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. dgibson@jcvi.org

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

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.

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

Automated unrestricted multigene recombineering

Sat, 16 May 2009 14:58:29 +0100

Nat Methods. 2009 May 3. [Epub ahead of print]

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.

[1] European Molecular Biology Laboratory, Grenoble Outstation, B.P. 181, Grenoble, France. [2] Unit of Virus Host-Cell Interactions, Unités Mixtes de Recherche 5233, Grenoble, France. [3] Eidgenössische Technische Hochschule Zürich, Institut für Molekularbiologie und Biophysik, Hönggerberg, Zürich, Switzerland. [4] These authors contributed equally to this work.

Structural and functional studies of...

Imaging intracellular RNA distribution and dynamics in living cells

Fri, 08 May 2009 23:17:18 +0100

Nat Methods. 2009 May;6(5):331-8.

Imaging intracellular RNA distribution and dynamics in living cells.

Tyagi S.

Public Health Research Institute, New Jersey Medical School, University of Medicine & Dentistry of New Jersey, Newark, New Jersey, USA. tyagisa@umdnj.edu

Powerful methods now allow the imaging of specific mRNAs in living cells. These methods enlist fluorescent proteins to illuminate mRNAs, use labeled oligonucleotide probes and exploit aptamers that render organic dyes fluorescent. The intracellular dynamics of mRNA synthesis, transport and localization can be analyzed at higher temporal resolution with these methods...

Ultramarine fluorescent protein with increased photostability and pH insensitivity

Fri, 08 May 2009 23:16:01 +0100

Nat Methods. 2009 May;6(5):351-3. Epub 2009 Apr 6.

An ultramarine fluorescent protein with increased photostability and pH insensitivity.

Tomosugi W, Matsuda T, Tani T, Nemoto T, Kotera I, Saito K, Horikawa K, Nagai T.

Laboratory for Nanosystems Physiology, Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido, Japan.

We report a pH-insensitive and photostable ultramarine fluorescent protein, Sirius, with an emission peak at 424 nm, the shortest emission wavelength among fluorescent proteins reported to date. The pH-insensitivity of Sirius allowed prolonged visualization of biological events in an...

Engineered luciferases for molecular sensing in living cells.

Fri, 08 May 2009 18:32:08 +0100

Curr Opin Biotechnol. 2009 Mar 17.

Engineered luciferases for molecular sensing in living cells.

Binkowski B, Fan F, Wood K.

Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, United States.

As a means for visualizing molecular physiology within living cells, new strategies are emerging for engineering luciferases into intracellular biosensors. These biosensors can be classified as bimolecular, relying on complementation of luciferase fragments, or intramolecular, relying on domain insertion within the luciferase structure. Multiple design strategies have recently surfaced for the development of intramolecular sensors, allowing...

Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP.

Tue, 02 Dec 2008 01:28:50 +0100

Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP.

Publication Date: 2008 Nov PMID: 18794860
Authors: Biteen, J. S. - Thompson, M. A. - Tselentis, N. K. - Bowman, G. R. - Shapiro, L. - Moerner, W. E.
Journal: Nat Methods

The commonly used, monomeric EYFP enabled imaging of intracellular protein structures beyond the optical resolution limit ('super-resolution' imaging) in living cells. By combining photoinduced activation of single EYFP fusions and time-lapse imaging, we obtained sub-40 nm resolution images of the filamentous superstructure of the bacterial actin protein MreB in live Caulobacter crescentus cells. These...

Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale ...

Tue, 02 Dec 2008 01:20:58 +0100

Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution.

Publication Date: 2008 Dec PMID: 19029906
Authors: Huang, B. - Jones, S. A. - Brandenburg, B. - Zhuang, X.
Journal: Nat Methods

The ability to directly visualize nanoscopic cellular structures and their spatial relationship in all three dimensions will greatly enhance our understanding of molecular processes in cells. Here we demonstrated multicolor three-dimensional (3D) stochastic optical reconstruction microscopy (STORM) as a tool to quantitatively probe cellular structures and their interactions. To facilitate STORM imaging, we generated photoswitchable probes in several distinct colors by covalently linking...

