Imaging volumetric dynamics at high speed in mouse and zebrafish brain with confocal light field microscopy.

Abstract:

:A detailed understanding of the function of neural networks and how they are supported by a dynamic vascular system requires fast three-dimensional imaging in thick tissues. Here we present confocal light field microscopy, a method that enables fast volumetric imaging in the brain at depths of hundreds of micrometers. It uses a generalized confocal detection scheme that selectively collects fluorescent signals from the in-focus volume and provides optical sectioning capability to improve imaging resolution and sensitivity in thick tissues. We demonstrate recording of whole-brain calcium transients in freely swimming zebrafish larvae and observe behaviorally correlated activities in single neurons during prey capture. Furthermore, in the mouse brain, we detect neural activities at depths of up to 370 μm and track blood cells at 70 Hz over a volume of diameter 800 μm × thickness 150 μm and depth of up to 600 μm.

journal_name

Nat Biotechnol

journal_title

Nature biotechnology

authors

Zhang Z,Bai L,Cong L,Yu P,Zhang T,Shi W,Li F,Du J,Wang K

doi

10.1038/s41587-020-0628-7

subject

Has Abstract

pub_date

2021-01-01 00:00:00

pages

74-83

issue

1

eissn

1087-0156

issn

1546-1696

pii

10.1038/s41587-020-0628-7

journal_volume

39

pub_type

杂志文章
  • Cloned transgenic cattle produce milk with higher levels of beta-casein and kappa-casein.

    abstract::To enhance milk composition and milk processing efficiency by increasing the casein concentration in milk, we have introduced additional copies of the genes encoding bovine beta- and kappa-casein (CSN2 and CSN3, respectively) into female bovine fibroblasts. Nuclear transfer with four independent donor cell lines resul...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt783

    authors: Brophy B,Smolenski G,Wheeler T,Wells D,L'Huillier P,Laible G

    更新日期:2003-02-01 00:00:00

  • Integrating cell-level kinetic modeling into the design of engineered protein therapeutics.

    abstract::Functional genomics and proteomics are identifying many potential drug targets for novel therapeutic proteins, and both rational and combinatorial protein engineering methods are available for creating drug candidates. A central challenge is the definition of the most appropriate design criteria, which will benefit cr...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1064

    authors: Rao BM,Lauffenburger DA,Wittrup KD

    更新日期:2005-02-01 00:00:00

  • Purification of recombinant proteins by fusion with thermally-responsive polypeptides.

    abstract::Elastin-like polypeptides (ELPs) undergo a reversible, inverse phase transition. Below their transition temperature (Tt), ELPs are soluble in water, but when the temperature is raised above Tt, phase transition occurs, leading to aggregation of the polypeptide. We demonstrate a method for purification of soluble fusio...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/15100

    authors: Meyer DE,Chilkoti A

    更新日期:1999-11-01 00:00:00

  • De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.

    abstract::Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogen...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.2979

    authors: Li YH,Zhou G,Ma J,Jiang W,Jin LG,Zhang Z,Guo Y,Zhang J,Sui Y,Zheng L,Zhang SS,Zuo Q,Shi XH,Li YF,Zhang WK,Hu Y,Kong G,Hong HL,Tan B,Song J,Liu ZX,Wang Y,Ruan H,Yeung CK,Liu J,Wang H,Zhang LJ,Guan RX

    更新日期:2014-10-01 00:00:00

  • Efficient siRNA delivery into primary cells by a peptide transduction domain-dsRNA binding domain fusion protein.

    abstract::RNA interference (RNAi) induced by short interfering RNA (siRNA) allows for discovery research and large-scale screening; however, owing to their size and anionic charge, siRNAs do not readily enter cells. Current approaches do not deliver siRNAs into a high percentage of primary cells without cytotoxicity. Here we re...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.1541

    authors: Eguchi A,Meade BR,Chang YC,Fredrickson CT,Willert K,Puri N,Dowdy SF

    更新日期:2009-06-01 00:00:00

  • Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.

    abstract::The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metagenomic sequencing could identify LRI pathogens much faster than culture, but methods are needed to remove the large amoun...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/s41587-019-0156-5

    authors: Charalampous T,Kay GL,Richardson H,Aydin A,Baldan R,Jeanes C,Rae D,Grundy S,Turner DJ,Wain J,Leggett RM,Livermore DM,O'Grady J

    更新日期:2019-07-01 00:00:00

  • Isolation of neuronal precursors by sorting embryonic forebrain transfected with GFP regulated by the T alpha 1 tubulin promoter.

    abstract::Neuronal precursor cells are widespread in the forebrain ventricular/subventricular zone, and may provide a cellular substrate for brain repair. Clonal lines derived from single progenitors can become progressively less representative of their parental precursors with time and passage in vitro. We have developed an al...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0298-196

    authors: Wang S,Wu H,Jiang J,Delohery TM,Isdell F,Goldman SA

    更新日期:1998-02-01 00:00:00

  • The pharmacological basis of anti-IgE therapy.

