Methods

idtracker.ai: tracking all individuals in small or large collectives of unmarked animals idtracker.ai: tracking all individuals in small or large collectives of unmarked animals, Published online: 14 January 2019; doi:10.1038/s41592-018-0295-5 The idtracker.ai software tracks freely moving animals in large groups of up to 100 individuals. The tool is versatile and has been applied to groups
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A robust and versatile platform for image scanning microscopy enabling super-resolution FLIM A robust and versatile platform for image scanning microscopy enabling super-resolution FLIM, Published online: 14 January 2019; doi:10.1038/s41592-018-0291-9 A single-photon detector array enables robust and versatile image scanning microscopy (ISM) on any confocal microscope. This implementation makes super-resolution FLIM possible and eases a
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Publication date: Available online 2 November 2018 Source: Methods Author(s): Prabuddha Waduge, Yogo Sakakibara, Christine S. Chow Abstract Among different RNA modifications, the helix 69 (H69) region of the bacterial ribosomal RNA (rRNA) contains three pseudouridines (Ψs). H69 is functionally important due to its location in the heart of the ribosome. Several structural and functional
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Publication date: Available online 2 November 2018 Source: Methods Author(s): Poonam R. Pandey, Pranita K. Rout, Aniruddha Das, Myriam Gorospe, Amaresh C. Panda Abstract Recent developments in high-throughput RNA sequencing methods coupled with innovative bioinformatic tools have uncovered thousands of circular (circ)RNAs. CircRNAs have emerged as a vast and novel class of regulatory RNAs with
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Publication date: Available online 30 October 2018 Source: Methods Author(s): Andrea Tanzer, Ivo L. Hofacker, Ronny Lorenz Abstract Chemical modifications of RNA nucleotides change their identity and characteristics and thus alter genetic and structural information encoded in the genomic DNA. tRNA and rRNA are probably the most heavily modified genes, and often depend on derivatization
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Publication date: Available online 28 October 2018 Source: Methods Author(s): Kaouthar Slama, Aurellia Galliot, Franziska Weichmann, Jasmin Hertler, Regina Feederle, Gunter Meister, Mark Helm Abstract In the growing field of RNA modification, precipitation techniques using antibodies play an important role. However, little is known about their specificities and protocols are missing to assess their effectiveness.
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Publication date: Available online 28 October 2018 Source: Methods Author(s): Joseph Hwang, Munmun Banerjee, Adam S. Venable, Zara Walden, John Jolly, Cathleen Zimmerman, Elizabeth Adkisson, Qiang Xiao Abstract Quantitation of biomarkers in biofluids plays a central role in basic research to management of patient care and is routinely used in clinical laboratories and academic institutions.
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Publisher Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR Publisher Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR, Published online: 02 January 2019; doi:10.1038/s41592-018-0300-z Publisher Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR
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Publication date: Available online 26 October 2018 Source: Methods Author(s): Hussain Jinnah, Randi J. Ulbricht Abstract The deamination of adenosine to inosine by RNA editing is a widespread post-transcriptional process that expands genetic diversity. Selective substitution of inosine for adenosine in pre-mRNA transcripts can alter splicing, mRNA stability, and the amino acid sequence of the
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Author Correction: Faster, sharper, and deeper: structured illumination microscopy for biological imaging Author Correction: Faster, sharper, and deeper: structured illumination microscopy for biological imaging, Published online: 29 December 2018; doi:10.1038/s41592-018-0296-4 Author Correction: Faster, sharper, and deeper: structured illumination microscopy for biological imaging
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Publication date: Available online 26 October 2018 Source: Methods Author(s): Cody M. Palumbo, Peter A. Beal Abstract Over 150 unique RNA modifications are now known including several nonstandard nucleotides present in the body of messenger RNAs. These modifications can alter a transcript’s function and are collectively referred to as the epitrancriptome. Chemically modified nucleoside analogs
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Publication date: Available online 22 October 2018 Source: Methods Author(s): Giulia Fabozzi, Amarendra Pegu, Richard A. Koup, Constantinos Petrovas Abstract Bispecific (bs) antibodies (Abs, bsAbs) are engineered immunoglobulins that contain two different antigen-binding sites in one molecule. bsAbs can be divided in two molecular formats; the IgG-like and non-IgG like. The structural elements of each
