Biotechnology articles within Nature Communications

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  • Article
    | Open Access

    Descriptive data in biomedical research are expanding rapidly, but functional validation methods lag behind. Here, authors present Logical Synthetic cis-regulatory DNA, a framework to design reporters that mark cellular states and pathways, showcasing its applicability to complex phenotypic states.

    • Carlos Company
    • , Matthias Jürgen Schmitt
    •  & Gaetano Gargiulo

  • Article
    | Open Access

    Aerogels are suitable for soft tissue engineering, but often come with brittleness. Here the authors develop a hybrid aerogel with micro- and nanofiber networks that optimizes tensile moduli and fracture energies and show that these materials are super-elastic, fostering rapid tissue ingrowth and allowing minimally invasive procedures.

    • S. M. Shatil Shahriar
    • , Alec D. McCarthy
    •  & Jingwei Xie

  • Article
    | Open Access

    Cell type annotation for single-cell data is challenging. Here, authors explore active and self-supervised learning and introduce adaptive reweighting as a tailored heuristic, demonstrating competitive performance and showing that incorporating prior knowledge enhances cell type annotation accuracy.

    • Michael J. Geuenich
    • , Dae-won Gong
    •  & Kieran R. Campbell

  • Article
    | Open Access

    Obtaining a comprehensive proteomic profile for complex samples is still an elusive task. Here, the authors present an LC-MS/MS workflow including micropillar arrays, wide isolation windows and AI-based data analysis to boost proteomic coverage and throughput for multiple proteomic samples.

    • Manuel Matzinger
    • , Anna Schmücker
    •  & Rupert L. Mayer

  • Article
    | Open Access

    Nanozymes used for antibacterial therapy conventionally have complex catalytic activities that cause multiple pathways in parallel and unwanted outcome. Here, the authors report a Cu-CeO2 single site nanozyme in which Cu single site modification can enhance the peroxidase-like activity and inhibit the hydroxyl radical antioxidant capacity of CeO2 to optimise the antibacterial effects.

    • Peng Jiang
    • , Ludan Zhang
    •  & Yuguang Wang

  • Article
    | Open Access

    Existing tools for structural variations (SVs) calling and merging often lead to fragmented SVs and the potential of introducing unnecessary errors. Here, the authors report the PanPop pipeline to address these issues by implementing sequence-aware SV merging algorithm to efficiently merge SVs of various types.

    • Zeyu Zheng
    • , Mingjia Zhu
    •  & Yongzhi Yang

  • Article
    | Open Access

    CRISPR-based gene drives have the potential to spread within populations and are considered as promising vector control tools. Here the authors show an anti-drive mosquito strain that prevents the spread and collapse of a population suppression gene drive in laboratory Anopheles mosquito large cage trials in complex ecological and behavioral conditions.

    • Rocco D’Amato
    • , Chrysanthi Taxiarchi
    •  & Ruth Müller

  • Article
    | Open Access

    CRISPR-Cas9 genome editing systems have great potential in cancer therapy. Here the authors report a gene-editing delivery system using functionalized nanovesicles derived from E. coli protoplasts to encapsulate Cas9-sgRNA ribonucleoprotein for the selective targeting of Pik3cg in tumor associated macrophages.

    • Mingming Zhao
    • , Xiaohui Cheng
    •  & Junfeng Zhang

  • Article
    | Open Access

    High-throughput electron microscopy demands minimal human intervention and high image quality. Here, authors introduce DeepFocus, a data-driven method for aberration correction in electron microscopy, robust for low SNR images, fast and easily adaptable to microscopes and samples. Peer Review Information: Nature Communications thanks Yang Zhang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

    • P. J. Schubert
    • , R. Saxena
    •  & J. Kornfeld

  • Article
    | Open Access

    Using All of Us pilot data, the authors compared short- and long-read performance across medically relevant genes and showcased the utility of long reads to improve variant detection and phasing in easy and hard to resolve medically relevant genes.