    abstract::The treatment of asthma and allergic rhinitis using unique, humanized anti-IgE monoclonal antibodies with very particular binding specificities is now supported by the results of multiple phase II and III human clinical studies. The therapeutic efficacy of this approach is attributable to several pharmacological mecha...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,评审

    doi:10.1038/72601

    authors: Chang TW

    更新日期:2000-02-01 00:00:00

  • Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.

    abstract::We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.2798

    authors: Sherwood RI,Hashimoto T,O'Donnell CW,Lewis S,Barkal AA,van Hoff JP,Karun V,Jaakkola T,Gifford DK

    更新日期:2014-02-01 00:00:00

  • Low probability of chloroplast movement from oilseed rape (Brassica napus) into wild Brassica rapa.

    abstract::Pollen-mediated movement of transgenes from transplastomic oilseed rape (Brassica napus) into wild relatives will be avoided if chloroplasts are maternally transmitted. We assess the probability of chloroplast exchange between conventional oilseed rape and wild Brassica rapa to model the future behavior of transplasto...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/7952

    authors: Scott SE,Wilkinson MJ

    更新日期:1999-04-01 00:00:00

  • Redirecting lipoic acid ligase for cell surface protein labeling with small-molecule probes.

    abstract::Live cell imaging is a powerful method to study protein dynamics at the cell surface, but conventional imaging probes are bulky, or interfere with protein function, or dissociate from proteins after internalization. Here, we report technology for covalent, specific tagging of cellular proteins with chemical probes. Th...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1355

    authors: Fernández-Suárez M,Baruah H,Martínez-Hernández L,Xie KT,Baskin JM,Bertozzi CR,Ting AY

    更新日期:2007-12-01 00:00:00

  • Lineage conversion induced by pluripotency factors involves transient passage through an iPSC stage.

    abstract::Brief expression of pluripotency-associated factors such as Oct4, Klf4, Sox2 and c-Myc (OKSM), in combination with differentiation-inducing signals, has been reported to trigger transdifferentiation of fibroblasts into other cell types. Here we show that OKSM expression in mouse fibroblasts gives rise to both induced ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3247

    authors: Bar-Nur O,Verheul C,Sommer AG,Brumbaugh J,Schwarz BA,Lipchina I,Huebner AJ,Mostoslavsky G,Hochedlinger K

    更新日期:2015-07-01 00:00:00

  • Engineered off-the-shelf therapeutic T cells resist host immune rejection.

    abstract::Engineered T cells are effective therapies against a range of malignancies, but current approaches rely on autologous T cells, which are difficult and expensive to manufacture. Efforts to develop potent allogeneic T cells that are not rejected by the recipient's immune system require abrogating both T- and natural kil...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/s41587-020-0601-5

    authors: Mo F,Watanabe N,McKenna MK,Hicks MJ,Srinivasan M,Gomes-Silva D,Atilla E,Smith T,Ataca Atilla P,Ma R,Quach D,Heslop HE,Brenner MK,Mamonkin M

    更新日期:2021-01-01 00:00:00

  • Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.

    abstract::Technologies that enable targeted manipulation of epigenetic marks could be used to precisely control cell phenotype or interrogate the relationship between the epigenome and transcriptional control. Here we describe a programmable, CRISPR-Cas9-based acetyltransferase consisting of the nuclease-null dCas9 protein fuse...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3199

    authors: Hilton IB,D'Ippolito AM,Vockley CM,Thakore PI,Crawford GE,Reddy TE,Gersbach CA

    更新日期:2015-05-01 00:00:00

  • Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.

    abstract::We describe tethered conformation capture (TCC), a method for genome-wide mapping of chromatin interactions. By performing ligations on solid substrates rather than in solution, TCC substantially enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and between chromosomes...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.2057

    authors: Kalhor R,Tjong H,Jayathilaka N,Alber F,Chen L

    更新日期:2011-12-25 00:00:00

  • Publisher Correction: Single-cell RNA-seq analysis software providers scramble to offer solutions.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41587-020-0510-7

    authors: Eisenstein M

    更新日期:2020-05-01 00:00:00

  • Author Correction: Brain leaks and consumer neurotechnology.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature biotechnology

    pub_type: 已发布勘误

    doi:10.1038/s41587-019-0167-2

    authors: Ienca M,Haselager P,Emanuel EJ

    更新日期:2019-07-01 00:00:00

  • Epigenetic modifications in pluripotent and differentiated cells.

    abstract::Epigenetic modifications constitute a complex regulatory layer on top of the genome sequence. Pluripotent and differentiated cells provide a powerful system for investigating how the epigenetic code influences cellular fate. High-throughput sequencing of these cell types has yielded DNA methylation maps at single-nucl...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,评审

    doi:10.1038/nbt.1684

    authors: Meissner A

    更新日期:2010-10-01 00:00:00

  • The impact of target site accessibility on the design of effective siRNAs.

