Volume 9 Issue 3, March 2012

Engineering light-induced gene expression

Heat maps are useful for visualizing multivariate data but must be applied properly.

A fluorescent protein fusion reports levels of the plant hormone auxin by succumbing to its degradation signal.

Rationally designed RNAs that work with the bacterial immune response allow targeted gene silencing in prokaryotes.

The integration of protein-protein interaction networks with structural information about the interacting protein partners creates a three-dimensional scaffold on which are mapped mutations involved in human disease.

Structure of modular DNA-recognition domain is revealed.

Engineered firefly enzymes use new substrates and emit at redder wavelengths.

An electronic circuit enables analysis of dynamic processivity of single molecules.

Researchers develop a genetic method for degradation of GFP protein fusions in cells and living flies.

Researchers are finding efficient ways to pick the most promising pluripotent stem cells.

Neuroimaging methods are beginning to provide promising ways of understanding the functional organization of the brain across species.

In living systems, chemical reactions and the geometry of cells feed back on each other. Methods for computational modeling are beginning to take this complexity into account.

Using two independent methods, researchers show that in vivo–grown crystals of soluble proteins and of membrane proteins grown in the lipidic sponge phase can be analyzed by serial femtosecond crystallography on an X-ray free electron laser.

The Open Microscopy Environment Remote Objects (OMERO) software platform provides a server-based system for managing and analyzing microscopy images and non-image data.

Automated tissue sectioning and two-photon imaging of fluorescently labeled and fixed mouse brains allows high-resolution tomographic imaging of the entire brain. The authors demonstrate performance using multiple GFP mouse lines, dye-based retrograde tracing and viral anterograde tracing.

Expression of a protein in Sf9 insect cells at high concentration triggers formation of in vivo crystals that can be analyzed by serial femtosecond X-ray crystallography.

Lipidic sponge phase crystallization yields membrane protein microcrystals that can be injected into an X-ray free electron laser beam, yielding diffraction patterns that can be processed to recover the crystal structure.

A light-inducible dimerization domain is used to create a genetically encoded, light-switchable transactivator of gene expression. The system allows rapid blue light–mediated activation of transgenes containing an appropriate activation sequence with low background and high induction.

The pairing of bisulfite padlock probes with a probe-design algorithm, library-free sequencing and an analysis pipeline provides a flexible and scalable method for quantifying cytosine methylation.

The authors report Alexa Fluor 633 hydrazide to be artery-specific and use it to measure arteriole dilation dynamics in vivo in response to visual stimuli in mouse, rat and cat neocortex. They find that sensory stimulus–evoked arteriole dilation reduces the fluorescence recorded from underlying neurons.

To examine functional correspondences between monkey and human brain areas, a method based on the temporal correlation of sensory-evoked functional magnetic resonance imaging responses is proposed. The study reveals putative homologous regions that have shifted to topologically unexpected locations during evolution.

Molecular processes in cells are not spatially homogenous. Reported here is an approach, implemented in the Simmune toolset, for modeling cellular processes within their dynamic spatial context.

A device for generating precise spatial and temporal patterns of airborne odorants is reported. In combination with machine vision tracking software, the authors use the device to monitor navigation of freely moving Drosophila melanogaster larvae.

An imaging chamber implanted over the mouse spinal cord enables long-term longitudinal two-photon microscopy of cellular dynamics in normal or pathological conditions.

Sensor proteins that exploit principles of linkage-specific avidity reveal topology-related functions of polyubiquitin in diverse cell types and pathways.