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CytoComp`s mission is to build the first microprocessor made from biological parts. It has an input output unit, which can both take a electrical as a biological signal. Thus you can monitor on your smartphone, what is going on in the biological system.
CytoComp will do what Intel has done with silicon with biological parts.
You can get a free review about biological computing if you go to this page
The backer of this campaign get some very interesting rewards.
For 1 Bitcoin ($119) you get exclusive early developer access to CytoComp`s CAD (computer assisted design platform, which allows you to custom design a biological microprocessor). Hurry - only 40 left!
If you do not have Bitcoins we can arrange a payment by PayPal. For that case please contact me at
This is a one time opportunity for developer and tinkeres to get exclusive access to a revolutionizing technology, which can have many applications.
Please help CytoComp to raise the remaining $4763.
Thanks for your support.
BTW this crowd funding campaign is part of a competition arranged by Stanford University. CytoComp is so far the leading top 1 most funded team. You can follow here http://startupmooc.org
Recent funds we have received via PayPal are even not added.
As this concept might be new for many, I wish in the following to explain a bit what biological computer can be used to. I will in the following also make some posts to focus on certain diseases.
Potential applications of biological computers
Biological computers possess some distinct advantages over silicon computers . These systems can self-assemble and self- reproduce, which might provide some economic advantages. Moreover, cells can be engineered to sense and respond to environmental signals, even under extreme conditions such as high temperature, high pressure, radioactivity or toxic chemicals. Biological systems have the ability to adapt to new information from a changed environment.
The ultimate goals of biocomputing are the monitoring and control of biological systems.
Monitoring of biological systems
Biological systems need to be monitored in respect to disease diagnostic, to drug screening, to understand experimental systems, and to observe the environment.
In line with this, a biocomputer has been utilized to detect multiple disease indicators, such as mRNA of disease-related genes associated with small-cell lung cancer and prostate cancer. Moreover, they can be used in experimental models, such as conditional transgenes or inducible expression systems. Environmental monitoring is another interesting application. A cell based biosensor using logic gates has been used to detect arsenic, mercury and copper ion levels.
Control of biological systems
Biocomputers can potentially be used to control development, cell differentiation and re-programming, as all these processes depend on gene regulatory networks. Another application area is tissue engineering and tissue regeneration. Metabolic engineering has the potential to produce from simple, inexpensive starting materials a large number of chemicals that are currently derived from nonrenewable resources or limited natural resources. The metabolic flux can potentially be controlled by a biocomputer . Interesting might also be to control the immune system by a biocomputer, e.g. in transplantation medicine . An important application area is the control of malign growth. Some interesting experiments with logic based biological devices have been executed to detect cancer cells (e.g. small-cell lung cancer, prostate cancer, HeLa cells), and to induce selective apoptosis of these cells. Furthermore, biocomputers can be used to engineer context-dependent programmable drugs. A biocomputer with a context-sensing mechanism, which can simultaneously sense different types of molecules, has been engineered. In the future it might be used to detect a broad range of molecular disease symptoms, and react with the release of a drug molecule suitable for the treatment of the specific condition. In line with this concept a programmable NOR-based device has been developed capable of differentiating between prokaryotic cell strains based on their unique expression profile.
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"The cost and accuracy of genome sequencing have improved dramatically. George Church asks why so few people are opting to inspect their genome.
Synthetic biology -- unlike any research discipline that precedes it -- has the potential to bypass the less predictable process of evolution to usher in a new and dynamic way of working with living systems.
byKoeppl H, Hafner M, Lu J."With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal design specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified design constraints are robustly satisfied. In this work we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction. The method is general and can hence be incorporated in a pipeline for the rational forward design of arbitrary devices in synthetic biology." http://bit.ly/18slJ5K
byNicolas Papon , Vincent Courdavault and Marc Clastre"Highlights
byMarkus J. Brçcker, Joanne M. L. Ho, George M. Church, Dieter Sçll, and Patrick ODonoghue"Selenocysteine (Sec) is naturally incorporated into proteins by recoding the stop codon UGA. Sec is not hardwired to UGA, as the Sec insertion machinery was found to be able to site-specifically incorporate Sec directed by 58 of the 64 codons. For 15 sense codons, complete conversion of the codon meaning from canonical amino acid (AA) to Sec was observed along with a tenfold increase in selenoprotein yield compared to Sec insertion at the three stop codons. This high-fidelity sense-codon recoding mechanism was demonstrated for Escherichia coli formate dehydrogenase and recombinant human thioredoxin reductase and confirmed by independent biochemical and biophysical methods. Although Sec insertion at UGA is known to compete against protein termination, it is surprising that the Sec machinery has the ability to outcompete abundant aminoacyl-tRNAs in decoding sense codons. The findings have implications for the process of translation and the information storage capacity of the biological cell."http://bit.ly/1964083
Cathal Garvey is the creator of the blog Indie Biotech, his personal endeavour to provide tools, materials and learning resources for biotechnology to indivi...
