SynBioFromLeukipposInstitute

*Please help to spread the word* Our campaign on #Microryza runs well. We have raised $280 that is 35% of what we needed. The time is short. Thus I ask all of you to make a personal post and spread it in as many social networks as possible. Use this link http://bit.ly/19lscEy Please send also your friends an email. If you know a science blogger, please ask them to support our campaign. If you have any other idea, please let us know. We need creativity. Looking forward to learn about your activity. 
Help us take open science to London! We submitted two papers produced by our synthetic biology lab to the International Workshop on Bio Design Automation that will take place this July in London, and got accepted. But we need your help to cover the registration fees, and travel costs for one of our members. Please lend us a hand and support open science!

 http://bit.ly/19lscEy PS the picture is a collage showing some of our group members 

by
Matthew T. Weinstock 

 http://bit.ly/11KQob0

*I need your help!* Many of you know Leukippos - a synthetic biology lab in the cloud. We are a group of people enthusiastic about synthetic biology and computer science. All our work is voluntary and free of charge. Many of you might know and like our daily posts about synthetic biology. Please, help us take open science to London! We submitted two papers produced by our synthetic biology lab to the International Workshop on Bio Design Automation that will take place this July in London, and got accepted. But we need your help to cover the registration fees, and travel costs for one of our members. Please lend us a hand and support open science! We really need this support. If you have little money, one $ can already make a difference! Thanks for your support and please RT this post! http://bit.ly/19lscEy ;

Synthetic biology to revolutionize treatment of infectious diseases

*Biomedicine Update: Genetic Engineering Changes How We Create Vaccines and Fight Disease*

by
lenrosen4

"Every year I get my influenza vaccine. So does my wife. We do this because our daughter was born with heart disease and we want to ensure that we don’t give her an unneeded bout of the flu which could compromise her health. But every year those who make the flu vaccine or using a best guess approach in formulating the serum.

Flu is an interesting virus. What occurs in the Southern Hemisphere’s winter may be the flu we get in the winter that follows here in the Northern Hemisphere. And of course, vice versa. So you would think that our bio-pharmaceutical industry would have plenty of notice on how to formulate an effective vaccine.

But last winter they got it wrong and lots of people who had the vaccine also got the flu because the variant that hit here in North America was not the one the industry thought we would get.

That’s why I’m interested in how synthetic biology, that is the genetic engineering of vaccines, can allow pharmaceutical companies to speed up the process of developing vaccines in response to viral outbreaks. This means creating a synthetic virus with genes harvested during a disease outbreak and incorporated into an engineered organism.."

http://bit.ly/19Yyr0w

By Katie Drummond 

"As first books go, Dr. Adam Rutherford probably couldn’t have chosen a vaster topic: an investigation into both the origins of life itself, and the incredible potential of its man-made future. In Creation: How Science is Reinventing Itself, Rutherford offers a historical account of biology’s biggest breakthroughs, before introducing readers to what he perceives as the next one on that list: synthetic biology, loosely defined as the radical engineering of new or novel life forms.

 Fortunately for readers, Rutherford is uniquely suited to write such a tome. A geneticist by training, Rutherford contributes regular science columns to The Guardian and recently ended an 11-year stint as an editor at Nature to host a new, weekly BBC show, Inside Science. We caught up with Rutherford, who resides in the UK, to talk about scientists playing God, the Supreme Court’s gene patent ruling… and his love affair with monochromatic clothing. Your new book, Creation, explores synthetic biology — which you say could have a similar impact on society to the Industrial Revolution or the advent of the internet. Why is synthetic biology so important, and how do you see it transforming our lives? The first thing to do is to describe what synthetic biology is, because definitions can differ. I’m hesitant to pin labels, but the primary aim of synthetic biology — and the easiest way to think about it — is the application of engineering techniques to biology, and the application of those techniques to real-world problems. Things like climate change, food production, fuel production, and even space travel...."

