Build engaged audiences through publishing by curation.
Sign up with Facebook
Sign up with Twitter
I don't have a Facebook or a Twitter account
Start a free trial of Scoop.it Business
Are you sure you want to delete this scoop?
A quantum computer is a serious piece of hardware. My colleagues and I build quantum computers from superconducting systems, quantum dots, lasers operating on nonlinear crystals,... Read Full Postelse
byOrlando de Lange, Andreas Binder, Thomas Lahaye"Whether rice, yeast, or fly there is barely a model organism not yet reached by transcription activator like effectors (TALEs) and their derivative fusion proteins. Insights into fundamental biology are now arriving on the back of work in the last years to develop these proteins as tools for molecular biology. This began with the publication of the simple cipher determining base-specific DNA recognition by TALEs in 2009 and now encompasses a huge variety of established fusion proteins mediating targeted modifications to transcriptome, genome, and recently, epigenome. Straightforward design and exquisite specificity, allowing unique sites to be targeted even within complex eukaryote genomes, are key to the popularity of this system. Synthetic biology is one field that is just beginning to make use of these properties with a number of recent publications demonstrating TALE-mediated regulation of synthetic genetic circuits. Intense interest has surrounded the CRISPR/Cas9 system within the last twelve months and it is already proving its mettle as a tool for targeted gene modifications and transcriptional regulation. However, questions over off-target activity and means for independent regulation of multiple Cas9-guide RNA pairs will have to be resolved before this method enters into the synthetic biology toolbox. TALEs are already showing promise as regulators of synthetic biological systems, a role that will likely be developed further in the coming years." http://bit.ly/1gnIM4O
This study establishes a proof-of-concept that a tattoo device can target intra-dermal drug delivery against cutaneous leishmaniasis (CL). The selected drug is oleylphosphocholine (OlPC) formulated as liposomes, particles known to be prone to macrophage ingestion. We first show that treatment of cultured Leishmania-infected macrophages with OlPC-liposomes results in a direct dose-dependent killing of intracellular parasites. Based on this, in vivo efficacy is demonstrated using a 10 day tattooing-mediated treatment in mice infected with L. major and L. mexicana. In both models this regimen results in rapid clinical recovery with complete regression of skin lesions by Day 28. Parasite counts and histopathology examination confirm high treatment efficacy at the parasitic level. Low amount of drug required for tattooing combined with fast clinical recovery may have a positive impact on CL patient management. This first example of tattoo-mediated drug delivery could open to new therapeutic interventions in the treatment of skin diseases.
*This forthcoming tome looks like it oughta be pretty happening. *It's a press release. *******************************************************************
byBruce Sterling"Synthetic Aesthetics
byMartyn Dade-Robertsona, Carolina Ramirez Figueroaa, Meng Zhang"This paper discusses the role that material ecologies might have in the emerging engineering paradigm of Synthetic Biology (hereafter SB). In this paper we suggest that, as a result of the paradigm of SB, a new way of considering the relationship between computation and material forms is needed, where computation is embedded into the material elements themselves through genetic programming. The paper discusses current trends to conceptualize SB in traditional engineering terms and contrast this from design speculations in terms of bottom up processes of emergence and self organization. The paper suggests that, to reconcile these positions, it is necessary to think about the design of new material systems derived from engineering living organisms in terms of a state space of production. The paper analyses this state space using the example of biomineralization, with illustrations from simple experiments on bacteria induced calcium carbonate. The paper suggests a framework involving three interconnected state spaces defined as: cellular (the control of structures within the cell structures within a cell, and specifically DNA and its expression through the process of transcription and translation); chemical (considered to occur outside the cell, but in direct chemical interaction with the interior of the cell itself); physical (which constitutes the physical forces and energy within the environment). We also illustrate, in broad terms, how such spaces are interconnected. Finally the paper will conclude by suggesting how a material ecologies approach might feature in the future development of SB." http://bit.ly/PkQNl6
A new microscope can be printed on a flat piece of paper and assembled in less than 10 minutes. And the parts to make it cost less than a dollar.
