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An open-source library of analytical tools for mapping large-scale patterns of brain activity using cluster computing finds structure in two-photon imaging data from mouse and whole-brain light-sheet functional imaging data from behaving larval zebrafish. Vladimirov et al., also in this issue, describes the light-sheet functional imaging system used here.
This paper describes automated methods for the accurate segmentation and tracking of tens of thousands of nuclei in time-lapse imaging data of developing embryos.
Application of the founder principle from population genetics to variant selection after recombineering allows the isolation of rare unselected recombinants.
The combination of selective 2'-hydroxyl acylation of RNA with high-throughput sequencing of the transcribed cDNA allows identification of chemically modified sites as mutations in the sequence that then yield highly accurate secondary-structure models of the RNA.
Ligand nanocalipers made using DNA nanotechnology are used to display ephrin-A5 at well-defined spatial intervals to study how nanoscale ligand spacing affects EphA2 receptor activation in breast cancer cells.
A synthetic library of nucleosomes, each with a DNA-barcode characteristic for a defined post-translational modification (PTM), is used to probe PTM-based recruitment and modulation of histone mark readers and writers.
This paper demonstrates that micropatterned human embryonic stem cell colonies can acquire spatial patterns reminiscent of those in the embryo and proposes their use to study early developmental processes in the human system.
The results of genome-wide association studies are combined with quantitative interaction proteomics to narrow down the list of putative causal disease genes and filter modest association signals.
A combination of a sensitive blue light–gated channelrhodopsin actuator and red-shifted Arch-based voltage sensors allows all-optical electrophysiology without cross-talk in cultured neurons or brain slices.
A simple, robust, chemically defined method for generating cardiomyocytes from human pluripotent stem cells is described. It should enable the identification of conditions for maturation of these cells.
A tetramethylrhodamine-labeled dimer of the cell-penetrating peptide TAT, named dfTAT, efficiently delivers proteins into live cells by facilitating endosomal escape.
This paper describes a single-vector strategy for flexible intersectional expression of genetically encoded reporters and tools in precisely defined cell types in the mouse.
A single-cell Western (scWestern) blotting technique allows quantitative measurements of up to 11 protein targets from ~2,000 individual cells in under 4 hours, expanding single-cell heterogeneity studies to the proteome.
The transformation of individual animal images acquired from videos into unique reference fingerprints allows for robust tracking of individuals in groups and reidentification of individuals between sightings and across different videos.
This paper reports the combination of thermogenetics with computer vision–controlled tracking to modulate neuronal activity in untethered fruit flies.
The high-throughput sequencing–RNA affinity profiling (HiTS-RAP) assay enables large-scale profiling of protein interactions with RNA libraries using a simple protocol on a high-throughput sequencer.
Bone marrow formed in a cylindrical PDMS device implanted in a mouse can be surgically removed and cultured for a week in vitro without losing any of the hallmarks of in vivo bone marrow niches.
Raven calculates assembly plans for complex genetic constructs from thousands of parts. It integrates user feedback on failed intermediate assemblies to improve the final outcome.
This framework for multiscale signal representation allows global analysis of genomic data at different length scales from base pairs to entire chromosomes and reveals the interplay of information encoded at different scales, such as the regulation of gene expression by methylation patterns that go beyond the single-gene scale.