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Move Over, Mother Nature

Move Over, Mother Nature | SynBioFromLeukipposInstitute | Scoop.it

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Amber Dance
"Working at the crossroads of biology and engineering, synthetic biologists are crafting genes, proteins, and organisms that evolution never came up with. They are creating bacteria that produce biofuels and yeast cells that manufacture medicines. They are swapping promoters, ribosome-binding sequences, and open reading frames as if they were Lego bricks.

“We are no longer constrained by what Mother Nature gives us,” says Claes Gustafsson, cofounder of the DNA synthesis company DNA2.0, in Menlo Park, California.

Now, the constraint is the toolkit. Traditional biologists can work with DNA sequences using a simple viewer or editor, but “the engineers need a whole new suite of tools,” says Natalie Kuldell, who teaches biological engineering at MIT.

The synthetic biologist’s mind-set is all about parts, those nucleic acid bricks they shuffle to design a desired gene or gene network. Previously, researchers dealt with plain-text sequences, in word-processing or spreadsheet files. Copying and pasting, “it’s very easy to make mistakes,” says Avi Robinson-Mosher, a postdoc who designs cancer drugs at Harvard’s Wyss Institute for Biologically Inspired Engineering. Synthetic biologists need computer-aided design tools akin to those used by other kinds of engineers.
...."
Fortunately, many synthetic biologists have backgrounds in computers and engineering, and are developing software of their own. Some programs make drawing up the plans for a new plasmid so effortless that high school students and untrained bio-hobbyists can do it. Others include simulators so researchers can predict how a new genetic circuit will work. Several are open-source, so computer-savvy biologists can customize them.

http://bit.ly/MpJiG3

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A few words about the intersection between art/design and science/synthetic biology

"The question about how art and science interact, and if art is an integrated part of scientific work, or should be banned from science, leads us back to discussions of the ancient Greek philosophers and their precursors. The fundamental question was: What is reality? Can we understand the world around us with the help of our senses, or is the world around us a product of our mental concepts? The answers to these questions never were straightforward, and have been heavily discussed during the last 2000 years. During the different periods of history, sometimes it was en vogue to believe that reality is defined by our senses (materialism) other times people preferred to believe that reality is mental (idealism).

The concept of idealism was profoundly formulated for the first time by Plato (428/7 - 348/7 BC). Later it was enlivened by different Neo-Platonic movements. E.g. Leonardo Da Vinci (1452 –1519), a follower of Neo-Platonism, did not make a clear distinction between art and science. If the reality of the world basically is a mental product, all mental products including art, play an as equally important role.

Idealistic scientific thinking fell out of favor by the end of the nineteenth century. The main paradigm was now materialism. Idealistic thinking was highly criticized as unscientific. The external world and its observation by experiments became the main subject of science. Reflection about how our brain is structuring the world, and its meaning for scientific discovery were excluded from scientific methodology. Materialistic, scientific approach survived as a leading paradigm until today. Such materialistic orientated science banned art and artistic thinking from science. Art was viewed as a separate area, which could not give valuable contributions to scientific discovery.

However, a number of twentieth century scientists are known to have concerned themselves with Neo-Platonic, artistic thinking, such as earlier described in e.g. Goethes (1749 – 1832) theory of color, a theory focused on the mental reception of color. Among these modern scientists are the logician and mathematician Kurt Goedel (1906 - 1978), the theoretical physicist Werner Heisenberg (1901 - 1976) the mathematical physicist and pioneer of chaos theory Mitchell Feigenbaum (born 1944), to mention a few. Feigenbaum has even said, “Goethe was right about color”! All the above-mentioned use mathematics as their scientific tool. ....."
http://bit.ly/ORwuZg

 
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Remotely Activated Protein-Producing Nanoparticles

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Avi Schroeder, Michael S. Goldberg, Christian Kastrup, Yingxia Wang, Shan Jiang, Brian J. Josep, Christopher G. Levins, Sneha T. Kannan, Robert Langer, and Daniel G. Anderson

