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A new method, R-scape, tests whether observed sequence covariation supports a conserved secondary structure in RNA. The program finds no evidence for previously proposed conserved secondary structures in several lncRNAs.
BUM-HMM is a statistically robust modeling pipeline for interpreting high-throughput RNA structure probing data, including that from transcriptome-wide experiments.
The far-red fluorescent protein mMaroon1 and a reporter based on stem-loop binding protein enables the generation of Fucci4, a 4-color cell cycle reporter system that can be used to distinguish all phases of the cell cycle. Also online, a paper by Laviv et al. uses mMaroon1 as a FRET acceptor for the newly developed CyRFP1.
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.
Two red fluorescent proteins with long Stokes shift enable simultaneous multicolor 2p imaging. CyRFP1 is well-suited for 2p structural imaging, and FRET sensors made with mCyRFP1 and mMaroon1enable multicolor 2pFLIM in brain slices. Also online, a paper by Bajar et al. reports the development of mMaroon1.
Photoactivatable derivatives of the bright and photostable Janelia Fluor dyes enable improved multicolor single-particle tracking and facile localization microscopy in cells.
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.
A method for producing multiprotein complexes engineered with site–specifically introduced noncanonical amino acids is described, enabling applications in biochemical and biophysical analysis, as well as in biotechnology.
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.
Random-access line scanning enables neural activity to be monitored at high speed in neurons and dendrites that are sparsely distributed in three dimensions. The approach is demonstrated in behaving mice.
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.
The combination of short and long crosslinkers during chromosome conformation capture allows the interrogation of structure from the nucleosome to the chromosome-wide level in yeast.
The incorporation of reversibly terminated deoxyinosine triphosphates during linear amplification allows the incorporation of one mutation per molecule and the generation of a systematic allelic series.
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.
The enzyme subtiligase can be used to catalyze expressed protein ligation of proteins of interest with peptides lacking an N-terminal cysteine. This enables the analysis of protein modifications in the context of the native primary sequence.