SynBioFromLeukipposInstitute
114.9K views | +2 today
Follow
 
Scooped by Gerd Moe-Behrens
onto SynBioFromLeukipposInstitute
Scoop.it!

Research reveals structure of key CRISPR complex

Research reveals structure of key CRISPR complex | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Veronica Meade-Kelly

"Researchers from MIT and the Broad Institute have teamed up with colleagues from the University of Tokyo to form the first high-definition picture of the Cas9 complex — a key part of the CRISPR-Cas system used by scientists as a genome-editing tool to silence genes and probe the biology of cells. Their findings, which are reported this week in Cell, are expected to help researchers refine and further engineer the tool to accelerate genomic research and bring the technology closer to use in the treatment of human genetic disease.

First discovered in bacteria in 1987, CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) have recently been harnessed as so-called genome-editing tools. These tools allow researchers to home in on “typos” within the three-billion-letter sequence of the human genome, and cut out or alter problematic sequences. The Cas9 complex, which includes the CRISPR “cleaving” enzyme Cas9 and an RNA “guide” that leads the enzyme to its DNA target, is key to this process. 
“We’ve come to view the Cas9 complex as the ultimate ‘guided missile’ that we can use to target precise sites in the genome,” says co-senior author Feng Zhang, the W.M. Keck Assistant Professor of Medical Engineering in MIT’s departments of Brain and Cognitive Sciences and Biological Engineering, and a member of the Broad Institute and MIT’s McGovern Institute for Brain Research. “This study provides a schematic of the entire system — it shows the missile (the Cas9 protein), the programming instructions (the guide RNA) that send it to the right location, and the target DNA. It also reveals the secret of how these pieces function together to make the whole system work.”
To deconstruct this system, Zhang approached the paper’s co-senior author, Osamu Nureki of the University of Tokyo. Together, they assembled a team to work out the complicated structure. 
“Cas9-based genome-editing technologies are proving to be revolutionary in a wide range of life sciences, enabling many new experimental techniques, so my colleagues and I were excited to work with Feng’s lab on this important research,” says first author Hiroshi Nishimasu, an assistant professor of biophysics and biochemistry who works in Nureki’s lab at the University of Tokyo. 
The two teams worked closely to reveal the structural details of the Cas9 complex and to test their functional significance. Their efforts revealed a division of labor within the Cas9 complex. The researchers determined that the Cas9 protein consists of two lobes: One lobe is involved in the recognition of the RNA and DNA elements, while the other lobe is responsible for cleaving the target DNA, causing what is known as a “double strand break” that disables the targeted gene. The team also found that key structures on Cas9 interface with the guide RNA, allowing Cas9 to organize itself around the RNA and the target DNA as it prepares to cut the strands.
Identifying the key features of the Cas9 complex should enable researchers to improve the genome-editing tool to better suit their needs. 
“Up until now, it has been very difficult to rationally engineer Cas9. Now that we have this structural information, we can take a principled approach to engineering the protein to make it more effective,” says Zhang, who is also a co-founder of Editas Medicine, a company that was started last year to develop Cas9 and other genome-editing technologies into a novel class of human therapeutics.
Currently, Cas9 is used in experiments to silence genes in mammalian cells — sometimes at multiple sites across the genome — and large libraries of RNA sequences have been created to guide Cas9 to genes of interest. However, the system can only target specific types of sites. Some studies have also shown that the RNA could lead Cas9 “off target,” potentially causing unexpected problems within the cellular machinery. 
The researchers plan to use this new, detailed picture of the Cas9 complex to address these concerns.
“Understanding this structure may help us engineer around the current limitations of the Cas9 complex,” says co-author F. Ann Ran, a graduate student in Zhang’s lab. “In the future, it could allow us to design versions of these editing tools that are more specific to our research needs. We may even be able to alter the type of nucleic acid sequences that Cas9 can target.”  
Such technological improvements will be needed if the CRISPR-Cas system is to evolve into a therapeutic tool for the treatment of genetic disease.
Dana Carroll, a professor of biochemistry at the University of Utah, says the new structural findings provide a basis for both understanding and modifying the CRISPR-Cas system. 
“Like many crystal structures, this one of the Cas9-sgRNA-DNA complex confirms and rationalizes many inferences from biological and biochemical studies, and it provides further insight into the functions of the complex. By doing so it suggests approaches to enhancing or modulating the activity of the Cas9 protein, some of which the authors have tested in a preliminary fashion,” says Carroll, who was not part of the research team.
The study was supported by the National Institute of Mental Health; an NIH Director’s Pioneer Award; the Japan Science and Technology Agency; the Japan Society for the Promotion of Science; the Keck, McKnight, Poitras, Merkin, Vallee, Damon Runyon, Searle Scholars, Klingenstein, and Simons foundations; as well as Bob Metcalfe and Jane Pauley.
Other researchers who worked on the study include Patrick D. Hsu, Silvana Konermann, Soraya Shehata, Naoshi Dohmae, and Ryuichiro Ishitani."



