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Nature Methods
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#1Lixue Shi (Columbia University)H-Index: 4
#2Xinwen Liu (Columbia University)
Last. Wei Min (Columbia University)H-Index: 33
view all 10 authors...
Understanding metabolism is indispensable in unraveling the mechanistic basis of many physiological and pathological processes. However, in situ metabolic imaging tools are still lacking. Here we introduce a framework for mid-infrared (MIR) metabolic imaging by coupling the emerging high-information-throughput MIR microscopy with specifically designed IR-active vibrational probes. We present three categories of small vibrational tags including azide bond, 13C-edited carbonyl bond and deuterium-l...
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#1Sebastian Strauss (LMU: Ludwig Maximilian University of Munich)H-Index: 4
#2Ralf Jungmann (LMU: Ludwig Maximilian University of Munich)H-Index: 28
DNA-PAINT’s imaging speed has recently been significantly enhanced by optimized sequence design and buffer conditions. However, this implementation has not reached an ultimate speed limit and is only applicable to imaging of single targets. To further improve acquisition speed, we introduce concatenated, periodic DNA sequence motifs, yielding up to 100-fold-faster sampling in comparison to traditional DNA-PAINT. We extend this approach to six orthogonal sequence motifs, now enabling speed-optimi...
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#1Elias Nehme (Technion – Israel Institute of Technology)H-Index: 4
#2Daniel Freedman (Google)H-Index: 4
Last. Yoav Shechtman (Technion – Israel Institute of Technology)H-Index: 19
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#1Issaku YamadaH-Index: 8
#2Masaaki Shiota (SUA: Soka University of America)H-Index: 1
Last. Noriaki Fujita (AIST: National Institute of Advanced Industrial Science and Technology)H-Index: 3
view all 15 authors...
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#1Wenkai Yi (Northwest University (United States))
#2Jingyu Li (CityU: City University of Hong Kong)
Last. Jing Ye (Fourth Military Medical University)
view all 15 authors...
We have developed CRISPR-assisted RNA-protein interaction detection method (CARPID), which leverages CRISPR-CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealin...
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#1Dora Mahecic (EPFL: École Polytechnique Fédérale de Lausanne)
#2Davide Gambarotto (University of Geneva)H-Index: 4
Last. Paul Guichard (University of Geneva)H-Index: 16
view all 11 authors...
Super-resolution microscopies have become an established tool in biological research. However, imaging throughput remains a main bottleneck in acquiring large datasets required for quantitative biology. Here we describe multifocal flat illumination for field-independent imaging (mfFIFI). By integrating mfFIFI into an instant structured illumination microscope (iSIM), we extend the field of view (FOV) to >100 × 100 µm2 while maintaining high-speed, multicolor, volumetric imaging at double the dif...
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#1Jolene Jie Lin Goh (Agency for Science, Technology and Research)
#1Jolene Jie Lin Goh (Agency for Science, Technology and Research)H-Index: 2
Last. Kok Hao Chen (Agency for Science, Technology and Research)H-Index: 11
view all 8 authors...
We present split-FISH, a multiplexed fluorescence in situ hybridization method that leverages a split-probe design to achieve enhanced specificity. Split-FISH reduces off-target background fluorescence, decreases false positives and enables accurate RNA profiling in uncleared tissues. We demonstrate the efficacy of split-FISH on various mouse tissues by quantifying the distribution and abundance of 317 genes in single cells and reveal diverse localization patterns for spatial regulation of the t...
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#1Elias Nehme (Technion – Israel Institute of Technology)H-Index: 4
#2Daniel Freedman (Google)H-Index: 4
Last. Yoav Shechtman (Technion – Israel Institute of Technology)H-Index: 19
view all 10 authors...
An outstanding challenge in single-molecule localization microscopy is the accurate and precise localization of individual point emitters in three dimensions in densely labeled samples. One established approach for three-dimensional single-molecule localization is point-spread-function (PSF) engineering, in which the PSF is engineered to vary distinctively with emitter depth using additional optical elements. However, images of dense emitters, which are desirable for improving temporal resolutio...
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#1Chris A. Brackey (Edin.: University of Edinburgh)
#2Davide Marenduzzo (Edin.: University of Edinburgh)H-Index: 46
Last. Nick Gilbert (Edin.: University of Edinburgh)H-Index: 23
view all 3 authors...
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organization and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation of experimental results. Polymer simulations and mechanistic modeling have been applied to explain experimental observations and their links to different aspects of genome function. Here we provide a guide for biologists, explaining different simulation appro...
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