Hyeshik Chang

Nature Methods 13, 5 (2016). doi:10.1038/nmeth.3699

Authors: Barbara J Hunnicutt & Martin Krzywinski

Apply visual grouping principles to add clarity to information flow in pathway diagrams.

Nature advance online publication 06 January 2016. doi:10.1038/nature16526

Authors: Benjamin P. Kleinstiver, Vikram Pattanayak, Michelle S. Prew, Shengdar Q. Tsai, Nhu T. Nguyen, Zongli Zheng & J. Keith Joung

Publication date: February 2016
Source:Trends in Cell Biology, Volume 26, Issue 2
Author(s): Nathan D. Lawson
Gene editing in zebrafish has begun to reveal discordance between mutant phenotypes and those associated with knockdown via morpholino oligonucleotides (MOs). These studies suggest that MOs should not be used as a standalone tool and underscore the need for guidelines that require defined mutants to assess gene function in zebrafish.

Publication date: 12 January 2016
Source:Cell Reports, Volume 14, Issue 2
Author(s): Spyros Darmanis, Caroline Julie Gallant, Voichita Dana Marinescu, Mia Niklasson, Anna Segerman, Georgios Flamourakis, Simon Fredriksson, Erika Assarsson, Martin Lundberg, Sven Nelander, Bengt Westermark, Ulf Landegren
Significant advances have been made in methods to analyze genomes and transcriptomes of single cells, but to fully define cell states, proteins must also be accessed as central actors defining a cell’s phenotype. Methods currently used to analyze endogenous protein expression in single cells are limited in specificity, throughput, or multiplex capability. Here, we present an approach to simultaneously and specifically interrogate large sets of protein and RNA targets in lysates from individual cells, enabling investigations of cell functions and responses. We applied our method to investigate the effects of BMP4, an experimental therapeutic agent, on early-passage glioblastoma cell cultures. We uncovered significant heterogeneity in responses to treatment at levels of RNA and protein, with a subset of cells reacting in a distinct manner to BMP4. Moreover, we found overall poor correlation between protein and RNA at the level of single cells, with proteins more accurately defining responses to treatment.

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Darmanis et al. present an approach to simultaneously measure levels of up to 96 transcripts and proteins in single cells. They apply this technique to study responses of glioblastoma cells to BMP4, a proposed therapeutic agent, and reveal heterogeneous responses and cell states.

Supplementary material is a ubiquitous feature of scientific articles, particularly in journals that limit the length of the articles. While the judicious use of supplementary material can improve the readability of scientific articles, its excessive use threatens the scientific review process and by extension the integrity of the scientific literature. In many cases supplementary material today is so extensive that it is reviewed superficially or not at all. Furthermore, citations buried within supplementary files rob other scientists of recognition of their contribution to the scientific record. These issues are exacerbated by the lack of guidance on the use of supplementary information from the journals to authors and reviewers. We propose that the removal of artificial length restrictions plus the use of interactive features made possible by modern electronic media can help to alleviate these problems. Many journals, in fact, have already removed article length limitations (as is the case for BMC Bioinformatics and other BioMed Central journals). We hope that the issues raised in our article will encourage publishers and scientists to work together towards a better use of supplementary information in scientific publishing.

Environment: Labs should cut plastic waste too

Nature 528, 7583 (2015). doi:10.1038/528479c

Authors: Mauricio A. Urbina, Andrew J. R. Watts & Erin E. Reardon

Many governments now impose charges for single-use plastic bags and bottles. As responsible researchers, we should cut back on disposable plastics (see also G.BistulfiNature502, 170;10.1038/502170a2013).We estimate that the 280 bench scientists in our bioscience department generated

Single-chip microprocessor that communicates directly using light

Nature 528, 7583 (2015). doi:10.1038/nature16454

Authors: Chen Sun, Mark T. Wade, Yunsup Lee, Jason S. Orcutt, Luca Alloatti, Michael S. Georgas, Andrew S. Waterman, Jeffrey M. Shainline, Rimas R. Avizienis, Sen Lin, Benjamin R. Moss, Rajesh Kumar, Fabio Pavanello, Amir H. Atabaki, Henry M. Cook, Albert J. Ou, Jonathan C. Leu, Yu-Hsin Chen, Krste Asanović, Rajeev J. Ram, Miloš A. Popović & Vladimir M. Stojanović

