Biotechnology articles within Nature Communications

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  • Article
    | Open Access

    Various GPCRs display constitutive ligand-independent activity, but it remains unclear whether ligand-dependent and -independent conformations differ. Here the authors demonstrate the recognition and blocking of G protein recruitment of either the ligand-bound active, or the constitutively active apo-conformation of the viral GPCR US28 by different nanobodies that target similar intracellular loops of the receptor.

    • Timo W. M. De Groof
    • , Nick D. Bergkamp
    •  & Martine J. Smit

  • Article
    | Open Access

    Self-powered implantable devices have the potential to extend device operation, though current energy harvesters are both insufficient and inconvenient. Here the authors report on a commercial coin battery-sized high-performance inertia-driven triboelectric nanogenerator based on body motion and gravity that can be used to charge a lithium-ion battery and integrated into a cardiac pacemaker.

    • Hanjun Ryu
    • , Hyun-moon Park
    •  & Sang-Woo Kim

  • Article
    | Open Access

    Current methods to estimate energy expenditure are either infeasible for everyday use or associated with significant errors. Here the authors present a Wearable System using inertial measurement units worn on the shank and thigh that estimates metabolic energy expenditure in real-time during common steady-state and time-varying activities.

    • Patrick Slade
    • , Mykel J. Kochenderfer
    •  & Steven H. Collins

  • Article
    | Open Access

    Finding durable, high-density media for data storage is necessary to support the ever-expanding generation of digital data. Here, the authors use peptide sequences to store digital data and retrieve them using tandem mass spectrometry, proving that peptides can be used as a storage medium.

    • Cheuk Chi A. Ng
    • , Wai Man Tam
    •  & Zhong-Ping Yao

  • Article
    | Open Access

    Single-cell RNA-seq reveals the cellular heterogeneity in development and disease. Here the authors present a single-nucleus RNA-seq2 that allows deep characterization of nuclei isolated from frozen archived tissues, apply it for transcriptional profiling of individual hepatocytes, and determine a functional crosstalk between liver zonation and ploidy.

    • M. L. Richter
    • , I. K. Deligiannis
    •  & C. P. Martinez-Jimenez

  • Article
    | Open Access

    Phospholipase A2 (PLA2) inhibitors have been shown to be able to treat acute pancreatitis, but are toxic with systemic application. Here the authors design a nanoparticle with macrophage membrane components to carry PLA2 inhibitor to macrophages and treat pancreatitis in mice, with no evidence of toxicity.

    • Qiangzhe Zhang
    • , Julia Zhou
    •  & Liangfang Zhang

  • Article
    | Open Access

    Shape memory scaffolds are needed for minimally invasive tissue repair and void filling. Here the authors report on the development of 4D printed polycarbonate-based scaffolds with surface degradation properties which fill voids without deforming tissue and allow for tissue ingrowth with reduced immune response.

    • Andrew C. Weems
    • , Maria C. Arno
    •  & Andrew P. Dove

  • Article
    | Open Access

    Limited understanding of the interactions between nanoparticle drug carriers and the blood-brain barrier underlies many translational failures in treatments of brain disorders. Here the authors use two-photon microscopy in mice to characterize the receptor-mediated transcytosis of nanoparticles at all steps of delivery from the blood to the brain in vivo.

    • Krzysztof Kucharz
    • , Kasper Kristensen
    •  & Martin Johannes Lauritzen

  • Article
    | Open Access

    Oncogenic RAS mutants remain difficult to target with small molecules. Here, the authors show that RAS-binding Affimer proteins inhibit RAS signaling while binding diverse regions on the RAS surface, suggesting the potential to use Affimers as tools to identify new binding pockets and pharmacophores.

    • Katarzyna Z. Haza
    • , Heather L. Martin
    •  & Darren C. Tomlinson

  • Article
    | Open Access

    Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.

