Methods

Publication date: 1 October 2018 Source: Methods, Volume 149 Author(s): Vanessa L. Hale, Patricio Jeraldo, Michael Mundy, Janet Yao, Gary Keeney, Nancy Scott, E. Heidi Cheek, Jennifer Davidson, Megan Green, Christine Martinez, John Lehman, Chandra Pettry, Erica Reed, Kelly Lyke, Bryan A. White, Christian Diener, Osbaldo Resendis-Antonio, Jaime Gransee, Tumpa Dutta, Xuan-Mai Petterson Abstract Multi-omic
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Publication date: 1 October 2018 Source: Methods, Volume 149 Author(s): Simon J.S. Cameron, Zoltán Takáts Abstract The interaction between microbial communities and their environment, such as the human gastrointestinal tract, has been an area of microbiology rapidly advanced, by developments in sequencing technology. However, these techniques are largely limited to the detection of the taxonomic
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Author Correction: Rapid and efficient induction of functional astrocytes from human pluripotent stem cells Author Correction: Rapid and efficient induction of functional astrocytes from human pluripotent stem cells, Published online: 04 December 2018; doi:10.1038/s41592-018-0264-z Author Correction: Rapid and efficient induction of functional astrocytes from human pluripotent stem cells
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Publication date: 1 October 2018 Source: Methods, Volume 149 Author(s): Mabel Guzman-Rodriguez, Julie A.K. McDonald, Richard Hyde, Emma Allen-Vercoe, Erika C. Claud, Prameet M. Sheth, Elaine O. Petrof Abstract The study of complex microbial communities has become a major research focus as mounting evidence suggests the pivotal role microbial communities play in host health and
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Publication date: 1 October 2018 Source: Methods, Volume 149 Author(s): Eleanor Jameson, Mussa Quareshy, Yin Chen Abstract The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in
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Comparing phenotypic variation between inbred and outbred mice Comparing phenotypic variation between inbred and outbred mice, Published online: 30 November 2018; doi:10.1038/s41592-018-0224-7 Inbred mice are preferred over outbred mice because it is assumed that they display less trait variability. We compared coefficients of variation and did not find evidence of greater trait stability in inbred
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An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas, Published online: 30 November 2018; doi:10.1038/s41592-018-0215-8 An ex vivo 3D culture model of mycobacterial granulomas recapitulates the in vivo physiology of these structures and enables longitudinal imaging studies. The platform allows genetic and
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Faster, sharper, and deeper: structured illumination microscopy for biological imaging Faster, sharper, and deeper: structured illumination microscopy for biological imaging, Published online: 26 November 2018; doi:10.1038/s41592-018-0211-z A Perspective on super-resolution structured illumination microscopy reviews advances in these methods and focuses on matching user needs in terms of imaging speed, sample depth, and desired resolution with
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Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments, Published online: 26 November 2018; doi:10.1038/s41592-018-0220-y Proximity-CLIP, a method that combines proximity-based protein biotinylation and UV crosslinking, profiles RNAs and ribonucleoproteins in any cellular compartment.
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Interpretation of an individual functional genomics experiment guided by massive public data Interpretation of an individual functional genomics experiment guided by massive public data, Published online: 26 November 2018; doi:10.1038/s41592-018-0218-5 YETI puts individual -omics experiments in the context of public genomics data by creating an integrated dataset-specific functional network, thus allowing more thorough interpretation of
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Found In Translation: a machine learning model for mouse-to-human inference Found In Translation: a machine learning model for mouse-to-human inference, Published online: 26 November 2018; doi:10.1038/s41592-018-0214-9 The machine learning approach FIT leverages public mouse and human expression data to improve the translation of mouse model results to analogous human disease.
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Content-aware image restoration: pushing the limits of fluorescence microscopy Content-aware image restoration: pushing the limits of fluorescence microscopy, Published online: 26 November 2018; doi:10.1038/s41592-018-0216-7 Content-aware image restoration (CARE) uses deep learning to improve microscopy images. CARE bypasses the trade-offs between imaging speed, resolution, and maximal light exposure that limit fluorescence imaging to enable discovery.
