Friday, March 31, 2017

Nature Methods Contents: April 2017 Volume 14 pp 325 - 456

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Nature Methods

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April 2017 Volume 14, Issue 4

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

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In This Issue


In This Issue   


Special Feature

Focus on deep imaging of live tissue
One of the goals of biological imaging is to watch biological processes where they occur – within living tissue or even within a living animal. But in vivo imaging presents a set of challenges that are not encountered when imaging relatively small, flat samples like cells. In this Focus issue, we bring together papers on methods for optical imaging within living tissue. Two Reviews discuss: microscopy methods for functional brain imaging and the principles and practicalities of the different flavours of light sheet microscopy. A Perspective describes the use of adaptive optics to correct aberrations in scattering samples. This issue also includes primary research papers on multiphoton microscopy, an editorial that reminds our readers of the many areas of this large and exciting field that we do not cover, and a collection of recent papers on deep imaging from Nature Research journals.



Focus on deep imaging of live tissue
Imaging beyond the coverslip   p325


This Month


Focus on deep imaging of live tissue
The Author File: Chris Xu   p327
Vivien Marx
Deep brain imaging with three-photon microscopy and a swim from the US to China.

Points of Significance: Tabular data   pp329 - 330
Naomi Altman and Martin Krzywinski
Tabulating the number of objects in categories of interest dates back to the earliest records of commerce and population censuses.




MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy   pp331 - 332
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng et al.
MotionCor2 software corrects for beam-induced sample motion, improving the resolution of cryo-EM reconstructions.

Automatic tracing of ultra-volumes of neuronal images   pp332 - 333
Hanchuan Peng, Zhi Zhou, Erik Meijering, Ting Zhao, Giorgio A Ascoli et al.
Automated tracing algorithms can extract neuronal morphology from fluorescent or brightfield images. UltraTracer scales up the capability of existing tracing algorithms to handle datasets of ever-increasing size.


Research Highlights


Connectomics at the single-cell level
Trans-synaptic tracing that starts from a single neuron provides a detailed view of that neuron's inputs.

A magnetic alternative to FRET
A new approach measures nanoscale distances based on magnetic resonance tuning.

SLICE-ing a genome's architecture
Thin slices through nuclei provide an unbiased view of the complex 3D organization of mammalian genomes.

Volumetric functional imaging two ways
Bessel focus scanning and stereoscopy speed up volumetric brain imaging.

DNA variants or DNA damage?
Cryptic, widespread DNA damage is commonly interpreted as sequence variation.

DNA variants or DNA damage?
Cryptic, widespread DNA damage is commonly interpreted as sequence variation.

Methods in Brief

STED with twice the depletion | Solution-state 13C NMR gets a boost | Optogenetic feedback in real time | Imaging fast subcellular dynamics with light sheets

Tools in Brief

A method for labeling methionines | One mouse to trap them all | Single-base editing | Genome scaffolding while you sequence

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Technology Feature


Choosing CRISPR-based screens in cancer   pp343 - 346
Vivien Marx
Many possibilities for parsing cancer emerge when labs combine gene editing and screens. And RNAi retains its spot in the menu of options.


News and Views


Nanopore sequencing meets epigenetics   pp347 - 348
Michael C Schatz
Advanced signal processing techniques enable the genome-wide analysis of methylation in native DNA using nanopore sequencing.

See also: Brief Communication by Simpson et al. | Brief Communication by Rand et al.




Focus on deep imaging of live tissue
In vivo imaging of neural activity   pp349 - 359
Weijian Yang and Rafael Yuste
Yang and Yuste review currently available technologies for optical imaging of neural circuits, comparing them to help researchers choose optimal ones for their applications.

Focus on deep imaging of live tissue
A guide to light-sheet fluorescence microscopy for multiscale imaging   pp360 - 373
Rory M Power and Jan Huisken
This Review introduces the fundamental considerations for building a light sheet microscope, describes the pros and cons associated with available implementations, and offers practical advice for users.




Focus on deep imaging of live tissue
Adaptive optical fluorescence microscopy   pp374 - 380
Na Ji
This Perspective introduces the development and use of adaptive optics in correcting aberrations in deep optical imaging applications.




Power analysis of single-cell RNA-sequencing experiments   pp381 - 387
Valentine Svensson, Kedar Nath Natarajan, Lam-Ha Ly, Ricardo J Miragaia, Charlotte Labalette et al.
A comparison framework applied to 15 single-cell RNA-seq protocols reveals differences in accuracy and sensitivity and discusses the utility of RNA spike-in standards.


