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A cellular engineering approach coupled with mass spectrometry allows the cell-of-origin of intra- and extracellular proteins to be determined from co-cultured cells.
A multiplexing strategy for data-independent acquisition (DIA)-based mass spectrometry addresses the limitation of low precursor selectivity to make DIA more practical for peptide analysis.
A method to tightly attach cell-derived extracellular matrix (ECM) to the culture surface is described. It is applied to generate bone marrow mesenchymal stem cell–derived ECM, which supports culture of human hematopoietic stem and progenitor cells.
Four spectrally distinct near-infrared fluorescent proteins based on bacterial phytochromes are described, expanding the possibilities for multicolor in vivo imaging experiments in nontransparent organisms.
Conditional genetic knockout is achieved in the rat by using zinc-finger nucleases to place loxP sites at specific genomic locations and introducing Cre recombinase under the control of a native promoter.
A semiconductor chip, coupled to an ion-sensitive field effect transistor (ISFET) pH sensor, can amplify and quantitate DNA in real time without dyes, cameras and external heating devices.
A mass spectrometry–based method using serial enrichments of different post-translational modifications (SEPTM) enables high-coverage proteomic analysis of multiple PTMs from a single biological sample.
Two methods for identifying protein isoforms that are concurrently phosphorylated and ubiquitylated are applied in yeast to identify phosphorylation sites that regulate ubiquitin proteasome–mediated proteome degradation.
A method for enzymatically producing long, high-purity, single-stranded DNA oligonucleotides should find many applications in basic research, in DNA nanotechnology and in clinical fields.
For genetically engineered circuits, the movement of RNA polymerase across the DNA during transcription needs to be tightly controlled. A large library of strong terminators will make circuit design easier and more efficient.
Algorithms that account for and overcome the intrinsic pixel-dependent readout noise from scientific complementary metal-oxide semiconductor (sCMOS) cameras prevent localization artifacts and avoid substantial compromises in localization uncertainty in single-molecule imaging. When combined with multi-emitter fitting, sCMOS cameras allow video-rate single-molecule switching nanoscopy.
The integration of microRNA target sequence features and data from cross-linking and immunoprecipitation of Argonaute proteins, implemented in the hidden Markov model–based framework MUMMIE, provides accurate prediction of microRNA targets.
This comparison of five RNA-seq library preparation methods highlights metrics for assessing the suitability of the methods for samples with low amounts of RNA and/or those with low-quality RNA.
Automated methods are described for the determination of survival curves in C. elegans, enabling rapid and statistically rigorous studies of lifespan in this organism.
Contact spotting with standard microarray printing tools can be used to generate high-density arrays of living mammalian cells, permitting the arraying of cell libraries without complex fluid manipulation.
An improved Brainbow toolbox for expression in the mouse is presented in this Resource. The collection includes transgenic lines, plasmids and viral vectors with improved performance and added capabilities relative to the original Brainbow constructs.