Data transport across short electrical wires is limited by both bandwidth and power density, which creates a performance bottleneck for semiconductor microchips in modern computer systems—from mobile phones to large-scale data centres. These limitations can be overcome by using optical communications based on chip-scale electronic–photonic systems enabled by silicon-based nanophotonic devices8. However, combining electronics and photonics on the same chip has proved challenging, owing to microchip manufacturing conflicts between electronics and photonics. Consequently, current electronic–photonic chips are limited to niche manufacturing processes and include only a few optical devices alongside simple circuits. Here we report an electronic–photonic system on a single chip integrating over 70 million transistors and 850 photonic components that work together to provide logic, memory, and interconnect functions. This system is a realization of a microprocessor that uses on-chip photonic devices to directly communicate with other chips using light. To integrate electronics and photonics at the scale of a microprocessor chip, we adopt a ‘zero-change’ approach to the integration of photonics. Instead of developing a custom process to enable the fabrication of photonics, which would complicate or eliminate the possibility of integration with state-of-the-art transistors at large scale and at high yield, we design optical devices using a standard microelectronics foundry process that is used for modern microprocessors. This demonstration could represent the beginning of an era of chip-scale electronic–photonic systems with the potential to transform computing system architectures, enabling more powerful computers, from network infrastructure to data centres and supercomputers.

Nature Reviews Molecular Cell Biology 17, 3 (2016). doi:10.1038/nrm.2015.20

Author: Eytan Zlotorynski

During transcription, the nascent RNA can anneal to its DNA template and form RNA–DNA hybrids (R-loops), thereby exposing the other DNA strand to transcription-associated mutagenesis (TAM). Chen et al. examined whether a greater propensity of transcripts to fold into stable RNA structures, which are

Cells are engineered for on-demand control of psoriasis Authors: Jeremy Di Domizio, Michel Gilliet

Publication date: 17 December 2015
Source:Cell, Volume 163, Issue 7
Author(s): Nico Battich, Thomas Stoeger, Lucas Pelkmans
A central question in biology is whether variability between genetically identical cells exposed to the same culture conditions is largely stochastic or deterministic. Using image-based transcriptomics in millions of single human cells, we find that while variability of cytoplasmic transcript abundance is large, it is for most genes minimally stochastic and can be predicted with multivariate models of the phenotypic state and population context of single cells. Computational multiplexing of these predictive signatures across hundreds of genes revealed a complex regulatory system that controls the observed variability of transcript abundance between individual cells. Mathematical modeling and experimental validation show that nuclear retention and transport of transcripts between the nucleus and the cytoplasm is central to buffering stochastic transcriptional fluctuations in mammalian gene expression. Our work indicates that cellular compartmentalization confines transcriptional noise to the nucleus, thereby preventing it from interfering with the control of single-cell transcript abundance in the cytoplasm.

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Variability between transcript levels in genetically identical cells is not random, but stems from tight adaptation to multiple properties at the single-cell level, including the microenvironment. Nuclear transport operates as a buffer to prevent random fluctuations in transcript levels from being transmitted to the cytoplasm.

Publication date: 17 December 2015
Source:Cell, Volume 163, Issue 7
Author(s): Kevin A. Janes
How stochastic is gene expression in mammalian cells? Not very, according to Battich et al., who report that single-cell variability in cytoplasmic mRNAs is remarkably predictable given measurements of a cell’s phenotypic state and microenvironment. The noise from transcriptional bursts is buffered by a hallmark of eukaryotes—the nucleus.

Teaser

How stochastic is gene expression in mammalian cells? Not very, according to Battich et al., who report that single-cell variability in cytoplasmic mRNAs is remarkably predictable given measurements of a cell’s phenotypic state and microenvironment. The noise from transcriptional bursts is buffered by a hallmark of eukaryotes—the nucleus.

Publication date: 17 December 2015
Source:Cell, Volume 163, Issue 7
Author(s): Leslie B. Vosshall

Publication date: 17 December 2015
Source:Cell, Volume 163, Issue 7
Author(s): Raju Tomer, Matthew Lovett-Barron, Isaac Kauvar, Aaron Andalman, Vanessa M. Burns, Sethuraman Sankaran, Logan Grosenick, Michael Broxton, Samuel Yang, Karl Deisseroth
The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca²⁺ imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function.

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By harnessing optical mechanisms that normally result in unwanted spherical aberrations, SPED light sheet microscopy allows high-speed mapping of biological structures such as the entire vertebrate nervous system and its activity at a cellular resolution.

