journal
MENU ▼
Read by QxMD icon Read
search

Nature Methods

journal
https://www.readbyqxmd.com/read/30397327/publisher-correction-transparent-danionella-translucida-as-a-genetically-tractable-vertebrate-brain-model
#1
Lisanne Schulze, Jörg Henninger, Mykola Kadobianskyi, Thomas Chaigne, Ana Isabel Faustino, Nahid Hakiy, Shahad Albadri, Markus Schuelke, Leonard Maler, Filippo Del Bene, Benjamin Judkewitz
The version of this paper originally published contained errors in reference citations: in the first paragraph of the Results section, the text "This extent of optical clarity probably results from the absence of skull above the brain22 . In our specimens, Nissl-stained coronal sections through the head showed that the skull surrounds the brain only laterally and ventrally" should have read "This extent of optical clarity probably results from the absence of skull above the brain21 . In our specimens, Nissl-stained coronal sections through the head22 showed that the skull surrounds the brain only laterally and ventrally...
November 5, 2018: Nature Methods
https://www.readbyqxmd.com/read/30397326/nanobody-immunostaining-for-correlated-light-and-electron-microscopy-with-preservation-of-ultrastructure
#2
Tao Fang, Xiaotang Lu, Daniel Berger, Christina Gmeiner, Julia Cho, Richard Schalek, Hidde Ploegh, Jeff Lichtman
Morphological and molecular characteristics determine the function of biological tissues. Attempts to combine immunofluorescence and electron microscopy invariably compromise the quality of the ultrastructure of tissue sections. We developed NATIVE, a correlated light and electron microscopy approach that preserves ultrastructure while showing the locations of multiple molecular moieties, even deep within tissues. This technique allowed the large-scale 3D reconstruction of a volume of mouse hippocampal CA3 tissue at nanometer resolution...
November 5, 2018: Nature Methods
https://www.readbyqxmd.com/read/30377379/a-mutant-cell-library-for-systematic-analysis-of-heparan-sulfate-structure-function-relationships
#3
Hong Qiu, Songshan Shi, Jingwen Yue, Meng Xin, Alison V Nairn, Lei Lin, Xinyue Liu, Guoyun Li, Stephanie A Archer-Hartmann, Mitche Dela Rosa, Melina Galizzi, Shunchun Wang, Fuming Zhang, Parastoo Azadi, Toin H van Kuppevelt, Wellington V Cardoso, Koji Kimata, Xingbin Ai, Kelley W Moremen, Jeffrey D Esko, Robert J Linhardt, Lianchun Wang
Heparan sulfate (HS) is a complex linear polysaccharide that modulates a wide range of biological functions. Elucidating the structure-function relationship of HS has been challenging. Here we report the generation of an HS-mutant mouse lung endothelial cell library by systematic deletion of HS genes expressed in the cell. We used this library to (1) determine that the strictly defined fine structure of HS, not its overall degree of sulfation, is more important for FGF2-FGFR1 signaling; (2) define the epitope features of commonly used anti-HS phage display antibodies; and (3) delineate the fine inter-regulation networks by which HS genes modify HS and chain length in mammalian cells at a cell-type-specific level...
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377378/neuroscience-models-choose-your-dimension
#4
Vivien Marx
No abstract text is available yet for this article.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377377/a-light-gated-potassium-channel-for-sustained-neuronal-inhibition
#5
Laura Alberio, Andrea Locarno, Andrea Saponaro, Edoardo Romano, Valérie Bercier, Shahad Albadri, Federica Simeoni, Silvia Moleri, Silvia Pelucchi, Alessandro Porro, Elena Marcello, Noemi Barsotti, Kerri Kukovetz, Arjen J Boender, Andrea Contestabile, Shizhen Luo, Aubin Moutal, Yingshi Ji, Giulia Romani, Monica Beltrame, Filippo Del Bene, Monica Di Luca, Rajesh Khanna, Henry M Colecraft, Massimo Pasqualetti, Gerhard Thiel, Raffaella Tonini, Anna Moroni
Currently available inhibitory optogenetic tools provide short and transient silencing of neurons, but they cannot provide long-lasting inhibition because of the requirement for high light intensities. Here we present an optimized blue-light-sensitive synthetic potassium channel, BLINK2, which showed good expression in neurons in three species. The channel is activated by illumination with low doses of blue light, and in our experiments it remained active over (tens of) minutes in the dark after the illumination was stopped...
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377376/species-level-functional-profiling-of-metagenomes-and-metatranscriptomes
#6
Eric A Franzosa, Lauren J McIver, Gholamali Rahnavard, Luke R Thompson, Melanie Schirmer, George Weingart, Karen Schwarzberg Lipson, Rob Knight, J Gregory Caporaso, Nicola Segata, Curtis Huttenhower
Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways...
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377375/a-call-for-public-archives-for-biological-image-data
#7
Jan Ellenberg, Jason R Swedlow, Mary Barlow, Charles E Cook, Ugis Sarkans, Ardan Patwardhan, Alvis Brazma, Ewan Birney
No abstract text is available yet for this article.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377374/crispr-sirius-rna-scaffolds-for-signal-amplification-in-genome-imaging
#8
Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Yu-Chieh Chung, David Grunwald, Shaojie Zhang, Thoru Pederson
Clustered regularly interspaced short palindromic repeats (CRISPR) guide RNA scaffolds have been adapted to carry multiple binding sites for fluorescent proteins to enhance brightness for live cell imaging of genomic loci. However, many of these modifications result in guide RNA instability and thus produce lower genome-labeling efficiency than anticipated. Here we introduce CRISPR-Sirius, based on octet arrays of aptamers conferring both enhanced guide RNA stability and brightness, and provide initial biological applications of this platform...
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377373/predicting-with-confidence-and-tolerance
#9
Naomi Altman, Martin Krzywinski
No abstract text is available yet for this article.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377372/de-novo-computational-rna-modeling-into-cryo-em-maps-of-large-ribonucleoprotein-complexes
#10
Kalli Kappel, Shiheng Liu, Kevin P Larsen, Georgios Skiniotis, Elisabetta Viani Puglisi, Joseph D Puglisi, Z Hong Zhou, Rui Zhao, Rhiju Das
Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA-protein assemblies, but nearly all maps determined with this method have biologically important regions where the local resolution does not permit RNA coordinate tracing. To address these omissions, we present de novo ribonucleoprotein modeling in real space through assembly of fragments together with experimental density in Rosetta (DRRAFTER). We show that DRRAFTER recovers near-native models for a diverse benchmark set of RNA-protein complexes including the spliceosome, mitochondrial ribosome, and CRISPR-Cas9-sgRNA complexes; rigorous blind tests include yeast U1 snRNP and spliceosomal P complex maps...
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377371/a-high-throughput-pipeline-for-validation-of-antibodies
#11
Krzysztof Sikorski, Adi Mehta, Marit Inngjerdingen, Flourina Thakor, Simon Kling, Tomas Kalina, Tuula A Nyman, Maria Ekman Stensland, Wei Zhou, Gustavo A de Souza, Lars Holden, Jan Stuchly, Markus Templin, Fridtjof Lund-Johansen
Western blotting (WB) is widely used to test antibody specificity, but the assay has low throughput and precision. Here we used preparative gel electrophoresis to develop a capture format for WB. Fractions with soluble, size-separated proteins facilitated parallel readout with antibody arrays, shotgun mass spectrometry (MS) and immunoprecipitation followed by MS (IP-MS). This pipeline provided the means for large-scale implementation of antibody validation concepts proposed by an international working group on antibody validation (IWGAV)...