 http://bit.ly/1f6sMsw

more...
No comment yet.
SynBioFromLeukipposInstitute
Your new post is loading...
Your new post is loading...
Scooped by Gerd Moe-Behrens
Scoop.it!

New technique could help scientists create a gene in just 1 day

New technique could help scientists create a gene in just 1 day | SynBioFromLeukipposInstitute | Scoop.it
Creating a new gene in a single day could soon be possible, thanks to a new technique that mimics the way the body copies its own DNA. Though the technology needs to clear a few more hurdles, it could one day let researchers speedily rewrite microbe genes, enabling them to synthesize new medicines and fuels on the fly.

“It’s the future,” says George Church, a geneticist at Harvard University who has pioneered numerous technologies to read and write DNA for synthetic biology. “This is going to be enormous.”

Researchers have been able to make DNA since the 1970s. The traditional approach takes DNA nucleotides—the chemical letters A, G, C, and T—and adds them, one by one, to a growing chain called an oligonucleotide, or oligo. But the process, which uses a series of toxic organic reagents, is typically slow and error-prone, limiting oligos to about 200 letters—a tiny fraction of the thousands of letters that make up most genes.

Our cells make DNA differently. A variety of enzymes called polymerases read a single strand of DNA and then synthesize a complementary strand that binds to it. That has prompted dreams of re-engineering polymerases to write new DNA.

Over the decades, most researchers have settled on one particular polymerase, called terminal deoxynucleotidyl transferase (TdT), because, unlike other polymerases, it can attach new nucleotides to an oligo strand without following a DNA template strand. Natural TdT does this to write millions of new variations of genes for antibodies, which the immune system can then select from to target invaders. But the natural enzyme adds new DNA letters randomly, rather than controlling the precise sequence of letters as researchers want to do.

Scientists have tried for years to make TdT add one nucleotide at a time and stop, before repeating the process with a different nucleotide, says Sebastian Palluk, a Ph.D. student who worked on the project in chemist Jay Keasling’s lab at the Lawrence Berkeley National Laboratory in California. They started by adding chemical groups to DNA’s four bases that act as “stop” signals. So, when TdT adds a modified A to an oligo of any length, it would be prevented from adding the next base. The oglio is then fished out, washed, and treated with another compound to cut off the blocking group, readying it for the next extension.

But TdT doesn’t work well with these modified nucleotides. “TdT is very picky,” Palluk says. One such system, for example, required about an hour to add each modified base, far too slow to be practical.

Palluk says he also tried to make this approach work. “I went down that route for 2 years,” he says. But he got to talking with Daniel Arlow, a fellow Ph.D. student in Keasling’s lab who was also trying to use enzymes to synthesize DNA. Eventually, the pair settled on a novel approach. They start with four separate pools for the four separate bases, each one with copies of TdT tethered to either A, G, C, or T. To grow their oligo, they add a base from one of the pools. After TdT adds the base to the end of the oligo, it remains tethered, blocking any additional copies of the enzyme from reacting with the oligo and extending it further. The now oligos are then fished out, and the tethers are snipped off. The free TdT is washed away, and the oligo is ready for the next base to be added.