Brief Communications


Focus on deep imaging of live tissue
In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain   pp388 - 390
Dimitre G Ouzounov, Tianyu Wang, Mengran Wang, Danielle D Feng, Nicholas G Horton et al.
Ouzounov et al. report calcium imaging with three-photon microscopy in the mouse brain. The approach enabled noninvasive recording of activity with high spatial and temporal resolution from GCaMP6-labeled neurons located as deep as the hippocampus.

Optogenetic control with a photocleavable protein, PhoCl   pp391 - 394
Wei Zhang, Alexander W Lohman, Yevgeniya Zhuravlova, Xiaocen Lu, Matthew D Wiens et al.
A photocleavable protein (PhoCl) that spontaneously dissociates into two fragments after illumination with violet light expands the toolkit for cellular optogenetics.

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput   pp395 - 398
Todd M Gierahn, Marc H Wadsworth II, Travis K Hughes, Bryan D Bryson, Andrew Butler et al.
Seq-Well provides similar scale and data quality to massively parallel, droplet-based single-cell RNA-seq methods in an easy to use, inexpensive and portable microwell format compatible with low-input samples.

Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED   pp399 - 402
M Jason de la Cruz, Johan Hattne, Dan Shi, Paul Seidler, Jose Rodriguez et al.
Fragmentation of large, imperfect crystals into nanocrystals by sonication, vortexing, or vigorous pipetting facilitates atomic-resolution analysis by the cryo-EM method MicroED.

Prospective identification of hematopoietic lineage choice by deep learning   pp403 - 406
Felix Buggenthin, Florian Buettner, Philipp S Hoppe, Max Endele, Manuel Kroiss et al.
A deep learning approach enables fast and robust prediction of hematopoietic stem cell lineage choice in time-lapse imaging three generations before conventional marker onset.

Detecting DNA cytosine methylation using nanopore sequencing   pp407 - 410
Jared T Simpson, Rachael E Workman, P C Zuzarte, Matei David, L J Dursi et al.
A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human genomic DNA without chemical treatment.

See also: News and Views by Schatz

Mapping DNA methylation with high-throughput nanopore sequencing   pp411 - 413
Arthur C Rand, Miten Jain, Jordan M Eizenga, Audrey Musselman-Brown, Hugh E Olsen et al.
A tool based on hidden Markov model and hierarchical Dirichlet process (HMM-HDP) can call two methylated cytosine variants and a methylated adenine variant directly from genomic DNA using nanopore sequencing data.

See also: News and Views by Schatz

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning   pp414 - 416
Bo Wang, Junjie Zhu, Emma Pierson, Daniele Ramazzotti and Serafim Batzoglou
The SIMLR software identifies similarities between cells across a range of single-cell RNA-seq data, enabling effective dimension reduction, clustering and visualization.

Salmon provides fast and bias-aware quantification of transcript expression   pp417 - 419
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry and Carl Kingsford
Salmon is a computational tool that uses sample-specific models and a dual-phase inference procedure to correct biases in RNA-seq data and rapidly quantify transcript abundances.

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Focus on deep imaging of live tissue
Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)   pp420 - 426
Alexander Song, Adam S Charles, Sue Ann Koay, Jeff L Gauthier, Stephan Y Thiberge et al.
vTwINS enables high-speed volumetric calcium imaging via a V-shaped point spread function and a dedicated data-processing algorithm. Song et al. apply this strategy to image population activity in the mouse visual cortex and hippocampus.

Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution   pp427 - 434
Gary C H Mo, Brian Ross, Fabian Hertel, Premashis Manna, Xinxing Yang et al.
New fluorescent biosensors enable the first super-resolution imaging of enzyme activity in live cells via fluorescence fluctuation increase by contact (FLINC).

Automated synaptic connectivity inference for volume electron microscopy   pp435 - 442
Sven Dorkenwald, Philipp J Schubert, Marius F Killinger, Gregor Urban, Shawn Mikula et al.
SyConn is a computational framework that infers the synaptic wiring of neurons in volume electron microscopy data sets with machine learning. It has been applied to zebra finch, mouse and zebrafish neuronal tissue samples.

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers   pp443 - 449
Franklin D Fuller, Sheraz Gul, Ruchira Chatterjee, E Sethe Burgie, Iris D Young et al.
A robust acoustic droplet ejection-drop-on-tape method delivers samples to an X-ray free-electron laser source for combined serial femtosecond crystallography and X-ray emission spectroscopy analysis, providing detailed insights into macromolecular reaction dynamics.

A genetic system to study Plasmodium falciparum protein function   pp450 - 456
Jakob Birnbaum, Sven Flemming, Nick Reichard, Alexandra Blancke Soares, Paolo Mesén-Ramírez et al.
Selection-linked integration in the Plasmodium genome allows for rapid selection of genes inserted at a genomic locus or induction of the inactivation of gene products.

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