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How are nature and computers related? - YouTube

Gerd Moe-Behrens's insight:

A platonic idea is an archetype, a blueprint, the essence of various phenomena of the same thing. 

Systemics and systems biology are such ideas, describing data processing systems in nature in terms of mathematics and formal logic. Systemic ideas have been used as a blueprint for silicon computing. Ideas derived from the observation of nature have also inspired computer models of nature. 

Engineering ideas behind silicon computer (such as standardized parts, switches, logic gates, input /output device, arithmetic logic unit, control unit, memory, and busses) have been used by synthetic biologists to build computers with biological parts, with the ultimate goal to control data processing in nature.


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Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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Alexandra Daisy Ginsberg: The dream of better | Design Indaba

Alexandra Daisy Ginsberg: The dream of better | Design Indaba | SynBioFromLeukipposInstitute | Scoop.it
By applying design thinking to emerging technologies Alexandra Daisy Ginsberg imagines a better future for us all.
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BioTechniques - Bringing Synthetic Biology to (Freeze-dried) Paper

BioTechniques - Bringing Synthetic Biology to (Freeze-dried) Paper | SynBioFromLeukipposInstitute | Scoop.it
Paper-based diagnostics such as pregnancy tests have been around for a while, but over the past few years researchers have been working to answer more complex biological questions. Now, synthetic biologists have developed portable,...
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How do I engineer a memory unit with biomolecules? Part 2 - YouTube

Gerd Moe-Behrens's insight:

A rewritable recombinase addressable data module, able to store data within a DNA sequence (simplified): 


Serine integrase and excisionase are used to invert and restore specific DNA sequences. The system has two potential inputs: a set and a reset transcription signal. 


This set signal drives expression of integrase which inverts a DNA element, functioning as a genetic data register. Flipping the register converts the flanking sites (triangle). The system is now in state 1 (S1). 


Alternatively a reset signal drives integrase and excisionase expression and restores register orientation and the flanking sites. The system is in its other state (S0). 


The register comprises a promoter, which is driving state dependent, strand-specific transcription of either red or green fluorescent protein, the two possible outputs of the system.



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Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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How do I build a finite state machine with biological parts? - YouTube

Gerd Moe-Behrens's insight:

Molecular implementation of a finite state machine. 


The definitions for this machine: The symbols a, b, and t (terminator) are implemented as a sequence of six specific nucleotides. The state (S1 or S0) of the machine is defined by a 5′ overhang (generated during the computing process) consisting of 4 specific nucleotides (inside the frames). The terminator defines the final symbol read. The machine consists of an input molecule, a transition molecule, an output detector and two enzymes Fokl and ligase. 

The input molecule consist of a Fokl recognition site (F), a spacer x (a certain defined number of nucleotides), a nucleotide sequence defining a and b, a sequence with the remaining symbols (rem = n numbers of a and b in a defined order) and the terminator sequence (t). Fokl is a restriction endonuclease which can bind to F. It cleaves the DNA (without further sequence specificity) on the sense strand 9 nucleotides downstream and the anti-sense strand 13 nucleotides upstream of the nearest nucleotide of the recognition site. Thus the space x defines where Fokl is cutting. The cleavage of the input molecule results in the first intermediate state (S0), an 5′ overhang, reading a. Ligase ligate this product with the transition molecule. This transition molecule determinates the transition between the states, in this example: if a is read, move from S0 to S0. Other transition molecules can be generated defining all the other possible transition rules. These molecules are designed such that the 4 bases long 3' overhang reads the symbol, the spacer x defines the cutting point of Fokl 1 and the state the machine will transit to. The input molecule and the transition molecule get ligated. A new digestion with Fokl leaves an 5' overhang representing S0 and a reading b. This cycle continues until all remaining symbols (rem) are read and state transitions are executed. The last digestion leaves a 5' overhang with a terminator sequence defining the final state, in general either S0 or S1 (in this example S0). The molecule in its final state, gets ligated to an output detector, engineered to recognize either state 0 or 1. This forms an output-reporting molecule, which can be detected by gel electrophoresis.