Ultimately, the approach should be cheap, Keasling says, because TdT is easy to manufacture in bacteria and yeast. It’s also fast. Most new nucleotides attach to the growing oligo in 10 to 20 seconds, Palluk, Arlow, Keasling, and their colleagues report today in Nature Biotechnology. For now, the tether snipping step still takes a minute. So synthesizing a whole gene will still likely take the better part of a day.

Church says the new approach is not quite ready to dethrone conventional DNA synthesis. So far, the group has made oligos only 10 bases long. And there are still a few writing problems, as the approach was only 98% accurate at writing DNA in the desired sequence, below the 99% accuracy of the traditional approach. “It’s cool for a first demonstration,” Palluk says. “But it’s not quite there yet.”

In order to write oligos up to 1000 bases long, the approach will likely need to be 99.9% accurate. If it gets there, Church says it could help revolutionize not just synthetic biology’s efforts to write and test new genes, but also enable efforts to write massive libraries of data in DNA to create a compact archive the firehoses of information coming from giant science projects such as astronomy surveys, which could then be fished out and read out later.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Synthetic receptors can rewire cell functions and minimize side-effects

Synthetic receptors can rewire cell functions and minimize side-effects | SynBioFromLeukipposInstitute | Scoop.it
One of the challenges of modern pharmacology is specificity. Despite therapeutic effects, drugs can often have side effects. The biological basis for this has to do with the proteins and receptors that the drug targets and binds to. Many target receptors are connected to more than one biochemical pathway or more commonly, the drug is not specific enough to exclusively bind one particular receptor.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

MIT engineers recruit microbes to help fight cholera

MIT engineers recruit microbes to help fight cholera | SynBioFromLeukipposInstitute | Scoop.it
MIT engineers have developed a probiotic mix of natural and engineered bacteria to diagnose and treat cholera, an intestinal infection that causes severe dehydration.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Genetic tool development and systemic regulation in biosynthetic technology

Biotechnol Biofuels. 2018 Jun 1;11:152. doi: 10.1186/s13068-018-1153-5. eCollection 2018.Review...
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Developing a Synthetic Biology Toolkit for Comamonas testosteroni, an Emerging Cellular Chassis for Bioremediation

ACS Synth Biol. 2018 Jun 3. doi: 10.1021/acssynbio.7b00430.[Epub ahead of print]...
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Bio Art | SVA Bio Art Lab, BFA Fine Arts – New York City