Original Article from The New England Journal of Medicine — Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV
*Biological Time Travel*"FROM GLOWING FISH to bacteria that can count, synthetic biologists are now able to create life forms never before seen on earth. “Historians and Ecclesiastes be damned,” says Sophia Roosth, assistant professor in the history of science. “In the first decades of the twenty-first century, a number of things are new under the sun.”
Ring chromosomes are structural aberrations commonly associated with birth defects, mental disabilities and growth retardation. Rings form after fusion of the long and short arms of a chromosome, and are sometimes associated with large terminal deletions. Owing to the severity of these large aberrations that can affect multiple contiguous genes, no possible therapeutic strategies for ring chromosome disorders have been proposed. During cell division, ring chromosomes can exhibit unstable behaviour leading to continuous production of aneuploid progeny with low viability and high cellular death rate. The overall consequences of this chromosomal instability have been largely unexplored in experimental model systems. Here we generated human induced pluripotent stem cells (iPSCs) from patient fibroblasts containing ring chromosomes with large deletions and found that reprogrammed cells lost the abnormal chromosome and duplicated the wild-type homologue through the compensatory uniparental disomy (UPD) mechanism. The karyotypically normal iPSCs with isodisomy for the corrected chromosome outgrew co-existing aneuploid populations, enabling rapid and efficient isolation of patient-derived iPSCs devoid of the original chromosomal aberration. Our results suggest a fundamentally different function for cellular reprogramming as a means of /`chromosome therapy/' to reverse combined loss-of-function across many genes in cells with large-scale aberrations involving ring structures. In addition, our work provides an experimentally tractable human cellular system for studying mechanisms of chromosomal number control, which is of critical relevance to human development and disease.
A great review by Yamanaka et al
byMacia J, Sole R"Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined."http://bit.ly/NseMxD
byAna Lúcia Leitãoa, Francisco J. Enguita"Secondary metabolic pathways of fungal origin provide an almost unlimited resource of new compounds for medical applications, which can fulfill some of the, currently unmet, needs for therapeutic alternatives for the treatment of a number of diseases. Secondary metabolites secreted to the extracellular medium (extrolites) belong to diverse chemical and structural families, but the majority of them are synthesized by the condensation of a limited number of precursor building blocks including amino acids, sugars, lipids and low molecular weight compounds also employed in anabolic processes. In fungi, genes related to secondary metabolic pathways are frequently clustered together and show a modular organization within fungal genomes. The majority of fungal gene clusters responsible for the biosynthesis of secondary metabolites contain genes encoding a high molecular weight condensing enzyme which is responsible for the assembly of the precursor units of the metabolite. They also contain other auxiliary genes which encode enzymes involved in subsequent chemical modification of the metabolite core. Synthetic biology is a branch of molecular biology whose main objective is the manipulation of cellular components and processes in order to perform logically connected metabolic functions. In synthetic biology applications, biosynthetic modules from secondary metabolic processes can be rationally engineered and combined to produce either new compounds, or to improve the activities and/or the bioavailability of the already known ones. Recently, advanced genome editing techniques based on guided DNA endonucleases have shown potential for the manipulation of eukaryotic and bacterial genomes. This review discusses the potential application of genetic engineering and genome editing tools in the rational design of fungal secondary metabolite pathways by taking advantage of the increasing availability of genomic and biochemical data."http://bit.ly/NsbMRQ
Synthetic Aesthetics: Investigating Synthetic Biology's Designs on Nature [Alexandra Daisy Ginsberg, Jane Calvert, Pablo Schyfter, Alistair Elfick, Drew Endy] on Amazon.com. *FREE* shipping on qualifying offers.
As the costs of DNA sequencing and synthesis drop precipitously, a host of computer science-meets-biotech startups are cropping up in Silicon Valley...
A tattoo may make a statement, but can it also help fight disease? Find out...