http://bit.ly/103FaRo

by
Hua Jiang , Sayed Ahmad Salehi , Marc D. Riedel , and Keshab K. Parhi

"We present a methodology for implementing discrete-time signal processing operations, such as filtering, with molecular reactions. The reactions produce time-varying output quantities of molecules as a function of time-varying input quantities according to a functional specification. This computation is robust and independent of the reaction rates, provided that the rate constants fall within coarse categories. We describe two approaches: one entails synchronization with a clock signal, implemented through sustained chemical oscillations; the other is “self-timed” or asynchronous. We illustrate the methodology by synthesizing a simple moving-average filter, a biquad filter, and a Fast Fourier Transform (FFT). Abstract molecular reactions for these filters and transforms are translated into DNA strand displacement reactions. The computation is validated through mass-action simulations of the DNA kinetics. Although a proof of concept for the time being, molecular filters and transforms have potential applications in fields such as biochemical sensing and drug delivery."
http://bit.ly/17V03D3

by
DANIELA HERNANDEZ

"The U.S. Supreme Court’s unanimous ruling that naturally occurring genes can’t be patented looks, on the surface, like terrible news for biotech companies. It would appear to strike down thousands of patents claiming intellectual property rights over isolated genetic sequences—the very DNA patents that anchor countless business plans.

 Yet biotech stocks saw a small increase on the Nasdaq Biotechnology Index yesterday, and the effect of the ruling was even more dramatic for Myriad Genetics, the Utah company whose patents were in question. Myriad’s stock price closed up nearly 10 percent, at one point topping $38. That’s the highest since 2009, the year the lawsuit against its patents on BRCA1 and BRCA2, two genes associated with early-onset breast and ovarian cancer, was filed. There’s a reason investors rejoiced over a decision that, superficially, seems to strip so many companies of their most valuable assets. John Wilbanks, chief commons officer at Sage Bionetworks, says that competitive advantage comes not from the DNA data itself but from the ways companies figure out to use it. “It’s clearly not as terrifying a ruling for the industry compared to what it could have been,” Wilbanks said. “It’s a decision that says that data is free, and that’s in line with what patent law has always said, which is that you can’t patent data. That’s what a gene sequence is. “By making that data free, there is a lot of room for public good and public and private innovation.” At the same time, the court did not strike down patents on “new applications of knowledge,” or on DNA whose sequence has been altered. In other words, biotechnologists still have plenty of room to develop proprietary innovations that use DNA data in new ways. Businesses can be build on genetic insights applied to new processes, methods or algorithms, which in most cases would still be patentable....."

http://bit.ly/1aeCtAv*

G8 science ministers endorse open access http://bit.ly/11lJmcJ

 http://bit.ly/19AfvoM

by
Guillermo Rodrigo and Alfonso Jaramillo

"Synthetic regulatory networks with prescribed functions are engineered by assembling a reduced set of functional elements. We could also assemble them computationally if the mathematical models of those functional elements were predictive enough in different genetic contexts. Only after achieving this will we have libraries of models of biological parts able to provide predictive dynamical behaviors for most circuits constructed with them. We thus need tools that can automatically explore different genetic contexts, in addition to being able to use such libraries to design novel circuits with targeted dynamics. We have implemented a new tool, AutoBioCAD, aimed at the automated design of gene regulatory circuits. AutoBioCAD loads a library of models of genetic elements and implements evolutionary design strategies to produce (i) nucleotide sequences encoding circuits with targeted dynamics that can then be tested experimentally and (ii) circuit models for testing regulation principles in natural systems, providing a new tool for synthetic biology. AutoBioCAD can be used to model and design genetic circuits with dynamic behavior, thanks to the incorporation of stochastic effects, robustness, qualitative dynamics, multiobjective optimization, or degenerate nucleotide sequences, all facilitating the link with biological part/circuit engineering."

http://bit.ly/160SRkS

Video: Living Factories: Engineering Cells to Manufacture Molecules http://bit.ly/11cCz8t

by
Sabrina Wend, Cristina Dal Bosco, [...], and Matias D. Zurbriggen

"Time-resolved quantitative analysis of auxin-mediated processes in plant cells is as of yet limited. By applying a synergistic mammalian and plant synthetic biology approach, we have developed a novel ratiometric luminescent biosensor with wide applicability in the study of auxin metabolism, transport, and signalling. The sensitivity and kinetic properties of our genetically encoded biosensor open new perspectives for the analysis of highly complex auxin dynamics in plant growth and development."

http://1.usa.gov/14ptd7R

by
Yu-Tzu Chena, Yen-Cheng Liua, Wei-Feng Fanga, Chao-Jyun Huanga, Shih-Kang Fana, Wen-Jone Chenb, Wei-Tien Changb, Chien-Hua Huangb, Jing-Tang Yanga,