"The development of responsive nanomaterials, nanoscale systems that actively respond to stimuli, is one general goal of nanotechnology. Here we develop nanoparticles that can be controllably triggered to synthesize proteins. The nanoparticles consist of lipid vesicles filled with the cellular machinery responsible for transcription and translation, including amino acids, ribosomes, and DNA caged with a photolabile protecting group. These particles served as nanofactories capable of producing proteins including green fluorescent protein (GFP) and enzymatically active luciferase. In vitro and in vivo, protein synthesis was spatially and temporally controllable, and could be initiated by irradiating micrometer-scale regions on the time scale of milliseconds. The ability to control protein synthesis inside nanomaterials may enable new strategies to facilitate the study of orthogonal proteins in a confined environment and for remotely activated drug delivery."

http://bit.ly/LEJcUM

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Mining the biodiversity of plants: a revolution in the making

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De Luca V, Salim V, Atsumi SM, Yu F.

"Only a small fraction of the immense diversity of plant metabolism has been explored for the production of new medicines and other products important to human well-being. The availability of inexpensive high-throughput sequencing is rapidly expanding the number of species that can be investigated for the speedy discovery of previously unknown enzymes and pathways. Exploitation of these resources is being carried out through interdisciplinary synthetic and chemical biology to engineer pathways in plant and microbial systems for improving the production of existing medicines and to create libraries of biologically active products that can be screened for new drug applications."
http://1.usa.gov/MgVAjU

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Support Grows for Open Access to Science Research

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Elliot Harmon
"In their excellent Washington Post opinion piece, Matt Cooper and Elizabeth Wiley suggest that federally funded research should be freely accessible over the Internet. They argue that when students lose their access to academic databases after graduation, society doesn’t get the same benefits it could from that research:

Students’ library cards are a passport to the specialized knowledge found in academic journal articles — covering medicine and math, computer science and chemistry, and many other fields. These articles contain the cutting edge of our understanding and capture the genius of what has come before. In no uncertain terms, access to journals provides critical knowledge and an up-to-date education for tomorrow’s doctors, researchers and entrepreneurs.
But should that access cease at graduation? Or would you rather a graduating medical student, perhaps your future doctor, be able to keep up with the latest advances? Would you rather an ambitious graduate student feel comfortable leaving the academy to found the next Google, knowing she still has access to the latest insight in her field and is able to build upon it?
Cooper and Wiley’s organizations — the National Association of Graduate-Professional Students and the American Medical Student Association, respectively — joined Creative Commons and many other allies in support of a petition on Whitehouse.gov for free access to scientific journal articles arising from taxpayer-funded research. The petition quickly reached its goal of 25,000 signatures, sending a clear message that it’s time for the government to rethink open access policies."

http://bit.ly/LWNA2K

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Programmable DNA Scissors Found for Bacterial Immune System « Berkeley Lab News Center

Programmable DNA Scissors Found for Bacterial Immune System « Berkeley Lab News Center | SynBioFromLeukipposInstitute | Scoop.it

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Lynn Yarris
"Genetic engineers and genomics researchers should welcome the news from the Lawrence Berkeley National Laboratory (Berkeley Lab) where an international team of scientists has discovered a new and possibly more effective means of editing genomes. This discovery holds potentially big implications for advanced biofuels and therapeutic drugs, as genetically modified microorganisms, such as bacteria and fungi, are expected to play a key role in the green chemistry production of these and other valuable chemical products.

Jennifer Doudna, a biochemist with Berkeley Lab’s Physical Biosciences Division and professor at the University of California (UC) Berkeley, helped lead the team that identified a double-RNA structure responsible for directing a bacterial protein to cleave foreign DNA at specific nucleotide sequences. Furthermore, the research team found that it is possible to program the protein with a single RNA to enable cleavage of essentially any DNA sequence.

“We’ve discovered the mechanism behind the RNA-guided cleavage of double-stranded DNA that is central to the bacterial acquired immunity system,” says Doudna, who holds appointments with UC Berkeley’s Department of Molecular and Cell Biology and Department of Chemistry, and is an investigator with the Howard Hughes Medical Institute (HHMI). “Our results could provide genetic engineers with a new and promising alternative to artificial enzymes for gene targeting and genome editing in bacteria and other cell types.” ...."

http://bit.ly/NdCbL3

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The "Death Carrot"

