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| Open AccessLipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission
The spatiotemporal regulation of membrane scaffolds recruitment and coupling between membrane deformation and fission in endocytosis are unclear. Here the authors show that lipid conversion at endocytic pits recruits SNX9, which couples local membrane constriction to fission in endocytosis.
- Johannes Schöneberg
- , Martin Lehmann
- & Frank Noé
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Article
| Open AccessMiCASA is a new method for quantifying cellular organization
There are few methods available that can quantify relationships between cell types in tissue images. Here the authors present a quantitative method to evaluate cellular organization, validated in the mouse thymus and spinal cord, called Multitaper Circularly Averaged Spectral Analysis (MiCASA).
- Andrew Sornborger
- , Jie Li
- & Nancy R. Manley
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| Open AccessDNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression
Cell cycle arrest after DNA damage is achieved by the expression of the CDK inhibitor p21. Here the authors show that spontaneous DNA damage incurred in unperturbed cell cycles, leads to cell populations exhibiting a bistable state, with p53 and p21 regulating the proliferation-quiescence decision.
- Alexis R. Barr
- , Samuel Cooper
- & Chris Bakal
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| Open AccessDefined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae
The three-dimensional architecture of genome-reduced bacteria is poorly understood. Here the authors combine Hi-C with super-resolution microscopy inMycoplasma pneumoniaeand provide evidence of how supercoiling and local organization influences gene regulation.
- Marie Trussart
- , Eva Yus
- & Luís Serrano
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| Open AccessA cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation
Embryonic development is a complex process where genetic and biochemical information direct morphogenesis. Here the authors describe MecaGen, an agent-based model and simulation platform of multicellular development designed to allow a quantitative comparison between simulations and real biological data.
- Julien Delile
- , Matthieu Herrmann
- & René Doursat
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| Open AccessMulti-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli
Multi-omics data integration is a great challenge. Here, the authors compile a database of E. coliproteomics, transcriptomics, metabolomics and fluxomics data to train models of recurrent neural network and constrained regression, enabling prediction of bacterial responses to perturbations.
- Minseung Kim
- , Navneet Rai
- & Ilias Tagkopoulos
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Article
| Open AccessSelf-organized centripetal movement of corneal epithelium in the absence of external cues
The cornea is formed of cells that originate from the outer circle of stem cells and that move towards its centre. Here, the authors show that the movement pattern is self-organised, requiring no cues, and that stem cell leakage may account for the presence of stem cells at the centre of the cornea.
- Erwin P. Lobo
- , Naomi C. Delic
- & J. Guy Lyons
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Article
| Open AccessA combined computational and structural model of the full-length human prolactin receptor
The prolactin receptor consists of a folded extracellular domain, a transmembrane domain and an intracellular intrinsically disordered domain. Here the authors use a combined experimental and computational approach to obtain a structure of a class I cytokine receptor, the human prolactin receptor.
- Katrine Bugge
- , Elena Papaleo
- & Birthe B. Kragelund
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| Open AccessArrhythmia risk stratification of patients after myocardial infarction using personalized heart models
Sudden arrhythmic death is a leading cause of mortality, however approaches to identify at-risk patients are of low sensitivity and specificity. Here, the authors develop a personalized approach to assess arrhythmia risk in post-infarction patients based on cardiac imaging and computational modelling that significantly outperforms existing clinical metrics.
- Hermenegild J. Arevalo
- , Fijoy Vadakkumpadan
- & Natalia A. Trayanova
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| Open AccessAccurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding
The folding of protein domains can occur concomitant with their synthesis, and the rates at which individual codons are translated by the ribosome can affect the folding process. Here the authors present a kinetic model that accurately predicts the probability that a nascent protein domain will co-translationally fold in vivo.
- Daniel A. Nissley
- , Ajeet K. Sharma
- & Edward P. O’Brien
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Article
| Open AccessContext influences on TALE–DNA binding revealed by quantitative profiling
TALE proteins are popular tools for genome engineering because they can recognize specific DNA sequences, however off-target effects are a routine problem. Here Rogers and Barrera et al. comprehensively map TALE–DNA interactions to develop a computational model to predict binding specificity.
- Julia M. Rogers
- , Luis A. Barrera
- & Martha L. Bulyk
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Article |
A network approach for identifying and delimiting biogeographical regions
There is currently no consensus on how best to identify and delimit biogeographical regions. Here the authors develop a network-based approach incorporating complex presence–absence patterns that can successfully identify commonly recognized biogeographical regions, and apply it to two large-scale data sets of plants and amphibians.
- Daril A. Vilhena
- & Alexandre Antonelli
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Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation
Sequential segmentation in development is best described in vertebrates, where it relies on cell proliferation and shows regular periodicity. Here, the authors show that in the flour beetle segments are added with irregular rate and their elongation during periods of fast growth relies mostly on cell movements.
- A. Nakamoto
- , S. D. Hester
- & T. A. Williams
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Notch1–Dll4 signalling and mechanical force regulate leader cell formation during collective cell migration
Many forms of collective cell migration are directed by specialized leader cells that have a distinct protrusive phenotype. Riahi et al.show that lateral inhibition mediated by Notch1–Dll4 signalling determines the stochastic emergence of leader cells in epithelial monolayers.
- Reza Riahi
- , Jian Sun
- & Pak Kin Wong
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| Open AccessSensory integration dynamics in a hierarchical network explains choice probabilities in cortical area MT
The activity of sensory neurons can be correlated with perceptual decisions and this effect may provide insights into how sensory information is processed during perceptual tasks. Here the authors develop a network model of sensory and decision-making areas and propose that the dynamics across the network hierarchy explains the choice probabilities.
- Klaus Wimmer
- , Albert Compte
- & Jaime de la Rocha
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| Open AccessProspective errors determine motor learning
Motor learning is characterized by diverse cognitive processes, which lack a unified theoretical framework. Here, Takiyama et al.present a model demonstrating that motor learning is determined by prospective errors, which they test in a specially designed visuomotor adaptation task.
- Ken Takiyama
- , Masaya Hirashima
- & Daichi Nozaki
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Article
| Open AccessHuman-to-mosquito transmission efficiency increases as malaria is controlled
Understanding the epidemiology of malaria transmission between humans and mosquitoes is crucial for successful disease control. Analysing data from an 18-year malaria control programme, Churcher et al. show that decreased parasite prevalence in humans can be found concurrently with an increase in transmission efficiency.
- Thomas S. Churcher
- , Jean-François Trape
- & Anna Cohuet
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| Open AccessMaster regulators of FGFR2 signalling and breast cancer risk
FGFR2 gene variation is associated with breast cancer risk but the molecular mechanism is unknown. Fletcher et al. provide a link between FGFR2 signalling and breast cancer susceptibility by demonstrating that FGFR2 signalling activates the ERa transcriptional network, which drives transcription of risk genes.
- Michael N. C. Fletcher
- , Mauro A. A. Castro
- & Kerstin B. Meyer
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| Open AccessIn silico method for modelling metabolism and gene product expression at genome scale
To describe the biochemical composition of an organism multiple data sets must be combined and this information can then be used forin silico analysis. By combining metabolism and transcription data, Lerman et al. discovered new regulons and improved the gene annotation for the simple organism Thermotoga maritima.
- Joshua A. Lerman
- , Daniel R. Hyduke
- & Bernhard O. Palsson