Chen T, Wang J, Zeng L, Li R, Li J, Chen Y, Lin Z.
"Cell reprogramming for microorganisms via engineered or artificial transcription factors and RNA polymerase mutants has presented a powerful tool for eliciting complex traits that are practically useful particularly for industrial strains, and for understanding at the global level the regulatory network of gene transcription. We previously further showed that an exogenous global regulator IrrE (derived from the extreme radiation-resistant bacterium Deinococcus radiodurans) can be tailored to confer Escherichia coli (E. coli) with significantly enhanced tolerances to different stresses. In this work, based on comparative transcriptomic and proteomic analyses of the representative strains E1 and E0, harboring the ethanol-tolerant IrrE mutant E1 and the ethanol-intolerant wild type IrrE, respectively, we found that the transcriptome and proteome of E. coli were extensively rewired by the tailored IrrE protein. Overall, 1196 genes (or approximately 27% of E. coli genes) were significantly altered at the transcriptomic level, including notably genes in the nitrate-nitrite-nitric oxide (NO) pathway, and genes for non-coding RNAs. The proteomic profile revealed significant up- or downregulation of several proteins associated with syntheses of the cell membrane and cell wall. Analyses of the intracellular NO level and cell growth under reduced temperature supported a close correlation between NO and ethanol tolerance, and also suggests a role for membrane fluidity. The significantly different omic profiles of strain E1 indicate that IrrE functions as a global regulator in E. coli, and that IrrE may be evolved for other cellular tolerances. In this sense, it will provide synthetic biology with a practical and evolvable regulatory "part" that operates at a higher level of complexity than local regulators. This work also suggests a possibility of introducing and engineering other exogenous global regulators to rewire the genomes of microorganism cells."
"Synthetic biology uses biological components to engineer new functionality in living organisms. Biological components are generally not as well characterized as their electronic counterparts. Therefore, systems produced with biological parts often exhibit unexpected or undesirable characteristics that are dependent on their interaction – also called crosstalk – with endogenous components from the organism where these systems are used.
One approach to dealing with this crosstalk would be to design a system that interacts so specifically that there is no possibility of crosstalk with endogenous components. Another approach is to use computational redesign of proteins and directed evolution to engineer “privileged” interfaces in the synthetic signaling system.
June Medford, Colorado State University, Fort Collins, CO, USA, and colleagues discuss current approaches in the field including the design of synthetic components, partially synthetic systems that utilize crosstalk to signal through endogenous components, computational redesign of proteins, and the use of heterologous components...."
Seema Singh "There may be deeper philosophical interpretations of life but for J Craig Venter, visionary geneticist who has been pushing the limits of genomics, life is a DNA software system; you change the system, you change the species. Just as all the marvels of computing derive from the binary codes of 00s and 11s, all life forms derive from a similar code, a Morse code of dots and dashes. To his credit, Venter and his team at the J Craig Venter Institute in Rockville, Maryland, are doing their best, more than anybody else, to ensure that in not-so-distant future, one can transfer the digital life code in email, to be downloaded on demand for various applications. He is even building a digital-biological converter, much akin to the telephone that converts digital information into sound, that will convert biological information into digital information. If that sounds too science-fiction-like, pinch yourself. It is reality, rather going to be reality very soon. For instance, take the pandemic flu vaccine. When H1N1, the swine flu bug, outbreak hit government agencies in 2009, it took almost six months to have the vaccine ready. Using the synthetic genomics tools and working with the US government and Swiss pharma major Novartis, Venter believes the next time such a crisis hits, the vaccines can be readied in less than a week....."
"The emerging field of synthetic biology enables the creation of living designs through science. Two concept designs explore and provoke dialogue about the future: 1) personal microbial culture and 2) packaging that creates its own contents...."
Fusun Yaman, Swapnil Bhatia, Aaron Adler, Douglas Densmore, and Jacob Beal
"Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal matching, and part matching. Feature matching ensures that the mapping satisfies the regulatory relationships in the abstract design. Signal matching ensures that the expression levels of functional units are compatible. Finally, part matching finds a DNA part sequence that can implement the design. Our software tool MatchMaker implements these three steps." http://bit.ly/L9BYbZ
"The ultimate design material is one that understands what it is to become. By way of an example, I’d like to think about how we might design a chicken.
Think of the creativity of Nature – which, in very real terms can:
• Transform an acorn into a giant oak tree • Change the colour of a chameleon • Evolve scales into feathers so that a creature can soar.
Throughout the ages we have sought to understand how one thing becomes another – and it really isn’t such a difficult thing to do:
• Ivy can be trained over frameworks to grow arches • Trees can be pleached to build fences • Plants and animals can be selectively bred to particular requirements.
The capacity to design things so that they become something else is real – provided we choose the right materials to work with. And now we have sophisticated technologies that can help us do this.
Over the last two decades there have been significant developments in the science of synthetic biology – the design and engineering of living things – where we can work at such small scales and with such precision – that we can consider some of life’s processes to actually be technology. This has enabled us to change the course of natural development.