"In treating cancer patients, one problem researchers face is how to deliver as much of the therapeutics as possible directly to cancer cells, while sparing normal cells. Many are working on various delivery systems using nanotech, synthetic biology approaches, RNA interference, and more. Now, a group at Johns Hopkins University led by Samuel Denmeade is taking inspiration from nature, says New Scientist's Hannah Krakauer. In its study published in Science Translational Medicine, the group describes how it engineered an analogue of thapsigargin, a toxic substance found in the flowering Thapsia garganica plant — nicknamed the "death carrot" by the ancient Greeks because of its toxicity to sheep and cattle. "Thapsigargin typically works by passing through cell membranes and shutting down calcium pumps — essential for cell survival — on the inside of cells," Krakauer says. By adding an extra peptide chain to the toxin, Denmeade's team changed it enough to keep it from entering cells until is encounters an enzyme called PSMA, which is found the surface of prostate cancer cells. "PSMA cleaves the extra chain off the toxin, setting it free to do its devastating business," Krakauer adds.

Further, the toxin doesn't just kill cancer cells that are undergoing growth, but can also kill dormant tumor cells, and non-cancerous cells used by tumors to help them grow. "You can envision it as a grenade," Denmeade tells Krakauer. "One guy pulls the pin, but it kills all the guys standing around." As the researchers' animal trials were successful, they are now moving to phase I clinical trials in prostate cancer, Krakauer adds."
http://bit.ly/Mcpfuv

Ref
Engineering a Prostate-Specific Membrane Antigen–Activated Tumor Endothelial Cell Prodrug for Cancer Therapy
by
Samuel R. Denmeade1,*, Annastasiah M. Mhaka1, D. Marc Rosen1, W. Nathaniel Brennen1, Susan Dalrymple1, Ingrid Dach2, Claus Olesen2, Bora Gurel1, Angelo M. DeMarzo1, George Wilding3, Michael A. Carducci1, Craig A. Dionne4, Jesper V. Møller2,5, Poul Nissen2,6, S. Brøgger Christensen7 and John T. Isaacs1
"Heterogeneous expression of drug target proteins within tumor sites is a major mechanism of resistance to anticancer therapies. We describe a strategy to selectively inhibit, within tumor sites, the function of a critical intracellular protein, the sarcoplasmic/endoplasmic reticulum calcium adenosine triphosphatase (SERCA) pump, whose proper function is required by all cell types for viability. To achieve targeted inhibition, we took advantage of the unique expression of the carboxypeptidase prostate-specific membrane antigen (PSMA) by tumor endothelial cells within the microenvironment of solid tumors. We generated a prodrug, G202, consisting of a PSMA-specific peptide coupled to an analog of the potent SERCA pump inhibitor thapsigargin. G202 produced substantial tumor regression against a panel of human cancer xenografts in vivo at doses that were minimally toxic to the host. On the basis of these data, a phase 1 dose-escalation clinical trial has been initiated with G202 in patients with advanced cancer."
http://bit.ly/NWMKXm

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*Found on Twitter*

We are LIVE! Win cash and global bragging rights for developing Open Source tools for Synthetic and DIY Biology at

http://sprize.synbiota.com/

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A Quixotic Solution: The Test-Tube Burger

A Quixotic Solution: The Test-Tube Burger | SynBioFromLeukipposInstitute | Scoop.it

By LESLIE KAUFMAN

"Four months ago, Mark Post, a professor of physiology at Maastricht University in the Netherlands, drew broad attention when he announced that he was close to producing a hamburger without a cow at his laboratory at a cost of about $330,000.

Dr. Post is literally growing meat from a single stem cell. (The cell for the meat is from the muscle of a special breed of Belgium cow that grows especially large and strong.)

While it is a complicated process, Dr. Post, whose research specialty is tissue engineering, said the science has already been developed by the medical community and the challenge now is honing the manufacturing process. He calls his innovation “no-kill meat,” but I think it might more accurately, albeit less appetizingly, be called petri dish meat.

This afternoon I attended a conference on technological innovation, organized by the Rockefeller Foundation, where Dr. Post was a featured speaker. Because his invention has the theoretical potential to relieve some pressures on the environment, I wanted to see how viable his idea was, business-wise.

