Friday, June 8, 2018

Nature Methods Contents: June 2018, Volume 15 No 6

If you are unable to see the message below, click here to view.
Nature Methods

Perfect your ISH with these 10 tips from Enzo! 

June 2018 Volume 15, Issue 6

This Month
Research Highlights
Technology Feature
Brief Communications
Amendments & Corrections

Let CST help build your next ChIP experiment!

Whether you are dreaming about your first ChIP experiment or are the resident expert in your lab, CST scientists have created a guide with tips and recommendations to ensure that your ChIP-qPCR and ChIP-seq experiments are successful.

Princeton University, Princeton Institute for the Science and Technology of Materials (PRISM), Nature Communications, Nature Materials, Nature Structural & Molecular Biology present:

Princeton — Nature Conference: Frontiers in Electron Microscopy for the Physical and Life Sciences
July 11-13, 2018, Princeton University, Princeton, NJ, USA 

Register now to secure your place.



Better research through metrology    p395

This Month


Laurent Cognet    p397
Vivien Marx

The curse(s) of dimensionality    pp399 - 400
Naomi Altman & Martin Krzywinski


Advanced Imaging with Proven Optics

Olympus is dedicated to your work, vision, and science. Through innovation and service, we seek to aide in your discoveries, advance your research, and inspire you to explore new possibilities. Our wide range of microscopes are built with the optical excellence and proven application expertise you can depend on. Your Science Matters™.

> Learn more about Olympus microscopes



MaxQuant goes Linux    p401
Pavel Sinitcyn, Shivani Tiwary, Jan Rudolph, Petra Gutenbrunner, Christoph Wichmann et al.

Advertisement webcasts

Nature Research Custom presents a webcast on: Multicolour Digital PCR for ctDNA detection in breast cancer

Date: 12 June 2018

Dr. Isaac Garcia-Murillas from ICR will address the technical challenges for clinical utility of liquid biopsy and ctDNA as a biomarker in breast cancer.

This webcast has been produced on behalf of the sponsor who retains sole responsibility for content 

Register for FREE 

Sponsored by: Stilla Technologies 

Research Highlights


Deep learning advances super-resolution imaging    p403
Rita Strack

A home for brain organoids    p404
Tal Nawy

RNAs that shape the genome    p405
Nicole Rusk

Simulating the imaging process in scattering tissue    p406
Nina Vogt

A pan-cancer atlas    p407
Tal Nawy

Analyzing Drosophila activity    p407
Nina Vogt

What hPSCs need    p407
Nicole Rusk

Hessian structured illumination microscopy    p407
Rita Strack

Cross-linking with SuFEx chemistry    p408
Allison Doerr

RBP census    p408
Nicole Rusk

Super-long single-molecule tracking    p408
Rita Strack

Tissue-specific oncogene screens    p408
Tal Nawy

A home for integrative structural models    p409
Allison Doerr

JOBS of the week
Scientific Director
ALBA Synchrotron
2018 International Talent Forum in Nankai University
Nankai University
Chief Research Officer
Ames Laboratory
Staff Scientist
VA Boston Healthcare System
Postdoctoral Scientist position
Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague)
More Science jobs from
Lab for Open Innovation in Science (LOIS)
Vienna, Austria
More science events from

Technology Feature


Stem cells: lineage tracing lets single cells talk about their past    pp411 - 414
Vivien Marx



Nanoparticles for super-resolution microscopy and single-molecule tracking    pp415 - 423
Dayong Jin, Peng Xi, Baoming Wang, Le Zhang, Jörg Enderlein et al.

This Perspective highlights recent advances in the use of nanoparticles in super-resolution microscopy and single-molecule tracking. It offers guidance for users interested in these tools and discusses potential future directions.


Brief Communications


Single-shot super-resolution total internal reflection fluorescence microscopy    pp425 - 428
Min Guo, Panagiotis Chandris, John Paul Giannini, Adam J. Trexler, Robert Fischer et al.

Instant structured illumination and total internal reflection fluorescence microscopy are combined to carry out time-lapse super-resolution TIRF imaging at frame rates up to 100 Hz, enabling observation of fast biological processes.


High-speed volumetric imaging of neuronal activity in freely moving rodents    pp429 - 432
Oliver Skocek, Tobias Nöbauer, Lukas Weilguny, Francisca Martínez Traub, Chuying Naomi Xia et al.

A miniature light-field microscope in combination with a signal-extraction approach enables high-speed volumetric calcium imaging in freely moving mice.


C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9–APEX2    pp433 - 436
Xin D. Gao, Li-Chun Tu, Aamir Mir, Tomás Rodriguez, Yuehe Ding et al.

dCas9 fused to ascorbate peroxidase (APEX2) biotinylates proteins around targeted loci so they can be enriched and characterized.


Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling    pp437 - 439
Samuel A. Myers, Jason Wright, Ryan Peckner, Brian T. Kalish, Feng Zhang et al.

After CRISPR-mediated targeting of the peroxidase APEX2 to a genomic locus of interest, the proteins at that locus are labeled, enriched and identified via quantitative proteomics.




BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes    pp440 - 448


BoxCar, a mass spectrometry data acquisition method, greatly increases sensitivity and the detection of low-abundance peptides with a minimal amount of instrument time.


Self-interference 3D super-resolution microscopy for deep tissue investigations    pp449 - 454
Pierre Bon, Jeanne Linarès-Loyez, Maxime Feyeux, Kevin Alessandri, Brahim Lounis et al.

Several methods make it possible to obtain depth information in 3D super-resolution microscopy. Here the authors exploit a self-interference phenomenon to allow deep imaging within tissue samples, as well as isotropic imaging.


Picky comprehensively detects high-resolution structural variants in nanopore long reads    pp455 - 460
Liang Gong, Chee-Hong Wong, Wei-Chung Cheng, Harianto Tjong, Francesca Menghi et al.

The computational pipeline Picky detects the full spectrum of structural variants and their breakpoints in long nanopore sequence reads.


Accurate detection of complex structural variations using single-molecule sequencing    pp461 - 468
Fritz J. Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad et al.

NGMLR and Sniffles perform highly accurate alignment and structural variation detection from long-read sequencing data.


Amendments & Corrections


Author Correction: High-speed volumetric imaging of neuronal activity in freely moving rodents    p469
Oliver Skocek, Tobias Nöbauer, Lukas Weilguny, Francisca Martínez Traub, Chuying Naomi Xia et al.

Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. With Nature Briefing, we'll keep you updated on the latest research, so you can focus on yours.

Click here to sign up.
nature events
Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here.
Find the latest scientific conferences, courses, meetings and symposia on For event advertising opportunities across the Nature Publishing Group portfolio please contact
More Nature Events

You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your account at:
(You will need to log in to be recognised as a registrant)

For further technical assistance, please contact our registration department

For print subscription enquiries, please contact our subscription department

For other enquiries, please contact our customer feedback department

Springer Nature | One New York Plaza, Suite 4500 | New York | NY 10004-1562 | USA

Springer Nature's worldwide offices:
London - Paris - Munich - New Delhi - Tokyo - Melbourne
San Diego - San Francisco - Washington - New York - Boston

Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at The Campus, 4 Crinan Street, London, N1 9XW.

© 2018 Macmillan Publishers Limited, part of Springer Nature. All Rights Reserved.

Springer Nature

No comments: