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Nature Protocols

Edoardo Balzani, Matteo Falappa, Fuat Balcà, Valter Tucci
Genetically modified mice are used as models for a variety of human behavioral conditions. However, behavioral phenotyping can be a major bottleneck in mouse genetics because many of the classic protocols are too long and/or are vulnerable to unaccountable sources of variance, leading to inconsistent results between centers. We developed a home-cage approach using a Chora feeder that is controlled by-and sends data to-software. In this approach, mice are tested in the standard cages in which they are held for husbandry, which removes confounding variables such as the stress induced by out-of-cage testing...
June 2018: Nature Protocols
Julia Vergalli, Estelle Dumont, Jelena Pajović, Bertrand Cinquin, Laure Maigre, Muriel Masi, Matthieu Réfrégiers, Jean-Marie Pagés
The efficacy of antibacterial molecules depends on their capacity to reach inhibitory concentrations in the vicinity of their target. This is particularly challenging for drugs directed against Gram-negative bacteria, which have a complex envelope comprising two membranes and efflux pumps. Precise determination of the bacterial drug content is an essential prerequisite for drug development. Here we describe three approaches that have been developed in our laboratories to quantify drugs accumulated in intact cells by spectrofluorimetry, microspectrofluorimetry, and kinetics microspectrofluorimetry (KMSF)...
June 2018: Nature Protocols
Rafael Laso-Pérez, Viola Krukenberg, Florin Musat, Gunter Wegener
Traditionally, the description of microorganisms starts with their isolation from an environmental sample. Many environmentally relevant anaerobic microorganisms grow very slowly, and often they rely on syntrophic interactions with other microorganisms. This impedes their isolation and characterization by classic microbiological techniques. We developed and applied an approach for the successive enrichment of syntrophic hydrocarbon-degrading microorganisms from environmental samples. We collected samples from microbial mat-covered hydrothermally heated hydrocarbon-rich sediments of the Guaymas Basin and mixed them with synthetic mineral medium to obtain sediment slurries...
June 2018: Nature Protocols
Andrew J Modzelewski, Sean Chen, Brandon J Willis, K C Kent Lloyd, Joshua A Wood, Lin He
CRISPR/Cas9 technology has transformed mouse genome editing with unprecedented precision, efficiency, and ease; however, the current practice of microinjecting CRISPR reagents into pronuclear-stage embryos remains rate-limiting. We thus developed CRISPR ribonucleoprotein (RNP) electroporation of zygotes (CRISPR-EZ), an electroporation-based technology that outperforms pronuclear and cytoplasmic microinjection in efficiency, simplicity, cost, and throughput. In C57BL/6J and C57BL/6N mouse strains, CRISPR-EZ achieves 100% delivery of Cas9/single-guide RNA (sgRNA) RNPs, facilitating indel mutations (insertions or deletions), exon deletions, point mutations, and small insertions...
June 2018: Nature Protocols
Simon Weiler, Joel Bauer, Mark Hübener, Tobias Bonhoeffer, Tobias Rose, Volker Scheuss
In vivo two-photon calcium imaging provides detailed information about the activity and response properties of individual neurons. However, in vitro methods are often required to study the underlying neuronal connectivity and physiology at the cellular and synaptic levels at high resolution. This protocol provides a fast and reliable workflow for combining the two approaches by characterizing the response properties of individual neurons in mice in vivo using genetically encoded calcium indicators (GECIs), followed by retrieval of the same neurons in brain slices for further analysis in vitro (e...
June 2018: Nature Protocols
Gunsagar S Gulati, Matthew P Murphy, Owen Marecic, Michael Lopez, Rachel E Brewer, Lauren S Koepke, Anoop Manjunath, Ryan C Ransom, Ankit Salhotra, Irving L Weissman, Michael T Longaker, Charles K F Chan
There are limited methods available to study skeletal stem, progenitor, and progeny cell activity in normal and diseased contexts. Most protocols for skeletal stem cell isolation are based on the extent to which cells adhere to plastic or whether they express a limited repertoire of surface markers. Here, we describe a flow cytometry-based approach that does not require in vitro selection and that uses eight surface markers to distinguish and isolate mouse skeletal stem cells (mSSCs); bone, cartilage, and stromal progenitors (mBCSPs); and five downstream differentiated subtypes, including chondroprogenitors, two types of osteoprogenitors, and two types of hematopoiesis-supportive stroma...
