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Nature Methods

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https://www.readbyqxmd.com/read/30202060/terminal-exon-characterization-with-tectool-reveals-an-abundance-of-cell-specific-isoforms
#1
Andreas J Gruber, Foivos Gypas, Andrea Riba, Ralf Schmidt, Mihaela Zavolan
Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization. We developed the terminal exon characterization (TEC) tool ( http://tectool.unibas.ch ), which can be used with RNA-sequencing data from any species for which a genome annotation that includes sites of RNA cleavage and polyadenylation is available...
September 10, 2018: Nature Methods
https://www.readbyqxmd.com/read/30202059/three-photon-imaging-of-mouse-brain-structure-and-function-through-the-intact-skull
#2
Tianyu Wang, Dimitre G Ouzounov, Chunyan Wu, Nicholas G Horton, Bin Zhang, Cheng-Hsun Wu, Yanping Zhang, Mark J Schnitzer, Chris Xu
Optical imaging through the intact mouse skull is challenging because of skull-induced aberrations and scattering. We found that three-photon excitation provided improved optical sectioning compared with that obtained with two-photon excitation, even when we used the same excitation wavelength and imaging system. Here we demonstrate three-photon imaging of vasculature through the adult mouse skull at >500-μm depth, as well as GCaMP6s calcium imaging over weeks in cortical layers 2/3 and 4 in awake mice, with 8...
September 10, 2018: Nature Methods
https://www.readbyqxmd.com/read/30202058/comrades-determines-in-vivo-rna-structures-and-interactions
#3
Omer Ziv, Marta M Gabryelska, Aaron T L Lun, Luca F R Gebert, Jessica Sheu-Gruttadauria, Luke W Meredith, Zhong-Yu Liu, Chun Kit Kwok, Cheng-Feng Qin, Ian J MacRae, Ian Goodfellow, John C Marioni, Grzegorz Kudla, Eric A Miska
The structural flexibility of RNA underlies fundamental biological processes, but there are no methods for exploring the multiple conformations adopted by RNAs in vivo. We developed cross-linking of matched RNAs and deep sequencing (COMRADES) for in-depth RNA conformation capture, and a pipeline for the retrieval of RNA structural ensembles. Using COMRADES, we determined the architecture of the Zika virus RNA genome inside cells, and identified multiple site-specific interactions with human noncoding RNAs.
September 10, 2018: Nature Methods
https://www.readbyqxmd.com/read/30158632/publisher-correction-calling-cell-biologists-to-try-cryo-et
#4
Vivien Marx
In the article originally published, Elizabeth Villa's affiliation should have been University of California, San Diego. This error has been corrected in the HTML and PDF versions of the paper.
August 29, 2018: Nature Methods
https://www.readbyqxmd.com/read/30104636/the-gagome-a-cell-based-library-of-displayed-glycosaminoglycans
#5
Yen-Hsi Chen, Yoshiki Narimatsu, Thomas M Clausen, Catarina Gomes, Richard Karlsson, Catharina Steentoft, Charlotte B Spliid, Tobias Gustavsson, Ali Salanti, Andrea Persson, Anders Malmström, Daniel Willén, Ulf Ellervik, Eric P Bennett, Yang Mao, Henrik Clausen, Zhang Yang
Glycosaminoglycans (GAGs) are essential polysaccharides in normal physiology and disease. However, understanding of the contribution of specific GAG structures to specific biological functions is limited, largely because of the great structural heterogeneity among GAGs themselves, as well as technical limitations in the structural characterization and chemical synthesis of GAGs. Here we describe a cell-based method to produce and display distinct GAGs with a broad repertoire of modifications, a library we refer to as the GAGOme...
August 13, 2018: Nature Methods
https://www.readbyqxmd.com/read/30171252/precision-and-accuracy-of-single-molecule-fret-measurements-a-multi-laboratory-benchmark-study
#6
Björn Hellenkamp, Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth, Soheila Rezaei Adariani, Benjamin Ambrose, Mikayel Aznauryan, Anders Barth, Victoria Birkedal, Mark E Bowen, Hongtao Chen, Thorben Cordes, Tobias Eilert, Carel Fijen, Christian Gebhardt, Markus Götz, Giorgos Gouridis, Enrico Gratton, Taekjip Ha, Pengyu Hao, Christian A Hanke, Andreas Hartmann, Jelle Hendrix, Lasse L Hildebrandt, Verena Hirschfeld, Johannes Hohlbein, Boyang Hua, Christian G Hübner, Eleni Kallis, Achillefs N Kapanidis, Jae-Yeol Kim, Georg Krainer, Don C Lamb, Nam Ki Lee, Edward A Lemke, Brié Levesque, Marcia Levitus, James J McCann, Nikolaus Naredi-Rainer, Daniel Nettels, Thuy Ngo, Ruoyi Qiu, Nicole C Robb, Carlheinz Röcker, Hugo Sanabria, Michael Schlierf, Tim Schröder, Benjamin Schuler, Henning Seidel, Lisa Streit, Johann Thurn, Philip Tinnefeld, Swati Tyagi, Niels Vandenberk, Andrés Manuel Vera, Keith R Weninger, Bettina Wünsch, Inna S Yanez-Orozco, Jens Michaelis, Claus A M Seidel, Timothy D Craggs, Thorsten Hugel
Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s...
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171251/comprehensive-mapping-of-ubiquitination
#7
Allison Doerr
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171250/crispr-and-immunity
#8
Nicole Rusk
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171249/absorption-based-multicolor-imaging
#9
Rita Strack
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171248/expansion-of-the-transgenic-toolkit-in-mouse
#10
Nina Vogt
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171247/organoid-hosts-for-parasitic-infection
#11
Tal Nawy
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171246/improved-photoacoustic-imaging-probes
#12
Rita Strack
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171245/three-tissues-to-gastrulation
#13
Tal Nawy
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171244/the-whole-fly-brain-in-detail
#14
Nina Vogt
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171243/profiling-the-dress-codes-of-rna-binding-proteins
#15
Vivien Marx
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171242/easing-the-burden-of-code-review
#16
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171241/toward-a-3d-genome-in-high-resolution
#17
Nicole Rusk
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171240/improving-probes-for-super-resolution
#18
Regan P Moore, Wesley R Legant
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171239/a-path-to-predict-rna-tertiary-structures
#19
Lei Tang
No abstract text is available yet for this article.
September 2018: Nature Methods
https://www.readbyqxmd.com/read/30171238/taking-inventory-with-shotgun-em
#20
Allison Doerr
No abstract text is available yet for this article.
September 2018: Nature Methods
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