Nature Methods Contents: February 2016 Volume 13 pp 103 - 183

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Advertisement We introduced our very first centrifuge in 1964 as an integral part of the Eppendorf Microliter System, and revolutionized life science research practices worldwide. Eppendorf micro centrifuges are designed to go beyond speed and capacity to offer you unparalleled ergonomic operation and superior temperature management. TABLE OF CONTENTS February 2016 Volume 13, Issue 2 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Review Brief Communications Articles Application Note Advertisement   Sputtered Metal Deep-UV Interference Filters Manufactured using single substrates of UV-grade fused silica and backed by warranty, these filters are available in  11 different passbands in a wide range of sizes, from 2mm-200mm. Laser damage thresholds >0.15 J/cm2 using a 355nm laser (10 ns pulse, 10 Hz), and suffer no degradation after 2 hours @ 300ºC. www.chroma.com Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Pre-made CRISPR-Cas9 Stable Cell Lines Stably expressing CRISPR Cas9 Ideal for CRISPR sgRNA validation, library screening, and sgRNA mediated knockouts and knockins Human: H1299 — Cas9 HEK293T — Cas9 HeLa — Cas9 A549 — Cas9 HEK293T — inducible Cas9 Mouse: Neuro2a — inducible Cas9 Learn more >>   In This Issue Top In This Issue    Editorial Top Improving databases for human variation   p103 doi:10.1038/nmeth.3762 To determine the true pathogenicity of genetic variants, data sharing is essential. This Month Top The Author File: Jason W. Chin   p105 Vivien Marx doi:10.1038/nmeth.3743 How to combine biology, chemistry and synthetic biology to add synthetic amino acids to a protein, and why creativity matters. Correspondence Top Solutions for quantifying P-value uncertainty and replication power   pp107 - 108 Laura C Lazzeroni, Ying Lu and Ilana Belitskaya-Lévy doi:10.1038/nmeth.3741 Response to Lazzeroni et al.   p108 Lewis G Halsey, Douglas Curran-Everett, Sarah L Vowler and Gordon B Drummond doi:10.1038/nmeth.3745 Estimation statistics should replace significance testing   pp108 - 109 Adam Claridge-Chang and Pryseley N Assam doi:10.1038/nmeth.3729 The mutation significance cutoff: gene-level thresholds for variant predictions   pp109 - 110 Yuval Itan, Lei Shang, Bertrand Boisson, Michael J Ciancanelli, Janet G Markle et al. doi:10.1038/nmeth.3739 Research Highlights Top Driving out malaria Laboratory tests show that gene drives could obliterate wild mosquito populations carrying the malaria parasite, or make them resistant to its transmission. Simple tools for difficult imaging Small chemical tweaks during tissue preparation make a big difference for imaging thick, complex biological samples. Watching proteins fold on the ribosome Researchers monitor cotranslational protein folding in real time. Taking a stab at neuronal heterogeneity Patch-seq integrates functional and molecular properties of single neurons to tackle heterogeneity in the brain. The condition-dependent proteome Absolute levels of the Escherichia coli proteome measured under 22 different conditions represent a valuable resource. Methods in Brief Counting stoichiometry with super-resolution image data | Mouse chimeras for testing human stem cell pluripotency | Comparing cancer genome analyses | Capturing lysine PTM–dependent interactions Tools in Brief Optogenetic mutagenesis in worms | Nanobody tools | A DIVERSE strategy for discovering peptide tags | Efficient unnatural amino acid incorporation Methods JOBS of the week Bioinformatics Scientist RWTH Aachen University, IZKF Computational Biology Group Assistant or Associate Faculty Member, Computational Immunologist Fred Hutchinson Cancer Research Center Postoctoral Fellow Memorial Sloan Kettering Cancer Center (MSKCC) PhD Students in Molecular Medicine & Bioinformatics Institute for Molecular Medicine Finland (FIMM) Bioinformatics Postdoctoral Fellow (VD-AY) La Jolla Institute for Allergy & Immunology More Science jobs from Methods EVENT 15th Conference on Methods and Applications in Fluorescence (MAF-15) 10th Sept - 13th Sept 2017 KU Leuven, Belgium More science events from Technology Feature Top Genetics: profiling DNA methylation and beyond   pp119 - 122 Vivien Marx doi:10.1038/nmeth.3736 Both tried-and-true and new assays are helping labs to assess methylation at particular loci and from single cells. News and Views Top Illuminating translation with ribosome profiling spectra   pp123 - 124 Pavel V Baranov and Audrey M Michel doi:10.1038/nmeth.3738 Software based on the spectral analysis of