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Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


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Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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How do I build a XOR gate in a biological arithmetic logic unit? - YouTube

Gerd Moe-Behrens's insight:

An inter cellular network based XOR gate: The system is built from four Escherichia coli colonies, whereas each colony consists of a strain engineered to contain a single gate. Three cell colonies (cell 1, 2, 3) containing NOR gates and a fourth (cell 4) a BUFFER gate (two subsequent NOT gates; if in = 0, so out = 0; or if in = 1, so out = 1). The cell colonies communicate through quorum sensing, which represent the “wires” of the system. If both inputs (a, b) are present, or if a and b are absent, the system has no output. If either a or b is present, yellow fluorescent protein (YFP) is expressed.


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Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


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Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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Lecture 11 - Synthetic Biology

In this month's lecture we cover the basics of synthetic biology and possible future applications of advances in this rapidly emerging field.
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Conferences and events | Biochemical Society - Synthetic Biology UK 2015

Conferences and events | Biochemical Society - Synthetic Biology UK 2015 | SynBioFromLeukipposInstitute | Scoop.it
Check out the latest conference and events from the Biochemical Society. Our programme covers a wide spectrum of topics; with events held in the UK and abroad.
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How do I build a NOR gate in a biological arithmetic logic unit? - YouTube

Gerd Moe-Behrens's insight:

A RNA aptamer based NOR gate: NOR is an OR gate followed by a NOT gate. Two subsequent RNA devices consist, in this case, each of three functional components: a sensor, made of a RNA aptamer (brown), an actuator component, made of a hammerhead ribozyme (purple), and a cobbling sequence between these parts, the transmitter (blue). 

Translation of the gene of interest (here GFP), encoded upstream of the device, is only possible in the case of the absence of both inputs (a and b).


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Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw


Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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Dr. Alicia Jackson: Programming the Living World, DARPA BiT | CodonOps

Dr. Alicia Jackson: Programming the Living World, DARPA BiT | CodonOps | SynBioFromLeukipposInstitute | Scoop.it
Dr. Alicia Jackson: Programming the Living World, DARPA BiT
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A Versatile Microfluidic Device for Automating Synthetic Biology - ACS Synthetic Biology (ACS Publications)

A Versatile Microfluidic Device for Automating Synthetic Biology - ACS Synthetic Biology (ACS Publications) | SynBioFromLeukipposInstitute | Scoop.it
RT @ACSSynBio: Learn more about a versatile microfluidic device for automating synthetic biology here: http://t.co/gFQFmJRjxv
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Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance

Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance | SynBioFromLeukipposInstitute | Scoop.it
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Why Bio is the New Digital - Joi Ito keynote - YouTube

From the 2015 Solid Conference. About Joichi Ito (MIT Media Lab): Media Lab Director Joi Ito is a leading thinker and writer on innovation, global technology...
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Synthetic tools for studying the chemical biology of InsP8

Chem Commun (Camb). 2015 Jul 8. [Epub ahead of print]
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Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota: Cell Systems

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota: Cell Systems | SynBioFromLeukipposInstitute | Scoop.it
Using Synthetic Biology to Develop Synthetic Genetic Circuits inside Mice. Scientists achieved up to 10,000-fold... http://t.co/yH8PXD5Np3
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How do I construct busses, wires in a biological microprocessor? - YouTube

Gerd Moe-Behrens's insight:

Wires in silicon microprocessors are made from solid state metals, whereas wires in biocomputers, in the systems engineered so far, consist of signaling molecules, such as regulatory proteins. 


The quorum sensing system we mentioned in the video: “How do I build a XOR gate in a biological arithmetic logic unit?” is one of many examples. In this concrete case are the quorum sensing (chemical signal) molecules used as wires between different logic gates.



BTW

Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw


Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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How do I engineer a memory unit with biomolecules? Part 1 - YouTube

Gerd Moe-Behrens's insight:

Shown is a simplified diagram of a modular memory device, which is a transcriptionally controlled network composed of two transcription factor encoding genes, a sensor gene and a positive (+) auto feedback gene 

(P-GAL = GAL 1/10 promoter, P-CYC = CYC 1 promoter, DNA BD = sequence encoding a DNA binding domain of the respective transcription factor). 


The network can be in three states, off, on and memory. 


The system is in off state, if it has never been exposed to a signal (here galactose). 


It is on, if galactose is present. In this case the signal induces the synthesis of a transcription factor, the sensor. This triggers the expression of another transcription factor able to bind to its own promoter. 


The system is in memory state, if the signal is removed. The auto feedback activator is able to initiate its own expression even if the inducing signal is lacking, which means that the system has stored information.