Bio Art | SVA Bio Art Lab, BFA Fine Arts – New York City | SynBioFromLeukipposInstitute | Scoop.it
SCALE Studies in Bio Art Wednesday June 13, 2018 6-8PM SVA BFA Fine Arts 335 W 16th St, New York, NY 10011   Participants: Clare Benson  Magdalena Dukiewicz Ryan Greer  Jane Hsi  Keika Okamoto E.R. Saba      Bio Art SVA Art and Science Laboratory Bio Art Lab. SVA BFA Fine Arts School of Visual Arts, New York The Bio Art Lab was founded in 2011 as part of the SVA’s BFA Fine Arts new facility consisting of 54,000 square feet in the heart of Chelsea, NYC.  The Lab was founded and is directed by Suzanne Anker, Chair of the BFA Fine Arts Department.  Conceived as a place where scientific tools and techniques become tools and techniques in art practice, the Lab is the result of many people’s expertise, research and sustained effort. Such deftness and collaborative efforts continue to remain crucial in developing this facility to its full potential. Joe Tekippe and Luis Navarro were responsible for all high-tech computer access including our full range of hardware and software installation and maintenance. More recently Michael Falk has coordinated, experimented with and set up the necessary photographic resources we need in place for our microscopic image making. Daniel Wapner and Sung Jin Choi used their skills to seamlessly build both stainless steel and aluminum stands housing our fish and plants. Mark Rosen set up a check-in check-out system for our library.  Brandon Ballengée added his knowledge concerning fresh water fish and frog tanks in addition to the acquisition of a chemical hood where the preservation of specimens and cleaning and staining of aquatic animals could take place. Dr. Ignacio Lopez-Coviella was a great consultant in developing our microscopic practices, pointing us in the direction of three types of microscopes: a compound microscope, a dissecting microscope and an inverted microscope.  Marine biologist Joe Di Giorgis expanded our collection of microscopes by loaning us a full array of dissecting microscopes and analyzing the camera requirements for each.  Molecular scientists, Oliver Medvedik and Ellen Jorgensen from Genspace consulted in regard to our incubators, HEPA filter and autoclave as well as helping to design projects relevant to Bio  Art practice. Ellen and Oliver are also our current “scientists in residence” working with students on the use of bio-materials for art projects and the barcoding of plants from the surrounding environment.  Tarah Rhoda researched labware, lab rules and formats for molecular cuisine and tissue culturing as well as lighting systems for plants and lab protocol, safety and workflow. Many student workers were instrumental in maintaining the live plants and organisms in the Lab with care, integrity, and enthusiasm. And I say the same for the various visiting artists who have shared their expertise with us (see separate link.) Scott Vaughn of  NY Aquarium in NYC manages our salt water aquarium which houses coral, an anemone, hermit crabs and starfish. Sebastian Cocioba from NY Botanics, introduced techniques for plant tissue culturing of African violets and venus fly-traps. He is also developing an “SVA” palette for painting with bacteria. Sebastian and Sung  have been helping us develop a molecular biology component  of our lab employing PCR practices, synthetic biology and forensics in analyzing molecular data. Raul Gomez Valverde has designed our micro website, www.bioart.sva.edu, and has produced outstanding pictures of student works produced in situ.  George Boorujy has donated marvelous taxidermied duck specimens which appear as if in flight.  And of course our great thanks to President David Rhodes and Provost Jeff Nesin for allowing us to go forward with this great resource.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Programming self-organizing multicellular structures with synthetic cell-cell signaling

A common theme in the self-organization of multicellular tissues is the use of cell-cell signaling networks to induce morphological changes. We used the modular synNotch juxtacrine signaling platform to engineer artificial genetic programs in which specific cell-cell contacts induced changes in cadherin cell adhesion. Despite their simplicity, these minimal intercellular programs were sufficient to yield assemblies with hallmarks of natural developmental systems: robust self-organization into multi-domain structures, well-choreographed sequential assembly, cell type divergence, symmetry breaking, and the capacity for regeneration upon injury. The ability of these networks to drive complex structure formation illustrates the power of interlinking cell signaling with cell sorting: signal-induced spatial reorganization alters the local signals received by each cell, resulting in iterative cycles of cell fate branching. These results provide insights into the evolution of multi-cellularity and demonstrate the potential to engineer customized self-organizing tissues or materials.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

The Global Synthetic Biology Summit

The Global Synthetic Biology Summit | SynBioFromLeukipposInstitute | Scoop.it
SynBioBeta 2018 comes to San Francisco on October 1-3, uniting biological engineers, entrepreneurs and investors for the Global Synthetic Biology Summit. Meet over 1000 attendees and 100 speakers, sponsors and exhibitors.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Do-it-yourself CRISPR genome editing kits bring genetic engineering to your kitchen bench

A synthetic biologist from NASA plans to make CRISPR-based genetic engineering as accessible as a home science kit, so you can bio-hack yeast and bacteria on your kitchen bench.​...
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9

Bio Protoc. 2018 Mar 20;8(6). pii: e2765. doi: 10.21769/BioProtoc.2765.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Bio-Algorithmic Workflows for Standardized Synthetic Biology Constructs