    • Joanne M. L. Ho
    • , Corwin A. Miller
    •  & Matthew R. Bennett

  • Article
    | Open Access

    Current near-IR optogenetic systems to regulate transcription consist of a number of large protein components. Here the authors report a smaller single-component near-IR system, iLight, developed from a bacterial phytochrome that they use to control gene transcription in bacterial and mammalian cells.

    • Andrii A. Kaberniuk
    • , Mikhail Baloban
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    The gene regulatory network controlling the bifurcation of common progenitors into the neural retina and retinal-pigmented epithelium programs remains poorly understood. Here the authors study transcriptome dynamics and chromatin accessibility during this process in zebrafish, revealing network redundancy, as well as context-dependent and sequential transcription factor activity.

    • Lorena Buono
    • , Jorge Corbacho
    •  & Juan-Ramón Martínez-Morales

  • Article
    | Open Access

    Here, the authors report de novo design, optimization and characterization of tRNAs that decode UGA stop codons in E. coli. The structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon suggests that distinct A-site ligands (tRNAs versus release factors) induce distinct conformation of the stop codon within the mRNA in the decoding center.

    • Suki Albers
    • , Bertrand Beckert
    •  & Zoya Ignatova

  • Article
    | Open Access

    Optimizing the concentration of different functional peptides on a surface can be a complex process. Here, the authors report on the use of a click immobilization strategy to create gradients of two different functional peptides on a surface to screen different density functions for rapid optimization.

    • Zhou Fang
    • , Junjian Chen
    •  & Chuanbin Mao

  • Article
    | Open Access

    Postsurgical adhesions are a problem during routine cardiothoracic procedures. Here, the authors report on a catechol functionalised hydrogel as an anti-adhesion material with improved retention on the heart which is biocompatible and biodegradable with minimal swelling, demonstrating application in vivo.

    • Masaki Fujita
    • , Gina M. Policastro
    •  & Karen L. Christman

  • Article
    | Open Access

    Base editing is one approach used to correct mutations causing cause Duchenne muscular dystrophy (DMD), but limitations are in the requirement for a specific PAM motif and the large size beyond the packaging capacity of adeno-associated virus (AAV). Here, the authors modify the NG-targeting adenine base editor to recognize a broader PAM, devise an intein split strategy to package the otherwise oversized adenine base editor into AAV, and show it efficiently restores dystrophin expression in muscle and heart when systemically injected in a mouse model of DMD

    • Li Xu
    • , Chen Zhang
    •  & Renzhi Han

  • Article
    | Open Access

    Single cell RNA-seq loses spatial information of gene expression in multicellular systems because tissue must be dissociated. Here, the authors show the spatial gene expression profiles can be both accurately and robustly reconstructed by a new computational method using a generative linear mapping, Perler.

    • Yasushi Okochi
    • , Shunta Sakaguchi
    •  & Honda Naoki

  • Article
    | Open Access

    Biomedical glues often face a challenge in providing strong adhesion and providing remodelling capabilities. Here the authors report on the development of a biocompatible and biodegradable protein-based coacervate adhesive and demonstrate application in haemostasis and wound healing using pig models.

    • Chao Ma
    • , Jing Sun
    •  & Andreas Herrmann

  • Article
    | Open Access

    Dysfunction of the lymphatic system leads to secondary lymphedema and results in degradation of quality of life. Here, the authors show that delivery of nucleoside-modified Vascular Endothelial Growth Factor C (VEGFC) mRNA, encapsulated in lipid nanoparticles, induces organ-specific lymphatic growth and reverses experimental lymphedema.

    • Dániel Szőke
    • , Gábor Kovács
    •  & Zoltán Jakus

  • Article
    | Open Access

    SERS assays have potential for multiplexed detection of biomarkers but differentiation of SERS tags remains a challenge. Here, the authors report the creation of 14 distinct geometrically controlled metal carbonyl tags and demonstrate multiplexed detection of nasopharyngeal carcinoma biomarkers from patient blood.

