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Nature Methods Contents: March 2018, Volume 15 No 3 pp 151 - 227

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Nature Methods

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TABLE OF CONTENTS

March 2018 Volume 15, Issue 3

Editorial
This Month
Correspondence
Research Highlights
Technology Feature
News and Views
Perspective
Brief Communications
Articles
Erratum
Corrigenda
 
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Nature Collection: 2017 Nobel Prize in Physiology or Medicine

The 2017 Nobel Prize in Physiology or Medicine was awarded to Jeffrey C. Hall, Michael Rosbash and Michael W. Young for their pioneering work in Drosophila that elucidated the molecular mechanisms controlling circadian rhythm. 

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Produced with support from: 
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npj Molecular Phenomics is an online-only, open access journal that provides a forum for cutting-edge scientific advances in the emerging field of phenomics, the study of the physical and chemical characteristics of an individual in quantitative terms. Part of the Nature Partner Journals series, npj Molecular Phenomics is published in partnership with Fudan University. The journal is now open for submissions.
 
 

Editorial

Top

Sharing epigenomes globally   p151
doi:10.1038/nmeth.4630
Epigenome reference data are continually being enriched—researchers should explore them, even if raw data access still presents some hurdles.
 

This Month

Top

The Author File: Miguel Angel Esteban   p153
Vivien Marx
doi:10.1038/nmeth.4626
A way to study the RNA interactome, baby RNA encounters, a sprinkle of poetry.
 

Correspondence

Top

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data   pp155 - 156
Caleb A Lareau and Martin J Aryee
doi:10.1038/nmeth.4583
 

Picky: a simple online PRM and SRM method designer for targeted proteomics   pp156 - 157
Henrik Zauber, Marieluise Kirchner and Matthias Selbach
doi:10.1038/nmeth.4607
 

Research Highlights

Top

Gas vesicles enable ultrasound imaging
Acoustic reporter genes that produce gas vesicles offer a way to image and locate microorganisms in mammalian hosts.

Tracking the protein-metabolite interactome
A method combining limited proteolysis with mass spectrometry systematically detects protein-metabolite interactions.

Gene factories made of droplets
How to make large synthetic gene libraries out of some beads, an oligo array and an emulsion.

Imaging allelic loci in live cells
SNP-CLING enables determining the dynamics of alleles on different chromosomes in live cells.

Transcriptomics in the NICHE
The combination of photoactivatable fluorescent markers with single-cell RNA-seq allows transcriptome analysis of cells from specific tissue locations.

Methods in Brief

Top

Cas goes rogue | Tilted light-sheet microscopy with 3D point-spread functions | Light-based RNA structure probing | Antibody function revealed in high throughput

Tools in Brief

Top

The Protein Contacts Atlas | A four-armed patch-clamping robot | An expanded set of full-length microbial marker genes | Tracking nanoparticles by eye

Methods
JOBS of the week
Dean of the Faculty of Science
The Chinese University of Hong Kong
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Columbia University
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Research Group Leader Opening
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Technology Feature

Top

Putting microfluidics in other people's hands   pp167 - 170
Vivien Marx
doi:10.1038/nmeth.4609
In microfluidics, sharing is hard. But practitioners are exploring new ways to share designs, devices and experience.
 

News and Views

Top

RNA dynamics revealed by metabolic RNA labeling and biochemical nucleoside conversions   pp171 - 172
Marisa A P Baptista and Lars Dölken
doi:10.1038/nmeth.4608
The combination of metabolic RNA labeling with biochemical nucleoside conversion now adds a broadly applicable temporal dimension to RNA sequencing.

See also: Article by Schofield et al.

Perspective

Top

STED super-resolved microscopy   pp173 - 182
Giuseppe Vicidomini, Paolo Bianchini and Alberto Diaspro
doi:10.1038/nmeth.4593
This Perspective reviews nanoscopy via stimulated emission depletion (STED), focusing on challenges for biologists and how technical advances are helping to meet these challenges.
 

Brief Communications

Top

EVIR: chimeric receptors that enhance dendritic cell cross-dressing with tumor antigens   pp183 - 186
Mario Leonardo Squadrito, Chiara Cianciaruso, Sarah K Hansen and Michele De Palma
doi:10.1038/nmeth.4579
Chimeric receptors expressed on the surface of antigen-presenting cells enable the uptake of cancer-cell-derived extracellular vesicles and the display of tumor antigens.
 

Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics   pp187 - 190
Clement M Potel, Miao-Hsia Lin, Albert J R Heck and Simone Lemeer
doi:10.1038/nmeth.4580
A twist on a common method used for enriching phosphorylated peptides for mass spectrometry-based proteomics analysis now reveals previously undetected and widespread histidine phosphorylation in Escherichia coli.
 

Ab initio electron density determination directly from solution scattering data   pp191 - 193
Thomas D Grant
doi:10.1038/nmeth.4581
An iterative structure factor retrieval algorithm allows electron densities to be directly calculated from solution scattering data, avoiding assumptions that limit modeling algorithms.
 

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Articles

Top

Supermultiplexed optical imaging and barcoding with engineered polyynes   pp194 - 200
Fanghao Hu, Chen Zeng, Rong Long, Yupeng Miao, Lu Wei et al.
doi:10.1038/nmeth.4578
A class of probes enables highly multiplexed imaging and barcoding applications with Raman microscopy.
 

Highly parallel direct RNA sequencing on an array of nanopores   pp201 - 206
Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd et al.
doi:10.1038/nmeth.4577
Direct sequencing of RNA molecules in real time using nanopores allows for the detection of splice variants and hold promises for profiling RNA modifications.
 

RNA-protein interaction detection in living cells   pp207 - 212
Muthukumar Ramanathan, Karim Majzoub, Deepti S Rao, Poornima H Neela, Brian J Zarnegar et al.
doi:10.1038/nmeth.4601
RaPID uses biotin ligases BirA[ast] and the faster acting BASU to label proteins in the proximity of an RNA motif of interest in living cells.
 

Capturing the interactome of newly transcribed RNA   pp213 - 220
Xichen Bao, Xiangpeng Guo, Menghui Yin, Muqddas Tariq, Yiwei Lai et al.
doi:10.1038/nmeth.4595
Labeling newly transcribed RNA with 5-ethynyluridine and adding biotin via click chemistry allows the analysis of the proteome bound to the various RNA species, including nascent RNA.
 

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding   pp221 - 225
Jeremy A Schofield, Erin E Duffy, Lea Kiefer, Meaghan C Sullivan and Matthew D Simon
doi:10.1038/nmeth.4582
TimeLapse-seq chemically recodes labeled s4U nucleosides to a cytidine derivative and monitors transcriptional dynamics.

See also: News and Views by Baptista & Dolken

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Corrigenda

Top

Corrigendum: Automated structure modeling of large protein assemblies using crosslinks as distance restraints   p226
Mathias Ferber, Jan Kosinski, Alessandro Ori, Umar J Rashid, María Moreno-Morcillo et al.
doi:10.1038/nmeth0318-226b
 

Corrigendum: Nm-seq maps 2'-O-methylation sites in human mRNA with base precision   pp226 - 227
Qing Dai, Sharon Moshitch-Moshkovitz, Dali Han, Nitzan Kol, Ninette Amariglio et al.
doi:10.1038/nmeth0318-226c
 

Erratum

Top

Erratum: Depleting endogenous proteins   p226
Ada Yee
doi:10.1038/nmeth0318-226a
 

Top
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