Volume 5 Issue 7, July 2008

Zebrafish researchers rejoice! Reverse genetics is now on the menu, thanks to zinc-finger nucleases.

Tiny droplets of water in oil can serve as miniature culture vessels for living single cells and multicellular organisms.

Recently discovered electrophilic probes open the door to activity-based protein profiling (ABPP) studies of a broader range of proteins.

A high-resolution interactome map that describes how proteins interact in living yeast cells is an invaluable reference for the research community.

Two complementary approaches, both using next-generation sequencing, have successfully tackled the scale and the complexity of mammalian transcriptomes, at once revealing unprecedented detail and allowing better quantification.

Strategies for the comprehensive identification of transcript isoforms produced from specific genomic loci make use of and expand existing tools and resources.

Advances in the application of microfluidics technology to biological assays using the model organism Caenorhabditis elegans help to automate otherwise time-consuming experiments.

The complete set of coding sequences, including all splice isoforms, is not known for any metazoan organism. Combination of a normalized pooling scheme and a new assembly algorithm with 454 sequencing yields a methodological pipeline for isoform discovery. The validated pipeline may now be applied genome-wide.

Conventional techniques for generating transgenic mice are quite costly, require substantial resources and necessitate killing the mouse. In contrast, in vivo electroporation of repopulating spermatogonial cells in the mouse testis can produce male mice for siring multiple distinctive transgenic founders for over a year.

Current approaches for live imaging of cellular actin dynamics have several drawbacks. Now the use of Lifeact, a 17-aa actin-binding peptide from yeast that is not present in higher eukaryotes, allows imaging of actin dynamics in live mammalian cells without disruption of function and without competition with endogenous binding proteins.

A combination of improved in vitro embryo culture and optical projection tomography allows development of the mouse limb bud to be monitored over time. Developmental changes seen in vitro are benchmarked against in vivo development, and tissue movements are quantitatively described.

Application of next-generation sequencing using the ABI SOLiD technology to mammalian transcriptome analysis enabled a survey of the content, the complexity and the developmental dynamics of the embryonic stem cell transcriptome in the mouse. Also in this issue, Mortazavi et al. report Illumina technology–based RNA-Seq analysis of the mouse transcriptome in three different tissues.

The mouse transcriptome in three tissue types has been analyzed using Illumina next-generation sequencing technology. This quantitative RNA-Seq methodology has been used for expression analysis and splice isoform discovery and to confirm or extend reference gene models. Also in this issue, another paper reports application of the ABI SOLiD technology to sequence the transcriptome in mouse embryonic stem cells.

A major bottleneck for genetic approaches in model organisms is the application of state-of-the-art technologies to phenotyping. Now, using a microfluidic chip, high-resolution imaging of fluorescent reporters and accurate sorting is demonstrated in an automated manner in Caenorhabditis elegans.

Cells in vivo are exposed not only to soluble factors but also to immobilized ligands. Controlled immobilization of functional growth factors yields dose-dependent responses in mouse embryonic stem cells in vitro and allows the effects of immobilized versus soluble ligands to be studied.

In designing microscopy software to take advantage of better hardware, developers are facing challenges of accessibility, functionality and usability.