Wetware news from www.synbio.org.uk

Design, construction and characterization of a set of insulated bacterial promoters.

Sat, 02 Oct 2010 23:12:20 +0100

Design, construction and characterization of a set of insulated bacterial promoters.: "Publication Date: 2010 Sep 15 PMID: 20843779
Authors: Davis, J. H. - Rubin, A. J. - Sauer, R. T.
Journal: Nucleic Acids Res

We have generated a series of variable-strength, constitutive, bacterial promoters that act predictably in different sequence contexts, span two orders of magnitude in strength and contain convenient sites for cloning and the introduction of downstream open-reading frames. Importantly, their design insulates these promoters from the stimulatory or repressive effects of many 5'- or 3'-sequence elements. We show that different promoters from our library produce...

A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization.

Sat, 02 Oct 2010 22:57:12 +0100

A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization.: "Publication Date: 2010 Sep 3 PMID: 20603133
Authors: Hoi, H. - Shaner, N. C. - Davidson, M. W. - Cairo, C. W. - Wang, J. - Campbell, R. E.
Journal: J Mol Biol

The use of green-to-red photoconvertible fluorescent proteins (FPs) enables researchers to highlight a subcellular population of a fusion protein of interest and to image its dynamics in live cells. In an effort to enrich the arsenal of photoconvertible FPs and to overcome the limitations imposed by the oligomeric structure of natural photoconvertible FPs, we...

Bathy phytochromes in rhizobial soil bacteria.

Sat, 02 Oct 2010 22:42:40 +0100

Bathy phytochromes in rhizobial soil bacteria.: "Publication Date: 2010 Oct PMID: 20675484
Authors: Rottwinkel, G. - Oberpichler, I. - Lamparter, T.
Journal: J Bacteriol

Phytochromes are biliprotein photoreceptors that are found in plants, bacteria, and fungi. Prototypical phytochromes have a Pr ground state that absorbs in the red spectral range and is converted by light into the Pfr form, which absorbs longer-wavelength, far-red light. Recently, some bacterial phytochromes have been described that undergo dark conversion of Pr to Pfr and thus have a Pfr ground state. We show here that such so-called bathy phytochromes are widely distributed among...

Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell ...

Sat, 02 Oct 2010 22:40:28 +0100

Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the Eut-BMC.: "Publication Date: 2010 Sep 17 PMID: 20851901
Authors: Takenoya, M. - Nikolakakis, K. - Sagermann, M.
Journal: J Bacteriol

The ethanolamine utilizing microcompartment of E. coli (Eut-BMC) is a polyhedrally shaped organelle that harbors specific enzymes for the catabolic degradation of ethanolamine. The compartment is composed of a proteinaceous shell structure that maintains a highly specialized environment for the biochemical reactions inside. Recent structural investigations have revealed hexagonally shaped assemblies of shell proteins that form a tightly packed 2-dimensional lattice...

The Carboxysome Shell Is Permeable to Protons.

Sat, 02 Oct 2010 22:38:00 +0100

The Carboxysome Shell Is Permeable to Protons.: "Publication Date: 2010 Sep 24 PMID: 20870775
Authors: Menon, B. B. - Heinhorst, S. - Shively, J. M. - Cannon, G. C.
Journal: J Bacteriol

Bacterial microcompartments (BMCs) are polyhedral organelles found in an increasingly wide variety of bacterial species. These structures, as typified by carboxysomes of cyanobacteria and many chemoautotrophs, function to compartmentalize important reaction sequences of metabolic pathways. Unlike their eukaryotic counterparts that are surrounded by lipid bilayer membranes, these microbial organelles are bounded by a thin protein shell that is assembled from multiple copies of a few different...

A new tagged-TEV protease: Construction, optimisation of production, purification and test activity.

Sat, 02 Oct 2010 22:12:12 +0100

A new tagged-TEV protease: Construction, optimisation of production, purification and test activity.: "Publication Date: 2010 Sep 9 PMID: 20817099
Authors: Miladi, B. - Bouallagui, H. - Dridi, C. - El Marjou, A. - Boeuf, G. - Di Martino, P. - Dufour, F. - Elm'selmi, A.
Journal: Protein Expr Purif

The Tobacco Etch Virus (TEV) protease is frequently used in the cleavage of recombinant fusion proteins because of its efficiency and high specificity. In this work, we present a new recombinant form of TEV termed Streptag II-TEV for high-level production and purification of TEV protease from Escherichia coli and...

Contrasting modes of evolution of the visual pigments in Heliconius butterflies.

Sat, 02 Oct 2010 22:08:34 +0100

Contrasting modes of evolution of the visual pigments in Heliconius butterflies.: "Publication Date: 2010 Oct PMID: 20478921
Authors: Yuan, F. - Bernard, G. D. - Le, J. - Briscoe, A. D.
Journal: Mol Biol Evol

The adult compound eyes of passion-vine butterflies in the genus Heliconius contain one more UV opsin than other butterflies. Together with an 11-cis-3-hydroxyretinal chromophore, their four opsin genes UVRh1, UVRh2, BRh, and LWRh produce four rhodopsins that are UV-, blue-, or long wavelength absorbing. One of the Heliconius UV opsin genes, UVRh2, was found to have evolved under positive selection following recent gene...

