Volume 6 Issue 8, August 2009

Computational biologists are often tempted to avoid providing a named software implementation of their new algorithm, but resisting this temptation helps avoid difficulties later on and benefits the wider community of biologists.

A prototype for a mass spectrometer with single-molecule sensitivity has prospects for single-cell proteomics.

A fluorescence resonance energy transfer (FRET)-based biosensor helps scientists monitor the activation of an essential signaling protein over the course of embryogenesis in Drosophila melanogaster.

Modification of a system for rapid amplification of misfolded prion proteins allows de novo generation of these infectious molecules and provides a glimpse of the diverse range of possible misfolded prion strains.

Researchers lay the foundation for networks that will self-destruct after being exposed to a predetermined number of stimuli.

A multilaboratory study designed to assess the reproducibility of multiple reaction monitoring (MRM) mass spectrometry–based proteomics demonstrates the promise of this technology for disease biomarker verification.

Cells can be delivered to the rodent brain noninvasively, via the nasal cavity.

Transposon mutagenesis coupled with microarray analysis helps to rapidly generate information about changing genotype-phenotype relationships in laboratory-evolved bacteria.

Real-time lineage tracing in flies gets a boost with three techniques to specifically label a progenitor's daughter cells.

A system for inducible protein degradation, originally developed for mammalian cells, is applied to essential viral proteins and will allow functional studies in a wide range of viruses.

This array-based discovery tool creates linkage between functional mutations and selectable markers across a bacterial genome and can thus distinguish between adaptive and neutral mutations.

A generally applicable approach to analyze intact membrane protein complexes by mass spectrometry is reported. This method allows subunit stoichiometry, lipid binding and the effects of post-translational modifications on complex formation to be explored.

Iterative cycles of metabolic modeling and experimental open reading frame verification in Chlamydomonas reinhardtii lay the groundwork for more accurate gene annotation and provide resources for metabolic engineering.

Nucleotide analogs modified with a free 3′ hydroxyl, maintaining the interactions at the polymerase active site, and a cleavable linker, attaching a fluorescent dye and an inhibitor, are efficient at reading homopolymer runs in a single-molecule sequencing reaction.

Multistage mass spectrometry and algorithms for spectral alignment and dereplication allow sequencing of nonribosomal peptides, pharmacologically important compounds that are not encoded in the genome but built by nonribosomal peptide synthetases.

This technique, adapted from mosaic analysis with double markers in mice, relies on mitotic recombination to reconstitute sequences encoding EGFP or mRFP1. After cell division, each daughter cell contains one fluorescent marker, causing a green and a red twin spot that can be traced through development.

A Gal4-based system in Drosophila reports on gene expression at a given developmental stage combined with lineage information on expression at earlier developmental stages.

High-throughput analyses of macromolecular shape and oligomeric state at ∼15 Å resolution are possible with a partially automated small angle X-ray scattering (SAXS) pipeline. Though X-ray crystallography provides higher-resolution structural information than SAXS, SAXS analysis is faster and has a higher success rate, which may have implications for how structural genomics research is performed.

Padlock probes, synthesized in large scale on programmable microarrays, capture expressed single-nucleotide polymorphisms for high-throughput sequencing in this method for RNA allelotyping. The approach combines the sensitivity of digital expression measurements with the efficiency of targeted resequencing to quantify allele specific gene expression in various tissues across several individuals.

With the realization that cells interact extensively with their surrounding microenvironments during growth and development, the challenge for researchers has become designing three-dimensional culture systems that more closely mimic those relationships.