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377370/anna-moroni
#12
Vivien Marx
No abstract text is available yet for this article.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377369/the-impact-of-the-nih-brain-initiative
#13
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377368/striped-unifrac-enabling-microbiome-analysis-at-unprecedented-scale
#14
LETTER
Daniel McDonald, Yoshiki Vázquez-Baeza, David Koslicki, Jason McClelland, Nicolai Reeve, Zhenjiang Xu, Antonio Gonzalez, Rob Knight
No abstract text is available yet for this article.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377367/high-speed-protein-crystallography
#15
Allison Doerr
No abstract text is available yet for this article.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377366/the-hit-and-return-system-enables-efficient-time-resolved-serial-synchrotron-crystallography
#16
Eike C Schulz, Pedram Mehrabi, Henrike M Müller-Werkmeister, Friedjof Tellkamp, Ajay Jha, William Stuart, Elke Persch, Raoul De Gasparo, François Diederich, Emil F Pai, R J Dwayne Miller
We present a 'hit-and-return' (HARE) method for time-resolved serial synchrotron crystallography with time resolution from milliseconds to seconds or longer. Timing delays are set mechanically, using the regular pattern in fixed-target crystallography chips and a translation stage system. Optical pump-probe experiments to capture intermediate structures of fluoroacetate dehalogenase binding to its ligand demonstrated that data can be collected at short (30 ms), medium (752 ms) and long (2,052 ms) intervals...
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377365/deep-learning-to-predict-microscope-images
#17
Roger Brent, Laura Boucheron
No abstract text is available yet for this article.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377364/spatial-organization-of-the-somatosensory-cortex-revealed-by-osmfish
#18
Simone Codeluppi, Lars E Borm, Amit Zeisel, Gioele La Manno, Josina A van Lunteren, Camilla I Svensson, Sten Linnarsson
Global efforts to create a molecular census of the brain using single-cell transcriptomics are producing a large catalog of molecularly defined cell types. However, spatial information is lacking and new methods are needed to map a large number of cell type-specific markers simultaneously on large tissue areas. Here, we describe a cyclic single-molecule fluorescence in situ hybridization methodology and define the cellular organization of the somatosensory cortex.
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377363/stability-affinity-and-chromatic-variants-of-the-glutamate-sensor-iglusnfr
#19
Jonathan S Marvin, Benjamin Scholl, Daniel E Wilson, Kaspar Podgorski, Abbas Kazemipour, Johannes Alexander Müller, Susanne Schoch, Francisco José Urra Quiroz, Nelson Rebola, Huan Bao, Justin P Little, Ariana N Tkachuk, Edward Cai, Adam W Hantman, Samuel S-H Wang, Victor J DePiero, Bart G Borghuis, Edwin R Chapman, Dirk Dietrich, David A DiGregorio, David Fitzpatrick, Loren L Looger
Single-wavelength fluorescent reporters allow visualization of specific neurotransmitters with high spatial and temporal resolution. We report variants of intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) that are functionally brighter; detect submicromolar to millimolar amounts of glutamate; and have blue, cyan, green, or yellow emission profiles. These variants could be imaged in vivo in cases where original iGluSnFR was too dim, resolved glutamate transients in dendritic spines and axonal boutons, and allowed imaging at kilohertz rates...
November 2018: Nature Methods
https://www.readbyqxmd.com/read/30377362/engineered-anti-crispr-proteins-for-optogenetic-control-of-crispr-cas9
#20
Felix Bubeck, Mareike D Hoffmann, Zander Harteveld, Sabine Aschenbrenner, Andreas Bietz, Max C Waldhauer, Kathleen Börner, Julia Fakhiri, Carolin Schmelas, Laura Dietz, Dirk Grimm, Bruno E Correia, Roland Eils, Dominik Niopek
Anti-CRISPR proteins are powerful tools for CRISPR-Cas9 regulation; the ability to precisely modulate their activity could facilitate spatiotemporally confined genome perturbations and uncover fundamental aspects of CRISPR biology. We engineered optogenetic anti-CRISPR variants comprising hybrids of AcrIIA4, a potent Streptococcus pyogenes Cas9 inhibitor, and the LOV2 photosensor from Avena sativa. Coexpression of these proteins with CRISPR-Cas9 effectors enabled light-mediated genome and epigenome editing, and revealed rapid Cas9 genome targeting in human cells...
November 2018: Nature Methods
journal
journal
40701
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"