byThomas E. Gorochowski , Eric van den Berg , Richard Kerkman , Johannes A Roubos , and Roel A.L. Bovenberg"Synthetic biology has developed numerous parts for the precise control of protein expression. However, relatively little is known about the burden these place on a host, or their reliability under varying environmental conditions. To address this, we made use of synthetic transcriptional and translational elements to create a combinatorial library of constructs that modulated expression strength of a green fluorescent protein. Combining this library with a microbioreactor platform, we were able to perform a detailed large-scale assessment of transient expression and growth characteristics of two Escherichia coli strains across several temperatures. This revealed significant differences in the robustness of both strains to differing types of protein expression, and a complex response of transcriptional and translational elements to differing temperatures. This study supports the development of reliable synthetic biological systems capable of working across different hosts and environmental contexts. Plasmids developed during this work have been made publicly available to act as a reference set for future research." http://bit.ly/18o4QJp
byHelen Shen"Scientists launch company to develop the therapeutic potential of gene-snipping enzymes.Instead of taking prescription pills to treat their ailments, patients may one day opt for genetic 'surgery' — using an innovative gene-editing technology to snip out harmful mutations and swap in healthy DNA.The system, called CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), has exploded in popularity in the past year, with genetic engineers, neuroscientists and even plant biologists viewing it as a highly efficient and precise research tool. Now, the gene-editing system has spun out a biotechnology company that is attracting attention from investors as well.
Scientists have finally turned human stem cells into lung cells, and say the breakthrough paves the way for using a patient's own cells for lung transplant.
byZhang M, Wang F, Li S, Wang Y, Bai Y, Xu X."Transcription activator-like effectors (TALEs), first identified in Xanthomonas bacteria, are naturally occurring or artificially designed proteins that modulate gene transcription. These proteins recognize and bind DNA sequences based on a variable numbers of tandem repeats. Each repeat is comprised of a set of ∼34 conserved amino acids; within this conserved domain, there are usually two amino acids that distinguish one TALE from another. Interestingly, TALEs have revealed a simple cipher for the one-to-one recognition of proteins for DNA bases. Synthetic TALEs have been used to successfully target genes in a variety of species, including humans. Depending on the type of functional domain that is fused to the TALE of interest, these proteins can have diverse biological effects. For example, after binding DNA, TALEs fused to transcriptional activation domains can function as robust transcription factors (TALE-TFs), while fused to restriction endonucleases (TALENs) can cut DNA. Targeted genome editing, in theory, is capable of modifying any endogenous gene sequence of interest; this can be performed in cells or organisms, and may be applied to clinical gene-based therapies in the future. With current technologies, highly accurate, specific, and reliable gene editing cannot be achieved. Thus, recognition and binding mechanisms governing TALE biology are currently hot research areas. In this review, we summarize the major advances in TALE technology over the past several years with a focus on the interaction between TALEs and DNA, TALE design and construction, potential applications for this technology, and unique characteristics that make TALEs superior to zinc finger endonucleases." http://bit.ly/IErZ3z
byJacqueline Vanacek"In April 2013, we celebrated the 10th anniversary of the completion of the Human Genome Project. Led by the National Institutes of Health, the Human Genome Project (HGP) was completed 2.5 years ahead of schedule and well under budget. “For the first time, anyone could freely read the fundamental instruction set needed to make a human body.”But it took years and billions of dollars to reach this point. How did we get here? And where are we headed? While those in the field point to “next gen sequencing” as a primary accelerator for the HGP, I wanted to explore what that meant.So I visited the nexus of the HGP — the National Human Genome Research Institute – to hear the history and tour the laboratory with NIH Intramural Sequencing Center (NISC) Director Jim Mullikin, PhD and Head of IT Systems Don Preuss from the National Center for Biotechnology Information (NCBI).The NIH Intramural Sequencing Center delivers high throughput DNA sequencing to support NHGRI’s basic research into both cause and treatments for genetic diseases. NISC experts “manufacture” high outputs of usable genomics data from samples of purified DNA or RNA for clinical investigators. And NCBI provides the advanced software tools and databases to study these “biologically important molecules.” The NISC tour included a look at past and present DNA sequencers with Jim Mullikin.