Abstract：
:Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium imaging of a local microcircuit and mesoscopic widefield calcium imaging of the entire cortical mantle in awake mice. Our multi-scale approach involves a microscope with an orthogonal axis design where the mesoscopic objective is oriented above the brain and the two-photon objective is oriented horizontally, with imaging performed through a microprism. We also introduce a viral transduction method for robust and widespread gene delivery in the mouse brain. These approaches allow us to identify the behavioral state-dependent functional connectivity of pyramidal neurons and vasoactive intestinal peptide-expressing interneurons with long-range cortical networks. Our imaging system provides a powerful strategy for investigating cortical architecture across a wide range of spatial scales.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Barson D,Hamodi AS,Shen X,Lur G,Constable RT,Cardin JA,Crair MC,Higley MJdoi
10.1038/s41592-019-0625-2subject
Has Abstractpub_date
2020-01-01 00:00:00pages
107-113issue
1eissn
1548-7091issn
1548-7105pii
10.1038/s41592-019-0625-2journal_volume
17pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract：:To enable sophisticated optogenetic manipulation of neural circuits throughout the nervous system with limited disruption of animal behavior, light-delivery systems beyond fiber optic tethering and large, head-mounted wireless receivers are desirable. We report the development of an easy-to-construct, implantable wire...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3536
更新日期：2015-10-01 00:00:00
abstract：:Photoconvertible fluorescent proteins are potential tools for investigating dynamic processes in living cells and for emerging super-resolution microscopy techniques. Unfortunately, most probes in this class are hampered by oligomerization, small photon budgets or poor photostability. Here we report an EosFP variant t...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1296
更新日期：2009-02-01 00:00:00
abstract：:We present general means to greatly increase the sensitivity of antibody-based assays. Augmentation relies on a 'tadpole' protein-DNA chimera whose protein moiety binds most classes of mammalian antibodies but not avian immunoglobulin Y (IgY). We used this tadpole in affinity capture assays followed by real-time PCR t...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth1127
更新日期：2007-12-01 00:00:00
abstract：:MicroRNA depletion by sequestration produces flexible hypomorphs that mimic mutants obtained by microRNA gene targeting. ...
journal_title：Nature methods
pub_type： 评论,杂志文章
doi：10.1038/nmeth1209-873
更新日期：2009-12-01 00:00:00
abstract：:Recent work has demonstrated that environmental factors experienced by parents can affect their offspring across multiple generations, and that such transgenerational transmission can depend on the germline. Causal evidence for the involvement of germ cells is rare, however, and the underlying molecular mechanisms rem...
journal_title：Nature methods
pub_type： 杂志文章,评审
doi：10.1038/nmeth.4181
更新日期：2017-02-28 00:00:00
abstract：:We introduce a nonintrusive method exploiting single-cell variability after cell division to validate protein localization. We found that Clp proteases, widely reported to form biologically relevant foci, were uniformly distributed in Escherichia coli cells, and that many commonly used fluorescent proteins caused seve...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1955
更新日期：2012-04-08 00:00:00
abstract：:Cell signaling, one of key processes in both normal cellular function and disease, is coordinated by numerous interactions between membrane proteins that change in response to stimuli. We present a split ubiquitin-based method for detection of integral membrane protein-protein interactions (PPIs) in human cells, terme...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2895
更新日期：2014-05-01 00:00:00
abstract：:Monomeric (m)Eos2 is an engineered photoactivatable fluorescent protein widely used for super-resolution microscopy. We show that mEos2 forms oligomers at high concentrations and forms aggregates when labeling membrane proteins, limiting its application as a fusion partner. We solved the crystal structure of tetrameri...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2021
更新日期：2012-05-13 00:00:00
abstract：:The importance of locating proteins in their context within cells has been heightened recently by the accomplishments in molecular structure and systems biology. Although light microscopy (LM) has been extensively used for mapping protein localization, many studies require the additional resolution of the electron mic...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth791
更新日期：2005-10-01 00:00:00
abstract：:We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scala...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth842
更新日期：2006-01-01 00:00:00
abstract：:The normalization of RNA-seq data is essential for accurate downstream inference, but the assumptions upon which most normalization methods are based are not applicable in the single-cell setting. Consequently, applying existing normalization methods to single-cell RNA-seq data introduces artifacts that bias downstrea...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.4263
更新日期：2017-06-01 00:00:00
abstract：: ...