    abstract::Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downst...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1404

    authors: Tafer H,Ameres SL,Obernosterer G,Gebeshuber CA,Schroeder R,Martinez J,Hofacker IL

    更新日期:2008-05-01 00:00:00

  • Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations.

    abstract::The ability to detect single protein molecules in blood could accelerate the discovery and use of more sensitive diagnostic biomarkers. To detect low-abundance proteins in blood, we captured them on microscopic beads decorated with specific antibodies and then labeled the immunocomplexes (one or zero labeled target pr...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.1641

    authors: Rissin DM,Kan CW,Campbell TG,Howes SC,Fournier DR,Song L,Piech T,Patel PP,Chang L,Rivnak AJ,Ferrell EP,Randall JD,Provuncher GK,Walt DR,Duffy DC

    更新日期:2010-06-01 00:00:00

  • Site-specific genomic integration produces therapeutic Factor IX levels in mice.

    abstract::We used the integrase from phage phiC31 to integrate the human Factor IX (hFIX) gene permanently into specific sites in the mouse genome. A plasmid containing attB and an expression cassette for hFIX was delivered to the livers of mice by using high-pressure tail vein injection. When an integrase expression plasmid wa...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt753

    authors: Olivares EC,Hollis RP,Chalberg TW,Meuse L,Kay MA,Calos MP

    更新日期:2002-11-01 00:00:00

  • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

    abstract::Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlatio...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.1511

    authors: Cox J,Mann M

    更新日期:2008-12-01 00:00:00

  • Hearts and minds.

    abstract::The nonprofit Pew Initiative on Food and Biotechnology is closing, but the need for an independent and neutral body to facilitate dialog on US biotech policy has never been greater. ...

    journal_title:Nature biotechnology

    pub_type: 社论

    doi:10.1038/nbt0207-143

    authors:

    更新日期:2007-02-01 00:00:00

  • Chaperones as thermodynamic sensors of drug-target interactions reveal kinase inhibitor specificities in living cells.

    abstract::The interaction between the HSP90 chaperone and its client kinases is sensitive to the conformational status of the kinase, and stabilization of the kinase fold by small molecules strongly decreases chaperone interaction. Here we exploit this observation and assay small-molecule binding to kinases in living cells, usi...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.2620

    authors: Taipale M,Krykbaeva I,Whitesell L,Santagata S,Zhang J,Liu Q,Gray NS,Lindquist S

    更新日期:2013-07-01 00:00:00

  • Profiling alternative splicing on fiber-optic arrays.

    abstract::The human transcriptome is marked by extensive alternative mRNA splicing and the expression of many closely related genes, which may be difficult to distinguish using standard microarray techniques. Here we describe a sensitive and specific assay for parallel analysis of mRNA isoforms on a fiber-optic microarray platf...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0402-353

    authors: Yeakley JM,Fan JB,Doucet D,Luo L,Wickham E,Ye Z,Chee MS,Fu XD

    更新日期:2002-04-01 00:00:00

  • High-throughput genome scaffolding from in vivo DNA interaction frequency.

    abstract::Despite advances in DNA sequencing technology, assembly of complex genomes remains a major challenge, particularly for genomes sequenced using short reads, which yield highly fragmented assemblies. Here we show that genome-wide in vivo chromatin interaction frequency data, which are measurable with chromosome conforma...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.2768

    authors: Kaplan N,Dekker J

    更新日期:2013-12-01 00:00:00

  • Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41587-020-0457-8

    authors: Röst HL,Rosenberger G,Navarro P,Gillet L,Miladinović SM,Schubert OT,Wolski W,Collins BC,Malmström J,Malmström L,Aebersold R

    更新日期:2020-03-01 00:00:00

  • Are university researchers at risk for patent infringement?

    abstract::Academic researchers have regularly ignored patents on key technologies as a strategy to maneuver around patent thickets and freedom-to-operate issues, but they may be more at risk than they realize. ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1107-1225

    authors: Yancey A,Stewart CN Jr

    更新日期:2007-11-01 00:00:00

  • CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes.

    abstract::High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based on clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) or its transcriptionally repressive variant, CRISPR-inter...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3536

    authors: Evers B,Jastrzebski K,Heijmans JP,Grernrum W,Beijersbergen RL,Bernards R

    更新日期:2016-06-01 00:00:00

  • Optogenetic control of endogenous Ca(2+) channels in vivo.

    abstract::Calcium (Ca(2+)) signals that are precisely modulated in space and time mediate a myriad of cellular processes, including contraction, excitation, growth, differentiation and apoptosis. However, study of Ca(2+) responses has been hampered by technological limitations of existing Ca(2+)-modulating tools. Here we presen...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3350

    authors: Kyung T,Lee S,Kim JE,Cho T,Park H,Jeong YM,Kim D,Shin A,Kim S,Baek J,Kim J,Kim NY,Woo D,Chae S,Kim CH,Shin HS,Han YM,Kim D,Heo WD

    更新日期:2015-10-01 00:00:00