Friday, July 28, 2017

Nature Methods Contents: August 2017 Volume 14 pp 753 - 825

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Nature Methods

Nikon's all-new DUVB is a high-sensitivity GaAsP detector for tunable virtual channel detection and spectral applications. Available for Nikon's A1 and C2 confocal microscope systems, the DUVB delivers flexible detection of fluorescent signals with higher sensitivity.

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August 2017 Volume 14, Issue 8

In This Issue
This Month
Research Highlights
Technology Feature
Brief Communications
Inspiration does not obey speed limits.

Announcing the ORCA-Lightning from Hamamatsu. Our new 12MP sCMOS camera engineered for high speed and low noise and ready for Lightsheet microscopy.

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In This Issue


In This Issue   




Sharing images   p753
Images are among the richest data types that biologists collect, yet most biological images are not available for reanalysis or reuse. This may be changing.


This Month


The Author File: Melike Lakadamyali   p755
Vivien Marx
DNA origami, super-resolution microscopy and creative flashes on a bike.


Points of Significance: Classification and regression trees   pp757 - 758
Martin Krzywinski and Naomi Altman
Decision trees are a simple but powerful prediction method.




Probes & Drugs portal: an interactive, open data resource for chemical biology   pp759 - 760
Ctibor Skuta, Martin Popr, Tomas Muller, Jindrich Jindrich, Michal Kahle et al.


sCMOS noise-correction algorithm for microscopy images   pp760 - 761
Sheng Liu, Michael J Mlodzianoski, Zhenhua Hu, Yuan Ren, Kristi McElmurry et al.


Research Highlights


Tailoring optogenetic illumination through tapered fibers
A tapered optical fiber delivers spatially precise and efficient optogenetic illumination to the rodent brain.

Synthetic epigenetic memory
Combining an inducible methyltransferase with a methylation-sensitive zinc finger creates an epigenetic memory circuit.

Developments in data-independent-acquisition mass spectrometry allow efficient and accurate quantitation of peptidoforms across large sample cohorts.

A community repository for microfluidics
The Metafluidics initiative encourages researchers to upload and share open-source microfluidics designs.

Super-resolution imaging with mCherry
A chemical caging strategy allows mCherry to be used for localization microscopy.

Methods in Brief

Speckle-free OCT | This is your brain on fiber | Interference-based force microscopy | Better 2D visualization of 3D image stacks

Tools in Brief

A switch for manipulating active neurons | Separating the primed from the naïve | An all-in-one cell cycle reporter | A comprehensive map of human protein complexes

JOBS of the week
Bioinformatics Scientist
King Abdullah University of Science and Technology (KAUST)
Junior Principal Investigator (Unit Leader)
IFOM the FIRC Institute of Molecualr Oncology
Postdoctoral fellow
University of Gothenburg, Institute of Biomedicine
Research Fellow in Single Molecule Biophysics
University of Leeds
Postdoctoral Scholar
The University of Iowa
More Science jobs from
4th World Congress on Cancer and Prevention Methods
Valencia, Spain
More science events from

Technology Feature


Genetics: new tales from ancient DNA   pp771 - 774
Vivien Marx
Coaxing ancient DNA to reveal its history delivers surprises and even improves ways of working with badly damaged present-day DNA.




Image Data Resource: a bioimage data integration and publication platform   pp775 - 781
Eleanor Williams, Josh Moore, Simon W Li, Gabriella Rustici, Aleksandra Tarkowska et al.
This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis.




Comparison of algorithms for the detection of cancer drivers at subgene resolution   pp782 - 788
Eduard Porta-Pardo, Atanas Kamburov, David Tamborero, Tirso Pons, Daniela Grases et al.
13 algorithms for the detection of cancer driver genes at the subgene level are assessed for their advantages and limitations.


Brief Communications


A DNA origami platform for quantifying protein copy number in super-resolution   pp789 - 792
Francesca Cella Zanacchi, Carlo Manzo, Angel S Alvarez, Nathan D Derr, Maria F Garcia-Parajo et al.
A DNA-origami-based calibration method determines and accounts for labeling stoichiometry and fluorophore photophysics to improve protein counting in quantitative super-resolution imaging.


Addressing preferred specimen orientation in single-particle cryo-EM through tilting   pp793 - 796
Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter et al.
The preferred specimen orientation problem limits accuracy and resolution in structure determination by cryo-EM. Collecting data at defined sample tilts yielded near-atomic-resolution structures for the influenza hemagglutinin trimer and ribosomal biogenesis intermediates.


RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps   pp797 - 800
Brandon Frenz, Alexandra C Walls, Edward H Egelman, David Veesler and Frank DiMaio
RosettaES, an algorithm that uses a fragment-based sampling strategy, improves macromolecular structure modeling from cryo-EM data at 3-5-Å resolution.


Visualizing adenosine-to-inosine RNA editing in single mammalian cells   pp801 - 804
Ian A Mellis, Rohit Gupte, Arjun Raj and Sara H Rouhanifard
inoFISH uses fluorescence in situ hybridization to visualize and localize adenosine-to-inosine-edited transcripts.

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.

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High-speed fixed-target serial virus crystallography   pp805 - 810
Philip Roedig, Helen M Ginn, Tim Pakendorf, Geoff Sutton, Karl Harlos et al.
A new sample-delivery method for serial X-ray crystallography exploits the full repetition rate of the X-ray free-electron laser at the LCLS facility, thus enabling efficient, high-speed data collection to solve the three-dimensional structures of viruses.


Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy   pp811 - 818
Tobias Nöbauer, Oliver Skocek, Alejandro J Pernía-Andrade, Lukas Weilguny, Francisca Martínez Traub et al.
The seeded iterative demixing strategy, when used in combination with light-field microscopy, enables calcium imaging at single-neuron resolution in the mouse brain at high volumetric imaging rates and depths of up to 380 [mu]m.


CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping   pp819 - 825
Shelly A Trigg, Renee M Garza, Andrew MacWilliams, Joseph R Nery, Anna Bartlett et al.
CrY2H-seq, a Cre recombinase reporter-mediated yeast two-hybrid method coupled with next-generation sequencing, enables ultra-high-throughput screening of transcription factor interactions in Arabidopsis thaliana.

When You Can’t PCR It, CATCH It

Cas9-assisted targeting of chromosome segments, or CATCH, is a method for extracting large DNA targets when you don’t know enough about the sequence to use standard enrichment protocols. With the SageHLS platform for purifying HMW DNA, this approach can be an alternative for scientists who would otherwise have to waste sequencing capacity on whole-genome analysis. Learn about HLS-CATCH in this case study.

November 2-3, 2017 | Hanover, Germany

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