Systems biology articles within Nature Communications

Featured

  • Article
    | Open Access

    While developmental phenotypes are often multigenic and involve environmental inputs, most research approaches involve perturbation of small numbers of genes. Here they use a synthetic evolution approach in Drosophila to show that adding extra copies of bicoid leads to rapid, system-wide phenotypic responses, potentiated by highly polygenic traits such as embryo size.

    • Xueying C. Li
    • , Lautaro Gandara
    •  & Justin Crocker
  • Article
    | Open Access

    It is known that spatially localized interactions can give rise to self-organized collective motion. Here, by studying pairwise interactions in juvenile zebrafish, authors reveal the role of reciprocal temporal coupling and find that temporal coordination considerably improves spatial responsiveness, such as reacting to changes in the direction of motion of a partner.

    • Guy Amichay
    • , Liang Li
    •  & Iain D. Couzin
  • Article
    | Open Access

    The use of orthogonal genetic code can help to prevent the escape of hazardous genes through horizontal gene transfer. Here, the authors develop a cell-free translation system with the Ser/Leu-swapped genetic code using a hybrid tRNA set and show its application in enhancing the production of superfolder GFP.

    • Tomoshige Fujino
    • , Ryogo Sonoda
    •  & Hiroshi Murakami
  • Article
    | Open Access

    Aberrant signalling pathway activity is relevant for tumour growth and resistance to therapy, but remains hard to understand and target. Here, the authors develop VESPA, a phosphoproteomics-based machine learning algorithm that can elucidate response and adaptation to drug perturbations in cancer signalling pathways.

    • George Rosenberger
    • , Wenxue Li
    •  & Andrea Califano
  • Perspective
    | Open Access

    Evolutionary and rational design approaches are commonly used to engineer biological systems but are typically seen at odds with each other. In this perspective the authors argue for the concept of an evolutionary design spectrum to help unify and compare these design methodologies to support more effective biological engineering.

    • Simeon D. Castle
    • , Michiel Stock
    •  & Thomas E. Gorochowski
  • Article
    | Open Access

    H2O2 stress is known to activate a slew of transcription factors that restore redox balance. Here, the authors use live-cell imaging and single-cell analysis to reveal that the transcription factors that are activated and their timing of activation is dose dependent.

    • Elizabeth Jose
    • , Woody March-Steinman
    •  & Andrew L. Paek
  • Article
    | Open Access

    Elucidating the gastroesophageal junction’s development is key to comprehending its disease susceptibility. Here, the authors mapped its development, uncovering cellular diversity and interaction dynamics using advanced spatiotemporal single-cell analysis.

    • Naveen Kumar
    • , Pon Ganish Prakash
    •  & Cindrilla Chumduri
  • Perspective
    | Open Access

    Engineering biology is a dynamic field that uses gene editing, synthesis, assembly, and engineering to design new or modified biological systems. Here the authors discuss the policy considerations and interventions needed to support a role for engineering biology in climate change mitigation.

    • Jonathan Symons
    • , Thomas A. Dixon
    •  & Isak S. Pretorius
  • Article
    | Open Access

    The unification of decision-making, communication, and memory would enable the programming of intelligent biotic systems. Here, the authors achieve this goal by engineering E. coli chassis cells with an array of inducible recombinases that mediate diverse genetic programs.

    • Brian D. Huang
    • , Dowan Kim
    •  & Corey J. Wilson
  • Article
    | Open Access

    The development of the human cerebellum is not well understood. Here, the authors analyse a large sample of neuroimaging scans from children and adolescents to develop growth models of the cerebellum which mirror age-related developmental trajectories of behaviour and function.

    • Carolin Gaiser
    • , Rick van der Vliet
    •  & Ryan L. Muetzel
  • Article
    | Open Access

    Production of proteins at scale and affordable cost has been a major need of the biotech sector for the last several decades. Here the authors present a design algorithm called UNILIB for boosting gene expression in eukaryotic cells developed using an oligo-library and machine learning approach, validated in both yeast and mammalian cells using unseen sequences.

    • Inbal Vaknin
    • , Or Willinger
    •  & Roee Amit
  • Article
    | Open Access

    Bispecific antibody architecture is often important for function but rarely optimized. Here, authors present a modular approach to assemble bispecifics in varied formats using a SpyTag/SpyCatcher approach called SpyMask, and build anti-HER2 bispecifics whose activities depend on binder orientation and bispecific geometry.

    • Claudia L. Driscoll
    • , Anthony H. Keeble
    •  & Mark R. Howarth
  • Article
    | Open Access

    Targeting the files containing content-of-interest is a challenge in DNA data storage. Here, the authors develop a CRISPR-powered search engine to quantitatively identify the keyword in files stored in DNA.

    • Jiongyu Zhang
    • , Chengyu Hou
    •  & Changchun Liu
  • Article
    | Open Access

    While tricarboxylic acid cycle (TCA cycle) is required for heterotrophic microbes, it reduces carbon yield of industrial products due to the release of excess CO2. Here, the authors construct an E. coli strain without a functional TCA cycle and demonstrate its feasibility as a chassis strain for production of four separate compounds.

    • Hang Zhou
    • , Yiwen Zhang
    •  & Baixue Lin
  • Article
    | Open Access

    Machine learning applied to large compendia of transcriptomic data has enabled the decomposition of bacterial transcriptomes to identify independently modulated sets of genes. Here the authors present iModulon-based engineering for precise identification of genes for cross-species function transfer to streamline synthetic biology for strain development and biomanufacturing.

    • Donghui Choe
    • , Connor A. Olson
    •  & Bernhard O. Palsson
  • Article
    | Open Access

    This work leverages a new diet database and six long term monitoring efforts of 361 taxa to build comparable pre- and post-heatwave ecosystem models. The study provides empirical demonstration of changes in ecosystem-wide patterns of energy flux and biomass in response to marine heatwaves.

    • Dylan G. E. Gomes
    • , James J. Ruzicka
    •  & Joshua D. Stewart
  • Article
    | Open Access

    Endocrinologists have traditionally focused on studying one hormone or organ system at a time. Here the authors use transcriptomic data from the mouse lemur to globally characterize primate hormonal signaling, describing hormone sources and targets, identifying conserved and primate specific regulation, and elucidating principles of the network.

    • Shixuan Liu
    • , Camille Ezran
    •  & James E. Ferrell Jr.
  • Article
    | Open Access

    Mass spectrometry-based proteomics faces the challenge of processing vast data amounts. Here, the authors introduce AlphaPept, an open-source, Python-based framework that offers high speed analysis and easy integration for large-scale proteome analysis.

    • Maximilian T. Strauss
    • , Isabell Bludau
    •  & Matthias Mann
  • Article
    | Open Access

    Gene expression is inherently dynamic, due to complex regulation and stochastic biochemical events. Here the authors train a deep neural network to predict and dynamically control gene expression in thousands of individual bacteria in real-time which they then apply to control antibiotic resistance and study single-cell survival dynamics.

    • Jean-Baptiste Lugagne
    • , Caroline M. Blassick
    •  & Mary J. Dunlop
  • Article
    | Open Access

    Cardiac macrophage contributes to the onset of cardiac fibrosis, but the underneath mechanisms remain unclear. Here the authors show that mouse cardiac macrophages from circulating monocytes may trans-differentiate into myofibroblast under hypertensive conditions for fibrosis development, with an AKLBH5/IL11 molecular axis modulating this macrophage-to-myofibroblast transition.

    • Tao Zhuang
    • , Mei-Hua Chen
    •  & Cheng-Chao Ruan
  • Article
    | Open Access

    The soil microbiome communicates with plant roots using a chemical language. Here, using p-coumaroyl-homoserine lactone as the synthetic communication signal, the authors demonstrate programmable microbe-to-plant communication from the sender in the soil bacteria to a receiver in the plant.

    • Alice Boo
    • , Tyler Toth
    •  & Christopher A. Voigt
  • Article
    | Open Access

    Conventional blue denim dyeing has both environmental and health-related consequences. Here, Bidart et al. use enzyme engineering to develop a viable method for the bulk production of indican and demonstrate dying processes which could significantly reduce the negative consequences of this billion-dollar industry.

    • Gonzalo Nahuel Bidart
    • , David Teze
    •  & Ditte Hededam Welner
  • Article
    | Open Access

    Recent protein design methods rely on large neural networks, yet it is unclear which dependencies are critical for determining function. Here, authors show that learning the per residue mutation preferences, without considering interactions, enables design of functional and diverse protein variants.

    • David Ding
    • , Ada Y. Shaw
    •  & Debora S. Marks
  • Article
    | Open Access

    Interfacing living systems with electronics for biosensing and biocomputing applications is challenging. Here, Gao et al. present hybrid transistors with electroactive bacteria capable of extracellular electron transfer, enabling transduction of biological computations to electrical readouts.

    • Yang Gao
    • , Yuchen Zhou
    •  & Benjamin K. Keitz
  • Article
    | Open Access

    Kinetic modeling of in vitro enzymatic reaction networks (ERNs) is severely hampered by the lack of training data. Here, authors introduce a methodology that combines an active learning-like approach and flow chemistry to create optimized datasets for an intricate ERN.

    • Bob van Sluijs
    • , Tao Zhou
    •  & Wilhelm T. S. Huck
  • Review Article
    | Open Access

    Engineering the form and function of root systems and their associated microbiota could provide a means to mitigate adverse climate-driven effects. Here, the authors review the recent developments in plant and rhizobacterial synthetic biology and highlight engineering targets for applications in root systems and rhizosphere.

    • Carin J. Ragland
    • , Kevin Y. Shih
    •  & José R. Dinneny
  • Article
    | Open Access

    Surgery poses significant risks for patients, with attempts to mitigate these risks using multimodal perioperative care pathways. Here, the authors show that preoperative hypercaloric carbohydrate drinks not only alleviate surgical stress but also demonstrates the replicability of this protection using FGF21 treatment alone.

    • Thomas Agius
    • , Raffaella Emsley
    •  & Alban Longchamp
  • Article
    | Open Access

    Age-associated myometrial dysfunction can cause complications during pregnancy and labor. Here, the authors report that aging myometrium is characterized by diminished contractile capillary cells, altered gene expression, and disrupted cellular communication leading to impaired angiogenesis, increased fibrosis and inflammation.

    • Paula Punzon-Jimenez
    • , Alba Machado-Lopez
    •  & Aymara Mas
  • Article
    | Open Access

    Achieving genetic circuits on single DNA molecules could have varied applications. Here, authors observed proteins emerging from single DNA molecules through coupled transcription-translation complexes, and show that nascent proteins lingered on DNA, regulating cascaded reactions on the same DNA and allowing the design of a pulsatile genetic circuit.

    • Ferdinand Greiss
    • , Nicolas Lardon
    •  & Roy Bar-Ziv
  • Article
    | Open Access

    Batch effects hinder multi-sample single-cell data analyses. Here, authors present STACAS, a scalable single-cell RNA-seq data integration tool that uses prior cell type knowledge to preserve biological variability, demonstrating robustness to noisy input cell type labels.

    • Massimo Andreatta
    • , Léonard Hérault
    •  & Santiago J. Carmona
  • Article
    | Open Access

    In contrast to their clinical success as inhibitors and targeting agents, antibodies have generally been ineffective as receptor agonists. Here, Romei et al. leverage a natural homotypic interface to tune antibody geometry, enabling optimization of agonist activity for multiple therapeutic targets.

    • Matthew G. Romei
    • , Brandon Leonard
    •  & Greg A. Lazar
  • Article
    | Open Access

    Xanthohumol is a prenylated flavonoid produced by hops and is an important flavor substance in beer. Here, the authors engineer brewing yeast for the de novo biosynthesis of xanthohumol from glucose by balancing the three parallel biosynthetic pathways.

    • Shan Yang
    • , Ruibing Chen
    •  & Yongjin J. Zhou
  • Article
    | Open Access

    Current cell annotation methods using high-plex spatial proteomics data are resource intensive and demand iterative expert input. Here, the authors present MAPS (Machine learning for Analysis of Proteomics in Spatial biology), an approach that facilitates rapid and precise cell type identification with human-level accuracy from spatial proteomics data.

    • Muhammad Shaban
    • , Yunhao Bai
    •  & Faisal Mahmood