Near-infrared fluorescent proteins.

Sat, 02 Oct 2010 21:44:17 +0100

Near-infrared fluorescent proteins.: "Publication Date: 2010 Oct PMID: 20818379
Authors: Shcherbo, D. - Shemiakina, I. I. - Ryabova, A. V. - Luker, K. E. - Schmidt, B. T. - Souslova, E. A. - Gorodnicheva, T. V. - Strukova, L. - Shidlovskiy, K. M. - Britanova, O. V. - Zaraisky, A. G. - Lukyanov, K. A. - Loschenov, V. B. - Luker, G. D. - Chudakov, D. M.
Journal: Nat Methods

Fluorescent proteins with emission wavelengths in the near-infrared and infrared range are in high demand for whole-body imaging techniques. Here we report near-infrared dimeric fluorescent proteins eqFP650 and...

Standard virtual biological parts

Fri, 02 Apr 2010 11:55:23 +0100

Standard virtual biological parts: A repository of modular modeling components for synthetic biology.
Cooling MT, Rouilly V, Misirli G, Lawson J, Yu...

BIOFAB announcement

Tue, 16 Mar 2010 14:05:19 +0100

Lab to be first ‘open-source’ for genetic parts

With seed money from the National Science Foundation, bioengineers from Stanford and UC-Berkeley, are ramping up efforts to characterize thousands of molecular players and processes critical to the engineering of microbes, so that eventually researchers can mix and match these...

Superfolder GFP

Fri, 27 Nov 2009 18:36:34 +0100

Introduction

Green Fluorescent Protein (GFP) offers efficient and convenient means of visualising the dynamic process of gene expression and of obtaining readout of the current state of complex gene regulatory networks – features of major interest for...

synthetic mammalian electro-genetic transcription circuit

Fri, 12 Jun 2009 08:06:08 +0100

A synthetic mammalian electro-genetic transcription circuit.

Enzymatic assembly of DNA molecules up to several hundred kilobases.

Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO.

Nat Methods. 2009 May;6(5):343-5. Epub 2009 Apr 12.

The J. Craig Venter Institute, Synthetic Biology Group, Rockville, Maryland, USA. [email protected]

We describe an isothermal, single-reaction method for assembling multiple overlapping DNA molecules by the concerted action of a 5' exonuclease, a DNA polymerase and a DNA ligase. First...

Automated unrestricted multigene recombineering

Tue, 09 Jun 2009 01:02:23 +0100

Automated unrestricted multigene recombineering for multiprotein complex production.

Bieniossek C, Nie Y, Frey D, Olieric N, Schaffitzel C, Collinson I, Romier C, Berger P, Richmond TJ, Steinmetz MO,Berger I.

Nat Methods. 2009 Jun;6(6):447-450. Epub 2009 May 3.

[1] European Molecular Biology Laboratory, Grenoble Outstation, B.P. 181, Grenoble, France. [2] Unit of Virus Host-Cell Interactions, Unités Mixtes de Recherche 5233,...

Resecting a double-strand break

Tue, 09 Jun 2009 00:04:31 +0100

At loose ends: resecting a double-strand break.

Cell. 2009 May 29;137(5):807-10.

Bernstein KA, Rothstein R.

Columbia University Medical Center, Department of Genetics & Development, New York, NY 10032, USA.

Double-strand break (DSB) repair is critical for maintaining genomic integrity and requires the processing of the 5' DSB ends. Recent studies have shed light on the mechanism and regulation of DNA end processing during DSB repair by homologous recombination.

A general strategy for the production of difficult-to-express inducer-dependent bacterial repressor proteins in Escherichia coli.

Christen EH, Karlsson M, Kämpf MM, Weber CC, Fussenegger M, Weber W.

Wetware news from www.synbio.org.uk

Design, construction and characterization of a set of insulated bacterial promoters.

A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization.

Bathy phytochromes in rhizobial soil bacteria.

Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell ...

The Carboxysome Shell Is Permeable to Protons.

A new tagged-TEV protease: Construction, optimisation of production, purification and test activity.

Contrasting modes of evolution of the visual pigments in Heliconius butterflies.

Near-infrared fluorescent proteins.

Standard virtual biological parts

BIOFAB announcement

Superfolder GFP

Introduction

synthetic mammalian electro-genetic transcription circuit

Automated unrestricted multigene recombineering

Resecting a double-strand break

Protein sequencing gone awry: 1 sample, 27 labs, 20 results

Automated unrestricted multigene recombineering

Imaging intracellular RNA distribution and dynamics in living cells

Ultramarine fluorescent protein with increased photostability and pH insensitivity