Livestock graze on 70 percent of the world’s arable land, Dr. Post said. They consume vast quantities of declining fresh-water supplies...."
http://nyti.ms/LBsQkj

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Genome Editing with CompoZr Custom Zinc Finger Nucleases (ZFNs)

Genome Editing with CompoZr Custom Zinc Finger Nucleases (ZFNs)

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Hansen K, Coussens MJ, Sago J, Subramanian S, Gjoka M, Briner D.
"Genome editing is a powerful technique that can be used to elucidate gene function and the genetic basis of disease. Traditional gene editing methods such as chemical-based mutagenesis or random integration of DNA sequences confer indiscriminate genetic changes in an overall inefficient manner and require incorporation of undesirable synthetic sequences or use of aberrant culture conditions, potentially confusing biological study. By contrast, transient ZFN expression in a cell can facilitate precise, heritable gene editing in a highly efficient manner without the need for administration of chemicals or integration of synthetic transgenes. Zinc finger nucleases (ZFNs) are enzymes which bind and cut distinct sequences of double-stranded DNA (dsDNA). A functional CompoZr ZFN unit consists of two individual monomeric proteins that bind a DNA "half-site" of approximately 15-18 nucleotides (see Figure 1). When two ZFN monomers "home" to their adjacent target sites the DNA-cleavage domains dimerize and create a double-strand break (DSB) in the DNA.(1) Introduction of ZFN-mediated DSBs in the genome lays a foundation for highly efficient genome editing. Imperfect repair of DSBs in a cell via the non-homologous end-joining (NHEJ) DNA repair pathway can result in small insertions and deletions (indels). Creation of indels within the gene coding sequence of a cell can result in frameshift and subsequent functional knockout of a gene locus at high efficiency.(2) While this protocol describes the use of ZFNs to create a gene knockout, integration of transgenes may also be conducted via homology-directed repair at the ZFN cut site. The CompoZr Custom ZFN Service represents a systematic, comprehensive, and well-characterized approach to targeted gene editing for the scientific community with ZFN technology. Sigma scientists work closely with investigators to 1) perform due diligence analysis including analysis of relevant gene structure, biology, and model system pursuant to the project goals, 2) apply this knowledge to develop a sound targeting strategy, 3) then design, build, and functionally validate ZFNs for activity in a relevant cell line. The investigator receives positive control genomic DNA and primers, and ready-to-use ZFN reagents supplied in both plasmid DNA and in-vitro transcribed mRNA format. These reagents may then be delivered for transient expression in the investigator's cell line or cell type of choice. Samples are then tested for gene editing at the locus of interest by standard molecular biology techniques including PCR amplification, enzymatic digest, and electrophoresis. After positive signal for gene editing is detected in the initial population, cells are single-cell cloned and genotyped for identification of mutant clones/alleles."
http://1.usa.gov/MU6Kap

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Modeling synthetic gene oscillators.

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O'Brien EL, Itallie EV, Bennett MR.
"Genetic oscillators have long held the fascination of experimental and theoretical synthetic biologists alike. From an experimental standpoint, the creation of synthetic gene oscillators represents a yardstick by which our ability to engineer synthetic gene circuits can be measured. For theorists, synthetic gene oscillators are a playground in which to test mathematical models for the dynamics of gene regulation. Historically, mathematical models of synthetic gene circuits have varied greatly. Often, the differences are determined by the level of biological detail included within each model, or which approximation scheme is used. In this review, we examine, in detail, how mathematical models of synthetic gene oscillators are derived and the biological processes that affect the dynamics of gene regulation."
http://1.usa.gov/MP5ntI

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Challenges and opportunities in synthetic biology for chemical engineers

Challenges and opportunities in synthetic biology for chemical engineers | SynBioFromLeukipposInstitute | Scoop.it

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Yunzi Luoa, Jung-Kul Leec, Huimin Zhaoa

 

"Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement..."

