For more than half a century scientists have looked on the DNA molecule as life's blueprint. Now biological engineers are beginning to see the molecule not as a static plan, but more like a snippet of life's computer code that they can program.
Penn State researchers are unraveling the mystery of how nature codes and recodes this program to address some of the world's biggest challenges, says Howard Salis, assistant professor of biological engineering and chemical engineering.
"You can engineer DNA to reprogram the metabolism of simple organisms and you can program them to make what you want, or to make it more efficiently, says Salis. "The trick is to understand how the organism interprets its DNA, and then to optimize new DNA sequences to rationally control its behavior."
This rapidly developing field, often referred to as synthetic biology, may one day allow biological engineers to design living systems just as reliably as engineers currently design and build airplanes, cars and trains, according to Salis. It also holds the key to products such as inexpensive biofuels, environmentally friendly plastics, and less expensive pharmaceuticals.
"Decoding the function of DNA -- what the DNA makes the organism do -- and then recoding it with a new human-desired function is central to synthetic biology," he says…"
"One of the most exciting and promising applications of 3D printing is bioprinting, the ability to manufacture living human tissue and possibly organs. And one of the most exciting companies in this field is Organovo.
Organovo (NYSE MKT: ONVO) designs and creates functional, three-dimensional human tissues for medical research and therapeutic applications. The Company collaborates with pharmaceutical and academic partners to develop human biological disease models in three dimensions. These 3D human tissues have the potential to accelerate the drug discovery process, enabling treatments to be developed faster and at lower cost. Keith Murphy, Chairman and Chief Executive Officer of Organovo, spoke last week at the Inside 3D Printing conference in San Jose, CA…."
"Last week’s DNA Science post caused an uproar because I suggested that some people might think life begins at a period other than conception. This week’s post continues that theme with how a researcher created life. But not just any researcher – J. Craig Venter, now head of Synthetic Genomics Inc (SGI).
A Great ReadI usually don’t read books about DNA, because I write books about DNA. But when offered a copy of Dr. Venter’s new book, Life at the Speed of Light, (Viking; publishing October 17), I couldn’t resist. Not just another tale of genome sequencing, Dr. Venter’s latest effort tackles synthetic biology – chemically creating a simple genome, then transferring it into a receptive cell minus its own genome. Creating life, plus sampling bits of various environments and trolling for genomes – metagenomics – are what he’s been up to since the human genome project days.I raced through the book, flashing back to grad school with every historical anecdote or recounted experiment that built to the ability to recapitulate the genetic headquarters of a living cell. Venter’s excitement is palpable, if a little reminiscent of Captain Kirk: “We were now ready to attempt to go where no one had gone before, to create a whole bacterial synthetic genome and try to produce the first synthetic cell.”…."
"In the very near future scientists will be able to design and 3D print synthetic DNA, at least that’s what Craig Venter is forecasting.
Venter has been lauded as one of the most seminal figures in modern biology. He came to fame for being the leader of the first team to sequence the human genome. Since then Venter has turned his interests towards synthetic biology. Essentially, Venter and his colleagues design and construct biological devices and systems that behave in a pre-programmed manner. The idea of synthetic biology has been around since 1974, but has only recently started to mature. Venter created the first synthetic organism in 2010. According to Venter, the widespread use of synthetic organisms might be just around the corner. Even more astonishing, he believes extra-terrestrial life could soon be synthesized, and 3D printed by robots like the Curiosity Rover. “The day is not far off when we will be able to send a robotically controlled genome-sequencing unit in a probe to other planets to read the DNA sequence of any alien microbe life that may be there,” claims Venter…."
