"The potential of advanced nanotechnology is getting some attention from mainstream media. Late last year The Guardian web site posted a brief article on the prospects for nanofactories and atomically precise manufacturing, featuring quotes from Christine Peterson and Robert Freitas. From “Nanofactories – a future vision” by Penny Sarchet"
"Can a wide range of complex biochemical behaviour arise from repeated applications of a highly reduced class of interactions? In particular, can the range of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands of DNA as the only component molecules. Various enzymatic manipulations of these mDNA molecules are simulated via toehold-mediated DNA strand displacement reactions. We provide a formal model to describe the required properties and operations of our mDNA, and show that our proposed DNA nanostructures and hybridization reactions provide these properties and functionality. Our meta-nucleotides are designed to form flexible linear assemblies (single-stranded mDNA (ssmDNA)) analogous to single-stranded DNA. We describe various isothermal hybridization reactions that manipulate our mDNA in powerful ways analogous to DNA-DNA reactions and the action of various enzymes on DNA. These operations on mDNA include (i) hybridization of ssmDNA into a double-stranded mDNA (dsmDNA) and heat denaturation of a dsmDNA into its component ssmDNA, (ii) strand displacement of one ssmDNA by another, (iii) restriction cuts on the backbones of ssmDNA and dsmDNA, (iv) polymerization reactions that extend ssmDNA on a template to form a complete dsmDNA, (v) synthesis of mDNA sequences via mDNA polymerase chain reaction, (vi) isothermal denaturation of a dsmDNA into its component ssmDNA, and (vii) an isothermal replicator reaction that exponentially amplifies ssmDNA strands and may be modified to allow for mutations."
More about this programme: http://www.bbc.co.uk/programmes/b01b45zh Synthetic biology has the radical aim to break down nature into spare parts so that we ca...
"In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This “liposome logic” approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in “top-down” synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of “bottom-up” liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie’s stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up."
The many different forms of cancer still pose one of the biggest challenges to human health. The fact that cancer cells are, crudely speaking, normal cells replicating out of control poses a number of significant problems.
"The development of new molecular approaches in biology and biotechnology introduced new scientific terms which include genome, genomics, methylome and methylomics. These are currently used in the literature of molecular and synthetic biology to refer various molecular concepts and applications. The present study is about the requirement of new “ome” and “omics” terms. This is because there are unique structural and functional aspects associated with genome and methylome at specific regions in the DNA sequence which are not explained by the two currently used terms methylome and genome. There is a requirement for new ome/omics terms to refer specific structural and functional matters associated with particular specialized zones in the DNA sequences. These genomic regions contain both the fifth base “methyl cytosine” and the other four coding bases. Methylated and non methylated DNA sequences are involved in gene expression of RNA and proteins, beside their role in the structural organization of the DNA sequence and the chromosome. In this study I suggest introducing two words which are derived from the established scientific terms “genome, genomics, methylome and methylomics”. The two new derived words are: gethylome and gethylomics. I suggest that these two words might be useful and could be used to explain various issues related to specific regions in the DNA sequence and chromosomes of eukaryotic organisms which contain the fifth base. Furthermore, gethylomics will help to refer more precisely to new applications in synthetic biology and genomics to design or redesign specific gethylomic circuits."
"...We have developed a genetic system capable of producing modular carbon-fixing microcompartments in a heterologous host. In doing so, we lay the groundwork for understanding these elaborate protein complexes and for the synthetic biological engineering of self-assembling molecular structures..."
RT @SpringerSysBio: Most accessed article from #Systems & #Synthetic #Biology journal this week: #Computational Study of #Liposome Logic http://t.co/J9YrDTI3...
central resource for events in human genetics and molecular biology (Third International ‘Frontiers in Synthetic Biology,Biofuels & Green Chemistry-2012- Meeting’ On ‘Synthetic Geno...)...
"Despite substantial progress in synthetic biology, we still lack the ability to engineer anything as complex as Nature has. One of the many reasons is that we lack the requisite tools for independently controlling the expression of multiple genes in parallel. While our toolbox is still spare, the situation is rapidly changing. This opinion discusses some recent approaches and open challenges in designing orthogonal regulators of gene expression in bacteria."
"Adrien Treuille, assistant professor of computer science at Carnegie Mellon University, discusses the online game EteRNA that has been developed jointly by CMU and Stanford University. EteRNA will engage a large and diverse group of players in the scientific discovery of principles underlying RNA design."
"In 1962, Hamilton Smith abandoned a career in medicine to follow his passion for the emerging field of molecular biology; within six years, he had made the discovery of a lifetime. As a new Johns Hopkins faculty member, Smith, together with his first graduate student, Kent Wilcox, geared up to study recombination in vitro but instead discovered the restriction enzyme “R” in Haemophilus influenzae. By cobbling together crude techniques, Smith, along with Wilcox and later Tom Kelly, showed that R cleaves DNA at a specific recognition sequence, a palindromic site, yielding blunt-ended DNA fragments. Now known as HindII, R proved to be the first of an enormous class of Type II restriction enzymes, and as such, presaged gene cloning, allowed DNA to be reproducibly fragmented and then sequenced, and enabled physical mapping of genomes. Smith went on to discover DNA methylases that constitute the other half of the bacterial host restriction and modification systems, as hypothesized by Werner Arber of Switzerland. Together with Arber and his Hopkins colleague Daniel Nathans, who first used the enzyme on SV40 DNA and demonstrated discrete bands on a tube gel, Smith shared the Nobel Prize for Physiology or Medicine in 1978.
Smith's curiosity and his gift for hands-on research continued to guide him through a highly productive career at Hopkins for more than three decades, when a chance meeting with Craig Venter, who had just launched The Institute for Genome Research (TIGR), turned his attention to sequencing the Haemophilus genome. In 1998, he gave up his faculty position at Hopkins and has been working with Venter ever since. Currently, Smith (Image 1) spearheads the highly visible synthetic biology program at the J. Craig Venter Institute (JCVI) in San Diego. And that is where I caught up with him in late October."
Silicon Valley has sprouted numerous hacker spaces in recent years, where software geeks get together to program and build new Web creations. Now there's a hangout for biohackers, too.
Sean A. Lynch, Ryan T. Gill. Metabolic Engineering (December 2011). The advancement of synthetic biology is thanks, in large part, to continuing improvements in DNA synthesis.
Technological advancements in the life sciences are continually pressing forward. The deliberative pattern tends to be similar as the technology unfolds: How does it work? How is it different than ...
What Is Life?: Investigating the Nature of Life in the Age of Synthetic Biology book download (What Is Life?: Investigating the Nature of Life in the Age of Synthetic Biology: What Is Life?
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