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Modular control of multiple pathways using engineered orthogonal T7 polymerases

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Karsten Temme, Rena Hill, Thomas H. Segall-Shapiro, Felix Moser and Christopher A. Voigt

"Synthetic genetic sensors and circuits enable programmable control over the timing and conditions of gene expression. They are being increasingly incorporated into the control of complex, multigene pathways and cellular functions. Here, we propose a design strategy to genetically separate the sensing/circuitry functions from the pathway to be controlled. This separation is achieved by having the output of the circuit drive the expression of a polymerase, which then activates the pathway from polymerase-specific promoters. The sensors, circuits and polymerase are encoded together on a ‘controller’ plasmid. Variants of T7 RNA polymerase that reduce toxicity were constructed and used as scaffolds for the construction of four orthogonal polymerases identified via part mining that bind to unique promoter sequences. This set is highly orthogonal and induces cognate promoters by 8- to 75-fold more than off-target promoters. These orthogonal polymerases enable four independent channels linking the outputs of circuits to the control of different cellular functions. As a demonstration, we constructed a controller plasmid that integrates two inducible systems, implements an AND logic operation and toggles between metabolic pathways that change Escherichia coli green (deoxychromoviridans) and red (lycopene). The advantages of this organization are that (i) the regulation of the pathway can be changed simply by introducing a different controller plasmid, (ii) transcription is orthogonal to host machinery and (iii) the pathway genes are not transcribed in the absence of a controller and are thus more easily carried without invoking evolutionary pressure."
http://bit.ly/KMwzr3

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A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity

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Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A. Doudna, Emmanuelle Charpentier

"CRISPR/Cas systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using crRNAs to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA base-paired to trans-activating tracrRNA forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand while the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing."
http://bit.ly/QJg7MS

Comment:
"*Programmable RNA Complex Could Speed Genome Editing in the Lab*
For bacteria, snipping apart DNA that bears certain signature sequences is a defense mechanism. For scientists working in the lab, the same strategy can be a powerful research tool. With a newly discovered component of an adaptive bacterial immune system, scientists have identified a targeted method of slicing DNA that they say can be easily customized for a variety of applications in the lab.

Tools that snip apart DNA strands in defined locations are essential for editing genomes in the laboratory to study or alter gene function. To target the specific site in the genome they are interested in, researchers often have to design and produce a protein that will recognize and bind to that particular DNA sequence, a laborious and time-consuming process.

“This system offers a straightforward way to cleave any desired site in a genome, which could be used to introduce new genetic information by coupling it to well-known cellular DNA recombination mechanisms.”
Jennifer A. Doudna...."
http://bit.ly/MyJGkY

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gubs, a behavior-based language for open system dedicated to synthetic biology

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Adrien Basso-Blandin and Franck Delaplace

"In this article, we propose a domain specific language, GUBS (Genomic Unified Behavior Specification), dedicated to the behavioral specification of synthetic biological devices, viewed as discrete open dynamical systems. gubs is a rule-based declarative language. By contrast to a closed system, a program is always a partial description of the behavior of the system. The semantics of the language accounts the existence of some hidden non-specified actions possibly altering the behavior of the programmed device. The compilation framework follows a scheme similar to automatic theorem proving, aiming at improving synthetic biological design safety."
http://bit.ly/OQ19aD

 
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The generation of "unNatural" products: Synthetic biology meets synthetic chemistry

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Goss RJ, Shankar S, Fayad AA.

"Covering: 2005 to 2012 Natural product analogue generation is important, providing tools for chemical biology, enabling structure activity relationship determination and insight into the way in which natural products interact with their target biomolecules. The generation of analogues is also often necessary in order to improve bioavailability and to fine tune compounds' activity. This review provides an overview of the catalogue of approaches available for accessing series of analogues. Over the last few years there have been major advances in genome sequencing and the development of tools for biosynthetic pathway engineering; it is therefore becoming increasingly easy to combine molecular biology and synthetic organic chemistry in order to enable expeditious access to series of natural products. This review outlines the various ways of combining biology and chemistry that have been applied to analogue generation, drawing upon a series of examples to illustrate each approach."
http://1.usa.gov/KTj39H

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Defining #syntheticbiology

What's in a name?

Abstract
Defining an emerging field can be challenging. Nature Biotechnology asked 20 experts for their views on the term 'synthetic biology'.

Similar to other new and trendy fields, synthetic biology has been defined so loosely that it can seem like all things to all people. Traditional genetic or metabolic engineering has been rebranded as synthetic biology, often to take advantage of the hype cycle that fuels investor interest.

http://bit.ly/KRIhFE

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DNA nanoLEGOlogy

Petya V Krasteva

"DNA's high chemical stability and programmable base-paired structure make it not only an ideal carrier of genetic information but also a promising material for engineering sophisticated nanodevices. Peng Yin and colleagues from the Wyss Institute at Harvard recently reported a robust bottom-up approach for the assembly of complex nanostructures in a single melting-annealing cycle from a mix of short synthetic DNAs.