by Prachi Agarwala, Satyaprakash Pandey, Dr. Souvik Maiti
"With the potential to engineer biological systems, synthetic biology is an emerging field that combines various disciplines of sciences. It encompasses combinations of DNA, RNA and protein modules for constructing desired systems and the “rewiring” of existing signalling networks. Despite recent advances, this field still lags behind in the artificial reconstruction of cellular processes, and thus demands new modules and switches to create “genetic circuits”. The widely characterised noncanonical nucleic acid secondary structures, G-quadruplexes are promising candidates to be used as biological modules in synthetic biology. Structural plasticity and functional versatility are significant G-quadruplex traits for its integration into a biological system and for diverse applications in synthetic circuits."
by Shenglong Zhang, J. Craig Blain, Daria Zielinsk, Sergei M. Gryaznovc, and Jack W. Szostak
"Recent advances suggest that it may be possible to construct simple artificial cells from two subsystems: a self-replicating cell membrane and a self-replicating genetic polymer. Although multiple pathways for the growth and division of model protocell membranes have been characterized, no self-replicating genetic material is yet available. Nonenzymatic template-directed synthesis of RNA with activated ribonucleotide monomers has led to the copying of short RNA templates; however, these reactions are generally slow (taking days to weeks) and highly error prone. N3′-P5′–linked phosphoramidate DNA (3′-NP-DNA) is similar to RNA in its overall duplex structure, and is attractive as an alternative to RNA because the high reactivity of its corresponding monomers allows rapid and efficient copying of all four nucleobases on homopolymeric RNA and DNA templates. Here we show that both homopolymeric and mixed-sequence 3′-NP-DNA templates can be copied into complementary 3′-NP-DNA sequences. G:T and A:C wobble pairing leads to a high error rate, but the modified nucleoside 2-thiothymidine suppresses wobble pairing. We show that the 2-thiothymidine modification increases both polymerization rate and fidelity in the copying of a 3′-NP-DNA template into a complementary strand of 3′-NP-DNA. Our results suggest that 3′-NP-DNA has the potential to serve as the genetic material of artificial biological systems."
"Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancellation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multidrug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications."
: Upcoming SynBio Events (Sunday, October 6 '13 - Monday, October 6 '14)
Sundays, October 6,6,13,20; November 10,17,243:00 PM to 7:00 PMBiotechnology Crash Course A great course that teaches you the basic techniques. Very similar to the Biohacker Boot Camp, but a more relaxed pace. If you've ever wanted to do a little biotech project of your own, or if you're just curious about what those guys do in the lab every day, this is the best course to start with. Isolate your own DNA and analyze it, make bacteria glow, and unleash your inner mad scientist in this hands-on course.
Monday, October 7; Tuesday, October 8; Wednesday, October 9; Thursday, October 106:00 PM to 9:00 PMBiohacker Boot Camp Boot Camp for biohackers! An intensive hands-on week that covers all the lab skills you need to start your own genomics or genetic engineering project. Monday, October 14; November 186:00 PM to 9:00 PMOpen DNA Barcoding Night Join us as we DNA Barcode plant samples from a remote Alaskan valley. This is one of our Open Nights, free to the general public. Tuesday, October 22; Wednesday, October 23; Thursday, October 24; Saturdays, November 9,16,236:00 PM to 9:00 PMIntro to Synthetic Biology New sessions of Intro to Synthetic Biology start October 22nd and November 9th!Never clone alone... join the class and build a biosensor.
iGem 2013: the Stanford-Brown Team California Academy of Sciences Simon Vecchioni just graduated from Brown and went through a number of “phases” in his college career, studying biology, animal behavior, and languages.
