens for chemical detection. While colorimetric chemicals are amenable to high-throughput screens, many value-added chemicals are not colorimetric and require sensors for high-throughput screening. Here, we use G-protein coupled receptors (GPCRs) known to bind medium-chain fatty acids in mammalian cells to rapidly construct chemical sensors in yeast. Medium-chain fatty acids are immediate precursors to the advanced biofuel fatty acid methyl esters, which can serve as a “drop-in” replacement for D2 diesel. One of the sensors detects even-chain C8–C12 fatty acids with a 13- to 17-fold increase in signal after activation, with linear ranges up to 250 μM. Introduction of a synthetic response unit alters both dynamic and linear range, improving the sensor response to decanoic acid to a 30-fold increase in signal after activation, with a linear range up to 500 μM. To our knowledge, this is the first report of a whole-cell medium-chain fatty acid biosensor, which we envision could be applied to the evolutionary engineering of fatty acid-producing microbes. Given the affinity of GPCRs for a wide range of chemicals, it should be possible to rapidly assemble new biosensors by simply swapping the GPCR sensing unit. These sensors should be amenable to a variety of applications that require different dynamic and linear ranges, by introducing different response units."

http://bit.ly/1IN4W3F
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Gerd Moe-Behrens
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Discussion  - 
 
A pioneer in biological computing
Heinz Förster 

His work focused on cybernetics, the exploration of regulatory systems, and who founded in 1958 the Biological Computer Lab (BCL) at the Department of Electrical Engineering at the University of Illinois. The work of the BCL was focused on the similarities in cybernetic systems and electronics and especially biology inspired computing.

Ref
A Muller, K.M
An Unfinished Revolution: Heinz von Foerster and the Biological Computer Laboratory / BCL 1958–1976Vienna Edition Echoraum (2007)

H Foerster, WR Ashby
Biological Computers
KE Schaefer (Ed.), Bioastronautics, The Macmillan Co, New York (1964), pp. 333–360

http://bit.ly/1PWi8C0 (Foto source)

http://bit.ly/YI13bF

There are some great interviews with him on YouTube.
Some from: Das Netz: Lutz Dammbeck und der Unabomber http://bit.ly/1djUkfD (worth to watch as a whole)

Also worth to watch 
http://bit.ly/1R31aUR
http://bit.ly/1R31kMa

Take a YouTube search by yourself and you will find several awesome videos.
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Gerd Moe-Behrens
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PNA as a Biosupramolecular Tag for Programmable Assemblies and Reactions http://bit.ly/1EeW9PR
Copyright © 2015 American Chemical Society. *E-mail: nicolas.winssinger@unige.ch. Biography. Sofia Barluenga received her Ph.D. with F. Aznar and J. Barluenga before joining the group of K. C. Nicolaou for postdoctoral training. She is currently a senior researcher at the University of Geneva.
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Gerd Moe-Behrens
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Engineering Aptazyme Switches for Conditional Gene Expression in Mammalian Cells Utilizing an In Vivo Screening Approach

by
Charlotte Rehm, Benedikt Klauser, Jörg S. Hartig

"Artificial RNA switches are an emerging class of genetic controllers suitable for synthetic biology applications. Aptazymes are fusions composed of an aptamer domain and a self-cleaving ribozyme. The utilization of aptazymes for conditional gene expression displays several advantages over employing conventional transcription factor-based techniques as aptazymes require minimal genomic space, fulfill their function without the need of protein cofactors, and most importantly are reprogrammable with respect to ligand selectivity and the RNA function to be regulated. Technologies that enable the generation of aptazymes to defined input ligands are of interest for the construction of biocomputing devices and biosensing applications. In this chapter we present a method that facilitates the in vivo screening of randomized pools of aptazymes in mammalian cells"

http://bit.ly/1dfqqZW
Artificial RNA switches are an emerging class of genetic controllers suitable for synthetic biology applications. Aptazymes are fusions composed of an aptamer domain and a self-cleaving ribozyme. The utilization of aptazymes for conditional gene expression displays several advantages over employing conventional transcription factor-based techniques as aptazymes require minimal genomic space, fulfill their function without the need of protein cofa...
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Gerd Moe-Behrens
owner

Discussion  - 
 
Living Computers Ultimate Goal

by
R. Colin Johnson

"Synthetic biology is "politically correct" name for twiddling with the origin of life itself. From splicing-in genes from other organisms to produce better vegetables—such as flounder genes to produce bruise-free tomatoes or jellyfish genes to potatoes which glow when they need to be watered or splicing human genes into cows to produce human breast milk or making completely new organisms from scratch.

In the electronics arena, the Semiconductor Research Corp. (Research Triangle Park, N.C.) started a Semiconductor Synthetic Biology (SSB) program in 2013 that is already beginning to bear fruit (pun intended). This fruit will ultimately cross human genes with semiconductors to create hybrid "cyborg-like" computers, but there are a lot of intermediate steps along the way.

"Our ultimate goal is to make living computers. Biological systems can do signal processing like human brains at very low power," professor Hua Wang from the Georgia Institute of Technology (Georgia Tech, Atlanta) a recipient of a grant from SRC's Synthetic Biology program told EE Times. "We want to see if we can build a CMOS hybrid life form, eventually, but right now we are combining CMOS and biological components for signal processing and sensing mechanisms."..."

 http://ubm.io/1F5Yunh
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Gerd Moe-Behrens
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CRISPR Meets Synthetic Biology: A Conversation with MIT’s Christopher Voigt

by
Kendall Morgan 

"As Christopher Voigt explains it, his lab at the Massachusetts Institute of Technology has been “working on new experimental and theoretical methods to push the scale of genetic engineering, with the ultimate objective of genome design.” It’s genetic engineering on a genomic scale, with the expectation for major advances in agriculture, materials, chemicals, and medicine.

As they’ve gone along, Voigt’s group has also been assembling the toolbox needed for anyone to begin considering genetic engineering projects in a very big way. In one of his latest papers, published in Molecular Systems Biology in November, Voigt and Alex Nielsen describe what’s possible when multi-input CRISPR/Cas genetic circuits are linked to the regulatory networks within E. coli host cells.
..."

http://bit.ly/1EbURK6
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Gerd Moe-Behrens
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A new magazine about biological computing curated by me

THE BIOLOGICAL MICROPROCESSOR

http://flip.it/Pb3xL
via #flipboard  
By Gerd Moe-Behrens | Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts....
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Gerd Moe-Behrens
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Design criteria for synthetic riboswitches acting on transcription

by
Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M.

"Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell."


http://bit.ly/1OZEe9c
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Gerd Moe-Behrens
owner

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Engineering a Bacterial Tape Recorder

by
Alexander Prokup andAlexander Deiters

"A method has been developed to produce and integrate single-stranded DNA into genomic locations in bacteria in response to exogenous signals. The system functions similarly to a cellular tape recorder by writing information into DNA and reading it at a later time. Much like other cellular memory platforms, its operation is based on DNA recombinase function. However, the scalability and recording capacity have been improved over previous designs. In addition, memory storage was reversible and could be recorded in response to analogue inputs, such as light exposure. This modular memory writing system is an important addition to the genomic editing toolbox available for synthetic biology."


http://bit.ly/1aeVV4X


Image from:
Bacteria become 'genomic tape recorders', recording chemical exposures in their DNA http://bit.ly/1HhoWqM
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