June 2018: Nature Protocols
Peter Chovanec, Daniel J Bolland, Louise S Matheson, Andrew L Wood, Felix Krueger, Simon Andrews, Anne E Corcoran
For high-throughput sequencing and quantification of immunoglobulin repertoires, most methodologies use RNA. However, output varies enormously between recombined genes due to different promoter strengths and differential activation of lymphocyte subsets, precluding quantitation of recombinants on a per-cell basis. To date, DNA-based approaches have used V gene primer cocktails, with substantial inherent biases. Here, we describe VDJ sequencing (VDJ-seq), which accurately quantitates immunoglobulin diversity at the DNA level in an unbiased manner...
June 2018: Nature Protocols
Matthew J Smola, Kevin M Weeks
This protocol is an extension to: Nat. Protoc. 10, 1643-1669 (2015); doi:10.1038/nprot.2015.103; published online 01 October 2015RNAs play key roles in many cellular processes. The underlying structure of RNA is an important determinant of how transcripts function, are processed, and interact with RNA-binding proteins and ligands. RNA structure analysis by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) takes advantage of the reactivity of small electrophilic chemical probes that react with the 2'-hydroxyl group to assess RNA structure at nucleotide resolution...
June 2018: Nature Protocols
Liwei Cao, Jolene K Diedrich, Yuanhui Ma, Nianshuang Wang, Matthias Pauthner, Sung-Kyu Robin Park, Claire M Delahunty, Jason S McLellan, Dennis R Burton, John R Yates, James C Paulson
N-glycans contribute to the folding, stability and functions of the proteins they decorate. They are produced by transfer of the glycan precursor to the sequon Asn-X-Thr/Ser, followed by enzymatic trimming to a high-mannose-type core and sequential addition of monosaccharides to generate complex-type and hybrid glycans. This process, mediated by the concerted action of multiple enzymes, produces a mixture of related glycoforms at each glycosite, making analysis of glycosylation difficult. To address this analytical challenge, we developed a robust semiquantitative mass spectrometry (MS)-based method that determines the degree of glycan occupancy at each glycosite and the proportion of N-glycans processed from high-mannose type to complex type...
June 2018: Nature Protocols
Jia-Xing Yue, Gianni Liti
Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process...
June 2018: Nature Protocols
Franziska Pfeiffer, Fabian Tolle, Malte Rosenthal, Gerhard Markus Brändle, Jörg Ewers, Günter Mayer
Aptamers are single-stranded oligonucleotides that are in vitro-selected to recognize their target molecule with high affinity and specificity. As they consist of the four canonical nucleobases, their chemical diversity is limited, which in turn limits the addressable target spectrum. Introducing chemical modifications into nucleic acid libraries increases the interaction capabilities of the DNA and thereby the target spectrum. Here, we describe a protocol to select nucleobase-modified aptamers by using click chemistry (CuAAC) to introduce the preferred chemical modification...
May 2018: Nature Protocols
Taras A Redchuk, Andrii A Kaberniuk, Vladislav V Verkhusha
Near-infrared (NIR, 740-780 nm) optogenetic systems are well-suited to spectral multiplexing with blue-light-controlled tools. Here, we present two protocols, one for regulation of gene transcription and another for control of protein localization, that use a NIR-responsive bacterial phytochrome BphP1-QPAS1 optogenetic pair. In the first protocol, cells are transfected with the optogenetic constructs for independently controlling gene transcription by NIR (BphP1-QPAS1) and blue (LightOn) light. The NIR and blue-light-controlled gene transcription systems show minimal spectral crosstalk and induce a 35- to 40-fold increase in reporter gene expression...
May 2018: Nature Protocols
Jonas Paulsen, Tharvesh Moideen Liyakat Ali, Philippe Collas
Chrom3D is a computational platform for 3D genome modeling that simulates the spatial positioning of chromosome domains relative to each other and relative to the nuclear periphery. In Chrom3D, chromosomes are modeled as chains of contiguous beads, in which each bead represents a genomic domain. In this protocol, a bead represents a topologically associated domain (TAD) mapped from ensemble Hi-C data. Chrom3D takes as input data significant pairwise TAD-TAD interactions determined from a Hi-C contact matrix, and TAD interactions with the nuclear periphery, determined by ChIP-sequencing of nuclear lamins to define lamina-associated domains (LADs)...