"Highlights

•DNA diagnosis is achieved in a microseparator based on particle aggregation/behaviour.•Target DNA is readily screened in the two-outlet PFF microseparator.•The concentration is determined in the six-outlet PFF microseparator.•The detection limit is around 33 pM.•The identification of single-nucleotide polymorphism (SNP) is realized.AbstractA novel aggregation-based biosensing method to achieve detection of oligonucleotides in a pinched-flow fractionation (PFF) microseparator was developed. Employing functionalized polystyrene microspheres, this method is capable of the direct detection of the concentration of a specific DNA sequence. The label-free target DNA hybridizes with probe DNA of two kinds on the surface of the microspheres and causes the formation of an aggregate, thus increasing the average size of the aggregate particles. On introducing the sample into a PFF microseparator, the aggregate particles locate at a specific position depending on the size of the aggregate. Through a multi-outlet asymmetric PFF microseparator, the aggregate particles become separated according to outlets. Because the size of the aggregate particles is proportional to the concentration of the target DNA, a rapid quantitative analysis is achievable with an optical microscope. A biological dose-response curve with concentration in a dynamic range 0.33 -- 10 nM has been achieved; the limit of detection is between 33 and 330 pM. The specificity of the method and the potential to detect single-nucleotide polymorphism (SNP) of known concentration were examined. The method features simple, direct and cheap detection, with a prospect of detecting other biochemical samples with distinct aggregation behaviour, such as heavy-metal ions, bacteria and proteins...."

http://bit.ly/10zp305

by
Oliver Purcell, Bonny Jain, Jonathan R. Karr, Markus W. Covert, and Timothy K. Lu

"Despite rapid advances over the last decade, synthetic biology lacks the predictive tools needed to enable rational design. Unlike established engineering disciplines, the engineering of synthetic gene circuits still relies heavily on experimental trial-and-error, a time-consuming and inefficient process that slows down the biological design cycle. This reliance on experimental tuning is because current modeling approaches are unable to make reliable predictions about the in vivo behavior of synthetic circuits. A major reason for this lack of predictability is that current models view circuits in isolation, ignoring the vast number of complex cellular processes that impinge on the dynamics of the synthetic circuit and vice versa. To address this problem, we present a modeling approach for the design of synthetic circuits in the context of cellular networks. Using the recently published whole-cell model of Mycoplasma genitalium, we examined the effect of adding genes into the host genome. We also investigated how codon usage correlates with gene expression and find agreement with existing experimental results. Finally, we successfully implemented a synthetic Goodwin oscillator in the whole-cell model. We provide an updated software framework for the whole-cell model that lays the foundation for the integration of whole- cell models with synthetic gene circuit models. This software framework is made freely available to the community to enable future extensions. We envision that this approach will be critical to transforming the field of synthetic biology into a rational and predictive engineering discipline...."



 http://stanford.io/14fdqc6

*Biology: The big challenges of big data* 

by
Vivien Marx

"Biologists are joining the big-data club. With the advent of high-throughput genomics, life scientists are starting to grapple with massive data sets, encountering challenges with handling, processing and moving information that were once the domain of astronomers and high-energy physicists1.

 With every passing year, they turn more often to big data to probe everything from the regulation of genes and the evolution of genomes to why coastal algae bloom, what microbes dwell where in human body cavities and how the genetic make-up of different cancers influences how cancer patients fare2. The European Bioinformatics Institute (EBI) in Hinxton, UK, part of the European Molecular Biology Laboratory and one of the world's largest biology-data repositories, currently stores 20 petabytes (1 petabyte is 1015 bytes) of data and back-ups about genes, proteins and small molecules. Genomic data account for 2 petabytes of that, a number that more than doubles every year3 (see 'Data explosion'). This data pile is just one-tenth the size of the data store at CERN, Europe's particle-physics laboratory near Geneva, Switzerland. Every year, particle-collision events in CERN's Large Hadron Collider generate around 15 petabytes of data — the equivalent of about 4 million high-definition feature-length films. But the EBI and institutes like it face similar data-wrangling challenges to those at CERN, says Ewan Birney, associate director of the EBI. He and his colleagues now regularly meet with organizations such as CERN and the European Space Agency (ESA) in Paris to swap lessons about data storage, analysis and sharing.  SOURCE: EMBL–EBIDownload PDF All labs need to manipulate data to yield research answers. As prices drop for high-throughput instruments such as automated genome sequencers, small biology labs can become big-data generators. And even labs without such instruments can become big-data users by accessing terabytes (1012 bytes) of data from public repositories at the EBI or the US National Center for Biotechnology Information in Bethesda, Maryland. Each day last year, the EBI received about 9 million online requests to query its data, a 60% increase over 2011...."