"Synthetic biology is built on the synthesis, engineering, and assembly of biological parts. Proteins are the first components considered for the construction of systems with designed biological functions because proteins carry out most of the biological functions and chemical reactions inside cells. Protein synthesis is considered to comprise the most basic levels of the hierarchical structure of synthetic biology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocesses. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables the rapid creation of protein molecules from diverse sources of genetic information. Cell-free protein synthesis is virtually free from the intrinsic constraints of cell-based methods and offers greater flexibility in system design and manipulability of biological synthetic machinery. Among its potential applications, cell-free protein synthesis can be combined with various man-made devices for rapid functional analysis of genomic sequences. This review covers recent efforts to integrate cell-free protein synthesis with various reaction devices and analytical platforms."
by Bryn L. Adams, Karen K. Carter, Min Guo , Hsuan-Chen Wu, Chen-Yu Tsao , Herman O. Sintim , James J. Valdes , and William E. Bentley
"In order to carry out innovative complex, multistep synthetic biology functions, members of a cell population often must communicate with one another to coordinate processes in a programmed manner. It therefore follows that native microbial communication systems are a conspicuous target for developing engineered populations and networks. Quorum sensing (QS) is a highly conserved mechanism of bacterial cell–cell communication and QS-based synthetic signal transduction pathways represent a new generation of biotechnology toolbox members. Specifically, the E. coli QS master regulator, LsrR, is uniquely positioned to actuate gene expression in response to a QS signal. In order to expand the use of LsrR in synthetic biology, two novel LsrR switches were generated through directed evolution: an “enhanced” repression and derepression eLsrR and a reversed repression/derepression function “activator” aLsrR. Protein modeling and docking studies are presented to gain insight into the QS signal binding to these two evolved proteins and their newly acquired functionality. We demonstrated the use of the aLsrR switch using a coculture system in which a QS signal, produced by one bacterial strain, is used to inhibit gene expression via aLsrR in a different strain. These first ever AI-2 controlled synthetic switches allow gene expression from the lsr promoter to be tuned simultaneously in two distinct cell populations. This work expands the tools available to create engineered microbial populations capable of carrying out complex functions necessary for the development of advanced synthetic products."
"Twenty years ago, sequencing the human genome was one of the most ambitious science projects ever attempted. Today, compared to the collection of genomes of the microorganisms living in our bodies, the ocean, the soil and elsewhere, each human genome, which easily fits on a DVD, is comparatively simple. Its 3 billion DNA base pairs and about 20,000 genes seem paltry next to the roughly 100 billion bases and millions of genes that make up the microbes found in the human body.
And a host of other variables accompanies that microbial DNA, including the age and health status of the microbial host, when and where the sample was collected, and how it was collected and processed. Take the mouth, populated by hundreds of species of microbes, with as many as tens of thousands of organisms living on each tooth. Beyond the challenges of analyzing all of these, scientists need to figure out how to reliably and reproducibly characterize the environment where they collect the data. “There are the clinical measurements that periodontists use to describe the gum pocket, chemical measurements, the composition of fluid in the pocket, immunological measures,” said David Relman, a physician and microbiologist at Stanford University who studies the human microbiome. “It gets complex really fast.”…."
"A team of students from the University of Exeter are making their final preparations before taking part in a prestigious international synthetic biology competition.
The multidisciplinary team of undergraduates will be competing against the very best of Europe at the annual international Genetically Engineered Machines (iGEM) event.The competition, which challenges student teams to design new synthetic biological systems and operate them in living cells using an engineering approach, takes place in Lyon from October 11-13.If they are successful at the European Jamboree, the Exeter team will travel to Boston to take part in the worldwide finals, to be held at MIT later this year.The 2013 team comprises of a diverse group of students from the Colleges of Life and Environmental Sciences (CLES) and Engineering, Mathematics and Physical Sciences (CEMPS).Their project, called 'Paint By COLI' and devised and led by the students themselves, has seen the team attempt to modify E.coli bacteria with light sensitive and pigment production genes, in order to produce a full colour biocamera.Bio-Photography is the application of genetically engineered bacteria to act as the light sensor of a camera, replacing digital sensors or photographic film.As the surface area of bacteria is on the order of microns, and so much smaller than a digital sensor, bio-cameras have the potential to produce images with far greater resolution than those offered by current digital photography.This opportunity to work as an interdisciplinary group allowed the team to capitalise on the varied approaches to problem-solving taken by researchers from different fields.With the support from The University of Exeter Annual Fund, CLES, CEMPS and academics from across the University, the group have been working on the competition over the summer. Local sixth-form students were invited to participate in the lab work through the Nuffield Research Placement Scheme, and the team held talks in the community to create awareness of the innovations in synthetic biology.Exeter competitor Frances Entwistle said: "iGEM has given us an opportunity to take everything we've learnt at Exeter so far and show that we can take it one step further. The lab work taught me so much about working hard, responsibly and with a team; it's an experience I'll never forget and I'd thoroughly recommend it to all of my fellow students."Dr Elizabeth Dridge, from Biosciences at the University of Exeter, helped coordinate the iGEM project and added: "It is a fantastic opportunity for students from different subject areas to learn from each other and work together on a self directed project. Interdisciplinary research is encouraged for researchers working at the University and it's great that we can offer this to our students as well."…"
"Scientists at The University of Texas at Austin have figured out how to make structures – like houses or cages – that are small enough to corral bacterial cells. The enclosures can be built in any shape and are 3-D printed using a modified laser, the team reported Oct. 7 in Proceedings of the National Academy of Sciences.