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Publication date: Available online 24 October 2018 Source: Methods Author(s): Peter A. Lobue, Ningxi Yu, Manasses Jora, Scott Abernathy, Patrick A. Limbach Abstract Research into post-transcriptional processing and modification of RNA continues to speed forward, as their ever-emerging role in the regulation of gene expression in biological systems continues to unravel. Liquid chromatography tandem mass
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Publication date: Available online 24 October 2018 Source: Methods Author(s): Felix Bormann, Francesca Tuorto, Cansu Cirzi, Frank Lyko, Carine Legrand Abstract RNA cytosine-5 methylation (m5C) has emerged as a key epitranscriptomic mark, which fulfills multiple roles in structural modulation, stress signaling and the regulation of protein translation. Bisulfite sequencing is currently the most accurate and
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Publication date: Available online 23 October 2018 Source: Methods Author(s): Gregory L. Moore, Matthew J. Bernett, Rumana Rashid, Erik W. Pong, Duc-Hanh T. Nguyen, Jonathan Jacinto, Araz Eivazi, Alex Nisthal, Juan E. Diaz, Seung Y. Chu, Umesh S. Muchhal, John R. Desjarlais Abstract Bispecific monoclonal antibodies can bind two protein targets simultaneously and enable therapeutic
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Publication date: Available online 23 October 2018 Source: Methods Author(s): Aldema Sas-Chen, Schraga Schwartz Abstract Post-transcriptional modification on mRNA has become a field of intense interest in recent years, and next-generation sequencing based technologies are constantly emerging to detect an increasing number of modifications at a transcriptome-wide level. Some of these approaches are based on
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Publication date: Available online 22 October 2018 Source: Methods Author(s): Jeanesse Scerri, Shawn Baldacchino, Christian Saliba, Christian Scerri, Godfrey Grech Abstract Patient stratification, prognosis and disease monitoring are three important aspects of personalized cancer medicine. With traditional serum tumour protein biomarkers showing lack of specificity and sensitivity, and tumour heterogeneity affecting the response to targeted
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Circuit interrogation in freely moving animals Circuit interrogation in freely moving animals, Published online: 20 December 2018; doi:10.1038/s41592-018-0275-9 Developments in imaging tools are making it possible to record activity from both large neuronal populations and subcellular components in freely moving animals. Although these developments are enabling relationships between brain activity and complex behaviors to be
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Reliability of human cortical organoid generation Reliability of human cortical organoid generation, Published online: 20 December 2018; doi:10.1038/s41592-018-0255-0 A protocol adapted to xeno- and feeder-free conditions is shown to generate reliable and consistent cortical brain organoids across differentiations and source stem cell lines, making it suitable for disease modeling and other applications.
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Long-read sequence and assembly of segmental duplications Long-read sequence and assembly of segmental duplications, Published online: 17 December 2018; doi:10.1038/s41592-018-0236-3 Segmental Duplication Assembler (SDA) uses long sequence reads to resolve segmental duplications that are collapsed in current genome assemblies. These assemblies correspond in total to the length of an average human chromosome.
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Multiplexed orthogonal genome editing and transcriptional activation by Cas12a Multiplexed orthogonal genome editing and transcriptional activation by Cas12a , Published online: 17 December 2018; doi:10.1038/s41592-018-0262-1 The length of the guide RNA for Cas12a-VPR determines whether a target gene is edited or activated and allows for multiplexed, combinatorial gene modifications.
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Imaging cellular ultrastructures using expansion microscopy (U-ExM) Imaging cellular ultrastructures using expansion microscopy (U-ExM), Published online: 17 December 2018; doi:10.1038/s41592-018-0238-1 U-ExM enables near-native expansion microscopy of samples in vitro and in cells. The combination of U-ExM with confocal microscopy and HyVolution revealed details of centriole chirality that were previously accessible only by electron microscopy.
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Deep learning enables cross-modality super-resolution in fluorescence microscopy Deep learning enables cross-modality super-resolution in fluorescence microscopy, Published online: 17 December 2018; doi:10.1038/s41592-018-0239-0 Deep learning enables cross-modality super-resolution imaging, including confocal-to-STED and TIRF-to-TIRF-SIM image transformation. Imaging of a larger FOV and greater depth of field is possible with higher resolution and SNR at lower light doses.
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U-Net: deep learning for cell counting, detection, and morphometry U-Net: deep learning for cell counting, detection, and morphometry, Published online: 17 December 2018; doi:10.1038/s41592-018-0261-2 A user-friendly ImageJ plugin enables the application and training of U-Nets for deep-learning-based image segmentation, detection and classification tasks with minimal labeling requirements.