journal_title：Nature methods
pub_type： 社论
doi：10.1038/s41592-018-0257-y
更新日期：2018-12-01 00:00:00
abstract：:To engineer a stem cell genome, we developed a technology for targeted elimination of chromosomes from mouse embryonic stem (ES)-somatic hybrid cells. Here we demonstrate the use of a universal chromosome elimination cassette (CEC) for elimination of a single embryonic stem cell (ESC)-derived chromosome 11 or 12, and ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth973
更新日期：2007-01-01 00:00:00
abstract：:Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral overlap between fluorophores. Here we demonstrate a simple but general strategy to drastically increase the ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2069
更新日期：2012-06-03 00:00:00
abstract：:Zinc-finger nucleases (ZFNs) drive efficient genome editing by introducing a double-strand break into the targeted gene. Cleavage is induced when two custom-designed ZFNs heterodimerize upon binding DNA to form a catalytically active nuclease complex. The importance of this dimerization event for subsequent cleavage a...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1539
更新日期：2011-01-01 00:00:00
abstract：:We introduce field synthesis, a theorem and method that can be used to synthesize any scanned or dithered light sheet, including those used in lattice light-sheet microscopy (LLSM), from an incoherent superposition of one-dimensional intensity distributions. Compared to LLSM, this user-friendly and modular approach of...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0327-9
更新日期：2019-03-01 00:00:00
abstract：:We must reliably map the interactomes of cellular macromolecular complexes in order to fully explore and understand biological systems. However, there are no methods to accurately predict how to capture a given macromolecular complex with its physiological binding partners. Here, we present a screening method that com...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3395
更新日期：2015-06-01 00:00:00
abstract：:Recent efforts in neuroscience research have been aimed at obtaining detailed anatomical neuronal wiring maps as well as information on how neurons in these networks engage in dynamic activities. Although the entire connectivity map of the nervous system of Caenorhabditis elegans has been known for more than 25 years,...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2637
更新日期：2013-10-01 00:00:00
abstract：:Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to defi...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0328-8
更新日期：2019-04-01 00:00:00
abstract：:We present a method to robustly discriminate clustered from randomly distributed molecules detected with techniques based on single-molecule localization microscopy, such as PALM and STORM. The approach is based on deliberate variation of labeling density, such as titration of fluorescent antibody, combined with quant...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3897
更新日期：2016-08-01 00:00:00
abstract：:Plants have evolved a unique system in which the plant hormone auxin directly induces rapid degradation of the AUX/IAA family of transcription repressors by a specific form of the SCF E3 ubiquitin ligase. Other eukaryotes lack the auxin response but share the SCF degradation pathway, allowing us to transplant the auxi...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1401
更新日期：2009-12-01 00:00:00
abstract：:Identifying groups of similar objects is a popular first step in biomedical data analysis, but it is error-prone and impossible to perform manually. Many computational methods have been developed to tackle this problem. Here we assessed 13 well-known methods using 24 data sets ranging from gene expression to protein d...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3583
更新日期：2015-11-01 00:00:00
abstract：:Single-molecule localization microscopy is a powerful tool for visualizing subcellular structures, interactions and protein functions in biological research. However, inhomogeneous refractive indices inside cells and tissues distort the fluorescent signal emitted from single-molecule probes, which rapidly degrades res...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-020-0816-x
更新日期：2020-05-01 00:00:00
abstract：:Biomolecular dynamics and stability are predominantly investigated in vitro and extrapolated to explain function in the living cell. We present fast relaxation imaging (FreI), which combines fluorescence microscopy and temperature jumps to probe biomolecular dynamics and stability inside a single living cell with high...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1435
更新日期：2010-04-01 00:00:00
abstract：:We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads f...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1517
更新日期：2010-11-01 00:00:00
abstract：:RNA-guided Cas9 nucleases derived from clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have dramatically transformed our ability to edit the genomes of diverse organisms. We believe tools and techniques based on Cas9, a single unifying factor capable of colocalizing RNA, DNA and protein,...
journal_title：Nature methods
pub_type： 杂志文章,评审
doi：10.1038/nmeth.2649
更新日期：2013-10-01 00:00:00
abstract：:Microfluidic channels provide a means to deliver barcodes encoding spatial information to a tissue, which allows co-profiling of gene expression and proteins of interest in a spatially resolved manner. ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-020-01043-w
更新日期：2021-01-01 00:00:00
abstract：:We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers' contributions to the biological sciences and more support of this development model from funders and instit...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2082
更新日期：2012-06-28 00:00:00
abstract：: ...
journal_title：Nature methods
pub_type： 评论,杂志文章
doi：10.1038/s41592-019-0315-0
更新日期：2019-02-01 00:00:00
abstract：:Small molecules are known to stabilize membrane proteins and to modulate their function and oligomeric state, but such interactions are often hard to precisely define. Here we develop and apply a high-resolution, Orbitrap mass spectrometry-based method for analyzing intact membrane protein-ligand complexes. Using this...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3771
更新日期：2016-04-01 00:00:00
