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Article
Open AccessA drug stabilizable GAL80ds for conditional control of gene expression via GAL4-UAS and CRISPR-Cas9 systems in Drosophila
The binary GAL4-UAS expression system has been widely used in Drosophila to achieve tissue-specific expression of genes. To further allow for simultaneous spatial and conditional control of gene expression in exi...
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Article
Open AccessMammalian cell growth characterisation by a non-invasive plate reader assay
Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here, we report the development of a high throughp...
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Protocol
A Directed Evolution Protocol for Engineering Minimal Transcription Factors, Based on CIS Display
Directed evolution is an efficient strategy for obtaining desired biomolecules. Since the 1990s, the emergence of display techniques has enabled high-throughput screening of functional proteins. However, class...
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Article
Open AccessA genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications
Mycoplasmas have exceptionally streamlined genomes and are strongly adapted to their many hosts, which provide them with essential nutrients. Owing to their relative genomic simplicity, Mycoplasmas have been used...
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Article
Trp-ing upon new repressors
Bioengineers have used directed evolution to generate a new family of synthetic transcription factors based on the tryptophan repressor. The evolved repressor family enables researchers to build new gene circu...
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Protocol
Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR
The ability to mutate a promoter in situ is potentially a very useful approach for gaining insights into endogenous gene regulation mechanisms. The advent of CRISPR/Cas systems has provided simple, efficient, ...
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Article
Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication
This protocol describes a phagemid-based intracellular evolution approach to generate and select for proteins with improved biological characteristics.
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Article
Open AccessEngineering orthogonal dual transcription factors for multi-input synthetic promoters
Synthetic biology has seen an explosive growth in the capability of engineering artificial gene circuits from transcription factors (TFs), particularly in bacteria. However, most artificial networks still empl...
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Article
Open AccessIdentifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis
Nonlinear responses to signals are widespread natural phenomena that affect various cellular processes. Nonlinearity can be a desirable characteristic for engineering living organisms because it can lead to mo...
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Article
Open AccessDeimmunization for gene therapy: host matching of synthetic zinc finger constructs enables long-term mutant Huntingtin repression in mice
Synthetic zinc finger (ZF) proteins can be targeted to desired DNA sequences and are useful tools for gene therapy. We recently developed a ZF transcription repressor (ZF-KOX1) able to bind to expanded DNA CAG...
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Article
Open AccessThe propagation of perturbations in rewired bacterial gene networks
What happens to gene expression when you add new links to a gene regulatory network? To answer this question, we profile 85 network rewirings in E. coli. Here we report that concerted patterns of differential exp...
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Article
Open AccessA shared mechanism of muscle wasting in cancer and Huntington’s disease
Skeletal muscle loss and dysfunction in aging and chronic diseases is one of the major causes of mortality in patients, and is relevant for a wide variety of diseases such as neurodegeneration and cancer. Musc...
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Article
Open AccessA unified design space of synthetic stripe-forming networks
Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case...
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Article
A cell in a computer
The small genomes of some bacteria could provide the first complete understanding of a biological system. A new computer model brings this goal closer, by calculating every process in a dividing Mycoplasma cell.
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Article
Zinc-finger nucleases: how to play two good hands
Zinc-finger nuclease dimers are more difficult to engineer than single DNA-binding domains, but the development of new methods could help.
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Article
Open AccessAvoiding transcription factor competition at promoter level increases the chances of obtaining oscillation
The ultimate goal of synthetic biology is the conception and construction of genetic circuits that are reliable with respect to their designed function (e.g. oscillators, switches). This task remains still to ...
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Article
This title is false
Comparing gene networks to Greek philosophy could help biologists to see the truth, argue Mark Isalan and Matthew Morrison.
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Article
Evolvability and hierarchy in rewired bacterial gene networks
Sequencing DNA from several organisms has revealed that duplication and drift of existing genes have primarily moulded the contents of a given genome. Though the effect of knocking out or overexpressing a part...
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Article
Localized transfection with magnetic beads coated with PCR products and other nucleic acids
The bead transfection method involves binding nucleic acids onto 3-μm-diameter paramagnetic beads, treating the beads with transfection reagent, and using them as scaffolds to direct transfection to individual...
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Article
Construction of semi-randomized gene libraries with weighted oligonucleotide synthesis and PCR
Randomized gene libraries may be constructed and screened to find novel candidates with particular functions, and the applications can range widely, from protein engineering to selecting new microRNAs. Here we...