Bacteria trapped in a square cage multiply over several hours. (J. Connell et al, PNAS)But instead of facilitating microbial cage-fighting matches, the microscopic structures should help scientists learn how infections spread and how bacteria talk with one another – a complex process involved in everything from population regulation to toxin release to the development of drug resistance. To cage cells, scientists first select a microbe to work with. For example, they may use Staphylococcus aureus, which causes skin infections and can mutate into the antibiotic-resistant superbug known as MRSA. Next, they suspend the bacteria in a warm, gelatin-based solution that contains light-sensitive molecules. Then they cool the mixture, which solidifies into a Jell-O like substance and traps bacteria where they are…."
Genetically engineered bacteria can be used to attack other bacterial species
"BIOFILMS are a problem in medicine. When bacteria gang up to form the continuous sheets that bear this name they are far harder to kill with antibiotics than when they just float around as individual cells. Biofilms on devices such as implants are thus difficult to shift, and those growing on the surfaces of human organs are frequently lethal. But Matthew Chang, a biochemical engineer at Nanyang Technological University in Singapore, has worked out a new way to attack them. His weapon is a different type of bacterium, which he has genetically engineered into a finely honed anti-biofilm missile.
The starting point for this new piece of biotechnology is a common gut bacterium called Escherichia coli. Though this species is best known to the wider world for causing food poisoning, most strains of it are benign, and it is one of the workhorses of genetics….."
"US scientists have taken another step towards the goal of creating self-replicating molecules like those thought to have spawned life on Earth. The researchers made RNA-like polymers capable of copying short sections of genetic code that they suggest could act as genomes in synthetic cells.
When life began, the cellular machinery for copying DNA had not yet evolved. So, as the theory goes, the first information-carrying molecules must have been self-replicators. Making self-replicators in the lab has proved difficult, although scientists have had some success using RNA molecules that are also enzymes capable of catalysing their own replication. The new study, however, led by Jack Szostak at Massachusetts General Hospital in Boston, US, focuses on another type of system – one that works without enzymes. Szostak’s team used phosphoramidate DNA, in which oxygen atoms in the phosphodiester bonds of DNA’s sugar-phosphate backbone are replaced by nitrogen. In previous work, they made phosphoramidate DNA copies from DNA or RNA templates, but they now show they can take a phosphoramidate DNA template and make a phosphoramidate DNA copy, mimicking ‘true’ self-replication and paving the way for self-reproducing synthetic cells. ‘This phosphoramidate system is actually rather nice, because it’s compatible with the kind of vesicles we use,’ says Szostak. ‘So if we could just improve the replication process a little bit more, we might be able to use it as the genome of protocell.’ Although the system only replicates a sequence of four bases, it makes use of a chemical modification to address what Philipp Holliger of the MRC Laboratory of Molecular Biology, UK, calls a ‘big stumbling block’ for self-replicating systems: copying accuracy. Copying depends on matching adenine–thymine (A-T) and guanine-cytosine (G-C) base pairs, so mismatches such as G–T lead to errors in the transmission of the genetic code. But Szostak’s tweak – replacing T with thio-T – increases A-T stability and, crucially, the copying accuracy. It’s not clear why thio-T makes A-T more stable, but the fact that it does raises further questions about the evolution of the genetic code. ‘You have to give an answer as to why these [modifications] were dropped,’ says Vitor Pinheiro, a synthetic biologist at the Institute of Structural and Molecular Biology, UK. Ignoring that difficult question for now, the tighter pairing also helps to increase the rate of copying – another stumbling block along the way to Szostak’s synthetic cells. There are, though, plenty more problems left to solve. Szostak himself listed a whole host of problems for his enzyme-free self-replicators in a recent review. ‘They’re taking them down one by one,’ says Holliger. ‘Hopefully at the end of it, you’ll be able to put all this together into a system that could truly perform self-replication. And that would obviously be a spectacular thing.’"