    • Duo Lin
    • , Chang-Lin Hsieh
    •  & Kien Voon Kong

  • Article
    | Open Access

    Cell based materials production has potential for generating diverse materials with a range of functions. Here, the authors report development of living fabrication of biohybrid semi interpenetrating polymer networks by encapsulating protein producing bacteria within polymer microcapsules.

    • Zhuojun Dai
    • , Xiaoyu Yang
    •  & Lingchong You

  • Article
    | Open Access

    The effect of fallopian tube’s curvature on sperm motion has not been studied in detail. Here, the authors use droplet microfluidics to create soft curved interfaces, revealing a dynamic switch in sperm motility from a progressive surface-aligned mode at low curvatures, to an aggressive surface-attacking mode at high curvatures.

    • Mohammad Reza Raveshi
    • , Melati S. Abdul Halim
    •  & Reza Nosrati

  • Article
    | Open Access

    A promising strategy to increase product synthesis from bacteria uses inducible systems to switch metabolism to production. Here, the authors use models to show how engineering positive feedback loops into the genetic circuitry creates a switch that requires only temporary induction with a cheap nutrient to switch metabolism irreversibly, and so drastically reduce inducer use and cost.

    • Ahmad A. Mannan
    •  & Declan G. Bates

  • Article
    | Open Access

    Current methods for the modular assembly of biomaterials are associated with limitations. Here the authors implement vapor-phase deposition to fabricate 3D polymeric materials that permit biomolecule functionalization, tunable mass transport and mechanical properties, as well as control over boundaries between compartments, and analyze the behavior of 3D encapsulated cells.

    • Chih-Yu Wu
    • , Ting-Ying Wu
    •  & Hsien-Yeh Chen

  • Perspective
    | Open Access

    Effective biological engineering requires the acknowledgement of evolution and its consideration during the design process. In this perspective, the authors present the concept of the evotype to reason about and shape the evolutionary potential of natural and engineered biosystems.

    • Simeon D. Castle
    • , Claire S. Grierson
    •  & Thomas E. Gorochowski

  • Article
    | Open Access

    Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.

    • Karoline Holler
    • , Anika Neuschulz
    •  & Jan Philipp Junker

  • Article
    | Open Access

    The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.

    • Jianping Zhang
    • , Timothy C. Hewitt
    •  & Evans S. Lagudah

  • Article
    | Open Access

    Current tissue engineering strategies lack materials that promote angiogenesis. Here the authors develop a microfluidic in vitro model in which chemokine-guided endothelial cell sprouting into a tunable hydrogel is followed by the formation of perfusable lumens to determine the material properties that regulate angiogenesis.

    • Jifeng Liu
    • , Hongyan Long
    •  & Britta Trappmann

  • Article
    | Open Access

    Existing studies of the chromatin accessibility, the primary mark of regulatory DNA, in Arabidopsis are based mainly on bulk samples. Here, the authors report the regulatory landscape of Arabidopsis thaliana roots at single-cell resolution.

    • Michael W. Dorrity
    • , Cristina M. Alexandre
    •  & Josh T. Cuperus

  • Article
    | Open Access

    Antibody-based Wnt agonists are able to phenocopy Wnt signaling in vivo resulting in increased bone density, repair, and strength. Here, the authors show that Wnt agonists can reverse bone loss associated with ovariectomy and build stronger bone when administered after fracture.

    • Tristan W. Fowler
    • , Troy L. Mitchell
    •  & Yang Li

  • Article
    | Open Access

    Macrophages perform diverse functions during immune responses, but the molecular mechanisms by which physical properties of the tissue regulate macrophage behavior remain unknown. Here the authors find that Piezo1 is a mechanosensor of stiffness, and that its activity modulates macrophage polarization responses.

    • Hamza Atcha
    • , Amit Jairaman
    •  & Wendy F. Liu

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