News & Views |
Featured
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Article |
Ion channels enable electrical communication in bacterial communities
Ion channels in bacterial biofilms are shown to conduct long-range electrical signals within the biofilm community through the propagation of potassium ions; as predicted by a simple mathematical model, potassium channel gating is shown to coordinate metabolic states between distant cells via electrical communication.
- Arthur Prindle
- , Jintao Liu
- & Gürol M. Süel
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News & Views |
Expression feels two pulses
Single-cell analyses reveal that combinatorial changes in the intracellular locations of transcription factors can tune the expression of the factors' target genes in response to environmental stimuli. See Article p.54
- Antoine Baudrimont
- & Attila Becskei
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Article |
Combinatorial gene regulation by modulation of relative pulse timing
Many gene-regulatory proteins have been shown to activate in pulses, but whether cells exploit the dynamic interaction between pulses of different regulatory proteins has remained unexplored; here single-cell videos show that yeast cells modulate the relative timing between the pulsatile transcription factors Msn2 and Mig1—a gene activator and a repressor, respectively—to control the expression of target genes in response to diverse environmental conditions.
- Yihan Lin
- , Chang Ho Sohn
- & Michael B. Elowitz
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Letter |
Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size
Saccharomyces cerevisiae controls its cell size through the differential size-dependency of the synthesis of the cell cycle activator Cln3 relative to the cell cycle inhibitor Whi5.
- Kurt M. Schmoller
- , J. J. Turner
- & Jan M. Skotheim
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Letter |
Sex‐specific demography and generalization of the Trivers–Willard theory
The Trivers–Willard theory proposing that maternal condition influences offspring sex ratio is extended by analysing how differences in mortality rates, age‐specific reproduction and life history tactics between males and females may affect adaptive offspring sex ratio adjustment in two systems.
- Susanne Schindler
- , Jean‐Michel Gaillard
- & Tim Coulson
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Article |
Panorama of ancient metazoan macromolecular complexes
Using biochemical fractionation and mass spectrometry, animal protein complexes are identified from nine species in parallel, and, along with genome sequence information, complex conservation is investigated and over one million protein–protein interactions are predicted in 122 eukaryotes.
- Cuihong Wan
- , Blake Borgeson
- & Andrew Emili
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Letter |
Single-cell messenger RNA sequencing reveals rare intestinal cell types
An algorithm that allows rare cell type identification in a complex population of single cells, based on single-cell mRNA-sequencing, is applied to mouse intestinal cells, revealing novel subtypes of enteroendocrine cells and showing that the Lgr5-expressing population consists of a homogenous stem cell population with a few rare secretory cells, including Paneth cells.
- Dominic Grün
- , Anna Lyubimova
- & Alexander van Oudenaarden
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Letter |
Protein synthesis by ribosomes with tethered subunits
A ribosome with tethered subunits, ‘Ribo-T’, is engineered by making a hybrid RNA composed of ribosomal RNA of large and small subunits; Ribo-T can support cell growth in vivo in the absence of wild-type ribosomes, and is used to establish a fully orthogonal ribosome–mRNA system.
- Cédric Orelle
- , Erik D. Carlson
- & Alexander S. Mankin
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Article |
Metabolic co-dependence gives rise to collective oscillations within biofilms
The emergence of long-range metabolic co-dependence within a biofilm drives oscillations in growth that resolve a social conflict between cooperation and competition, thereby increasing community-level fitness against chemical attack.
- Jintao Liu
- , Arthur Prindle
- & Gürol M. Süel
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News & Views |
Network evolution hinges on history
The effects of mutations in proteins can depend on the occurrence of previous mutations. It emerges that such historical contingency is also important during the evolution of gene regulatory networks. See Letter p.361
- Aaron M. New
- & Ben Lehner
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Letter |
Intersecting transcription networks constrain gene regulatory evolution
Epistatic interactions, whereby a mutation's effect is contingent on another mutation, have been shown to constrain evolution within single proteins, and how such interactions arise in gene regulatory networks has remained unclear; here the appearance of pheromone-response regulator binding sites in the regulatory DNA of the a-specific genes of Saccharomyces cerevisiae are shown to have required specific changes in a second pathway during the evolution from its common ancestor with Candida albicans.
- Trevor R. Sorrells
- , Lauren N. Booth
- & Alexander D. Johnson
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Letter |
Single-cell chromatin accessibility reveals principles of regulatory variation
A single-cell method for probing genome-wide chromatin accessibility has been developed; the results provide insight into the relationship between cell-to-cell variation associated with specific trans-factors and cis-elements, as well insights into the relationship between chromatin accessibility and three-dimensional genome organization.
- Jason D. Buenrostro
- , Beijing Wu
- & William J. Greenleaf
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Letter |
A noisy linear map underlies oscillations in cell size and gene expression in bacteria
Quantification of single-cell growth over long periods of time in E. coli shows transient oscillations in cell size, with periods stretching across more than ten generations; a noisy negative feedback on cell-size control is proposed in which cells with a small initial size tend to divide later than cells with a large initial size with implications for the genetic and physiological processes required.