“First Generation” DNA SequencingNHGRI defines DNA sequencing as a “laboratory technique used to determine the exact sequence of bases (A, C, G and T) in a DNA molecule. The DNA base sequence carries the information a cell needs to assemble protein and RNA molecules” which govern how our bodies are built and function.While recently deceased genomics pioneer and Nobel Laureate Frederick Sanger developed rapid DNA sequencing chemical methods in the 1970s, it was not until ten years later, in 1986, that the first fully automated DNA sequencing instrument appeared on the market.These early automated sequencers were used in the Human Genome Project and could decipher about 700-1000 base-pair long DNA fragments at a time. There was no ability or expectation to decipher and map a full human genome back then. And with 3 billion DNA building blocks making up a single human genome, the HGP required thousands of scientists mapping thousands of fragments to eventually be reconstructed into one complete sequence.Back then, each DNA sequencer cost about $1 million. And when one considers how labor-intensive this early work was, it’s easy to understand why it took 13 years and cost about $3.5 billion in total to map the 99% of the Human Genome DNA blueprint that is identical for all of us.“Next Generation” DNA SequencingWhen Dr. Francis Collins, then Director of NHGRI, challenged the genomics community to reduce the cost of mapping a personal genome from $100 million to $1000, advances in DNA sequencers skyrocketed.The subsequent miniaturization of sequencers has allowed for smaller DNA sample sizes, less chemical reagents and the ability to run multiple DNA samples in parallel. All of these factors have dramatically reduced the time and cost of analysis.Today, a variety of sequencers exists, ranging from those that can survey a full human genome in eleven days to jumpstart a research investigation — to solid state sequencers that can do a partial analysis in just a day for quality control or to zero in on a specific chromosome.Where DNA Sequencing Is HeadedEven with so many advances in DNA sequencing, there is another wave yet to come! For example, Jim Mullikin talked about the Genome in a Bottle Consortium’s collaboration with the National Institute of Standards. NIST will develop whole genome reference materials to ensure accuracy of high throughput DNA sequencing done in a clinical setting. Recent studies show that false positives or negatives in genetic variants or mutations could arise from different sequencing and bioinformatics analysis methods. The reference materials would ensure that any risk is minimized.Finally, Don Preuss described the emerging genome-in-a-box concept, with a myriad of vendor approaches. For example, from Harvard Medical School, George Church’s Knome company is offering a “plug-and-play” human genome interpretation system. It combines hardware and genomic interpretation software to simplify getting “useful medical information from a patient’s DNA.” This approach supports data privacy and regulatory compliance.Genomics leader Illumina’s “lab in a box” model permits customers to “upload their DNA sequences to a cloud-based data storage and analysis system for interpretation.” And Bina Technologies offers a pay-per-use Genomic Analysis Platform or on premise appliance that can process a whole human genome in only 4 hours......" http://onforb.es/IJzvuR
RT @TeselaGen: A New Paper In Synthetic Biology Sheds “Light” On Future: http://t.co/82kugjtlbm #synbio #cyanobacteria #photosynthesis #sys…
"this is how I envisioned synthetic biology would look": comment on Murray paper on a designed concentration tracker http://t.co/80i5zZRNGN
bySun ZZ, Yeung E, Hayes CA, Noireaux V, Murray RM."Accelerating the pace of synthetic biology experiments requires new approaches for rapid prototyping of circuits from individual DNA regulatory elements. However, current testing standards require days to weeks due to cloning and in vivo transformation. In this work, we first characterized methods to protect linear DNA strands from exonuclease degradation in an Escherichia coli based transcription-translation cell-free system (TX-TL), as well as mechanisms of degradation. This enabled the use of linear DNA PCR products in TX-TL. We then compared expression levels and binding dynamics of different promoters on linear DNA and plasmid DNA. We also demonstrated assembly technology to rapidly build circuits entirely in vitro from separate parts. Using this strategy, we prototyped a four component genetic switch in under 8 h entirely in vitro. Rapid in vitro assembly has future applications for prototyping multiple component circuits if combined with predictive computational models." http://bit.ly/1bOWl07
byMaryJoe K Rice and Warren C Ruder"Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems."http://bit.ly/1kn5g8d
DNA sequencing seems to be an eternal theme for human due to the desire of ascertaining the nature of life.
