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The RNA-element selection assay (RESA) probes regulatory elements in vivo and identifies protein binding partners and the nucleotides that contribute most to the regulation.
A lentiviral library expressing Cpf1 guide RNAs and containing target sequences allows high-throughput profiling of highly active guide RNAs and is the basis for cindel, a webtool to predict the activity at any given target sequence.
A method to screen proteins for enzymatic activity by incubating purified or overexpressed proteins with a metabolite extract and measuring changes in metabolite abundance using mass spectrometry enables high-throughput characterization of functionally uncharacterized proteins in Escherichia coli.
Stroke is often modeled in rodents by surgically occluding vessels. SIMPLE is an alternative approach that involves the magnet-induced accumulation of nanoparticles. Because of its reversible nature, this method can be used to study both occlusion and subsequent reperfusion of blood vessels.
The mechanical properties of tissues can be measured by deforming magnetically responsive microdroplets that are implanted in the tissue. Serwane et al. apply this method to study the mechanical properties of tissues in the living zebrafish embryo.
A hybrid approach merges networks of time-correlated distances determined by single-molecule FRET to uncover local and global dynamics of the multidomain protein Hsp90 in solution at multiple timescales.
An instrumental setup for atmospheric pressure MALDI-based mass spectrometry imaging with improved lateral resolution enables subcellular-level details to be resolved.
DMS-MaPseq enables genome-wide and target-specific RNA secondary structure probing of even rare or heterogeneously structured RNAs in vivo and was used to study structure involved in translation regulation as well as nascent transcripts.
BUM-HMM is a statistically robust modeling pipeline for interpreting high-throughput RNA structure probing data, including that from transcriptome-wide experiments.
Two-photon scanning microscopy is inherently slow and thus limits volumetric calcium imaging. Prevedel et al. achieve increased volumetric imaging speed by tailoring the excitation volume via light sculpting.
Recruiting a hyperactive cytidine deaminase via the guide RNA to dCas9 allows for the introduction of diverse point mutations at the CRISPR target locus to create complex libraries of variants for protein engineering or dissection of protein function.
The combination of orthogonal dCas9 with two chemical-inducible dimerization systems allows precise induction of gene activation and repression as well as the creation of Boolean logic gates.
The covalent insertion of fluorophore-labeled DNA adaptors by Tn5 transposase into open chromatin allows its imaging and subsequent analysis by sequencing from exactly the same samples.
The open-source FALCON and FALCON-Unzip software utilize long-read sequencing data to generate contiguous, accurate and phased diploid assemblies, even from genomes that are highly heterozygous.
An Escherichia coli-based genetic selection system, constructed from a split antibiotic resistance protein individually tethered to ubiquitin and a target protein, helps discover ubiquitin cascade pathway interactions.
A ‘conditional proteomics’ approach, as applied here to identify proteins involved in zinc homeostasis, utilizes an activatable labeling reagent to tag proteins affected by a particular biological condition in the cell, enabling them to be isolated and identified using mass spectrometry.
The combination of cellular barcoding and treatment with a library of small molecules before injecting the treated cells into mice allows the screening for compounds that inhibit metastatic seeding.