BTW

Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw


Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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What is a finite state machine? - YouTube

Gerd Moe-Behrens's insight:

Control unit: 


A finite state machine, is a theoretical model which can help to understand what is going on in the control unit. 


Simplified: Symbols a and b are written on a tape, which is read by the machine letter by letter from left to right. In this example the tape ends with the final letter b. Each letter provides the instruction to the machine into which state (S1, or S0) it should move; here a means move to state 0 (S0) and b codes the instruction move to state 1 (S1). The finite state of the machine in this example is thus S1. 



BTW

Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw


Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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Generating Effective Models and Parameters for RNA Genetic Circuits | CodonOps

Generating Effective Models and Parameters for RNA Genetic Circuits | CodonOps | SynBioFromLeukipposInstitute | Scoop.it
Generating Effective Models and Parameters for RNA Genetic Circuits
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Generating Effective Models and Parameters for RNA Genetic Circuits

Generating Effective Models and Parameters for RNA Genetic Circuits
Gerd Moe-Behrens's insight:

by

Chelsea Y. Hu Jeffrey D. Varner , and Julius B. Lucks *


"RNA genetic circuitry is emerging as a powerful tool to control gene expression. However, little work has been done to create a theoretical foundation for RNA circuit design. A prerequisite to this is a quantitative modeling framework that accurately describes the dynamics of RNA circuits. In this work, we develop an ordinary differential equation model of transcriptional RNA genetic circuitry, using an RNA cascade as a test case. We show that parameter sensitivity analysis can be used to design a set of four simple experiments that can be performed in parallel using rapid cell-free transcription-translation (TX-TL) reactions to determine the 13 parameters of the model. The resulting model accurately recapitulates the dynamic behavior of the cascade, and can be easily extended to predict the function of new cascade variants that utilize new elements with limited additional characterization experiments. Interestingly, we show that inconsistencies between model predictions and experiments led to the model-guided discovery of a previously unknown maturation step required for RNA regulator function. We also determine circuit parameters in two different batches of TX-TL, and show that batch-to-batch variation can be attributed to differences in parameters that are directly related to the concentrations of core gene expression machinery. We anticipate the RNA circuit models developed here will inform the creation of computer aided genetic circuit design tools that can incorporate the growing number of RNA regulators, and that the parametrization method will find use in determining functional parameters of a broad array of natural and synthetic regulatory systems.'


http://bit.ly/1CQEEX3

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SULSA 2015 Research Symposium | SULSA

SULSA 2015 Research Symposium | SULSA | SynBioFromLeukipposInstitute | Scoop.it
The heat is on, but SULSA server meltdown is fixed, so you can sign up for Life 2.0:The Synthetic Biology of New Life http://t.co/DWjmigiCXy
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How do I build an NOT gate in a biological arithmetic logic unit? - YouTube

Gerd Moe-Behrens's insight:

Deoxyribozyme based NOT gate: 


The deoxyribozyme (DNA based catalyst) is in an active form, if no input (in) is present (in = 0). Cleavage activity results in this case in a fluorescent oligonucleotid (F) as output. An oligonucleotide input (in) (in = 1) leads to hybridization of the input strand (green) with the closed loop strand, which is marked purple. This results in an inactive, open loop and the absences of a fluorescent product. 



BTW

Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


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Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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How do I build an AND gate in a biological arithmetic logic unit? - YouTube

Arithmetic logic unit: Shown are four basic Boolean logic gates (AND, NOT, NOR, and XOR), their symbols and respective truth tables. 1 means that the input (...
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Engineered particles 'may become antibiotics of the future'

Engineered particles 'may become antibiotics of the future' | SynBioFromLeukipposInstitute | Scoop.it
Using synthetic biology, researchers have engineered particles called phagemids that cause harmful bacteria to malfunction and cease replicating without bursting open.
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High-Throughput Synthetic Biology: Synthesizing Designer Yeast through Automation and Acoustic Liquid Handling | Webinars | GEN

High-Throughput Synthetic Biology: Synthesizing Designer Yeast through Automation and Acoustic Liquid Handling | Webinars | GEN | SynBioFromLeukipposInstitute | Scoop.it
Get the latest in biotechnology through daily news coverage as well as analysis, features, tutorials, webinars, podcasts, and blogs. Learn about the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and commercialization.
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