"Researchers who have assembled a trove of genetic and medical data on 100,000 northern Californians unveiled their initial findings here this week at the annual meeting of the American Society of Human Genetics (ASHG). The effort, which may be the largest such "biobank" in the United States, has already yielded an intriguing connection between mortality and telomeres, the protective DNA sequences that cap chromosome ends, and found new links between genetic variants and disease traits. And that's just the beginning, say the biobank's curators at Kaiser Permanente (KP), the giant health care organization.
The project is one of many that aim to collect medical and DNA data on vast numbers of people and look for links between diseases, lifestyle factors, traits, and genes. More than a decade ago, the company deCODE genetics in Iceland led the way with a biobank now holding data on 140,000 Icelanders; and the UK Biobank, which has enrolled 500,000 people but hasn't yet tested their DNA, may be the largest such study in the world...."
"ABSTRACT: BACKGROUND: Synthetic biology approaches can make a significant contribution to the advance of metabolic engineering by reducing the development time of recombinant organisms. However, most of synthetic biology tools have been developed for Escherichia coli. Here we provide a platform for rapid engineering of C. glutamicum, a microorganism of great industrial interest. This bacteria, used for decades for the fermentative production of amino acids, has recently been developed as a host for the production of several economically important compounds including metabolites and recombinant proteins because of its higher capacity of secretion compared to traditional bacterial hosts like E. coli. Thus, the development of modern molecular platforms may significantly contribute to establish C. glutamicum as a robust and versatile microbial factory. RESULTS: A plasmid based platform named pTGR was created where all the genetic components are flanked by unique restriction sites to both facilitate the evaluation of regulatory sequences and the assembly of constructs for the expression of multiple genes. The approach was validated by using reporter genes to test promoters, ribosome binding sites, and for the assembly of dual gene operons and gene clusters containing two transcriptional units. Combinatorial assembly of promoter (tac, cspB and sod) and RBS (lacZ, cspB and sod) elements with different strengths conferred clear differential gene expression of two reporter genes, eGFP and mCherry, thus allowing transcriptional "fine-tuning"of multiple genes. In addition, the platform allowed the rapid assembly of operons and genes clusters for co-expression of heterologous genes, a feature that may assist metabolic pathway engineering. CONCLUSIONS: We anticipate that the pTGR platform will contribute to explore the potential of novel parts to regulate gene expression, and to facilitate the assembly of genetic circuits for metabolic engineering of C. glutamicum. The standardization provided by this approach may provide a means to improve the productivity of biosynthetic pathways in microbial factories for the production of novel compounds."
Tae Seok Moon, Chunbo Lou, Alvin Tamsir, Brynne C. Stanton & Christopher A. Voigt
"Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics1. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits2, 3, 4, 5, 6, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has been limited to a few circuits1, 7. Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output. This allows the gates to be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. Each gate consists of a transcription factor that requires a second chaperone protein to activate the output promoter. Multiple activator–chaperone pairs are identified from type III secretion pathways in different strains of bacteria. Directed evolution is applied to increase the dynamic range and orthogonality of the circuits. These gates are connected in different permutations to form programs, the largest of which is a 4-input AND gate that consists of 3 circuits that integrate 4 inducible systems, thus requiring 11 regulatory proteins. Measuring the performance of individual gates is sufficient to capture the behaviour of the complete program. Errors in the output due to delays (faults), a common problem for layered circuits, are not observed. This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells."
In response to the recent publication of “Hacking the President’s DNA,” I’ve been fielding a lot of general questions about synthetic biology. I thought I’d put together a little primer for my readers.
The science and ethics of synthetic biology and what it means for the UK will be the subject of a Royal Society of Chemistry debate to be streamed live to the Great Hall of the Wills Memorial Building at the University of Bristol on Wednesday 14...
"In a conversation at an expo at Duke University last week, an executive with Oracle and I discussed my new project on sustainability and synthetic biology. He curiously asked if I made monsters. Honestly, I was not aware that profession even existed.
Clearly, there is a need for more education on this emerging technology. Books on synthetic biology are rare. This is unfortunate. In order to fill that void, scientists and writers are providing the needed discussions to supplement the existing highly technical articles. In Rob Carlson’s Biology is Technology (2010), he argues biology has long been a technology. In Revolutions, released earlier this year, based on philosophical and historical discussions I argue that synthetic biology is the logical extension of genomics.
So, why is synthetic biology important? Many scientists believe an influenza pandemic is impending. We have an astronomical federal deficit; there are developing countries with fast growing populations with pollution and a carbon footprint to match. ...." http://bit.ly/TFotIe
How far would you go to modify yourself using the latest medical technology?
*How Science Can Build a Better You*
By DAVID EWING DUNCAN
"IF a brain implant were safe and available and allowed you to operate your iPad or car using only thought, would you want one? What about an embedded device that gently bathed your brain in electrons and boosted memory and attention? Would you order one for your children? Enlarge This Image
Chris Kim In a future presidential election, would you vote for a candidate who had neural implants that helped optimize his or her alertness and functionality during a crisis, or in a candidates’ debate? Would you vote for a commander in chief who wasn’t equipped with such a device?...." http://nyti.ms/VqsHWq
"In a series of articles we are highlighting the work of some of the leading synthetic biology researchers in the UK. Here we profile how synthetic biology could deliver benefits in the area of health.