"One of the big challenges for the Internet of Things (IoT) is how to collect and share data from the physical world when sensors use proprietary interfaces. Unlike the world of the Internet, which has grown explosively through well-defined interfaces, much of sensor data remains locked in proprietary embedded sensor systems. It turns out the Internet of Things may evolve to incorporate elements of the natural world it senses.
The Center for Biomedical Innovation at MIT hosted a recent conference on the role of standards in biologics, since that industry faces similar challenges measuring and exchanging data about biological processes. Natural interfaces already exist between biological systems components, where the challenge has been to replicate that functionality using manufactured systems. However, biological systems such as diseases can be extraordinarily complex and respond to treatment differently according to complex network effects, explained Veronique Klemer, an executive editor for Nature Publishing Group, speaking at the event. Thus replicating an experiment that has been published in a top journal may only be possible thirty percent of the time, she said. The ISO's Good Manufacturing Process standards that have been adapted for bio-manufacturing and laboratory research environments may be useful in addressing the reproducibility issue. Further translational research in this area may be useful. The desire to replace human and animal testing of new drugs with synthetic-biology substitutes is driving interest in this area. Ron Weiss, director of the Synthetic Biology Center at MIT, noted the similarity between the equations of chemistry and the equations of sub-threshold analog electronics. The formulation of an organ-to-organ protocol is one example of research in analog synthetic biology. Other examples are in lab-on-a-chip specifications that promise to revolutionize both research and medicine through lower costs, better sensitivity, portability, and higher throughput. The MIT biomedical center and similar groups can help bring together stakeholders from academic research, industry, and the regulatory community. Together they can define interfaces between complex biological systems, components, and processes to facilitate the translation of science into new products in biology -- and IoT."
Sabrina Wend , Hanna J. Wagner, Konrad Müller, Matias D. Zurbriggen, Wilfried Weber, and Gerald Radziwill
"Light-dependent dimerization is the basis for recently developed noninvasive optogenetic tools. Here we present a novel tool combining optogenetics with the control of protein kinase activity to investigate signal transduction pathways. Mediated by Arabidopsis thalianaphotoreceptor cryptochrome 2, we activated the protein kinase C-RAF by blue light-dependent dimerization, allowing for decoupling from upstream signaling events induced by surface receptors. The activation by light is fast, reversible, and not only time but also dose dependent as monitored by phosphorylation of ERK1/2. Additionally, light-activated C-RAF controls serum response factor-mediated gene expression. Light-induced heterodimerization of C-RAF with a kinase-dead mutant of B-RAF demonstrates the enhancing role of B-RAF as a scaffold for C-RAF activity, which leads to the paradoxical activation of C-RAF found in human cancers. This optogenetic tool enables reversible control of protein kinase activity in signal duration and strength. These properties can help to shed light onto downstream signaling processes of protein kinases in living cells."
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