The idea to use DNA as a scaffold in molecular engineering was conceived about 30 years ago when, inspired by M.C. Escher's woodwork 'Depth', crystallographer Ned Seeman reasoned that interlocking branched DNAs could be used as tiles to build carrier lattices for crystallization of target molecules. The concept launched the field of DNA nanotechnology and led to the first reports on the assembly of basic geometric shapes, tubes and lattices from DNA tiles. Nevertheless, complex nanoshapes remained largely out of reach, with experts sharing the intuition that imprecise ratios among the building tiles would lead to jammed assembly....."
http://bit.ly/LGoFnr

 
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Genome-based microbiology—From -omics research to systems and synthetic biology

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Alfred Pühler

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Synthetic antibody libraries.

*Synthetic antibody libraries*

by
Nelson B, Sidhu SS.
"Synthetic antibody libraries are constructed using designed synthetic DNA that facilitates the use of highly optimized human frameworks and enables the introduction of defined chemical diversity at positions that are most likely to contribute to antigen recognition. Using a relatively simple design based on a single human framework into which diversity is restricted to four complementarity-determining regions and two amino acids (tyrosine and serine), these synthetic antibody libraries are capable of generating specific antibodies against a diverse range of protein antigens. Moreover, by using the methods described here, more complex libraries can be constructed that are able to produce synthetic antibodies with affinities and specificities beyond the capacity of natural antibodies. Since these methods rely entirely upon standard supplies, equipment, and methods, construction of such libraries can be performed by any molecular biology laboratory."
http://1.usa.gov/KOPciF

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New Phytologist Synthetic Biology Workshop: Novel ProteinsWeeding the Gems

New Phytologist Synthetic Biology Workshop: Novel ProteinsWeeding the Gems | SynBioFromLeukipposInstitute | Scoop.it

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Charis Cook
"As exciting as this research in this post is, to me as a humble traditional molecular biologist the most impressive ‘toolboxes’ were the truly synthetic ones involving no genes at all. Dek Woolfson (University of Bristol) and Samuel Stupp (Northwestern University, USA) presented astonishing work on custom peptides.

The Woolfson group is working towards making a toolbox for building proteins. They chose to work on α-helical coiled-coils because these peptide structures have that essential orthogonality built in – the correct peptides form coiled-coils irrespective of the surrounding domains, which can then be customised to fit the designer’s requirements. The group is now able to synthesise a number of structures using coiled-coils....."
http://bit.ly/MAd3m5

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The Gold Standard: Gold Nanoparticle Libraries To Understand the Nano-Bio Interface

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Alkilany AM, Lohse SE, Murphy CJ.
"Since the late 1980s, researchers have prepared inorganic nanoparticles of many types-including elemental metals, metal oxides, metal sulfides, metal selenides, and metal tellurides-with excellent control over size and shape. Originally many researchers were primarily interested in exploring the quantum size effects predicted for such materials. Applications of inorganic nanomaterials initially centered on physics, optics, and engineering but have expanded to include biology. Many current nanomaterials can serve as biochemical sensors, contrast agents in cellular or tissue imaging, drug delivery vehicles, or even as therapeutics. In this Account we emphasize that the understanding of how nanomaterials will function in a biological system relies on the knowledge of the interface between biological systems and nanomaterials, the nano-bio interface. Gold nanoparticles can serve as excellent standards to understand more general features of the nano-bio interface because of its many advantages over other inorganic materials. The bulk material is chemically inert, and well-established synthetic methods allow researchers to control its size, shape, and surface chemistry. Gold's background concentration in biological systems is low, which makes it relatively easy to measure it at the part-per-billion level or lower in water. In addition, the large electron density of gold enables relatively simple electron microscopic experiments to localize it within thin sections of cells or tissue. Finally, gold's brilliant optical properties at the nanoscale are tunable with size, shape, and aggregation state and enable many of the promising chemical sensing, imaging, and therapeutic applications. Basic experiments with gold nanoparticles and cells include measuring the toxicity of the particles to cells in in vitro experiments. The species other than gold in the nanoparticle solution can be responsible for the apparent toxicity at a particular dose. Once the identity of the toxic agent in nanoparticle solutions is known, researchers can employ strategies to mitigate toxicity. For example, the surfactant used at high concentration in the synthesis (0.1 M) of gold nanorods remains on their surface in the form of a bilayer and can be toxic to certain cells at 200 nM concentrations. Several strategies can alleviate the toxic response. Polyelectrolyte layer-by-layer wrapping can cover up the surfactant bilayer, or researchers can exchange the surfactant with chemically similar molecules. Researchers can also replace the surfactant with a biocompatible thiol or use a polymerizable surfactant that can be "stitched" onto the nanorods and reduce its lability. In all these cases, however, proteins or other molecules from the cellular media cover the engineered surface of the nanoparticles, which can drastically change the charges and functional groups on the nanoparticle surface."