byRichard A. Stein"“Science is more than a body of knowledge, it’s a way of thinking,” remarked Carl Sagan, and probably his words were never more powerfully relevant than for portraying one of the newest biomedical felds, systems biology.A recent symposium inaugurating the depart- ment of systems biology at Columbia Univer- sity Medical Center comes at a very auspi- cious time, one in which biomedical sciences, chemistry, physics, engineering, bioinformat- ics, and computer sciences are converging to shape a vibrant new discipline.As Lee Goldman, M.D., M.P.H., execu- tive vice president for health and biomedical sciences at the Columbia University College of Physicians and Surgeons pointed out dur- ing the opening remarks, this new feld “rep- resents so much about our future.”Within a relatively short time, we have re- alized the possibility of sequencing and map- ping the genome of virtually any organism. Concomitantly, as increasingly sophisticated technologies allow whole-genome sequences to be completed within hours to days, navigat- ing the vast datasets has become the foremost challenge, opening a gap in our ability to un- derstand and interpret their significance....." http://bit.ly/18dDwmj
Metabolic modelling in the development of cell factories by synthetic biology
byPaula Tuulia Jouhten"Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory."http://bit.ly/1gaBRk7
byYunzi Luo,Hua Huang,Jing Liang,Meng Wang,Lu Lu,Zengyi Shao,Ryan E. Cobb& Huimin Zhao"Polycyclic tetramate macrolactams (PTMs) are a widely distributed class of natural products with important biological activities. However, many of these PTMs have not been characterized. Here we apply a plug-and-play synthetic biology strategy to activate a cryptic PTM biosynthetic gene cluster SGR810-815 from Streptomyces griseus and discover three new PTMs. This gene cluster is highly conserved in phylogenetically diverse bacterial strains and contains an unusual hybrid polyketide synthase-nonribosomal peptide synthetase, which resembles iterative polyketide synthases known in fungi. To further characterize this gene cluster, we use the same synthetic biology approach to create a series of gene deletion constructs and elucidate the biosynthetic steps for the formation of the polycyclic system. The strategy we employ bypasses the traditional laborious processes to elicit gene cluster expression and should be generally applicable to many other silent or cryptic gene clusters for discovery and characterization of new natural products. http://bit.ly/IS5mcQcomment:*New method of DNA editing allows synthetic biologists to unlock secrets of a bacterial genome*byAnonymous"A group of University of Illinois researchers, led by Centennial Chair Professor of the Department of Chemical and Biomolecular Engineering Huimin Zhao, has demonstrated the use of an innovative DNA engineering technique to discover potentially valuable functions hidden within bacterial genomes. Their work was reported in a Nature Communications article on December 5, 2013.
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The ‘reading’ of DNA is a solved technological problem but what about ‘writing’ DNA? Could we program or reprogram biological systems and even generate new life forms? In this Friday Evening Discourse at the Ri, Paul Freemont explores how the powerful fusion of molecular biology, design and engineering could lead to a ‘Biotechnological Revolution’ and considers the implications of the extraordinary field of synthetic biology.
Scientists launch company to develop the therapeutic potential of gene-snipping enzymes
A showcase of the best infographics from around the web
byPorcar M, Peretó J."Synthetic Biology is a singular, revolutionary scenario with a vast range of practical applications but, is SB research really based on engineering principles? Is it contributing to the artificial synthesis of life or using approaches "sophisticated" enough to fall outside the scope of biotechnology or metabolic engineering? We have reviewed the state of the art on synthetic biology and we conclude that most research projects actually describe an extension of metabolic engineering. We draw this conclusion because the complexity of living organisms, their tight dependence on evolution and our limited knowledge of the interactions between the molecules they are made of, actually make life difficult to engineer. We therefore propose the term synthetic biology should be used more sparingly."