SynBioFromLeukipposInstitute

by
Helen 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.

http://bit.ly/1bhL7uM

by
Zhang 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

by
Jacqueline 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 Sequencing
NHGRI 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 Sequencing
When 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 Headed
Even 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

by
Tanaya Joshi

"Being from a very different background than my fellow bloggers, it can be a challenge to find a topic to write about. I mean, I’m an Industrial Design major and that’s pretty far from science and labs and stuff, right? WRONG!

 http://bit.ly/IAPmdZ

*Researchers find a missing component in effort to create primitive, synthetic cells*

by
Anonymous

"A team of Massachusetts General Hospital (MGH) investigators working to create "protocells" – primitive synthetic cells consisting of a nucleic acid strand encased within a membrane-bound compartment – have accomplished an important step towards their goal. In the November 28 issue of Science, the investigators describe a solution to what could have been a critical problem – the potential incompatibility between a chemical requirement of RNA copying and the stability of the protocell membrane.

by
Sachin Rawat

"A recent addition to the list of discoveries that stay neglected for long before their full potential is realized – CRISPR – may revolutionize genetic engineering. Two and a half decades after its discovery in the bacterial systems, Clustered Regularly Interspaced Short Palindromic Repeats are now being seen as the tools to edit genomes with precision like never before.

 http://bit.ly/1jKU6dd

by
+Jonny Serfaty 

"Sunny Allen was always interested in science, but overwhelming workloads and lack of encouragement led her to study linguistics instead. Five years of waitressing later, she decided to go back to school and start a second degree in biology and programming, which led her into the world of DIY bio. Now she is helping to get a new DIY bio lab started in the Bay area and working on a huge project to make affordable bioreactors available to the public.

 http://bit.ly/1htoFHF

by

Christian Durand

"From helping produce more energy-efficient biofuels to increasing global access to life-saving medications, the emerging field of synthetic biology has the potential to provide solutions for many of humanity’s problems.
 
At Concordia, the Centre for Applied Synthetic Biology (CASB) — Canada’s first dedicated research centre — is leading the way. It brings biologists, engineers, computer scientists and social scientists together to develop tools and technologies with practical applications in environmental and health management.
 
On November 26, the university held a round table to explore new interdisciplinary approaches to the research and teaching of this vast and ethically complex discipline. “Synthetic Biology: Interdisciplinary Perspectives” was hosted by the Individualized Program at the School of Graduate Studies. Academics from all four faculties — Arts and Science, Fine Arts, Engineering and Computer Science, and the John Molson School of Business — attended, including CASB co-directors Vincent Martin, the Canada Research Chair in Microbial Genomics, and Nawwaf Kharma, an associate professor in Electrical and Computer Engineering.
 
The event’s keynote speaker was Brittany Wray, a filmmaker, radio documentary producer and self-described “biologist-turned-artist” who has been researching synthetic biology for three years. She completed Concordia’s graduate diploma in Communication Studies in 2010.
 
In an interview before Tuesday’s round table, Wray explained the basics.
 
What exactly is synthetic biology?
 
Brittany Wray: Synthetic biology is the field of science where an engineering mindset gets applied to biology in an attempt to build things out of nature from an intentional design perspective.
 
It is always a tricky discipline to define because it takes many forms, from work that aims to make genetic devices that modify an organism in a specific way, to whole genome engineering where the entire genetic information in an organism is organized by a scientist from the bottom up.
 
What are some practical examples?
 
BW: Synthetic biology is being developed largely for biofuels and medicine. For example, a company has recently made a synthetic yeast that creates biofuel as a product of its metabolism. Another recent development has been the invention of the cheapest anti-malarial drug to hit the medical world.
 
Synthetic biology can also be used to create synthetic versions of some coveted food ingredients, like vanilla or saffron. The applications are far ranging — from biosensors, to cell communication and protein transfer devices, to strategies for interspecies communication. 
 
What impact can this emerging field have on society?
 
BW: Synthetic biology is often propped up as the big fix to some of the big problems we face around sustainability, and the deep environmental trenches we've gotten ourselves into after many decades of industrialized life. It garners a lot of excitement because of its potential to produce fuel in far more sustainable ways. But the question remains, of course, can it do so on such a large scale?
 
It also has the potential to help us see health problems before it is too late. A synthetic biosensor could test for meat spoilage before it goes to markets. There are any other number of scenarios where invisible issues arise — and sometimes go wrong — when things are not examined on the level of their biology.
 
Synthetic biology may also be able to provide far greater numbers of people with accessible pharmaceuticals, because it would lower the manufacturing costs of medications.
 
But synthetic biology is not regarded as a magic bullet. To go back to the example of cheap pharmaceuticals, many argue that synthetic biology will have detrimental effects on societies in the places like the global south. In those countries, many farmers’ livelihoods depend on growing the non-synthetic versions of artemisia — a pre-cursor to the malaria vaccine — or vanilla, and they will not be able to compete with corporately manufactured synthetic versions of their crops. 
 
Why is an interdisciplinary approach important in synthetic biology?
 
BW: There is a very exciting and diverse set of interests that are focused on synthetic biology at the moment. Do-it-yourself biologists are interested in making the tools to access and use biotechnology more openly. Ethicists, anthropologists and other natural scientists are trying to understand the moral issues involved in doing this type of work, and the impacts it will have on human and non-human communities for years to come.
 
Essentially, there's a Pandora's box at play in terms of how this technology could be used. The more interested, critical and thoughtful minds we have working on it at once, the more productive a deliberation we can have. And hopefully that will give rise to the responsible insight we need in order to use synthetic biology as beneficially as possible with the least amount of harm. "

http://bit.ly/1eMzD7z