Tuesday, January 31, 2017

Nature Methods Contents: February 2016 Volume 14 pp 97 - 207

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February 2017 Volume 14, Issue 2

In This Issue
This Month
Research Highlights
Technology Feature
News and Views
Brief Communications

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Nature Milestones: Antibodies

Nature Milestones: Antibodies chronicles the history of antibodies from their earliest description in antisera, their structure, generation and function, right through to their recent application in cancer immunotherapy. It also includes a timeline and a collection of seminal papers reproduced from Springer Nature. 

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Produced with support from: 

nature.com webcasts

Pixels to data: Quantitative cell biology using high-content imaging and analysis.

Date: Tuesday 28 February 2017

Time: 8AM PST, 11AM EST, 4PM GMT, 5PM CET 



In This Issue


In This Issue   



Stand up for science   p97
Uncertainty reigns in many domains as the Trump administration takes power. Science is no exception. Federal support for biological research must continue. And scientists must not be silenced by political pressure.

This Month


The Author File: Hyongbum (Henry) Kim   p99
Swimming to a way of testing thousands of guide RNAs at once.



Multicut brings automated neurite segmentation closer to human performance   pp101 - 102
Thorsten Beier, Constantin Pape, Nasim Rahaman, Timo Prange, Stuart Berg et al.

eC-CLEM: flexible multidimensional registration software for correlative microscopies   pp102 - 103
Perrine Paul-Gilloteaux, Xavier Heiligenstein, Martin Belle, Marie-Charlotte Domart, Banafshe Larijani et al.

Research Highlights


Native chromosome conformation
Isolation of nuclei in an isotonic buffer retains chromosome loops and allows the probing of intrinsic loop conformation.

Designer proteases for post-translational modifications
Researchers have engineered a protease specific for a post-translational modification.

Stem cells from the young and old
Donor age impacts the epigenetic state and mutational burden of induced pluripotent stem cells.

Putting the brakes on CRISPR-Cas9
Researchers identify biological inhibitors of Cas9 nuclease activity and block genome editing in cultured human cells.

Genetic tools for magnetic resonance imaging
Genetically encoded reporters can be used for noninvasive cell tracking or molecular imaging with magnetic resonance imaging technologies.

Methods in Brief

A functional assay for promoters | Count on FRET for stoichiometry | Probing protein mechanics with an electric field | Optimized optical recordings of voltage sensors

Tools in Brief

Special delivery for live-cell imaging | Stretchable multichannel wireless implants | Many models of microbial metabolism | Nanopore-based protein fingerprinting

JOBS of the week
Postdoctoral Researchers
Institute of Animal Physiology and Genetics, Czech Academy of Sciences
Associate Research Scientist
Columbia University
Postdoctoral Position at USC
University of Southern California
Professorship in Biological Sciences
University of Southampton
Interdisciplinary Postdoctoral Fellowship in Tumor Biology
Johns Hopkins University
More Science jobs from
Methods in Computational Neuroscience
Woods Hole, USA
More science events from



Win-win data sharing in neuroscience   pp112 - 116
Giorgio A Ascoli, Patricia Maraver, Sumit Nanda, Sridevi Polavaram and Rubén Armañanzas
In this Commentary, Ascoli et al. discuss recipes for setting up public data sharing initiatives based on their experiences with NeuroMorpho.Org.

Technology Feature


Pursuing the simple life   pp117 - 121
Michael Eisenstein
Efforts to pare away cellular genomes are yielding streamlined biosynthetic factories and deeper insights into the core processes of biology.

News and Views


Cool and dynamic: single-molecule fluorescence-based structural biology   pp123 - 124
Timothy D Craggs
New methods exploit single-molecule measurements to study protein structure and dynamics.

See also: Brief Communication by Weisenburger et al. | Article by Hellenkamp et al.



How best to identify chromosomal interactions: a comparison of approaches   pp125 - 134
James O J Davies, A Marieke Oudelaar, Douglas R Higgs and Jim R Hughes
In this Review, the authors compare commonly used chromosome conformation capture techniques, describing their respective strengths and weaknesses, and provide advice for the end user on which approach and analysis method to use.



Simulation-based comprehensive benchmarking of RNA-seq aligners   pp135 - 139
Giacomo Baruzzo, Katharina E Hayer, Eun Ji Kim, Barbara Di Camillo, Garret A FitzGerald et al.
Benchmarking on synthetic data reveals differences between common RNA-seq alignment software tools, particularly for complex genomic regions.

