Publications
101 results found
Schaerli Y, Munteanu A, Gili M, et al., 2014, A unified design space of synthetic stripe-forming networks, Nature Communications, Vol: 5, Pages: 1-10, ISSN: 2041-1723
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-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.
Diambra L, Senthivel VR, Menendez DB, et al., 2014, Cooperativity To Increase Turing Pattern Space for Synthetic Biology, ACS Synthetic Biology
Herrman F, Isalan M, 2014, High-throughput ‘On Chip’ Protein and Nucleic Acid Transfection (2nd Edition), eLS, Publisher: John Wiley and Sons, Inc., ISBN: 9780470015902
Transfection describes the nonviral introduction of exogenous molecules into eukaryotic cells. Numerous transfection methods have been developed to transfer nucleic acids, proteins and other macromolecules across the plasma membrane efficiently. These include physical methods, such as electroporation, magnetofection and microinjection, as well as a chemical or biological carrier-mediated methods. Chemical transfection reagents such as cationic lipids or polymers are widely used, either alone or in combination with scaffolds. Biological methods include delivery with cell-penetrating protein domain fusions such as trans-activator of transcription protein from human immunodeficiency virus, VP22 or Antennapedia peptides. Certain proteins such as zinc-finger nucleases, which are used for targeted genome modification, even appear to have intrinsic cell-penetrating properties. To facilitate large-scale genomic and proteomic studies there is an increasing need for automated high-throughput transfection platforms. Several such platforms have been developed, including multiwell plates, transfection microarrays and microfluidic chip formats. Overall, the different advantages and applications of these diverse methods to deliver cargo into cells are discussed.
Carvalho A, Barcena Menendez D, Raj Senthivel V, et al., 2013, Genetically encoded sender-receiver system in 3D mammalian cell culture, ACS Synthetic Biology, Vol: 3, Pages: 264-272, ISSN: 2161-5063
Engineering spatial patterning in mammalian cells, employing entirely genetically encoded components, requires solving several problems. These include how to code secreted activator or inhibitor molecules and how to send concentration-dependent signals to neighboring cells, to control gene expression. The Madin–Darby Canine Kidney (MDCK) cell line is a potential engineering scaffold as it forms hollow spheres (cysts) in 3D culture and tubulates in response to extracellular hepatocyte growth factor (HGF). We first aimed to graft a synthetic patterning system onto single developing MDCK cysts. We therefore developed a new localized transfection method to engineer distinct sender and receiver regions. A stable reporter line enabled reversible EGFP activation by HGF and modulation by a secreted repressor (a truncated HGF variant, NK4). By expanding the scale to wide fields of cysts, we generated morphogen diffusion gradients, controlling reporter gene expression. Together, these components provide a toolkit for engineering cell–cell communication networks in 3D cell culture.
Sanders PGT, Cotterell J, Sharpe J, et al., 2013, Transfecting RNA quadruplexes results in few transcriptome perturbations, RNA BIOLOGY, Vol: 10, Pages: 205-210, ISSN: 1547-6286
- Author Web Link
- Cite
- Citations: 3
Schaerli Y, Isalan M, 2013, Building synthetic gene circuits from combinatorial libraries: screening and selection strategies, MOLECULAR BIOSYSTEMS, Vol: 9, Pages: 1559-1567, ISSN: 1742-206X
- Author Web Link
- Cite
- Citations: 25
Isalan M, 2013, Zinc Fingers, Encyclopedia of Biological Chemistry (Second Edition), Editors: Lennarz, Lane, Publisher: Elsevier
Garriga-Canut M, Agustin-Pavon C, Herrmann F, et al., 2012, Synthetic zinc finger repressors reduce mutant huntingtin expression in the brain of R6/2 mice, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: E3136-E3145, ISSN: 0027-8424
- Author Web Link
- Open Access Link
- Cite
- Citations: 118
Peccoud J, Isalan M, 2012, The PLOS ONE Synthetic Biology Collection: Six Years and Counting, PLOS ONE, Vol: 7, ISSN: 1932-6203
- Author Web Link
- Open Access Link
- Cite
- Citations: 7
Isalan M, 2012, SYSTEMS BIOLOGY A cell in a computer, NATURE, Vol: 488, Pages: 40-41, ISSN: 0028-0836
- Author Web Link
- Cite
- Citations: 6
Isalan M, 2012, Zinc-finger nucleases: how to play two good hands, NATURE METHODS, Vol: 9, Pages: 32-34, ISSN: 1548-7091
- Author Web Link
- Cite
- Citations: 47