- Yu Tanouchi
- , Anand Pai
- & Lingchong You
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Letter |
Condensin-driven remodelling of X chromosome topology during dosage compensation
Genome-wide chromosome conformation capture analysis in C. elegans reveals that the dosage compensation complex, a condensin complex, remodels the X chromosomes of hermaphrodites into a sex-specific topology distinct from autosomes while regulating gene expression chromosome-wide.
- Emily Crane
- , Qian Bian
- & Barbara J. Meyer
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Letter |
Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour
Little is known about how individual cells within a group of cells exposed to the same external signals can produce a specific individual response to their local microenvironment; a quantitative analysis of cell crowding reveals that single cells can autonomously sense local crowding though their ability to spread and activate focal adhesion kinase (FAK), which ultimately results in changes in cellular lipid composition.
- Mathieu Frechin
- , Thomas Stoeger
- & Lucas Pelkmans
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Letter |
hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1
A method, termed hiCLIP, has been developed to determine the RNA duplexes bound by RNA-binding proteins, revealing an unforeseen prevalence of long-range duplexes in 3′ untranslated regions (UTRs), and a decreased incidence of SNPs in duplex-forming regions; the results also show that RNA structure is able to regulate gene expression.
- Yoichiro Sugimoto
- , Alessandra Vigilante
- & Jernej Ule
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News & Views |
Defiant daughters and coordinated cousins
Genetically identical cells can have many variable properties. A study of correlations between cells in a lineage explains paradoxical inheritance laws, in which mother and daughter cells seem less similar than cousins. See Letter p.468
- Andreas Hilfinger
- & Johan Paulsson
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Letter |
Lineage correlations of single cell division time as a probe of cell-cycle dynamics
Precise measurement of cell-cycle duration in thousands of mammalian cells reveals correlations among cousin cells, but no such correlations between mother and daughter cells; recapitulating this finding using a deterministic model suggests that observed cellular heterogeneities in cell-cycle duration may be attributable to deterministic processes, and eventually be controlled.
- Oded Sandler
- , Sivan Pearl Mizrahi
- & Nathalie Q. Balaban
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News Q&A |
The mathematics behind Internet virality
Computational social scientist Sharad Goel studies the spread of memes such as #TheDress.
- Davide Castelvecchi
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News & Views |
Roadmap for regulation
A package of papers investigates the functional regulatory elements in genomes that have been obtained from human tissue samples and cell lines. The implications of the project are presented here from three viewpoints. See Articles p.317, p.331, p.337 & p.344 and Letters p.350, p.355, p.360 & p.365
- Casey E. Romanoski
- , Christopher K. Glass
- & Genevieve Almouzni
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News Feature |
Sex redefined
The idea of two sexes is simplistic. Biologists now think there is a wider spectrum than that.
- Claire Ainsworth
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Article
| Open AccessIntegrative analysis of 111 reference human epigenomes
This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease.
- Anshul Kundaje
- , Wouter Meuleman
- & Manolis Kellis
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Article |
An Arabidopsis gene regulatory network for secondary cell wall synthesis
The full complement of transcriptional regulators that affect synthesis of the plant secondary cell wall remains largely undetermined; here, the network of protein–DNA interactions controlling secondary cell wall synthesis of Arabidopsis thaliana is determined, showing that gene expression is regulated by a series of feed-forward loops to ensure that the secondary cell wall is deposited at the right time and in the right place.
- M. Taylor-Teeples
- , L. Lin
- & S. M. Brady
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Letter |
Protein quality control at the inner nuclear membrane
A protein degradation pathway is found at the inner nuclear membrane that is distinct from, but complementary to, endoplasmic-reticulum-associated protein degradation, and which is mediated by the Asi protein complex; a genome-wide library screening of yeast identifies more than 20 substrates of this pathway, which is shown to target mislocalized integral membrane proteins for degradation.
- Anton Khmelinskii
- , Ewa Blaszczak
- & Michael Knop
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News |
Microsoft billionaire takes on cell biology
New Allen institute will create simulations of cell behaviour.
- Ewen Callaway
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Article |
Deconstructing transcriptional heterogeneity in pluripotent stem cells
This study uses single-cell expression profiling of pluripotent stem cells after various perturbations, and uncovers a high degree of variability that can be inherited through cell divisions—modulating microRNA or external signalling pathways induces a ground state with reduced gene expression heterogeneity and a distinct chromatin profile.
- Roshan M. Kumar
- , Patrick Cahan
- & James J. Collins
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News |
Data bank struggles as protein imaging ups its game
Hybrid methods to solve structures of molecular machines create a storage headache.
- Ewen Callaway
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News & Views |
A compass for stem-cell differentiation
The development of CellNet — network-biology software that determines how cell types generated in vitro relate to their naturally occurring counterparts — could improve our ability to produce desirable cells in culture.
- Franz-Josef Müller
- & Jeanne F. Loring
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News |
Ambitious plans for BRAIN project unveiled
US National Institutes of Health’s share of the BRAIN neuroscience initiative calls for a ten-fold increase in funding.