Brief Communications


Cryogenic optical localization provides 3D protein structure data with Angstrom resolution   pp141 - 144
Siegfried Weisenburger, Daniel Boening, Benjamin Schomburg, Karin Giller, Stefan Becker et al.
The positions of fluorophores can be localized in single proteins with Angstrom-scale resolution using Cryogenic Optical Localization in 3D (COLD), a complementary approach to traditional structural biology techniques.

See also: News and Views by Craggs

cGAL, a temperature-robust GAL4-UAS system for Caenorhabditis elegans   pp145 - 148
Han Wang, Jonathan Liu, Shahla Gharib, Cynthia M Chai, Erich M Schwarz et al.
Standardized driver and effector lines that use optimized GAL4 from a cryophilic yeast species enable bipartite control of transgene expression in Caenorhabditis elegans.

Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging   pp149 - 152
Francesco Cutrale, Vikas Trivedi, Le A Trinh, Chi-Li Chiu, John M Choi et al.
Hyper-Spectral Phasors allow unmixing of multiple signals even under conditions with low signal-to-noise ratios, and they enable highly multiplexed 5D imaging of live zebrafish embryos labeled with conventional fluorophores.

Focus on the neuroscience toolbox 

Nature Neuroscience presents a special focus issue on the neuroscience toolbox highlighting recent technological advances, approaches and collaborative initiatives that are enabling new avenues of research. 

Access the Focus free online for six months

Produced with support from: 
The Kavli Foundation



In vivo high-throughput profiling of CRISPR-Cpf1 activity   pp153 - 159
Hui K Kim, Myungjae Song, Jinu Lee, A Vipin Menon, Soobin Jung et al.
A lentiviral library expressing Cpf1 guide RNAs and containing target sequences allows high-throughput profiling of highly active guide RNAs and is the basis for cindel, a webtool to predict the activity at any given target sequence.

Control of cerebral ischemia with magnetic nanoparticles   pp160 - 166
Jie-Min Jia, Praveen D Chowdary, Xiaofei Gao, Bo Ci, Wenjun Li et al.
Stroke is often modeled in rodents by surgically occluding vessels. SIMPLE is an alternative approach that involves the magnet-induced accumulation of nanoparticles. Because of its reversible nature, this method can be used to study both occlusion and subsequent reperfusion of blood vessels.

Scalable whole-genome single-cell library preparation without preamplification   pp167 - 173
Hans Zahn, Adi Steif, Emma Laks, Peter Eirew, Michael VanInsberghe et al.
Direct library preparation (DLP) is a robust and economic method for preparing large numbers of single-cell whole-genome sequencing libraries without preamplification, to study copy-number heterogeneity at the cell level and other variant types at the clone or population level.

Multidomain structure and correlated dynamics determined by self-consistent FRET networks   pp174 - 180
Björn Hellenkamp, Philipp Wortmann, Florian Kandzia, Martin Zacharias and Thorsten Hugel
A hybrid approach merges networks of time-correlated distances determined by single-molecule FRET to uncover local and global dynamics of the multidomain protein Hsp90 in solution at multiple timescales.

See also: News and Views by Craggs

In vivo quantification of spatially varying mechanical properties in developing tissues   pp181 - 186
Friedhelm Serwane, Alessandro Mongera, Payam Rowghanian, David A Kealhofer, Adam A Lucio et al.
The mechanical properties of tissues can be measured by deforming magnetically responsive microdroplets that are implanted in the tissue. Serwane et al. apply this method to study the mechanical properties of tissues in the living zebrafish embryo.

Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli   pp187 - 194
Daniel C Sévin, Tobias Fuhrer, Nicola Zamboni and Uwe Sauer
A method to screen proteins for enzymatic activity by incubating purified or overexpressed proteins with a metabolite extract and measuring changes in metabolite abundance using mass spectrometry enables high-throughput characterization of functionally uncharacterized proteins in Escherichia coli.

Rapidly evolving homing CRISPR barcodes   pp195 - 200
Reza Kalhor, Prashant Mali and George M Church
Homing guide RNAs that target Cas9 to their own loci generate diverse barcodes that can trace the lineage of cells.

RESA identifies mRNA-regulatory sequences at high resolution   pp201 - 207
Valeria Yartseva, Carter M Takacs, Charles E Vejnar, Miler T Lee and Antonio J Giraldez
The RNA-element selection assay (RESA) probes regulatory elements in vivo and identifies protein binding partners and the nucleotides that contribute most to the regulation.

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