Volume 7 Issue 7, July 2010

Fly brains light the way for neurobehavioral circuits.

Researchers synthesized the first functional synthetic bacterial genome; repeating this feat with different bacteria will require further methodological development.

New strategies expand the genetic toolkit for transgene expression, lineage tracing and mosaic analysis of gene function in flies and mammalian cells.

Live-cell time-lapse imaging of somatic cells undergoing reprogramming raises interesting questions about the mechanism of the process.

Nanoscale robots can be programmed to walk a DNA origami track.

Raw data of millions of sequences used to assemble the reference genomes of ten organisms are analyzed in search of mismatches indicative of editing events. Findings include candidate sites for in vivo DNA and RNA editing, and a common sequencing error.

A technique combining laser and electron pulses is used to achieve nanometer and femtosecond resolution in biological imaging.

To keep pace with accelerating sequencing machines, genomics researchers clean house and move toward the cloud.

Simplified methods to map transcription start sites allow the exploration of transcription-initiation landscapes in rare cell types.

New technical feats make it possible to monitor the activity of identified neurons in awake behaving Drosophila melanogaster.

With a combination of microscopic and computational methods, the lineage of cells produced by divisions in the meristems of growing plants can now be tracked over time.

A method to analyze the sequence of C-terminal peptides using a combination of a specific enrichment approach and mass spectrometry is described, allowing the study of C-terminal proteolytic processing on a global scale. Also in this issue, Van Damme et al. describe a related method for simultaneous C- and N-terminal peptide analysis.

A method to simultaneously analyze C- and N-terminal peptides using a combination of strong cation exchange, diagonal chromatography and mass spectrometry is described, allowing the screening of protease substrates on a global scale. Also in this issue, Schilling et al. describe a related method for analyzing the sequence of C-terminal peptides.

A genetically encoded ratiometric biosensor not based on fluorescence resonance energy transfer (FRET), ClopHensor, allows concurrent measurement of intracellular pH and chloride by providing an internal control for pH-dependent fluorescence changes. Measurements of chloride levels in acidic large dense core vesicles showed high concentrations of chloride.

The misfolded form of the prion protein, PrP^Sc, can be quantified in a variety of tissues and fluids using a quantitative version of the popular protein misfolding cyclic amplification (PMCA) assay.

Paired-end reads consisting of 5′ transcription start sites and 3′ downstream sequences from transcripts in Drosophila melanogaster reveal distinct initiation patterns at different fly promoters and show that 5′ caps originating in coding regions are added posttranscriptionally.

Capturing the 5′ end of transcripts from an input of only 1,000 cells and linking the transcription start sites to downstream sequences allows the analysis of complex transcriptome architecture.

This technique allows functional imaging of neurons in head-fixed Drosophila while the fly walks on an air-supported ball. Using a genetically encoded calcium sensor, the activity of motion-sensitive neurons in the fly optic lobe was recorded while the flies were presented with visual stimuli. Activity in these cells correlated with robust optomotor behavior in the walking flies.

This software integrates data from multiple samples and single-nucleotide polymorphism and comparative genome hybridization array platforms to detect and genotype copy-number variants (CNVs). It has high accuracy in the detection of short deletions and amplifications and will be valuable for genome-wide CNV analyses in population studies.

A set of computational and imaging approaches, called MARS-ALT, permits three-dimensional tracking of plant tissue development, including cell lineaging, at cellular resolution. It is applied to the study of floral development in Arabidopsis.

Expression of the transporter SID-1 in Caenorhabditis elegans neurons renders the cells sensitive to systemic RNAi and permits previously unidentified neuronal phenotypes to be uncovered. This expression also reduces RNAi in nonneuronal cell types, allowing examination of neuronal functions of lethal genes.

By micropatterning cells in polarized shapes the global distribution of endomembranes can be compared and subtle but statistically significant changes can be detected from only tens of cells.