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Publication date: Available online 27 September 2018 Source: Methods Author(s): John S.Y. Lim, Graham D. Wright, Brian Burke, Wei Xie Abstract For decades, components of the mammalian nuclear envelope (NE), such as the nuclear lamina and nuclear pore complexes (NPCs), have been largely resistant to quantitative cell biological analysis using conventional fluorescence microscopy. This is
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Publication date: Available online 25 September 2018 Source: Methods Author(s): Na-Young Kwon, Youngjin Kim, Jie-Oh Lee Abstract Diabodies are bispecific antibody fragments that have two antigen binding Fv domains. They are unique among hundreds of different formats of bispecific antibodies because they are small and rigid enough to be crystallized. Diabodies are generated by connecting
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Publication date: Available online 22 September 2018 Source: Methods Author(s): Eduardo Andrés-León, Ana M. Rojas Abstract Messenger RNAs (mRNAs) fulfil specific biological roles in cells and, thus, their expression may be adapted to suit specific circumstances. This is in part achieved through selective gene transcription and post-transcriptional events, the regulation of which must be tightly
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Publication date: Available online 12 September 2018 Source: Methods Author(s): Jan-Hendrik Spille, Micca Hecht, Valentin Grube, Won-ki Cho, Choongman Lee, Ibrahim I. Cissé Abstract The MS2 system is a powerful tool for investigating transcription dynamics at the single molecule directly in live cells. In the past, insertion of the RNA-labelling cassette at specific gene loci
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Publication date: Available online 28 September 2018 Source: Methods Author(s): Jared Hennen, Kwang-Ho Hur, Siddarth Reddy Karuka, G.W. Gant Luxton, Joachim D. Mueller Abstract Analysis of fluorescence fluctuation experiments by the mean-segmented Q (MSQ) method was recently used to successfully characterize the oligomeric state and mobility of proteins within the nuclear envelope (NE) of living
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Publication date: Available online 29 September 2018 Source: Methods Author(s): James M. Kinross Abstract Health based games have significant potential as therapeutic interventions due to the inherent mechanisms associated with social and individual game play and their capacity for sensor integration, data capture analysis and patient feedback. Moreover, they are low cost and they can
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Publication date: 1 October 2018 Source: Methods, Volume 149 Author(s): Santosh Lamichhane, Partho Sen, Alex M. Dickens, Matej Orešič, Hanne Christine Bertram Abstract It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we
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Publication date: 1 October 2018 Source: Methods, Volume 149 Author(s): Markus Egert, Severin Weis, Sylvia Schnell Abstract The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ
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Publication date: Available online 1 October 2018 Source: Methods Author(s): Sophia Hober, Sarah Lindbo, Johan Nilvebrant Abstract Non-immunoglobulin scaffolds represent a proven group of small affinity proteins that can be engineered in vitro to similar affinity and potency as monoclonal antibodies. Several novel candidate biotherapeutics that exploit the potential advantages scaffold proteins hold over larger
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Cell-type-specific and projection-specific brain-wide reconstruction of single neurons Cell-type-specific and projection-specific brain-wide reconstruction of single neurons, Published online: 19 November 2018; doi:10.1038/s41592-018-0184-y An AAV-based platform achieves sparse yet bright labeling of neurons with cell-type specificity. This technology will facilitate the reconstruction of neurons in the mouse brain.
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Fast, in vivo voltage imaging using a red fluorescent indicator Fast, in vivo voltage imaging using a red fluorescent indicator, Published online: 12 November 2018; doi:10.1038/s41592-018-0188-7 VARNAM is a red-shifted genetically encoded voltage sensor based on the Ace opsin. It is applied in Drosophila, mouse brain slices and behaving mice. It can be readily combined
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Closed-loop all-optical interrogation of neural circuits in vivo Closed-loop all-optical interrogation of neural circuits in vivo, Published online: 12 November 2018; doi:10.1038/s41592-018-0183-z A closed-loop all-optical strategy allows manipulation of neurons on the basis of their ongoing activity and can be used to clamp neuronal activity to a preset level, boost sensory-evoked activity or yoke together
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Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure, Published online: 05 November 2018; doi:10.1038/s41592-018-0177-x NATIVE is a correlative light and electron microscopy approach that is based on nanobody-mediated immunohistochemistry. The approach does not require harsh permeabilization and preserves ultrastructure
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Publisher Correction: Transparent Danionella translucida as a genetically tractable vertebrate brain model Publisher Correction: Transparent <i>Danionella translucida</i> as a genetically tractable vertebrate brain model, Published online: 05 November 2018; doi:10.1038/s41592-018-0217-6 Publisher Correction: Transparent Danionella translucida as a genetically tractable vertebrate brain model
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Spatial organization of the somatosensory cortex revealed by osmFISH Spatial organization of the somatosensory cortex revealed by osmFISH, Published online: 30 October 2018; doi:10.1038/s41592-018-0175-z osmFISH applies automated cycles of single-molecule fluorescence in situ hybridization without barcoding to provide spatial gene expression in tissue sections at high sensitivity, accuracy and throughput.
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FLIRT: fast local infrared thermogenetics for subcellular control of protein function FLIRT: fast local infrared thermogenetics for subcellular control of protein function, Published online: 30 October 2018; doi:10.1038/s41592-018-0168-y FLIRT enables spatiotemporally precise control of protein function in C. elegans by harnessing existing temperature-sensitive mutations. Proteins can be inactivated at desired sites by infrared laser light
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Diploid genome in 3D Diploid genome in 3D, Published online: 30 October 2018; doi:10.1038/s41592-018-0208-7 Dip-C, a descendent of the 3C method, reveals 3D genome structures of single diploid human cells.
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A call for public archives for biological image data A call for public archives for biological image data, Published online: 30 October 2018; doi:10.1038/s41592-018-0195-8 Public data archives are the backbone of modern biological research. Biomolecular archives are well established, but bioimaging resources lag behind them. The technology required for imaging archives is now available, thus
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emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging, Published online: 22 October 2018; doi:10.1038/s41592-018-0167-z A software tool, emClarity, implements several improvements in cryo-electron tomography image-processing algorithms to achieve sub-nanometer resolution for diverse macromolecular structures.
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Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study, Published online: 16 October 2018; doi:10.1038/s41592-018-0193-x Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
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Transparent Danionella translucida as a genetically tractable vertebrate brain model Transparent <i>Danionella translucida</i> as a genetically tractable vertebrate brain model, Published online: 15 October 2018; doi:10.1038/s41592-018-0144-6 The combination of transparency, small brain size and genetic access positions Danionella translucida as a promising model organism for functional imaging of neuronal circuits, especially during complex behaviors in
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