F-pili dynamics by live-cell imaging.

Tue, 02 Dec 2008 01:18:10 +0100

F-pili dynamics by live-cell imaging.

Publication Date: 2008 Nov 18 PMID: 19004777
Authors: Clarke, M. - Maddera, L. - Harris, R. L. - Silverman, P. M.
Journal: Proc Natl Acad Sci U S A

Bacteria have evolved numerous mechanisms for cell-cell communication, many of which have important consequences for human health. Among these is conjugation, the direct transfer of DNA from one cell to another. For gram-negative bacteria, conjugation requires thin, flexible filaments (conjugative pili) that are elaborated by DNA donor cells. The structure, function, and especially the dynamics of conjugative pili are poorly understood. Here,...

Cationic gold microparticles for biolistic delivery of nucleic acids.

Sun, 30 Nov 2008 20:25:56 +0100

Cationic gold microparticles for biolistic delivery of nucleic acids.

Publication Date: 2008 Nov PMID: 19007338
Authors: Svarovsky, S. - Borovkov, A. - Sykes, K.
Journal: Biotechniques

Here we report preparation and properties of positively charged gold microparticles, and their use for biolistic DNA delivery. Micron-sized gold microparticles were modified by building self-assembling polyethylenimine monolayers on their surfaces, which enabled their electrostatic interaction with negatively charged molecules such as DNA. One milligram of the surface-modified microparticles was able to bind directly to up to 3.5 microg of DNA, exceeding the 1 microg/mg limit of the conventional protocols. The...

Improving membrane voltage measurements using FRET with new fluorescent proteins

Wed, 27 Aug 2008 02:21:02 +0100

Nature Methods 5, 683 (2008). doi:10.1038/nmeth.1235

Authors: Hidekazu Tsutsui, Satoshi Karasawa, Yasushi Okamura & Atsushi Miyawaki

We used two new coral fluorescent proteins as fluorescence resonance energy transfer (FRET) donor and acceptor to develop a voltage sensor, named Mermaid, that displays ∼40% changes in emission ratio per 100 mV, allowing for direct visualization of electrical activities in cultured excitable cells. Notably, Mermaid has fast on-off kinetics at warm (∼33 °C) temperatures and can report voltage spikes comparable to action potentials.

[From Improving membrane voltage measurements using FRET with new fluorescent proteins]

Combination of novel GFP mutant TSapphire and DsRed variant mOrange to set up a versatile in ...

Wed, 27 Aug 2008 00:56:06 +0100

Publication Date: 2008 Jul 16 PMID: 18621983
Authors: Bayle, V. - Nussaume, L. - Bhat, R. A.
Journal: Plant Physiol

Forster resonance energy transfer (FRET) measurements based on fluorescence lifetime imaging microscopy (FLIM) are increasingly being used to assess molecular conformations and associations in living systems. Reduction in the excited state lifetime of the donor fluorophore in the presence of an appropriately positioned acceptor is taken as a strong evidence of FRET. Traditionally CFP has been widely used as a donor fluorophore in FRET experiments. However given its...

Light-activated DNA binding in a designed allosteric protein.

Wed, 27 Aug 2008 00:35:09 +0100

Publication Date: 2008 Aug 5 PMID: 18667691
Authors: Strickland, D. - Moffat, K. - Sosnick, T. R.
Journal: Proc Natl Acad Sci U S A

An understanding of how allostery, the conformational coupling of distant functional sites, arises in highly evolvable systems is of considerable interest in areas ranging from cell biology to protein design and signaling networks. We reasoned that the rigidity and defined geometry of an alpha-helical domain linker would make it effective as a conduit for allosteric signals. To test this idea, we rationally designed...

Wetware news from www.synbio.org.uk

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

Engineered luciferases for molecular sensing in living cells.

Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP.

Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale ...

F-pili dynamics by live-cell imaging.

Cationic gold microparticles for biolistic delivery of nucleic acids.

Improving membrane voltage measurements using FRET with new fluorescent proteins

Combination of novel GFP mutant TSapphire and DsRed variant mOrange to set up a versatile in ...

Light-activated DNA binding in a designed allosteric protein.