Systems biology articles within Nature Communications

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  • Article
    | Open Access

    Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here the authors develop a high throughput non-invasive method for tracking suspension and adhesion mammalian cell growth based on plate reader measures to characterize engineered cell lines.

    • Alice Grob
    • , Chiara Enrico Bena
    •  & Francesca Ceroni

  • Article
    | Open Access

    Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, the authors identify microbial interactions as a mechanism underlying flavour formation in Cheddar cheese.

    • Chrats Melkonian
    • , Francisco Zorrilla
    •  & Ahmad A. Zeidan

  • Review Article
    | Open Access

    As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. In this review, the authors outline design strategies for the DNA, RNA, and protein-level circuits and the hybrid “multi-level” circuits.

    • Yuanli Gao
    • , Lei Wang
    •  & Baojun Wang

  • Article
    | Open Access

    Co-fractionation mass spectrometry (CF-MS) is a powerful technique for mapping protein interactions under physiological conditions. Here, the authors uniformly re-process 411 CF-MS experiments and carry out meta-analyses of protein abundance, protein-protein interactions, and phosphorylation sites in the resulting resource.

    • Michael A. Skinnider
    • , Mopelola O. Akinlaja
    •  & Leonard J. Foster

  • Article
    | Open Access

    Little is known about how malaria parasites adapt the speed of their development to their mosquito vectors. Using an evolutionary modelling framework, this study predicts that the metabolic status of mosquitoes shapes the parasites’ life-history strategies and transmission dynamics.

    • Paola Carrillo-Bustamante
    • , Giulia Costa
    •  & Elena A. Levashina

  • Article
    | Open Access

    Reconstructing transcriptome-wide spatially-resolved gene expressions requires modelling nonlinear patterns and spatial structures in RNA profiling data. Here, authors introduce a graph-guided neural hierarchical tensor decomposition model that incorporates spatial and functional relations for the task.

    • Tianci Song
    • , Charles Broadbent
    •  & Rui Kuang

  • Article
    | Open Access

    Analysis of newly synthesized proteins upon perturbation can provide detailed insights into immediate proteome remodeling, which drives cellular responses. Here, the authors report an optimized semi-automated workflow for the quantitative analysis of the newly synthesized proteome.

    • Toman Borteçen
    • , Torsten Müller
    •  & Jeroen Krijgsveld

  • Article
    | Open Access

    Global epistasis can be used to reconstruct fitness landscapes and infer adaptive trajectories. Here, the authors investigate how environmental variation impacts patterns of global epistasis, finding that global epistasis in the malaria parasite P. falciparum can be modulated by drug concentration in the environment.

    • Juan Diaz-Colunga
    • , Alvaro Sanchez
    •  & C. Brandon Ogbunugafor

  • Article
    | Open Access

    In Saccharomyces cerevisiae, the left arm of chromosome XII only requires 12 genes to maintain cell viability, whereas 25 genes are needed for robust fitness. Here the authors demonstrate that the entire arm can be replaced by a neochromosome with completely artificial sequences.

    • Shuangying Jiang
    • , Zhouqing Luo
    •  & Junbiao Dai

  • Article
    | Open Access

    Different membrane proteins dynamically polarize to organize signal transduction, but the underlying mechanism is unclear. Here, the authors show that a differential diffusion mediated partitioning process is sufficient to drive such spatiotemporal patterning of membrane-associated signaling proteins.

    • Tatsat Banerjee
    • , Satomi Matsuoka
    •  & Pablo A. Iglesias

  • Article
    | Open Access

    Using a microfluidic single-cell aging platform, the authors report how single-cell lifespan varies across more than 300 yeast strains, each missing a single gene. Their top hit, Sis2, was found to regulate yeast lifespan in a dose-dependent fashion.

    • Tolga T. Ölmez
    • , David F. Moreno
    •  & Murat Acar

  • Article
    | Open Access

    Imbalance in the growth rate of two organs can perturb their appropriate scaling. Here, Stojanovski et al., identify a mechanism involving the mechanotransducer YAP-1 which ensures proper proportions of the pharynx and the body length of C. elegans.

    • Klement Stojanovski
    • , Ioana Gheorghe
    •  & Benjamin D. Towbin

  • Article
    | Open Access

    Many real-world systems are characterized by bursty dynamics with interchanging periods of intense activity and quiescence. The authors propose a method to construct temporal networks that match a given activity pattern, and apply it to empirical bursty patterns.

    • Anzhi Sheng
    • , Qi Su
    •  & Joshua B. Plotkin

  • Article
    | Open Access

    Multiplex histology faces the challenge of integrating tissue architecture with the identification of relevant spatial cellular phenotypes. Using community ecology principles, the authors propose NIPMAP, a tool for niche-phenotype mapping of multiplex histology data.

    • Anissa El Marrahi
    • , Fabio Lipreri
    •  & Jean Hausser

  • Article
    | Open Access

    Channel networks are key to coastal wetland functioning. Here, the authors show how vegetation enhances network branching, and hypothesize that this may enhance the storm surge buffering capacity of wetlands and their resilience under sea-level rise.

    • Roeland C. van de Vijsel
    • , Jim van Belzen
    •  & Johan van de Koppel

  • Article
    | Open Access

    Identifying memory and state switching in single cells remains elusive. Here, the authors develop a method, scMemorySeq, by combining cell barcoding and scRNA-seq and apply it to human melanoma cells to track lineages as they switch states between a drug-susceptible state and a state primed for drug resistance.

    • Guillaume Harmange
    • , Raúl A. Reyes Hueros
    •  & Sydney M. Shaffer

  • Article
    | Open Access

    The detoxification pathway photorespiration has been thought to be photoprotective in dynamic light. The authors report that, instead, growth in dynamic light buffers plants against photorespiratory lesions by reducing photosynthesis and inducing metabolite re-routing.

    • Thekla von Bismarck
    • , Philipp Wendering
    •  & Ute Armbruster

  • Article
    | Open Access

    The rational design and implementation of synthetic mammalian communication systems can unravel fundamental design principles of cell communication circuits and offer a framework for engineering of designer cell consortia with potential applications in cell therapeutics. Here the authors present a synthetic communication platform in mammalian cells based on diffusible dipeptide ligands and synthetic receptors, that is by design highly orthogonal, scalable, and programmable.

    • Anna-Maria Makri Pistikou
    • , Glenn A. O. Cremers
    •  & Tom F. A. de Greef

  • Perspective
    | Open Access

    The utilization of one-carbon assimilation pathways for bioproduction represents a promising direction towards a more sustainable bio-based economy. Here, the authors compare the thermodynamic efficiencies and energy demand of C1-assimilation pathways and discuss their implementation for energy, material, and food production.

    • Simone Bachleitner
    • , Özge Ata
    •  & Diethard Mattanovich

  • Article
    | Open Access

    Genetic code expansion (GCE) is a protein engineering tool that enables programmed and site-specific installation of noncanonical amino acids into proteins. Here, authors show that cellular stress remodelling boosts GCE in mammalian cells including GCE realized by orthogonally translating organelles.

    • Mikhail E. Sushkin
    • , Christine Koehler
    •  & Edward A. Lemke

  • Article
    | Open Access

    In this work, Bay et al describe the construction of the first genome-scale metabolic model for the parasitic whipworm, Trichuris muris and use it to identify novel metabolic pathways and predict critical enzymes and essential metabolites for worm survival.

    • Ömer F. Bay
    • , Kelly S. Hayes
    •  & Ian S. Roberts

  • Article
    | Open Access

    Understanding disease progression dynamics is critical for diagnostics and treatment, but capturing dynamics is difficult. Here, the authors present a method for modelling disease progression from high dimensional molecular data that enables patient stratification and high-risk disease state identification, showcased in bladder cancer.

    • Amit Frishberg
    • , Neta Milman
    •  & Shai S. Shen-Orr

  • Perspective
    | Open Access

    Using one carbon (C1) molecules as primary feedstock for bioproduction holds great potential for a circular and carbon neutral economy. Here, the authors discuss the potential of merging knowledge gained from natural and synthetic C1-trophic organisms to expedite the development of efficient C1-based biomanufacturing.

    • Enrico Orsi
    • , Pablo Ivan Nikel
    •  & Stefano Donati

  • Article
    | Open Access

    Control of HIV and SIV infection is largely thought to be achieved through direct lysis of target cells. Here, using mathematical modelling of viral load data from rhesus macaques, the authors propose that virus control is best explained by the combination of cytolytic and non-cytolytic effects.

    • Benjamin B. Policicchio
    • , Erwing Fabian Cardozo-Ojeda
    •  & Ruy M. Ribeiro

  • Article
    | Open Access

    Synthetic auxotrophy in which cell viability depends on the presence of an unnatural amino acid provides a powerful strategy to restrict unwanted propagation of genetically modified organisms in open environments and potentially prevent industrial espionage. Here the authors establish a general framework for the creation and optimization of synthetic auxotrophs in yeast.

    • Tiantian Chang
    • , Weichao Ding
    •  & Xian Fu

  • Article
    | Open Access

    DNA is an alternative to data storage materials for its durability, density, and energetics. Here the authors demonstrate the storage of digital information on DNA molecules using base-editing.

    • Afsaneh Sadremomtaz
    • , Robert F. Glass
    •  & Reza Zadegan

  • Article
    | Open Access

    Myelofibrosis is a form of myeloproliferative neoplasm with few treatment options available. Here, the authors profiled drug responses and proteomics ex vivo and identify molecularly-guided treatment strategies, including HDAC and BET inhibitors for CALR mutant myelofibrosis patients.

    • Mattheus H. E. Wildschut
    • , Julien Mena
    •  & Berend Snijder

  • Article
    | Open Access

    Designing promoters with desired properties is crucial in synthetic biology. Here, authors introduce DeepSEED, an AI-aided flanking sequence optimisation framework which combines expert knowledge with deep learning techniques to efficiently design promoters in both eukaryotic and prokaryotic cells.

    • Pengcheng Zhang
    • , Haochen Wang
    •  & Xiaowo Wang

  • Article
    | Open Access

    Generating and controlling cell collective behavior is important for synthetic biology and bioproduction. Here, the authors show the diversification dynamic and the fitness cost associated with cell switching are coupled in yeast and bacteria, and demonstrate the feasibility of controlling diversification regimes.

    • Lucas Henrion
    • , Juan Andres Martinez
    •  & Frank Delvigne

  • Article
    | Open Access

    Using a multi-OMICS approach, Haas et al identify 54 human genes and 16 host-targeting chemical compounds that regulate influenza A virus infection in lung epithelial cells, including AHNAK and COBP1 which are also essential for SARS-CoV-2 infection.

    • Kelsey M. Haas
    • , Michael J. McGregor
    •  & Nevan J. Krogan

  • Article
    | Open Access

    Plastic pollution is rapidly increasing worldwide, causing adverse impacts on the environment, wildlife and human health. Here the authors present a synthetic microbial consortium that efficiently degrades polyethylene terephthalate hydrolysate and upcycles it to desired chemicals through cellular division of labor.

    • Teng Bao
    • , Yuanchao Qian
    •  & Ting Lu

  • Article
    | Open Access

    Single-cell proteomics by Mass Spectrometry (scpMS) provides unparalleled insights into cellular mechanisms from a proteome-centric standpoint. Here, the authors leverage sensitivity-tailored data acquisition methods to profile cell state heterogeneity in cultured model systems.

    • Valdemaras Petrosius
    • , Pedro Aragon-Fernandez
    •  & Erwin M. Schoof

  • Article
    | Open Access

    TMAO is known to be atherothrombotic. Here the authors show that i) kidney function is the main determinant of serum TMAO, ii) TMAO increases kidney scarring with TGF-β1 signalling and iii) anti-diabetic drugs with reno-protective properties such as GLP1R agonists reduce plasma TMAO.

    • Petros Andrikopoulos
    • , Judith Aron-Wisnewsky
    •  & Marc-Emmanuel Dumas

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