- Sara Reardon
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Letter |
Rapid and tunable post-translational coupling of genetic circuits
Protease competition is used to produce rapid and tunable coupling of genetic circuits, enabling a coupled clock network that can encode independent environmental cues into a single time series output, a form of frequency multiplexing in a genetic circuit context.
- Arthur Prindle
- , Jangir Selimkhanov
- & Jeff Hasty
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News |
First synthetic yeast chromosome revealed
US-based project recruited dozens of undergraduates to stitch DNA fragments together.
- Ewen Callaway
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Article |
A promoter-level mammalian expression atlas
A study from the FANTOM consortium using single-molecule cDNA sequencing of transcription start sites and their usage in human and mouse primary cells, cell lines and tissues reveals insights into the specificity and diversity of transcription patterns across different mammalian cell types.
- Alistair R. R. Forrest
- , Hideya Kawaji
- & Yoshihide Hayashizaki
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News |
Medicine gets up close and personal
Long-term study will monitor healthy people in detail — and encourage them to respond to the results.
- W. Wayt Gibbs
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News & Views |
How bacteria choose a lifestyle
In a bacterial population, some cells stay single and motile, whereas others settle down and form chains. A study now investigates the mechanisms that determine these outcomes. See Article p.481
- James C. W. Locke
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Article |
Memory and modularity in cell-fate decision making
This study shows that Bacillus subtilis switches from a solitary, motile lifestyle to a multicellular, sessile state in a random, memoryless fashion, but that the underlying gene network is buffered against its own stochastic variation to tightly time the reverse transition; thus bacteria keep track of time to force their progeny to cooperate during the earliest stage of multicellular growth.
- Thomas M. Norman
- , Nathan D. Lord
- & Richard Losick
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Outlook |
Q&A: A lateral thinker
The winner of the 2007 Nobel Prize in Chemistry Gerhard Ertl ponders biology's big questions with Diane Wu.
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News Feature |
Systems ecology: Biology on the high seas
How Eric Karsenti's quest to understand the cell launched a trip around the world.
- Claire Ainsworth
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Letter |
Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins
The lipid-binding profiles of all lipid-transfer proteins in Saccharomyces cerevisiae are determined and a new subfamily of oxysterol-binding proteins that function in phosphatidylserine homeostasis and transport is identified.
- Kenji Maeda
- , Kanchan Anand
- & Anne-Claude Gavin
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News & Views |
Metabolite turns master regulator
The phenomenon of catabolite repression enables microorganisms to use their favourite carbon source first. New work reveals α-ketoacids as key effectors of this process, with their levels regulating gene expression. See Article p.301
- Joshua D. Rabinowitz
- & Thomas J. Silhavy
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Article |
Coordination of bacterial proteome with metabolism by cyclic AMP signalling
Cyclic AMP, one of the earliest discovered and most intensely studied signalling molecules in molecular biology, is widely believed to signal the carbon status in mediating catabolite repression in bacteria; here a quantitative approach reveals a much broader physiological role for cAMP signalling, whereby it coordinates the allocation of proteomic resources with the global metabolic needs of the cell, including, for example, nitrogen or sulphur.
- Conghui You
- , Hiroyuki Okano
- & Terence Hwa
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Letter |
A latent capacity for evolutionary innovation through exaptation in metabolic systems
A computational analysis of the ability of a metabolic reaction network to synthesize all biomass from a single source of carbon and energy shows that when such networks are required to be viable on one particular carbon source, they are typically also viable on multiple other carbon sources that were not targets of selection.
- Aditya Barve
- & Andreas Wagner
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Article |
Temporal regulation of EGF signalling networks by the scaffold protein Shc1
The Shc1 scaffold mediates a switch in the signaling output of the epidermal growth factor receptor tyrosine kinase over time through recruitment of successive waves of proteins with distinct biological functions.
- Yong Zheng
- , Cunjie Zhang
- & Tony Pawson
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Article |
The Mycobacterium tuberculosis regulatory network and hypoxia
Mycobacterium tuberculosis has the ability to survive within the host for months to decades in an asymptomatic state, and adaptations to hypoxia are thought to have an important role in pathogenesis; here a systems-wide reconstruction of the regulatory network provides a framework for understanding mycobacterial persistence in the host.
- James E. Galagan
- , Kyle Minch
- & Gary K. Schoolnik
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News |
Plants perform molecular maths
Arithmetic division guides plants' use of energy at night.
- Heidi Ledford
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Letter |
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
By exploring the phageome in mice, antibiotic treatment is shown to lead to enrichment of phage-encoded genes that are related to antibiotic resistance.
- Sheetal R. Modi
- , Henry H. Lee
- & James J. Collins
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Q&A |
Turning point: Hana El-Samad
Engineer takes a career risk in moving to biology.
- Virginia Gewin
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Letter |
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Single-cell RNA sequencing is used to investigate the transcriptional response of 18 mouse bone-marrow-derived dendritic cells after lipopolysaccharide stimulation; many highly expressed genes, such as key immune genes and cytokines, show bimodal variation in both transcript abundance and splicing patterns. This variation reflects differences in both cell state and usage of an interferon-driven pathway involving Stat2 and Irf7.
- Alex K. Shalek
- , Rahul Satija
- & Aviv Regev
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