From gene switches to mammalian designer cells: present and future prospects

Nature has evolved a treasury of biological molecules that are logically connected to networks, enabling cells to maintain their functional integrity. Similar to electronic circuits, cells operate as information-processing systems that dynamically integrate and respond to distinct input signals. Synthetic biology aims to standardize and expand the natural toolbox of biological building blocks to engineer novel synthetic networks in living systems. Mammalian cells harboring integrated designer circuits could work as living biocomputers that execute predictable metabolic and therapeutic functions. This review presents design principles of mammalian gene circuits, highlights recent developments, and discusses future challenges and prospects.

Slides for Recruiting Talk for WHU-iGEM-2013

New march to 2013’s iGEM, new WHU-iGEM team.

Here attached the link to my  presentation on Dec 8, 2012 at the Recruiting Talk. The slides formatted in html are deployed at my github site, and thus internet browser, like Chrome or Firefox,  supporting Html5 is highly recommended for better visualization.

My presentation is based on A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell. 2012. Students with mathematics, statistics background are welcome.

The English version will be uploaded soon~~~



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p.s. The slides intend to draw attention of undergraduates with modeling/statistics background, and at the same time remind students from life sciences of the fact that biology has become executive, not just only readable or writable. A new era is coming. Interdisciplinary collaboration platform is now provided by iGEM.


Designing and using RNA scaffolds to assemble proteins in vivo

RNA scaffolds are synthetic noncoding RNA molecules with engineered 3D folding harnessed to spatially organize proteins in vivo. Here we provide a protocol to design, express and characterize RNA scaffolds and their cognate proteins within 1 month. The RNA scaffold designs described here are based on either monomeric or multimeric units harboring RNA aptamers as protein docking sites. The scaffolds and proteins are cloned into inducible plasmids and expressed to form functional assemblies. RNA scaffolds find applications in many fields in which in vivo organization of biomolecules is of interest. RNA scaffolds provide extended flexibility compared with DNA or protein scaffolding strategies through programmed modulation of multiple protein stoichiometry and numbers, as well as the proteins’ relative distances and spatial orientations. For synthetic biology, RNA scaffolds provide a new platform that can be used to increase yields of sequential metabolic pathways.


Tool Developer Website Summary
mfold University of Albany RNA folding software; folding temperature and ionic conditions are fixed
NUPACK California Institute of Technology RNA software suite for design and folding analysis with the option of designing RNA reaction pathways
RNA Designer University of British Columbia RNA design tool using the dot-bracket format; temperature and GC content are adjustable
RBS Calculator Penn State University Predicts translation initiation rate in bacteria; takes into account RNA secondary structures for predictions
Nucleotide BLAST National Center for Biotechnology Information BLAST compares nucleotide sequences to sequence database and calculates the statistical significance of any match
Primer-BLAST National Center for Biotechnology Information Uses the popular primer3 engine to design primers; results are submitted to BLAST to check for unwanted endogenous match
BioNumbers Harvard Medical School Registry of useful biological numbers, including genomic GC contents
genormPLUS Biogazelle Algorithm to determine the most stable reference genes from a set of tested candidate reference genes in a given qPCR sample panel

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

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (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, whereas 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.


–end && reference

— later I’ll explain a little bit.