http://bit.ly/16o9ozW

by
+David Bikard  Wenyan Jiang, Poulami Samai, Ann Hochschild, Feng Zhang and Luciano A. Marraffini

"The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease that participates in the CRISPR-Cas immune defense against prokaryotic viruses. We describe the use of a Cas9 nuclease mutant that retains DNA-binding activity and can be engineered as a programmable transcription repressor by preventing the binding of the RNA polymerase (RNAP) to promoter sequences or as a transcription terminator by blocking the running RNAP. In addition, a fusion between the omega subunit of the RNAP and a Cas9 nuclease mutant directed to bind upstream promoter regions can achieve programmable transcription activation. The simple and efficient modulation of gene expression achieved by this technology is a useful asset for the study of gene networks and for the development of synthetic biology and biotechnological applications.>>"


http://bit.ly/16k79xv

*Supreme Court Decision Opens the Doors to A Boom in Synthetic Biology* 

by
Morgan Clendaniel

"Today’s Supreme Court ruling on the patenting of human genes was a boost to the field of synthetic biology. While human genes cannot be directly patented, the Court found, so-called complementary DNA can. This is DNA that is synthesized from the rNA in a genetic template and then cloned. The Court found that while naturally occurring DNA is not a human creation, "the lab technician unquestionably creates something new when cDNA is made. "

Synthetic biology relies on this synthesized cDNA. Synthetic biology has been in the news lately for many reasons. Last Friday a unique Kickstarter campaign closed with almost $500,000 in donations (well over a $65,000 goal). As a result, three young DIY bio enthusiasts will distribute to almost 6,000 backers, who kicked in at least $40 each, packages of synthetically genetically engineered seeds that supposedly will allow each of them to grow bioluminescent house plants--Arabidopsis and eventually roses--at home. Synthetic biology is an emerging and controversial scientific field that uses gene-writing software to compile DNA sequences, in this case, taken and modified from a firefly, that are then printed onto a blotter. The Glowing Plants project will use a "Gene Gun" to "fire" particles of gold coated in DNA into living cells. The use of the gun does an end run around USDA regulations that govern the use of viruses or other pathogens to modify DNA. The project started at Singularity University. It’s designed as a public demonstration of the power of DIY Biology. And herein lies the problem for some critics. The potential applications of synthetic biology are to create immensely useful, lifesaving things, like a cure for Alzheimer’s disease, or a rice crop that needs as little water as a cactus, or an algae or other single-celled species that can produce near-perfect petroleum analogues from the sun or from toxic chemicals. These glowing plants don’t do any of that, and scientists and environmentalists question if the wow factor is really worth the risk. Though the project is technically legal, its sheer hubris has kickstarted some serious from scientists and environmental groups that object to the release of these seeds to the public, with the chance that the DNA will get into the natural gene pool with unknown consequences. An anti-synthetic bio group called ETC has started a fundraising drive of their own, dubbed a "Kickstopper." "To date all [experts] have agreed that no synthetic organisms should yet be released into the environment without 'precaution,' 'prudent vigilance,' regulation, monitoring and other sober and sensible safeguards. Yet now the US government appears ready to avert its eyes," they write on their website. And a on Avaaz.org has over 13,000 signatures. Other scientists object that it’s unlikely that the small plant will actually be able to process enough energy to visibly glow, even slightly or for a few seconds at a time. The journal Nature notes that the Glowing Plants project is among other genetically modified, glow in the dark creature to be available to the public soon. A company called BioGlow in St. Louis also intends to sell glowing houseplants. Commercially available synthetically engineered animals, to say nothing of human cDNA, are still far away, but if they appear, they’ll be protected by intellectual property law."

http://bit.ly/11cFDBA