Wednesday, January 31, 2018

Nature Methods Contents: February 2018, Volume 15 No 2 pp 91 - 149

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Nature Methods

Can you trust your Antibody? Implications for disease research.
A recent publication in Scientific Reports rigorously tested nine commercially available antibodies for specificity and sensitivity and found that only one, from Cell Signaling Technology, met all validation criteria. Read this open-access article to explore the potentially serious implications of non-specific antibodies and disease research.
Read more now.

February 2018 Volume 15, Issue 2

This Month
Research Highlights
Technology Feature
Brief Communications
Application Note

NSK Manipulation System 

Simplify and automate your micromanipulator workflow.

Easy-to-use, PC-based system enables inexperienced operators to perform high-skill tasks, and automation reduces repetition and increases efficiency. Proprietary piezo-actuator enables highly accurate cell perforation with minimal damage. Ideal for ICSI, DNA injection, and research applications.

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All of your valuable samples deserve the best treatment. 

With continuous quality assurance throughout the entire production process, you are guaranteed the highest quality consumables for ultimate reliability and reproducibility of your precious experiments. Eppendorf consumables — quality beyond measure.
Nature Collection: 2017 Nobel Prize in Chemistry 

Nature Research present this Collection of articles celebrating the 2017 Nobel Prize in Chemistry to Jacques Dubochet, Joachim Frank and Richard Henderson, recognised "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution". 

Access here >>

Produced with support from 
Thermo Fisher Scientific 



The good referee   p91
Referees provide an invaluable service in advancing science. We offer some food for thought about how to effectively peer review methods papers.

This Month


The Author File: Jennifer Phillips-Cremins   p93
Vivien Marx
To better explore how genomes fold takes disparate fields and a love of math.

Research Highlights


Putting a stamp on single cells
Virus stamping can target single cells in complex tissues, both in culture and in vivo.

Off-the-shelf super-resolution microscopy in whole cells
The combination of DNA-PAINT and spinning-disk confocal microscopy makes super-resolution microscopy in whole cells affordable and easy to implement.

Humanized yeast—erasing 1.3 billion years of evolution
Cellular engineering that allows budding yeast to survive with the four core human histones opens the door to exploring the function of histone variants and their modifications.

Epigenetic profiles to classify bacterial sequences
Methylation patterns can help determine the origin of metagenomic sequences.

Automated brain mapping
A computational framework enables automated annotation, analysis, and sharing of mouse brain data at single-cell resolution.

Methods in Brief


Single-organelle sequencing | Myelin quantification at nanoscale | Assessing protein activity in single cells | Single-molecule imaging and force spectroscopy at extended depth

Tools in Brief


Big Papi uncovers genetic interactions | A colorful series of bioorthogonal probes | Biobanking breast cancers | Cell-type-specific proteomics in the in vivo mouse brain

JOBS of the week
Postdoctoral Fellow
University of Pennsylvania - Perelman School of Medicine
Postdoctoral Fellow
University Health Network (Toronto)
Bioinformatician / Computational Biologist (PhD)
University of Helsinki

Postdoctoral Fellowship
The University of Texas MD Anderson Cancer Center
More Science jobs from
Materials, Methods & Technologies 2018, 20th International Conference
Elenite, Bulgaria
More science events from

Technology Feature


Meet some code-breakers of noncoding RNAs   pp103 - 106
Vivien Marx
The regulome—the part of the genome that regulates function—includes noncoding RNAs with varied functions yet to be deciphered.



Interactome INSIDER: a structural interactome browser for genomic studies   pp107 - 114
Michael J Meyer, Juan Felipe Beltrán, Siqi Liang, Robert Fragoza, Aaron Rumack et al.
Based on machine learning-predicted interaction interfaces, this resource enables interpretation of genomic variants and disease mutations in light of the protein-protein interactome.

Brief Communications


Mapping the 3D orientation of piconewton integrin traction forces   pp115 - 118
Joshua M Brockman, Aaron T Blanchard, Victor Pui-Yan Ma, Wallace D Derricotte, Yun Zhang et al.
Molecular force microscopy employs a combination of fluorescence polarization microscopy and molecular tension sensors to determine the orientation of cellular forces. The technology is demonstrated for integrin-mediated forces in platelets and fibroblasts.

Detecting hierarchical genome folding with network modularity   pp119 - 122
Heidi K Norton, Daniel J Emerson, Harvey Huang, Jesi Kim, Katelyn R Titus et al.
3DNetMod identifies nested topologically associating domains (TADs) and subTADs from Hi-C data.

GIGGLE: a search engine for large-scale integrated genome analysis   pp123 - 126
Ryan M Layer, Brent S Pedersen, Tonya DiSera, Gabor T Marth, Jason Gertz et al.
GIGGLE is a genome interval search engine that enables extremely fast queries of genome features from thousands of genome annotation sets.



Biotinylation by antibody recognition—a method for proximity labeling   pp127 - 133
Daniel Z Bar, Kathleen Atkatsh, Urraca Tavarez, Michael R Erdos, Yosef Gruenbaum et al.
Proximity-based labeling represents a useful approach for mapping protein environment, but current methods for this are limited to application to cell lines. This approach is now extended to primary human tissues with a method that uses antibodies to guide proximity labeling.

BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance   pp134 - 140
Alexandra A Duarte, Ewa Gogola, Norman Sachs, Marco Barazas, Stefano Annunziato et al.
Mouse tumor organoids are characterized as a model to study tumor biology and drug resistance.

Resolving systematic errors in widely used enhancer activity assays in human cells   pp141 - 149
Felix Muerdter, Łukasz M Boryń, Ashley R Woodfin, Christoph Neumayr, Martina Rath et al.
Using the ORI of plasmids used in enhancer assays as the sole core promoter and inhibiting the interferon I response triggered by plasmid transfection greatly reduces false positive and negative results in single-candidate and massively parallel enhancer assays and enables genome-wide enhancer screens.

Animation on CRISPR: Gene editing and beyond 

The CRISPR-Cas9 system has revolutionised gene editing, but cutting DNA isn't all it can do.

This Animation, from Nature Methods, explores where CRISPR might be headed next. 

Watch the Animation >> 

Produced with support from: 

Application Note


Making difficult things easier and simpler with a manipulation system   

Nature Mentoring Collection 

Offering advice and support to scientist mentors and their mentees 

Access the Collection 
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