Nature advance online publication 16 December 2015. doi:10.1038/nature16162

Authors: TJ Brunette, Fabio Parmeggiani, Po-Ssu Huang, Gira Bhabha, Damian C. Ekiert, Susan E. Tsutakawa, Greg L. Hura, John A. Tainer & David Baker

A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. Here we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.

In evaluating research investments, it is important to establish whether the expertise gained by researchers in conducting their projects propagates into the broader economy. For eight universities, it was possible to combine data from the UMETRICS project, which provided administrative records on graduate students supported by funded research, with data from the U.S. Census Bureau. The analysis covers 2010–2012 earnings and placement outcomes of people receiving doctorates in 2009–2011. Almost 40% of supported doctorate recipients, both federally and nonfederally funded, entered industry and, when they did, they disproportionately got jobs at large and high-wage establishments in high-tech and professional service industries. Although Ph.D. recipients spread nationally, there was also geographic clustering in employment near the universities that trained and employed the researchers. We also show large differences across fields in placement outcomes. Authors: Nikolas Zolas, Nathan Goldschlag, Ron Jarmin, Paula Stephan, Jason Owen- Smith, Rebecca F. Rosen, Barbara McFadden Allen, Bruce A. Weinberg, Julia I. Lane

Ambitious international data-sharing initiatives have existed for years in fields such as genomics, earth science, and astronomy. But to realize the promise of widespread sharing of scientific data, intellectual property, data privacy, national security, and other legal and policy obstacles must be overcome (1). Although these issues have attracted much attention in some circles, they have often taken a back seat to addressing technical challenges. Yet failure to account for legal and policy issues at the outset of a large transborder data-sharing project can lead to undue resource expenditures and data-sharing structures that may offer fewer benefits than hoped. Drawing on our experience with the Belmont Forum, a multinational earth change–research program, we propose a framework to help plan data-sharing arrangements with a focus on early-stage decisions including options for legal interoperability. Authors: Jorge L. Contreras, Jerome H. Reichman

The system of tenure for university faculty in the United States arose in the late 19th to early 20th centuries to guarantee that academics would not be capriciously dismissed if they conducted research on controversial topics, pursued “unpromising” research, or did not conform to conventional beliefs. Much in the world has changed in the past 100 years, from the demographics of the academic workforce and the scale of the educational enterprise, to the pace of discovery and the legal statutes surrounding retirement. These changes prompt a reexamination: Is tenure the best way to nurture scholarly growth and academic freedom, or has its cost become too much to bear? Author: Marcia McNutt

by Rui Fang, Walter N. Moss, Michael Rutenberg-Schoenberg, Matthew D. Simon

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.

No description available

Lab staple agar hit by seaweed shortage

Nature 528, 7581 (2015). http://www.nature.com/doifinder/10.1038/528171a

Author: Ewen Callaway

Dwindling algae harvest imperils reagent essential for culturing microbes.

Nature Medicine 21, 1384 (2015). doi:10.1038/nm1215-1384

Authors: Randy Levinson, Alison Farrell, Michael Basson, Kevin Da Silva, Victoria Aranda, Christine Borowski, Hannah Stower & Brett Benedetti

This year saw a whirlwind of insights gleaned into topics ranging from heart cell proliferation to organoid modeling. Here are a few of the research papers detailing some of these intriguing discoveries.

Citations to previous literature are extensively used to measure the quality and diffusion of knowledge. However, we know little about the different ways in which a study can be cited; in particular, are papers cited to point out their merits or their flaws? We elaborated a methodology to characterize “negative”...

Bacterial RNases catalyze the turnover of RNA and are essential for gene expression and quality surveillance of transcripts. In Escherichia coli, the exoribonucleases RNase R and polynucleotide phosphorylase (PNPase) play critical roles in degrading RNA. Here, we developed an optical-trapping assay to monitor the translocation of individual enzymes along RNA-based...

by Richard de Grijs

by Mark P. Simmons

by William K. Michener

Nature Medicine 21, 1373 (2015). doi:10.1038/nm.4009

Aging is receiving more attention as a risk factor for human disease. With the correct modeling of human heterogeneity and consideration of the environmental factors involved in the aging process, we may be able to delay the onset of human disease.

