by Pablo I. Nikel,Esteban Martínez-García& Víctor de Lorenzo
"Much of contemporary synthetic biology research relies on the use of bacterial chassis for plugging-in and plugging-out genetic circuits and new-to-nature functionalities. However, the microorganisms that are the easiest to manipulate in the laboratory are often suboptimal for downstream industrial applications, which can involve physicochemical stress and harsh operating conditions. In this Review, we advocate the use of environmental Pseudomonas strains as model organisms that are pre-endowed with the metabolic, physiological and stress-endurance traits that are demanded by current and future synthetic biology and biotechnological needs."
Yusuf E. Murgha, Jean-Marie Rouillard, Erdogan Gulari
"Custom-defined oligonucleotide collections have a broad range of applications in fields of synthetic biology, targeted sequencing, and cytogenetics. Also, they are used to encode information for technologies like RNA interference, protein engineering and DNA-encoded libraries. High-throughput parallel DNA synthesis technologies developed for the manufacture of DNA microarrays can produce libraries of large numbers of different oligonucleotides, but in very limited amounts. Here, we compare three approaches to prepare large quantities of single-stranded oligonucleotide libraries derived from microarray synthesized collections. The first approach, alkaline melting of double-stranded PCR amplified libraries with a biotinylated strand captured on streptavidin coated magnetic beads results in little or no non-biotinylated ssDNA. The second method wherein the phosphorylated strand of PCR amplified libraries is nucleolyticaly hydrolyzed is recommended when small amounts of libraries are needed. The third method combining in vitro transcription of PCR amplified libraries to reverse transcription of the RNA product into single-stranded cDNA is our recommended method to produce large amounts of oligonucleotide libraries. Finally, we propose a method to remove any primer binding sequences introduced during library amplification."
Biomedical engineer James Collins of Boston and Harvard universities and the Howard Hughes Medical Institute, will give a BSA Distinguished Lecture, titled "Life Redesigned: The Emergence of Synthetic Biology," at the U.S. Department of Energy's Brookhaven National Laboratory on Wednesday, April 30.
by Eduardo Antonio Della Pia, Randi Westh Hansen, Manuela Zoonens, Karen L. Martinez
"Amphipols are amphipathic polymers that stabilize membrane proteins isolated from their native membrane. They have been functionalized with various chemical groups in the past years for protein labeling and protein immobilization. This large toolbox of functionalized amphipols combined with their interesting physico-chemical properties give opportunities to selectively add multiple functionalities to membrane proteins and to tune them according to the needs. This unique combination of properties makes them one of the most versatile strategies available today for exploiting membrane proteins onto surfaces for various applications in synthetic biology. This review summarizes the properties of functionalized amphipols suitable for synthetic biology approaches." http://bit.ly/1h0r7QB
by Arthur Prindle,Jangir Selimkhanov,Howard Li,Ivan Razinkov,Lev S. Tsimring& Jeff Hasty
"One promise of synthetic biology is the creation of genetic circuitry that enables the execution of logical programming in living cells. Such ‘wet programming’ is positioned to transform a wide and diverse swathe of biotechnology ranging from therapeutics and diagnostics to water treatment strategies. Although progress in the development of a library of genetic modules continues apace1, 2, 3, 4, a major challenge for their integration into larger circuits is the generation of sufficiently fast and precise communication between modules5, 6. An attractive approach is to integrate engineered circuits with host processes that facilitate robust cellular signalling7. In this context, recent studies have demonstrated that bacterial protein degradation can trigger a precise response to stress by overloading a limited supply of intracellular proteases8, 9, 10. Here we use protease competition to engineer rapid and tunable coupling of genetic circuits across multiple spatial and temporal scales. We characterize coupling delay times that are more than an order of magnitude faster than standard transcription-factor-based coupling methods (less than 1 min compared with ~20–40 min) and demonstrate tunability through manipulation of the linker between the protein and its degradation tag. We use this mechanism as a platform to couple genetic clocks at the intracellular and colony level, then synchronize the multi-colony dynamics to reduce variability in both clocks. We show how the coupled clock network can be used to encode independent environmental inputs into a single time series output, thus enabling frequency multiplexing (information transmitted on a common channel by distinct frequencies) in a genetic circuit context. Our results establish a general framework for the rapid and tunable coupling of genetic circuits through the use of native ‘queueing’ processes such as competitive protein degradation."
The possibility of the deliberate creation of living organisms from elementary materials that are not themselves alive has engaged the human imagination for a very long time. Putting aside Genesis I, which is singularly lacking in any physical details on the bringing forth of life from the waters and the dust, we think immediately of the classical Greek story of the sculptor Pygmalion. Enamored of the unresponsive goddess Aphrodite, he ...
by Aoki W, Saito M, Manabe R3 Mori H4, Yamaguchi Y2 Tamiya E2
"We propose 'integrated synthetic genetics' as a novel methodology that integrates reductive and synthetic approaches used in life science research. Integrated synthetic genetics enables determinations of sets of genes required for the functioning of any biological subsystem. This method utilizes artificial cell-like compartments, including a randomly introduced whole gene library, strictly defined components for in vitro transcription and translation and a reporter that fluoresces 'only when a particular function of a target biological subsystem is active.' The set of genes necessary for the target biological subsystem can be identified by isolating fluorescent artificial cells and multiplex next-generation sequencing of genes included in these cells. The importance of this methodology is that screening for the set of genes involved in a subsystem and reconstructing the entire subsystem can be done simultaneously. This methodology can be applied to any biological subsystem of any species and may remarkably accelerate life science research."
"An international team of researchers has embarked on the creation of a synthetic eukaryotic genome and now report the synthesis of a redesigned Saccharomyces cerevisiae chromosome. Boeke and colleagues built a fully functional chromosome III (which they term synIII) that contained hundreds of alterations, including the removal of introns, transposons…"
I hope the internet will stay under US control. If I think about the alternatives, the US will be the most likely guardian for a free internet, despite the recent surveillance scandals. Science need a free internet.
LOUISVILLE, Ky. (AP) -- It may sound far-fetched, but scientists are attempting to build a human heart with a 3-D printer.Ultimately, the goal is to create a new heart for a patient with their own cells that could be transplanted. It is an ambitious project to first, make a heart and then get it to work in a patient, and it could be years — perhaps decades — before a 3-D printed heart would ever be put in a person.The technology, though, is not all that futuristic: Researchers have already used 3-D printers to make splints, valves and even a human ear.
"Cellular biocircuit design has taken a major step forward. The circuit reuses the cell's own protein-degradation system to synchronize the expression of two synthetic modules throughout an entire bacterial population."
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