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Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells, Published online: 17 December 2018; doi:10.1038/s41592-018-0259-9 DART-seq alters droplet sequencing in a simple and flexible way to simultaneously profile the transcriptome and multiplexed targeted RNAs, such as viral transcripts and immunoglobulin chains, in single cells.
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Yamuna Krishnan Yamuna Krishnan, Published online: 10 December 2018; doi:10.1038/s41592-018-0263-0 A probe for a journey into bubbles and why it’s good to be both inventor and discoverer.
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A pH-correctable, DNA-based fluorescent reporter for organellar calcium A pH-correctable, DNA-based fluorescent reporter for organellar calcium, Published online: 10 December 2018; doi:10.1038/s41592-018-0232-7 The DNA-based, ratiometric fluorescent reporter CalipHluor enables quantitative imaging of pH and calcium in acidic organelles with single-organelle resolution. The probe was used to identify a lysosome-specific Ca2+ importer in animals.
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fMRIPrep: a robust preprocessing pipeline for functional MRI fMRIPrep: a robust preprocessing pipeline for functional MRI, Published online: 10 December 2018; doi:10.1038/s41592-018-0235-4 fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
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Publication date: Available online 4 October 2018 Source: Methods Author(s): Soohyun Kim, Hyori Kim, Dong Hyun Jo, Jeong Hun Kim, Su Ree Kim, Dongmin Kang, Dobeen Hwang, Junho Chung Abstract Antibody selection for antibody-drug conjugates (ADCs) has traditionally depended on its internalization into the target cell, although ADC efficacy also relies on recycling of the
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Publication date: Available online 5 October 2018 Source: Methods Author(s): Ines Rodrigues Lopes, Ricardo Jorge Silva, Ines Caramelo, Ana Eulalio, Miguel Mano Abstract MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally modulate gene expression and orchestrate a wide range of biological and pathological processes. The use of high-throughput screening technologies, in particular microscopy-based screenings (also
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Publication date: Available online 9 October 2018 Source: Methods Author(s): Shobbir Hussain Abstract Well over a hundred types of naturally occurring covalent modifications can be made to ribonucleotides in RNA molecules. Moreover, several types of such modifications are each known to be catalysed by multiple enzymes which largely appear to modify distinct sites within the
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Publication date: Available online 9 October 2018 Source: Methods Author(s): Azeet Narayan, Rofina Johnkennedy, Maheen Zakaria, Victor Lee, Abhijit A. Patel Abstract META RNA profiling is a simple and inexpensive method to measure the expression of multiple targeted RNAs across many samples. By assigning sample-specific tags up-front during reverse-transcription, cDNAs from multiple samples can be
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Publication date: Available online 22 October 2018 Source: Methods Author(s): Jessica F. Williams, Simon G.J. Mochrie, Megan C. King Abstract Nuclear morphology is indicative of cellular health in many contexts. In order to robustly and quantitatively measure nuclear size and shape, numerous experimental methods leveraging fluorescence microscopy have been developed. While these methods are useful
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Publication date: Available online 13 October 2018 Source: Methods Author(s): Hirotake Shiraiwa, Atsushi Narita, Mika Kamata-Sakurai, Takahiro Ishiguro, Yuji Sano, Naoka Hironiwa, Takashi Tsushima, Hiroaki Segawa, Toshiaki Tsunenari, Yosuke Ikeda, Yoko Kayukawa, Mizuho Noguchi, Tetsuya Wakabayashi, Akihisa Sakamoto, Hiroko Konishi, Taichi Kuramochi, Mika Endo, Kunihiro Hattori, Junichi Nezu, Tomoyuki Igawa Abstract The antibody drug market
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Publication date: Available online 9 October 2018 Source: Methods Author(s): Lei Han, Huifang Zong, Yuexian Zhou, Zhidi Pan, Jie Chen, Kai Ding, Yueqing Xie, Hua Jiang, Baohong Zhang, Huili Lu, John Gilly, Jianwei Zhu Abstract High product purity, preserving natural IgG architecture, and excellent production efficiency are highly desirable in bispecific antibody manufacturing. We have
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Publication date: 1 October 2018 Source: Methods, Volume 149 Author(s): Benjamin H. Mullish, Alexandros Pechlivanis, Grace F. Barker, Mark R. Thursz, Julian R. Marchesi, Julie A.K. McDonald Abstract There is an ever-increasing recognition that bile acids are not purely simple surfactant molecules that aid in lipid digestion, but are a family of molecules contributing to
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