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This review describes methods for increasing the activity and accuracy of the CRISPR-Cas9 system and discusses approaches for assessing off-target cleavage.
Applications of focused ion beams for biological ultrastructure and chemical imaging, with a particular emphasis on the coupling of this technology with scanning electron microscopy, are discussed in this Review.
Correlated light and electron microscopy (CLEM) gives context to biomolecules studied with fluorescence microscopy. This Review discusses recent improvements and guides readers on probes, instrumentation and sample preparation to implement CLEM.
A proteogenomic approach to analyzing mass spectrometry–based proteomic data enables the discovery of novel peptides, provides peptide-level evidence of gene expression, and assists in refining gene models. Strategies for building custom sequence databases, applications benefitting from a proteogenomic approach, and challenges in interpreting data are discussed in this Review. Also in this issue, Alfaro et al. discuss the use of proteogenomic approaches for studying cancer biology.
This Review discusses large-scale de novo DNA synthesis via oligos or arrays, describes gene assembly and error correction and considers applications for large-scale DNA synthesis.
This Review introduces tools to build transcriptional circuits and explains how the choice of different tools can affect circuit behavior and how its operation can be affected by the cellular host.
This second Review introduces readers to the many algorithms used to localize fluorophores in localization-based super-resolution imaging and offers practical advice to guide their choice and usage.
This first of two review articles provides an overview and practical introduction to the precise and accurate localization of single emitters for single-particle tracking and super-resolution localization microscopy.
Fourteen scientists who participated in a recent workshop to identify and address challenges of epigenome-wide association studies summarize their recommendations in this Review.
This Review of force-distance curve-based atomic force microscopy highlights the unique capabilities of the technique to simultaneously image the architecture of complex biological systems and map their physical, chemical and biological properties at nanometer resolution.
At macroscopic scales, the human connectome comprises anatomically distinct brain areas, the structural pathways connecting them and their functional interactions. Annotation of phenotypic associations with variation in the connectome and cataloging of neurophenotypes promise to transform our understanding of the human brain. In this Review, we provide a survey of magnetic resonance imaging–based measurements of functional and structural connectivity. We highlight emerging areas of development and inquiry and emphasize the importance of integrating structural and functional perspectives on brain architecture.
The beginning of the 21st century has seen a renaissance in light microscopy and anatomical tract tracing that together are rapidly advancing our understanding of the form and function of neuronal circuits. The introduction of instruments for automated imaging of whole mouse brains, new cell type–specific and trans-synaptic tracers, and computational methods for handling the whole-brain data sets has opened the door to neuroanatomical studies at an unprecedented scale. We present an overview of the present state and future opportunities in charting long-range and local connectivity in the entire mouse brain and in linking brain circuits to function.
A review of zymography techniques is presented. Zymography approaches yield valuable information about enzyme forms and localization of activity in tissues or in whole organisms.
Representative members of the bioimage informatics community review the computational steps and some of the primary software tools available to biologists who are acquiring and analyzing microscopy-based digital image data, with a focus on open-source options.
In this Review, the authors provide a guide through to the different steps involved in selected reaction monitoring as well as discuss its applications.
In this Review, the authors take the reader through the steps needed to analyze bisulfite-treated DNA, pointing out different considerations for data in base or color space, to ensure high-quality methylome analysis.
This Review covers recent technological developments to label and manipulate genes in selected populations of cells in Drosophila melanogaster. The Review is intended as a user guide to help with the selection of the best expression systems and clonal analysis techniques for developmental studies in the fly.
In this Review, the authors thoroughly discuss solution-state NMR spectroscopy methods used for characterizing the dynamic structure landscape of RNA molecules, from picosecond to second timescale motions.
Presented is a Review of the principles and practice of optical sectioning microscopy using planar illumination or structured illumination with descriptions of the advantages and disadvantages of these techniques.