ribosome profiling improves the detection of translated segments in RNA molecules. See also: Article by Calviello et al. Hidden in the mist no more: physical force in cell biology   pp124 - 125 Karin Wang, Li-Heng Cai, Bo Lan and Jeffrey J Fredberg doi:10.1038/nmeth.3744 To drive its migration through a fibrillar matrix—and thus to spread, invade or metastasize—a cancer cell must exert physical forces. The first visualization of these forces in three dimensions reveals surprising migration dynamics. See also: Article by Steinwachs et al. Review Top Editing the epigenome: technologies for programmable transcription and epigenetic modulation   pp127 - 137 Pratiksha I Thakore, Joshua B Black, Isaac B Hilton and Charles A Gersbach doi:10.1038/nmeth.3733 Brief Communications Top Inverted light-sheet microscope for imaging mouse pre-implantation development   pp139 - 142 Petr Strnad, Stefan Gunther, Judith Reichmann, Uros Krzic, Balint Balazs et al. doi:10.1038/nmeth.3690 An inverted light-sheet microscope enables imaging of mouse embryos from zygote to blastocyst with minimal photodamage and high resolution for automatic lineage tree reconstruction, allowing new insight into cell fate specification. Nanoscale optomechanical actuators for controlling mechanotransduction in living cells   pp143 - 146 Zheng Liu, Yang Liu, Yuan Chang, Hamid Reza Seyf, Asegun Henry et al. doi:10.1038/nmeth.3689 Optomechanical actuator nanoparticles collapse upon illumination with near-infrared light. Appropriately coated, they can be used to mechanically trigger cellular processes such as focal adhesion formation or T cell activation. TRP channel mediated neuronal activation and ablation in freely behaving zebrafish   pp147 - 150 Shijia Chen, Cindy N Chiu, Kimberly L McArthur, Joseph R Fetcho and David A Prober doi:10.1038/nmeth.3691 Heterologous TRP channels can be used to stimulate or ablate neurons in response to their chemical or thermal agonists in zebrafish larvae, providing a set of tools orthogonal to optogenetic manipulation. Articles Top Small airway-on-a-chip enables analysis of human lung inflammation and drug responses in vitro   pp151 - 157 Kambez H Benam, Remi Villenave, Carolina Lucchesi, Antonio Varone, Cedric Hubeau et al. doi:10.1038/nmeth.3697 The small airway-on-a-chip allows the recapitulation of human lung pathophysiology in vitro and analysis of responses to drugs. Genetic code expansion in stable cell lines enables encoded chromatin modification   pp158 - 164 Simon J Elsässer, Russell J Ernst, Olivia S Walker and Jason W Chin doi:10.1038/nmeth.3701 Stable integration of genes that facilitate the incorporation of unnatural amino acids into the amber stop codon in genes of interest allows targeted integration of acetyl-lysine into histone H3.3 and the investigation of its effects in mouse embryonic stem cells. Detecting actively translated open reading frames in ribosome profiling data   pp165 - 170 Lorenzo Calviello, Neelanjan Mukherjee, Emanuel Wyler, Henrik Zauber, Antje Hirsekorn et al. doi:10.1038/nmeth.3688 RiboTaper quantifies the three-nucleotide periodicity in Ribo-seq data to find translated open reading frames (ORFs). The de novo inferred set of ORFs comprehensively defines the cellular proteome across a wide expression range and comprises few additional translated noncoding regions. See also: News and Views by Baranov & Michel Three-dimensional force microscopy of cells in biopolymer networks   pp171 - 176 Julian Steinwachs, Claus Metzner, Kai Skodzek, Nadine Lang, Ingo Thievessen et al. doi:10.1038/nmeth.3685 Measuring the forces generated by cells is not trivial in materials that behave in a nonlinear fashion. An equation that captures this behavior and finite-element modeling can be used to derive these forces from the material deformations around cells. See also: News and Views by Wang et al. Engineering an allosteric transcription factor to respond to new ligands   pp177 - 183 Noah D Taylor, Alexander S Garruss, Rocco Moretti, Sum Chan, Mark A Arbing et al. doi:10.1038/nmeth.3696 The combination of computational protein design and single-site saturation mutagenesis enables engineering of allosteric transcription factors to respond to new small molecules. Application Note Top Diagenode® Premium RRBS technology: cost-effective DNA methylation mapping with superior coverage    Anne-Clémence Veillard, Paul Datlinger, Miklos Laczik, Sharon Squazzo and Christoph Bock Top 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 natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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