May 2018: Nature Protocols
Kallol Gupta, Jingwen Li, Idlir Liko, Joseph Gault, Cherine Bechara, Di Wu, Jonathan T S Hopper, Kevin Giles, Justin L P Benesch, Carol V Robinson
With the recent success in determining membrane protein structures, further detailed understanding of the identity and function of the bound lipidome is essential. Using an approach that combines high-energy native mass spectrometry (HE-nMS) and solution-phase lipid profiling, this protocol can be used to determine the identity of the endogenous lipids that directly interact with a protein. Furthermore, this method can identify systems in which such lipid binding has a major role in regulating the oligomeric assembly of membrane proteins...
May 2018: Nature Protocols
Hadi T Nia, Meenal Datta, Giorgio Seano, Peigen Huang, Lance L Munn, Rakesh K Jain
Solid stress, distinct from both tissue stiffness and fluid pressure, is a mechanical stress that is often elevated in both murine and human tumors. The importance of solid stress in tumor biology has been recognized in initial studies: solid stress promotes tumor progression and lowers the efficacy of anticancer therapies by compressing blood vessels and contributing to hypoxia. However, robust, reproducible, and objective methods that go beyond demonstration and bulk measurements have not yet been established...
May 2018: Nature Protocols
Katarzyna B Handing, Ewa Niedzialkowska, Ivan G Shabalin, Misty L Kuhn, Heping Zheng, Wladek Minor
Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies...
May 2018: Nature Protocols
Keyin Liu, Xiuqi Kong, Yanyan Ma, Weiying Lin
Carbon monoxide (CO) is a key gaseous signaling molecule in living cells and organisms. This protocol illustrates the synthesis of a highly sensitive Nile Red (NR)-Pd-based fluorescent probe, NR-PdA, and its applications for detecting endogenous CO in tissue culture cells, ex vivo organs, and zebrafish embryos. In the NR-PdA synthesis process, 3-diethylamine phenol reacts with sodium nitrite in the acidic condition to afford 5-(diethylamino)-2-nitrosophenol hydrochloride (compound 1), which is further treated with 1-naphthalenol at a high temperature to provide the NR dye via a cyclization reaction...
May 2018: Nature Protocols
David Lando, Srinjan Basu, Tim J Stevens, Andy Riddell, Kai J Wohlfahrt, Yang Cao, Wayne Boucher, Martin Leeb, Liam P Atkinson, Steven F Lee, Brian Hendrich, Dave Klenerman, Ernest D Laue
Fluorescence imaging and chromosome conformation capture assays such as Hi-C are key tools for studying genome organization. However, traditionally, they have been carried out independently, making integration of the two types of data difficult to perform. By trapping individual cell nuclei inside a well of a 384-well glass-bottom plate with an agarose pad, we have established a protocol that allows both fluorescence imaging and Hi-C processing to be carried out on the same single cell. The protocol identifies 30,000-100,000 chromosome contacts per single haploid genome in parallel with fluorescence images...
May 2018: Nature Protocols
Yu Liu, Erik Holmstrom, Ping Yu, Kemin Tan, Xiaobing Zuo, David J Nesbitt, Rui Sousa, Jason R Stagno, Yun-Xing Wang
Site-specific incorporation of labeled nucleotides is an extremely useful synthetic tool for many structural studies (e.g., NMR, electron paramagnetic resonance (EPR), fluorescence resonance energy transfer (FRET), and X-ray crystallography) of RNA. However, specific-position-labeled RNAs >60 nt are not commercially available on a milligram scale. Position-selective labeling of RNA (PLOR) has been applied to prepare large RNAs labeled at desired positions, and all the required reagents are commercially available...
May 2018: Nature Protocols
Matthew C Canver, Maximilian Haeussler, Daniel E Bauer, Stuart H Orkin, Neville E Sanjana, Ophir Shalem, Guo-Cheng Yuan, Feng Zhang, Jean-Paul Concordet, Luca Pinello
CRISPR (clustered regularly interspaced short palindromic repeats) genome-editing experiments offer enormous potential for the evaluation of genomic loci using arrayed single guide RNAs (sgRNAs) or pooled sgRNA libraries. Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target potential. In addition, computational tools have been developed to analyze deep-sequencing data resulting from genome-editing experiments. However, these tools are typically developed in isolation and oftentimes are not readily translatable into laboratory-based experiments...
May 2018: Nature Protocols
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