Constante M, Gruenberg R, Isalan M, 2011, A Biobrick Library for Cloning Custom Eukaryotic Plasmids, PLOS ONE, Vol: 6, ISSN: 1932-6203
- Author Web Link
- Open Access Link
- Cite
- Citations: 11
Herrmann F, Garriga-Canut M, Baumstark R, et al., 2011, p53 Gene Repair with Zinc Finger Nucleases Optimised by Yeast 1-Hybrid and Validated by Solexa Sequencing, PLOS ONE, Vol: 6, ISSN: 1932-6203
- Author Web Link
- Open Access Link
- Cite
- Citations: 28
Munteanu A, Constante M, Isalan M, et al., 2010, Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation, BMC SYSTEMS BIOLOGY, Vol: 4
- Author Web Link
- Open Access Link
- Cite
- Citations: 11
Isalan M, 2009, Gene networks and liar paradoxes, BIOESSAYS, Vol: 31, Pages: 1110-1115, ISSN: 0265-9247
- Author Web Link
- Open Access Link
- Cite
- Citations: 16
Isalan M, Morrison M, 2009, This title is false, NATURE, Vol: 458, Pages: 969-969, ISSN: 0028-0836
- Author Web Link
- Cite
- Citations: 7
Michalodimitrakis K, Isalan M, 2009, Engineering prokaryotic gene circuits, FEMS MICROBIOLOGY REVIEWS, Vol: 33, Pages: 27-37, ISSN: 0168-6445
- Author Web Link
- Open Access Link
- Cite
- Citations: 35
Isalan M, Lemerle C, Michalodimitrakis K, et al., 2008, Evolvability and hierarchy in rewired bacterial gene networks, NATURE, Vol: 452, Pages: 840-U2, ISSN: 0028-0836
- Author Web Link
- Open Access Link
- Cite
- Citations: 228
Fajardo-Sanchez E, Stricher F, Paques F, et al., 2008, Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences, NUCLEIC ACIDS RESEARCH, Vol: 36, Pages: 2163-2173, ISSN: 0305-1048
- Author Web Link
- Open Access Link
- Cite
- Citations: 41
EMMANUEL FAJARDO SANCHEZ, SYLVESTRE GRIZOT, MARK ISALAN, et al., 2008, Obligate heterodimer meganucleases and uses thereof
An obligate heterodimer meganuclease consisting of a first and a second monomer, deriving from two different homodimeric LAGLIDADG endonuclease monomers (parent monomers), and having at least one pairof mutations interesting corresponding residues of said parent monomers which make an intermolecular interaction between the two monomers of each parent homodimeric LAGLIDADG endonuclease, a vector encoding said meganuclease, a cell, an animal or a plant modified by said vector and the use of said meganuclease and derived products for molecular biology, genome engineering and genome therapy.
Herrmann F, Isalan M, 2008, High-throughput ‘On Chip’ Protein and Nucleic Acid Transfection, Encyclopedia of Life Sciences, Editors: Finazzi-Agrò, Publisher: John Wiley & Sons
Isalan M, 2006, Construction of semi-randomized gene libraries with weighted oligonucleotide synthesis and PCR, NATURE PROTOCOLS, Vol: 1, Pages: 468-475, ISSN: 1754-2189
- Author Web Link
- Cite
- Citations: 12
Santori MI, Gonzalez C, Serrano L, et al., 2006, Localized transfection with magnetic beads coated with PCR products and other nucleic acids, NATURE PROTOCOLS, Vol: 1, Pages: 526-531, ISSN: 1754-2189
- Author Web Link
- Cite
- Citations: 8
Guidez F, Howell L, Isalan M, et al., 2005, Histone acetyltransferase activity of p300 is required for transcriptional repression by the promyelocytic leukemia zinc finger protein, MOLECULAR AND CELLULAR BIOLOGY, Vol: 25, Pages: 5552-5566, ISSN: 0270-7306
- Author Web Link
- Cite
- Citations: 87
Isalan M, Lemerle C, Serrano L, 2005, Engineering gene networks to emulate <i>Drosophila</i> embryonic pattern formation, PLOS BIOLOGY, Vol: 3, Pages: 488-496, ISSN: 1544-9173
- Author Web Link
- Open Access Link
- Cite
- Citations: 95
Isalan M, Santori MI, Gonzalez C, et al., 2005, Localized transfection on arrays of magnetic beads coated with PCR products, NATURE METHODS, Vol: 2, Pages: 113-118, ISSN: 1548-7091
- Author Web Link
- Cite
- Citations: 32
Guidez F, Howell L, Isalan M, et al., 2004, Histone acetyltransferase activity of p300 is required for transcriptional repression by the Promyelocytic Leukemia Zinc Finger protein, 46th Annual Meeting of the American-Society-of-Hematology, Publisher: AMER SOC HEMATOLOGY, Pages: 106A-106A, ISSN: 0006-4971
Patel SD, Isalan M, Gavory G, et al., 2004, Inhibition of human telomerase activity by an engineered zinc finger protein that binds G-quadruplexes, BIOCHEMISTRY, Vol: 43, Pages: 13452-13458, ISSN: 0006-2960
- Author Web Link
- Cite
- Citations: 43
Isalan M, Choo Y, 2004, Phage display of zinc fingers and other nucleic acid-binding motifs: Phage display – A Practical Approach, Editors: Clackson, Publisher: Oxford University Press
Isalan M, 2004, Zinc Fingers, Encyclopedia of Biological Chemistry (First Edition), Editors: Lennarz, Lane, Publisher: Elsevier/Academic Press
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.