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The Strand-seq method independently sequences each parental strand of template DNA from single proliferating cells. It can be used to detect sister chromatid exchange and other chromosomal abnormalities at high resolution and to correct contig misorientations in genome assemblies, with potential for strand-inheritance and haplotyping studies.
A synthetic peptide library in conjunction with liquid chromatography–tandem mass spectrometry identifies the specificities of endo- and exopeptidases without requiring enrichment of substrates or products.
A genetic tool that converts bacterial regulators of translational initiation into regulators of transcriptional elongation is described. This adaptor is used to engineer several transcriptional attenuators and activators that can be predictably assembled into higher-order gene regulatory functions.
Removing phosphopantetheine-tagged labels from acyl carrier proteins (ACPs) and ACP fusion proteins contributes to a versatile labeling method in which tags can be iteratively swapped.
A G protein–coupled receptor (GPCR) signaling assay based on ectodomain shedding of a membrane-bound proform of alkaline phosphatase-tagged TGFα provides a platform for studying poorly characterized Gα12/13-coupled GPCRs. The assay allowed identification of three orphan GPCRs as Gα12/13-coupled lysophosphatidylserine receptors.
Development of the bright green and red fluorescent proteins, Clover and mRuby2, creates a fluorescence resonance energy transfer (FRET) pair with the highest Förster radius among existing ratiometric FRET pairs. Substitution of this pair for current FRET pairs in several existing sensors reliably and substantially improves sensor performance.
A high-resolution 4C-seq protocol involving two restriction digests and a revised analysis pipeline allows robust detection of physical interactions between regulatory DNA elements.
A dual-trap force-clamp configuration is used to apply a constant load between a binding protein and a single intermittently interacting biological polymer. This allows high-resolution measurements of short-lived molecular complexes and reveals previously undetected complex regulation of the myosin working stroke.
This paper reports genetic manipulation of the malaria parasite Plasmodium falciparum with zinc-finger nucleases. It demonstrates gene disruption as well as replacement and site-specific editing of both an integrated reporter and an endogenous gene.
An integrated system composed of a microfluidic device, computer-vision tools and statistical methods for automatically handling, imaging, classifying and sorting C. elegans organisms is presented. The system performs automated screens of subcellular phenotypes and is used here to identify genes involved in synaptogenesis.
Gene synthesis is currently limited by the need to use error-prone oligonucleotide building blocks. Dial-out PCR overcomes the sequence verification bottleneck by using unique sequence tags and massively parallel sequencing to identify and selectively retrieve error-free DNA molecules of interest from complex mixtures.
A method is presented to model cell proliferation from tracked automated time-lapse imaging of cell populations. The resulting fractional proliferation graphs permit visualization of dynamic changes in the dividing and nondividing subsets of the population.
A combination of protein correlation profiling–stable isotope labeling by amino acids in cell culture and size-exclusion chromatography allows stoichiometric analysis of changes in the human interactome in response to a growth factor.
Precise mass measurement on single mammalian cells is combined with imaging to monitor changes in cellular mass during the cell cycle over many generations.
The mouse cancer model 'Multi-Hit' allows for the evaluation of oncogene cooperativities in tumor development based on stochastic Cre-recombination events. Cells with cooperating oncogenes are positively selected and give rise to tumors. The approach is used to study Ras downstream effector pathways in tumorigenesis.
A flexible, environmentally controlled experimental setup for the study of terrestrial animal dispersal is reported. Its unprecedented scale should enable studies in spatial ecology and permit tests of conservation strategies in the face of environmental change.