To use a very explicit example we could introduce jellyfish genes into pets such as, mice, fish and cats so they can glow under dark light.
Matter has never been so strange or creative.
Yet because when we design - we use living things in such a limited set of circumstances - such as, gardening and agriculture – we equate design with working with inert materials with predictable properties.
Synthetic biology is changing this by bringing living materials – which share some of the qualities of living things – into our everyday manufacturing and social spaces. It is influencing design practice so profoundly that it is even shaping our cities......" http://bit.ly/PQSVQb
Authors: Di Camillo B, Sanavia T, Martini M, Jurman G, Sambo F, Barla A, Squillario M, Furlanello C, Toffolo G, Cobelli C
"MOTIVATION: The identification of robust lists of molecular biomarkers related to a disease is a fundamental step for early diagnosis and treatment. However, methodologies for the discovery of biomarkers using microarray data often provide results with limited overlap. These differences are imputable to 1) dataset size (few subjects with respect to the number of features); 2) heterogeneity of the disease; 3) heterogeneity of experimental protocols and computational pipelines employed in the analysis. In this paper, we focus on the first two issues and assess, both on simulated (through an in silico regulation network model) and real clinical datasets, the consistency of candidate biomarkers provided by a number of different methods. METHODS: We extensively simulated the effect of heterogeneity characteristic of complex diseases on different sets of microarray data. Heterogeneity was reproduced by simulating both intrinsic variability of the population and the alteration of regulatory mechanisms. Population variability was simulated by modeling evolution of a pool of subjects; then, a subset of them underwent alterations in regulatory mechanisms so as to mimic the disease state. RESULTS: The simulated data allowed us to outline advantages and drawbacks of different methods across multiple studies and varying number of samples and to evaluate precision of feature selection on a benchmark with known biomarkers. Although comparable classification accuracy was reached by different methods, the use of external cross-validation loops is helpful in finding features with a higher degree of precision and stability. Application to real data confirmed these results. "
The world may soon see the first examples of synthetic life, artificial organisms constructed in a laboratory. These will be unique organisms, not close copies of existing cells, said their creator Dr Craig Venter.
Brock A. Peters, Bahram G. Kermani, Andrew B. Sparks, Oleg Alferov, Peter Hong, Andrei Alexeev, Yuan Jiang, Fredrik Dahl, Y. Tom Tang, Juergen Haas, Kimberly Robasky, Alexander Wait Zaranek, Je-Hyuk Lee, Madeleine Price Ball, Joseph E. Peterson, Helena Perazich, George Yeung, Jia Liu, Linsu Chen, Michael I. Kennemer, Kaliprasad Pothuraju, Karel Konvicka, Mike Tsoupko-Sitnikov, Krishna P. Pant, Jessica C. Ebert et al
"Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ~100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10–20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications."
"This report presents the findings of a series of public workshops and stakeholder interviews on the science and issues surrounding synthetic biology. The project took place during 2009-2010 and was carried out by the TNS-BMRB, initiated by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC), and with support of the Department for Business, Innovation and Skills’ Sciencewise program me......"
Yang G, Wang S, Wei H, Ping J, Liu J, Xu L, Zhang W.
"Synthesis of long DNA fragments is often associated with mutations and requires multiple DNA manipulation steps. A novel DNA synthesis method, referred to as patch oligodeoxynucleotide synthesis (POS) to assembly long DNA fragments is presented here. This method involves connection of two types of oligodeoxynucleotides: long constructional oligonucleotides (COs) and short patch oligonucleotides (POs). Long COs were connected by a ligase with the aid of POs, which were complementary to both adjacent COs to help remove secondary structures during assembly. The partial double-stranded DNA template that was formed was then amplified by PCR. Accordingly, we synthesized SV40 polyadenylation signal sequences (187 bp), a codon-optimized yellow fluorescent protein gene (678 bp), and Rattus norvegicus catenin β1 (2,352 bp). This presented method can be broadly applied to synthesize DNA fragments of varying lengths with great convenience." http://1.usa.gov/NGhfid
Malyshev DA, Dhami K, Quach HT, Lavergne T, Ordoukhanian P, Torkamani A, Romesberg FE.
"The natural four-letter genetic alphabet, comprised of just two base pairs (dA-dT and dG-dC), is conserved throughout all life, and its expansion by the development of a third, unnatural base pair has emerged as a central goal of chemical and synthetic biology. We recently developed a class of candidate unnatural base pairs, exemplified by the pair formed between d5SICS and dNaM. Here, we examine the PCR amplification of DNA containing one or more d5SICS-dNaM pairs in a wide variety of sequence contexts. Under standard conditions, we show that this DNA may be amplified with high efficiency and greater than 99.9% fidelity. To more rigorously explore potential sequence effects, we used deep sequencing to characterize a library of templates containing the unnatural base pair as a function of amplification. We found that the unnatural base pair is efficiently replicated with high fidelity in virtually all sequence contexts. The results show that, for PCR and PCR-based applications, d5SICS-dNaM is functionally equivalent to a natural base pair, and when combined with dA-dT and dG-dC, it provides a fully functional six-letter genetic alphabet."