Rapid diagnostics The E. coli O157:H7 strain causes a serious infection, which can lead to acute kidney failure and death in up to 5% of cases. Worryingly, the number of outbreaks is on the rise. A critical stage in dealing with infection is in confirming which strain is causing the problem – current detection methods take between 12 and 14 hours.
Professor Tim Dafforn from the University of Birmingham is developing a rapid E. coli detection system using a novel spectroscopic technique called linear dichroism, which detects molecules when they line up in solution if you stir it – just like when you stir a bowl of spaghetti and the strands align around your fork.
He realised that the method could be used to detect long, thin nanoparticles formed from a filamentous virus called M13. M13 is a bacteriophage – a family of viruses that attack bacteria. Using synthetic biology, Dafforn has engineered M13 to 'stick' to chosen target molecules, in this case E.coli.
Just as meatballs disturb aligned spaghetti, bacteria stuck to the virus particles causes them to separate and tangle, a change which can be detected in under two minutes. Image: Professor Tim Dafforn
And, just as meatballs disturb aligned spaghetti, bacteria stuck to the virus particles causes them to separate and tangle, a change which can be detected in under two minutes. The method also has potential to be used for many different bacteria simply by changing the target binding site. A spin-out company, Linear Diagnostics, has been set up by the team to develop the technology. ...." http://bit.ly/TpZPag
"When Heidi Rehm surveys a patient’s genes and finds a variant she’s never seen before, she improvises. First Rehm, who directs a clinical genetics testing laboratory at Partners HealthCare in Cambridge, Massachusetts, checks through as many as ten databases to learn whether that variant has ever been associated with disease. Then she may ask colleagues at other clinical sequencing laboratories whether they have seen it. But the launch this week of a database known as ClinVar will make her job much easier — and allow her to ask more sophisticated questions.
Related stories Share alike Genome interpreter vies for place in clinical market Rapid test pinpoints newborns' genetic diseases in days More related stories Developed by the US National Institutes of Health (NIH) National Center for Biotechnology Information (NCBI) in Bethesda, Maryland, ClinVar integrates dozens of existing databases. It also provides, for the first time, a central place in which clinical testing laboratories can deposit their data, because most currently keep their data within the laboratory. By aggregating such information, ClinVar’s creators hope to accelerate clinicians’ understanding of the effects of variants as well as reveal whether different laboratories are interpreting the same variant in different ways.
“There is a growing recognition that a clinical lab may see a mutation once or never, so it’s better if all those data could be pooled,” explains James Ostell, chief of the information engineering branch at the NCBI and a member of the ClinVar team. Such information could not only help laboratories to improve quality, it could also prompt research on new variants...."
"In recent years, high-throughput discovery of macromolecular protein structures and complexes has played a major role in advancing a more systems-oriented view of protein interaction and signaling networks. The design of biological systems often employs structural information or structure-based protein design to successfully implement synthetic signaling circuits or for rewiring signaling flows. Here, we summarize the latest advances in using structural information for studying protein interaction and signaling networks, and in synthetic biology approaches. We then provide a perspective of how combining structural biology with engineered cell signaling modules—using additional information from quantitative biochemistry and proteomics, gene evolution, and mathematical modeling—can provide insight into signaling modules and the general design principles of cell signaling. Ultimately, this will improve our understanding of cell- and tissue-type-specific signal transduction. Integrating the quantitative effects of disease mutations into these systems may provide a basis for elucidating the molecular mechanisms of diseases."
Months of painstaking work in the laboratory at Bielefeld University‘s Center for Biotechnology (CeBiTec) have paid off: the 15 students participating in this year’s ‘international Genetically Engineered Machine competition’ (iGEM) at the...
The Alliance for Nanomedical Technologies has received an Enhanced CAT Award for $2.8 million over two years from the state of New York, through its New York State Office of Science, Technology and Academic Research (NYSTAR).
One possible pathway from current technology to advanced nanotechnology that will comprise atomically precise manufacturing implemented by atomically precise machinery is through adaptation and extension of the complex molecular machine systems...
"Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial overproduction of various products. As such, it deals with the engineering (construction and optimization) of native as well as non-natural routes of product synthesis, aided in the latter task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest about pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits and non-linear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, these areas do not constitute a coherent definition of synthetic biology with distinct intellectual foundation and well defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products while the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits."
We are a developing a device which aims to improve your diabetes diagnostic and treatment. We are doing this survey in order to find out where you need improvement. We would very much appreciate, if you could answer the questions of this survey. The information is totally anonymous. Thanks so much for your time.
+David Gifford just informed me about this exiting challenge: "Synthetic Biology design contest challenges. Challenge B to design sequences to add Formaldehyde resistance to the arabidopsis plant is underway, with the first deadline coming soon on November 21! Challenge A special programming challenge is also underway to design CAD programming modules to help with the Promoter Design Challenge. You only need access to a computer browser to enter! If you win we will make a real plant with your designs. And there are prizes! "
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