This Article addresses copyright as a viable form of intellectual property protection for living, organic creations of science and art. The United States Supreme Court’s decision in Association for Molecular Pathology v. Myriad Genetics, Inc. narrowed patent-eligible protection over living components of humans or other organisms. Synthetic biologists are expected to look with renewed focus on copyright law for the intellectual property protection of biological creations. The contribution of this Article is to reveal that the same issues are raised with regard to the copyrightability of the works of synthetic biology as are raised by pictorial, graphic, and sculptural arts that use and produce living media as their works. The current contours of copyrightability present four identical questions that are particularly relevant to and difficult to answer in the context of science and art that purports to create works of living media: Is living media copyrightable subject matter? What is authorship (or who is an author) of living media? What does it mean to create a fixed and tangible work of living media? What constitutes an original creation of living media under the originality doctrines of merger and scenes a faire? This Article will provide an analytical framework for rethinking the contours of copyright so as to answer these questions by comparing contemporary scientific methods of creation with artistic methods in order to determine the copyright narratives and metaphors of subject matter, authorship, creation, and originality that best address the concerns underlying these four questions and allow copyright protection over the works.  Association for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107 (Jun. 13, 2013) (isolated DNA sequences not patentable).
byChiarabelli, Cristiano; Luisi, Pier Luigi"Although both the most popular form of synthetic biology (SB) and chemical synthetic biology (CSB) share the biotechnologically useful aim of making new forms of life, SB does so by using genetic manipulation of extant microorganism, while CSB utilises classic chemical procedures in order to obtain biological structures which are non-existent in nature. The main query concerning CSB is the philosophical question: why did nature do this, and not that? The idea then is to synthesise alternative structures in order to understand why nature operated in such a particular way. We briefly present here some various examples of CSB, including those cases of nucleic acids synthesised with pyranose instead of ribose, and proteins with a reduced alphabet of amino acids; also we report the developing research on the “never born proteins” (NBP) and “never born RNA” (NBRNA), up to the minimal cell project, where the issue is the preparation of semi-synthetic cells that can perform the basic functions of biological cells." http://bit.ly/1crgtqj
byJay Keasling "Most Americans may not be familiar with synthetic biology, but they may come to appreciate its advances someday soon. Synthetic biology focuses on creating technologies for designing and building biological organisms. A multidisciplinary effort, it calls biologists, engineers, software developers, and others to collaborate on finding ways to understand how genetic parts work together, and then to combine them to produce useful applications.
Agilis Biotherapeutics, LLC, a synthetic biology-based company focused on developing DNA-based therapeutics for rare genetic diseases, announced today
SYS-CON Media, NJ, The world's leading i-technology media company on breaking technology news.
bySamuel H. Sternberg, Sy Redding, Martin Jinek, Eric C. Greene & Jennifer A. Doudna"The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA–DNA base-pairing to target foreign DNA in bacteria. Cas9–guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9–RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9–RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9–RNA. Competition assays provide evidence that DNA strand separation and RNA–DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA."http://bit.ly/1cdwW1l
byPatrick M. Shi1, Jan Zarzycki, Krishna K. Niyogi and Cheryl A. Kerfeld"Global photosynthetic productivity is limited by the enzymatic assimilation of CO2 into organic carbon compounds. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the carboxylating enzyme of the Calvin-Benson (CB) cycle, poorly discriminates between CO2 and O2, leading to photorespiration and the loss of fixed carbon and nitrogen. With the advent of synthetic biology, it is now feasible to design, synthesize and introduce biochemical pathways in vivo. We engineered a synthetic photorespiratory bypass based on the 3-hydroxypropionate bi-cycle into the model cyanobacterium, Synechococcus elongatus sp. PCC 7942. The heterologously expressed cycle is designed to function as both a photorespiratory bypass and an additional CO2-fixing pathway, supplementing the CB cycle. We demonstrate the function of all six introduced enzymes and identify bottlenecks to be targeted in subsequent bioengineering. These results have implications for efforts to improve photosynthesis, and for the "green" production of high-value products of biotechnological interest." http://bit.ly/1kvbwPS
George Church, Ph.D., a Core Faculty member at the Wyss Institute and Professor of Genetics at Harvard Medical School, explains how fluorescent in situ sequencing…