Methods Mol Biol. 2018;1772:363-372. doi: 10.1007/978-1-4939-7795-6_20.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

CRISPR-Cas9-Mediated Genome Editing and Transcriptional Control in Yarrowia lipolytica

Methods Mol Biol. 2018;1772:327-345. doi: 10.1007/978-1-4939-7795-6_18.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Tools for Biohackers: Here Come 3 Mini-Labs

Tools for Biohackers: Here Come 3 Mini-Labs | SynBioFromLeukipposInstitute | Scoop.it
These desktop gadgets should make DIY genetic engineering much easier...
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Student disruptors invent new way to synthesise DNA | Cosmos

Frustrated at the slow pace of putting code together, two young researchers took things into their own hands. Elizabeth Finkel reports.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Optogenetic Hack Advances Synthetic Morphogenesis

Optogenetic Hack Advances Synthetic Morphogenesis | SynBioFromLeukipposInstitute | Scoop.it
Get the latest in biotechnology through daily news coverage as well as analysis, features, tutorials, webinars, podcasts, and blogs. Learn about the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and...
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

New machine learning approach could accelerate bioengineering

Scientists have developed a way to use machine learning to dramatically accelerate the design of microbes that produce biofuel....
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Journal of Biosensors and Bioelectronics - Open Access Journals

Journal of Biosensors and Bioelectronics - Open Access Journals | SynBioFromLeukipposInstitute | Scoop.it
Journal of Biosensors and Bioelectronics discusses the latest research innovations and important developments in this field.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

CRISPR/dCas9-mediated multiplex gene repression in Streptomyces

Biotechnol J. 2018 Jun 3:e1800121. doi: 10.1002/biot.201800121.[Epub ahead of print]...
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

On an algorithmic definition for the components of the minimal cell

On an algorithmic definition for the components of the minimal cell | SynBioFromLeukipposInstitute | Scoop.it
Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology

Living organisms are differentiated by their genetic material-millions to billions of DNA bases encoding thousands of genes. These genes are translated into a vast array of proteins, many of which have functions that are still unknown. Previously, it was believed that simply knowing the genetic sequence of an organism would be the key to unlocking all understanding. However, as DNA sequencing technology has become affordable, it has become clear that living cells are governed by complex, multilayered networks of gene regulation that cannot be deduced from sequence alone. Synthetic biology as a field might best be characterized as a learn-by-building approach, in which scientists attempt to engineer molecular pathways that do not exist in nature. In doing so, they test the limits of both natural and engineered organisms.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Artificial metalloenzyme flips switch in cells

Artificial metalloenzyme flips switch in cells | SynBioFromLeukipposInstitute | Scoop.it
Cell-penetrating assembly uncages hormone, turning on gene circuit...
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Water-Based Digital Fabrication Platforms : fabrication platform

Water-Based Digital Fabrication Platforms : fabrication platform | SynBioFromLeukipposInstitute | Scoop.it
fabrication platform - In her water-based digital fabrication platform project, architect and professor Neri Oxman embraces water as nature’s architectural tool and...
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

neri oxman and MIT develop digitally produced water-based renewable material

neri oxman and MIT develop digitally produced water-based renewable material | SynBioFromLeukipposInstitute | Scoop.it
neri oxman and the MIT mediated matter group have developed a water-based digital fabrication platform using a renewable polymer from the ocean.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

Construction and Integration of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells

Methods Mol Biol. 2018;1772:347-359. doi: 10.1007/978-1-4939-7795-6_19.
more...
No comment yet.
Scooped by Gerd Moe-Behrens
Scoop.it!

At GP-write, scientists take first steps on way to synthetic human genome

At GP-write, scientists take first steps on way to synthetic human genome | SynBioFromLeukipposInstitute | Scoop.it
At the third meeting of GP-write, researchers decide to create virus-resistant human cells...
more...
No comment yet.