Publication date: 3 December 2015
Source:Cell, Volume 163, Issue 6
Author(s): Gagan D. Gupta, Étienne Coyaud, João Gonçalves, Bahareh A. Mojarad, Yi Liu, Qianzhu Wu, Ladan Gheiratmand, David Comartin, Johnny M. Tkach, Sally W.T. Cheung, Mikhail Bashkurov, Monica Hasegan, James D. Knight, Zhen-Yuan Lin, Markus Schueler, Friedhelm Hildebrandt, Jason Moffat, Anne-Claude Gingras, Brian Raught, Laurence Pelletier
The centrosome is the primary microtubule organizing center of the cells and templates the formation of cilia, thereby operating at a nexus of critical cellular functions. Here, we use proximity-dependent biotinylation (BioID) to map the centrosome-cilium interface; with 58 bait proteins we generate a protein topology network comprising >7,000 interactions. Analysis of interaction profiles coupled with high resolution phenotypic profiling implicates a number of protein modules in centriole duplication, ciliogenesis, and centriolar satellite biogenesis and highlights extensive interplay between these processes. By monitoring dynamic changes in the centrosome-cilium protein interaction landscape during ciliogenesis, we also identify satellite proteins that support cilia formation. Systematic profiling of proximity interactions combined with functional analysis thus provides a rich resource for better understanding human centrosome and cilia biology. Similar strategies may be applied to other complex biological structures or pathways.

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In vivo proximity-dependent biotinylation (BioID) generates a protein interaction map of the human centrosome-cilium interface, revealing protein modules critical for centrosome and cilium biogenesis and pervasive and dynamic interplay between the two processes.

Publication date: 3 December 2015
Source:Cell, Volume 163, Issue 6
Author(s): Evan Murray, Jae Hun Cho, Daniel Goodwin, Taeyun Ku, Justin Swaney, Sung-Yon Kim, Heejin Choi, Young-Gyun Park, Jeong-Yoon Park, Austin Hubbert, Margaret McCue, Sara Vassallo, Naveed Bakh, Matthew P. Frosch, Van J. Wedeen, H. Sebastian Seung, Kwanghun Chung
Combined measurement of diverse molecular and anatomical traits that span multiple levels remains a major challenge in biology. Here, we introduce a simple method that enables proteomic imaging for scalable, integrated, high-dimensional phenotyping of both animal tissues and human clinical samples. This method, termed SWITCH, uniformly secures tissue architecture, native biomolecules, and antigenicity across an entire system by synchronizing the tissue preservation reaction. The heat- and chemical-resistant nature of the resulting framework permits multiple rounds (>20) of relabeling. We have performed 22 rounds of labeling of a single tissue with precise co-registration of multiple datasets. Furthermore, SWITCH synchronizes labeling reactions to improve probe penetration depth and uniformity of staining. With SWITCH, we performed combinatorial protein expression profiling of the human cortex and also interrogated the geometric structure of the fiber pathways in mouse brains. Such integrated high-dimensional information may accelerate our understanding of biological systems at multiple levels.

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A simple technique, termed SWITCH, for synchronizing key chemical reactions in tissue processing enables scalable tissue preservation and repeated labeling and imaging of biomolecules.

Publication date: 3 December 2015
Source:Cell, Volume 163, Issue 6
Author(s): Michael Boutros, Florian Heigwer, Christina Laufer
Image-based screening is used to measure a variety of phenotypes in cells and whole organisms. Combined with perturbations such as RNA interference, small molecules, and mutations, such screens are a powerful method for gaining systematic insights into biological processes. Screens have been applied to study diverse processes, such as protein-localization changes, cancer cell vulnerabilities, and complex organismal phenotypes. Recently, advances in imaging and image-analysis methodologies have accelerated large-scale perturbation screens. Here, we describe the state of the art for image-based screening experiments and delineate experimental approaches and image-analysis approaches as well as discussing challenges and future directions, including leveraging CRISPR/Cas9-mediated genome engineering.

Teaser

Image-based screening is used to measure a variety of phenotypes in cells and whole organisms. Combined with perturbations such as RNA interference, small molecules, and mutations, such screens are a powerful method for gaining systematic insights into biological processes. Screens have been applied to study diverse processes, such as protein-localization changes, cancer cell vulnerabilities, and complex organismal phenotypes. Recently, advances in imaging and image-analysis methodologies have accelerated large-scale perturbation screens. Here, we describe the state of the art for image-based screening experiments and delineate experimental approaches and image-analysis approaches as well as discussing challenges and future directions, including leveraging CRISPR/Cas9-mediated genome engineering.