SynBioFromLeukipposInstitute

Novel advances in the design of three-dimensional bio-scaffolds to control cell fate: translation from 2D to 3D

by
Santos E, Hernández RM, Pedraz JL, Orive G.
"Recreating the most critical aspects of the native extracellular matrix (ECM) is fundamental to understand and control the processes regulating cell fate and cell function. From the ill-defined complexity to the controlled simplicity, we discuss the different strategies that are being carried out by scientists worldwide to achieve the latest advances in the sophistication of three-dimensional (3D) scaffolds, stressing their impact on cell biology, tissue engineering and regenerative medicine. Synthetic and naturally derived polymers like polyethylene glycol, alginate, agarose, etc., together with micro- and nanofabrication techniques are allowing the creation of 3D models where biophysical and biochemical variables can be modified with high precision, orthogonality and even in real-time."

http://1.usa.gov/KmjVBg

Remotely controlled gene expression

by
Sarah A. Stanley, Jennifer E. Gagner, Shadi Damanpour, Mitsukuni Yoshida, Jonathan S. Dordick, Jeffrey M. Friedman

"Medical applications of nanotechnology typically focus on drug delivery and biosensors. Here, we combine nanotechnology and bioengineering to demonstrate that nanoparticles can be used to remotely regulate protein production in vivo. We decorated a modified temperature-sensitive channel, TRPV1, with antibody-coated iron oxide nanoparticles that are heated in a low-frequency magnetic field. When local temperature rises, TRPV1 gates calcium to stimulate synthesis and release of bioengineered insulin driven by a Ca2+-sensitive promoter. Studying tumor xenografts expressing the bioengineered insulin gene, we show that exposure to radio waves stimulates insulin release from the tumors and lowers blood glucose in mice. We further show that cells can be engineered to synthesize genetically encoded ferritin nanoparticles and inducibly release insulin. These approaches provide a platform for using nanotechnology to activate cells."
http://bit.ly/L8uyJS

by

Bhartiya D, Kapoor S, Jalali S, Sati S, Kaushik K, Sachidanandan C, Sivasubbu S, Scaria V.
"Introduction: Long non-coding RNAs (lncRNAs) are a recently discovered class of non-coding functional RNA which has attracted immense research interest. The growing corpus of literature in the field provides ample evidence to suggest the important role of lncRNAs as regulators in a wide spectrum of biological processes. Recent evidence also suggests the role of lncRNAs in the pathophysiology of disease processes. Areas covered: The authors discuss a conceptual framework for understanding lncRNA-mediated regulation as a function of its interaction with other biomolecules in the cell. They summarize the mechanisms of the known functions of lncRNAs in light of this conceptual framework, and suggest how this insight could help in discovering novel targets for drug discovery. They also argue how certain emerging technologies could be of immense utility, both in discovering potential therapeutic targets as well as in further therapeutic development. Expert opinion: The authors propose how the field could immensely benefit from methodologies and technologies from six emerging fields in molecular and computational biology. They also suggest a futuristic area of lncRNAs design as a potential offshoot of synthetic biology, which would be an attractive field, both for discovery of targets as well as a therapeutic strategy."

http://1.usa.gov/Ld2Itz

Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters

by
Blazeck J, Garg R, Reed B, Alper H.
"A dynamic range of well-controlled constitutive and tunable promoters are essential for metabolic engineering and synthetic biology applications in all host organisms. Here we apply a synthetic hybrid promoter approach for the creation of strong promoter libraries in the model yeast, Saccharomyces cerevisiae. Synthetic hybrid promoters are composed of two modular components- the enhancer element, consisting of tandem repeats or combinations of upstream activation sequences (UAS), and the core promoter element. We demonstrate the utility of this approach with three main case studies. First, we establish a dynamic range of constitutive promoters and in doing so expand transcriptional capacity of the strongest constitutive yeast promoter, P(GPD) , by 2.5-fold in terms of mRNA levels. Second, we demonstrate the capacity to impart synthetic regulation through a hybrid promoter approach by adding galactose activation and removing glucose repression. Third, we establish a collection of galactose-inducible hybrid promoters that span a nearly 50-fold dynamic range of galactose-induced expression levels and increase the transcriptional capacity of the Gal1 promoter by 15%. These results demonstrate that promoters in S. cerevisiae, and potentially all yeast, are enhancer limited and a synthetic hybrid promoter approach can expand, enhance, and control promoter activity."

http://1.usa.gov/JfGEw5

"In this paper, I discuss the aetiological account of biological interests, developed by Varner (1998), in the context of artefactual organisms envisioned by current research in synthetic biology. In “Sections 2–5”, I present Varner's theory and criticise it for being incapable of ascribing non-derivative interests to artefactual organisms due to their lack of a history of natural selection. In “Sections 6–7”, I develop a new alternative to Varner's account, building on the organisational theory of biological teleology and function. I argue that the organisational account of biological interest is superior to Varner's aetiological account because it (i) can accommodate both artefactual and naturally evolved organisms, (ii) provides a non-arbitrary and practical way of determining biological interests, (iii) supports the claim that organisms have interests in a sense in which artefacts do not, and (iv) avoids the possibility of there being a conflict between what an organismic part is supposed to do and what is in the interest of the organism."

by

Harris H Wang, Hwangbeom Kim, Le Cong, Jaehwan Jeong, Duhee Bang & George M Church

"Multiplex automated genome engineering (MAGE) uses short oligonucleotides to scarlessly modify genomes; however, insertions >10 bases are still inefficient but can be improved substantially by selection of highly modified chromosomes. Here we describe 'coselection' MAGE (CoS-MAGE) to optimize biosynthesis of aromatic amino acid derivatives by combinatorially inserting multiple T7 promoters simultaneously into 12 genomic operons. Promoter libraries can be quickly generated to study gain-of-function epistatic interactions in gene networks."

http://bit.ly/KciEg1

by

Shuobing Chen, Haoqian Zhang, Handuo Shi, Weiyue Ji, Jingchen Feng, Yan Gong, Zhenglin Yang, Qi Ouyang
Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Peking University, Beijng, 100871, China

"Synthetic biology aims to rationally construct biological devices with required functionalities. Methods that automate the design of genetic devices without post-hoc adjustment, therefore, are highly desired. Here we provide a method to predictably design genetic toggle switches with predetermined bistability. To accomplish this task, a biophysical model that links Ribosome Binding Site (RBS) DNA sequence to toggle switch bistability was first developed by integrating a stochastic model with RBS design method. Then, to parameterize the model, a library of genetic toggle switch mutants was experimentally built, followed by establishing the equivalence between RBS DNA sequences and switch bistability. To test this equivalence, RBS nucleotide sequences for different specified bistability were in silico designed and experimentally verified. Results show that the deciphered equivalence is highly predictive for the toggle switch design with predetermined bistability. This method can be generalized to quantitative design of other probabilistic genetic devices in synthetic biology."

http://bit.ly/ItPEhH

GENOME SEQUENCING
by

Elizabeth Pennisi
"Oxford Nanopore Technologies is set to achieve the first commercialization of a long-awaited and oft-doubted technology called nanopore sequencing. The technology, based on protein pores so tiny that 25,000 of them can fit on the cross section of a human hair, could be the next big thing in genome sequencing and analysis. Although they've gotten much cheaper and smaller in recent years, machines that read DNA and RNA still usually cost hundreds of thousands of dollars, take up entire lab benches, and require much upfront and postsequencing processing to generate a genome. Nanopore sequencing could change all that. But some scientists say many technical hurdles remain to be overcome before nanopore devices produce actual sequence data."

http://bit.ly/IPqcl6