http://1.usa.gov/QjR2Yv

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'Turkey tail' tree fungus could filter oestrogen from water (Wired UK)

'Turkey tail' tree fungus could filter oestrogen from water (Wired UK) | SynBioFromLeukipposInstitute | Scoop.it

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Liat Clark
"A tree fungus filter that removes oestrogen present in water is one of the proposals in an annual international synthetic biology competition, the International Genetically Engineered Machine.

The entry, submitted by 15 students at Germany's Bielefeld University, explains how the oxidase enzyme laccases -- present in the Trametes versicolor fungus (also known as turkey tail, because of its appearance) -- breaks down the aromatase enzymes present in synthetic oestrogens such as the oral contraceptive pill. These synthetic oestrogens end up in the water supply when women who are taking the pill or hormone replacement therapy go to the toilet.

By the time the touring competition comes to Europe in October 2012 the team, which has already isolated the responsible laccases genes, hopes to present exactly how the break-down occurs and have a prototype, biodegradable filter ready. In the meantime they are seeking funding from biotechnology companies to help with the extensive costs associated with this kind of lab research and development.

If successful, the model could be used to create filters for other potentially harmful pollutants in the public water supply, including pesticides and drugs.

The effects of oestrogen present in public water supplies is not definitively known, but over the years concerns have been raised that rising levels are linked to a rise in prostate cancer. A 2011 study submitted by the University of Toronto confirmed that there was a "significant association" between the two, and prior to this the issue of rising oestrogen levels was flagged up in a 2002 UK Environment Agency report detailing how male river fish were exhibiting female reproductive organs.

Oestrogen ethinylestradiol is the compound most commonly used in ...."
http://bit.ly/Ld02Mr

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Stabilizing Structure-Switching Signaling RNA Aptamers by Entrapment in Sol-Gel Derived Materials for Solid-Phase Assay

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Carrasquilla C, Lau PS, Li Y, Brennan JD.
"Structure-switching, fluorescence-signaling DNA and RNA aptamers have been reported as highly versatile molecular recognition elements for biosensor development. While structure-switching DNA aptamers have been utilized for solid-phase sensing, equivalent RNA aptamers have yet to be successfully utilized in solid-phase sensors due to their lack of chemical stability and susceptibility to nuclease attack. In this study, we examined entrapment into sol-gel derived organic-inorganic composite materials as a platform for immobilization of structure-switching fluorescence-signaling RNA aptamer reporters, using both the synthetic theophylline- and naturally occurring thiamine pyrophosphate-binding RNA aptamers as test cases. Structure-switching versions of both aptamers were entrapped into a series of sol-gel derived composites, ranging from highly polar silica to hydrophobic methylsilsesquioxane-based materials, and the target-binding and signaling capabilities of these immobilized aptamers were assessed relative to solution. Both immobilized aptamers demonstrated sensitivity and selectivity similar to that of free aptamers when entrapped in a composite material derived from 40% (v/v) methyltrimethoxysilane/tetramethoxysilane. Importantly, this material also conferred protection from nuclease degradation and imparted long-term chemical stability to the RNA reporter systems. Given the versatility of sol-gel entrapment for development of biosensors, microarrays, bioaffinity columns, and other devices, this entrapment method should provide a useful platform for numerous solid-phase RNA aptamer-based devices."
http://1.usa.gov/MWGz0F

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