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The NIH BRAIN Initiative is currently in its fifth year. We reflect on its impact on methods development at a time when the program’s future direction is under discussion.
Public data archives are the backbone of modern biological research. Biomolecular archives are well established, but bioimaging resources lag behind them. The technology required for imaging archives is now available, thus enabling the creation of the first public bioimage datasets. We present the rationale for the construction of bioimage archives and their associated databases to underpin the next revolution in bioinformatics discovery.
Two cell-based resources producing a broad repertoire of glycosaminoglycan structures will facilitate new applications in the glycosciences field and beyond.
A type of neural network first described in 2015 can be trained to translate between images of the same field of view acquired by different modalities. Trained networks can use information inherent in grayscale images of cells to predict fluorescent signals.
A review of cellular barcoding fundamentals and applications, including powerful approaches for lineage reconstruction, genetic screening, and the recording of cellular activity and neuroanatomy.
A CHO cell library displaying a near-complete repertoire of glycosaminoglycan (GAG) modifications provides a resource for cell-based binding assays, recombinant proteoglycan expression, and assembly of GAG glycan microarrays.
A library of mutant mouse lung endothelial cells expressing a comprehensive repertoire of heparin sulfate structure modifications enables studies of the structure–function relationships of this complex polysaccharide.
A data-collection strategy using a fixed-target crystallography chip allows time-resolved serial synchrotron crystallography experiments to determine enzyme intermediate structures with time resolutions of milliseconds to seconds.
This paper describes a platform for carrying out antibody-based capture and mass spectrometry in parallel, and tests the feasibility of this platform for high-throughput validation of antibodies.
The deep neural network smNet extracts multiplexed parameters such as 3D position, orientation and wavefront distortion from emission patterns of single molecules.
Convolutional neural networks enable prediction of fluorescently labeled structures from three-dimensional time-lapse transmitted-light images. Applications include multiplexed long time-lapse imaging and prediction of fluorescence in electron micrographs.
FLIRT enables spatiotemporally precise control of protein function in C. elegans by harnessing existing temperature-sensitive mutations. Proteins can be inactivated at desired sites by infrared laser light targeted to the region(s) of interest.
Multiple MS2 loops inserted in the first loop of an sgRNA after the spacer sequence stabilize the sgRNA and allow recruitment of multicolor fluorescent proteins for imaging of low-repeat genomic loci.
osmFISH applies automated cycles of single-molecule fluorescence in situ hybridization without barcoding to provide spatial gene expression in tissue sections at high sensitivity, accuracy and throughput.
Variants of the genetically encoded sensor iGluSnFR extend the range of conditions under which glutamate neurotransmission can be visualized. In addition, chromatic variants of iGluSnFR improve compatibility with various illumination schemes.
Guide Swap challenges the hypothesis that Cas9–sgRNA binding is irreversible. The authors find that instead, nontargeting sgRNAs are swapped for targeting sgRNAs in the Cas9 complex. The method allows genome-scale functional screens in primary cells
A software tool, emClarity, implements several improvements in cryo-electron tomography image-processing algorithms to achieve sub-nanometer resolution for diverse macromolecular structures.
HUMAnN2 uses a tiered sequence search to provide rapid and accurate species-level functional profiles of microbial communities from metagenomic and metatranscriptomic data.
BLINK2 is a light-activated potassium channel for optogenetic inhibition of neuronal activity. Alberio et al. apply the tool in systems as diverse as cultured rat neurons, mouse brain slices, behaving zebrafish and a rat model of neuropathic pain.
The combination of transparency, small brain size and genetic access positions Danionella translucida as a promising model organism for functional imaging of neuronal circuits, especially during complex behaviors in adults.