    • M. Mahmoud
    • , Y. Huang
    •  & F. J. Sedlazeck

  • 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

    Efforts to produce aromatic monomers through catalytic lignin depolymerization were focused on aryl–ether bond cleavage, while the carbon–carbon bonds of a large fraction of aromatic monomers in lignin are difficult to cleave. Here, the authors report a catalytic autoxidation method using manganese and zirconium salts as catalysts to cleave the C–C bonds in lignin-derived dimers and oligomers from pine and poplar.

    • Chad T. Palumbo
    • , Nina X. Gu
    •  & Gregg T. Beckham

  • Article
    | Open Access

    Miniature gene editing tools are highly desired for efficient in vivo delivery and disease treatment. Here, the authors reported engineering hypercompact TnpB-ωRNA for robust gene editing with minimal off-target effect in cultured cells and use it to rescue fatal genetic liver disease in a tyrosinaemia mouse model.

    • Zhifang Li
    • , Ruochen Guo
    •  & Chunlong Xu

  • Article
    | Open Access

    Surgery is a primary therapeutic modality for treating melanoma, but it is challenging to tackle tumor recurrence/metastasis and postsurgical wounds. Here the authors report a sprayable hydrogel capable of long-lasting and controllable oxygen supply for preventing tumor recurrence/metastasis and simultaneously promoting wound healing during the postsurgical treatment of melanoma.

    • Shuiling Chen
    • , Yang Luo
    •  & Shaobing Zhou

  • Article
    | Open Access

    Different approaches have been described for the transdermal delivery of drugs. Here the authors report the design of a fluorocarbon modified chitosan-based non-invasive transdermal platform for the delivery of biomacromolecules, such as viral antigens for vaccines or immune checkpoint inhibitors for melanoma immunotherapy.

    • Wenjun Zhu
    • , Ting Wei
    •  & Zhuang Liu

  • Article
    | Open Access

    Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. Here the authors present an engineered yeast strain with 83 sparsely distributed loxPsym sites across the genome can genrerate large-scale genomic rearrangements, which benefits cell fitness under stress and boosts the SCRaMbLE system when combined with synthetic chromosomes.

    • Li Cheng
    • , Shijun Zhao
    •  & Junbiao Dai

  • Article
    | Open Access

    Synthetic microbial communities are suitable for mixed substrates fermentation and long metabolic pathway engineering. Here, the authors combine fermentation experiments with mathematical modeling to reveal the effect of compositional and temporal changes on division of labor in cellulosic ethanol production using two yeast strains.

    • Jonghyeok Shin
    • , Siqi Liao
    •  & Yong-Su Jin

  • Article
    | Open Access

    Aedes aegypti is the main vector of several major pathogens including dengue, Zika and chikungunya viruses. Here the authors find that a CRISPR/Cas9 based split gene drive in Aedes aegypti could successfully bias inheritance up to 89% over successive generations in a multi-cage trial with further deep sequencing suggesting that the multiplexing design could mitigate resistance allele formation.

    • Michelle A. E. Anderson
    • , Estela Gonzalez
    •  & Luke Alphey

  • Article
    | Open Access

    The efficacy of drug-eluting stents remains limited due to delayed reendothelialization, impaired intimal remodeling, and potentially increased late restenosis. Here the authors propose a one-produces-multi stent coating, a drug-free strategy that supports in situ healing of vascular tissues, as demonstrated in rabbit and porcine models.

    • Haoshuang Wu
    • , Li Yang
    •  & Yunbing Wang

  • Article
    | Open Access

    Adipose stem cells are promising therapeutic agents in tissue regeneration. Here the authors develop a lipid nanoparticle/RNA engineering platform to enhance the protein production of these cells, which demonstrate superior healing efficacy in a mouse model of diabetic cutaneous wounds.

    • Yonger Xue
    • , Yuebao Zhang
    •  & Yizhou Dong

  • Article
    | Open Access

    The rapid identification of drug-resistant bacteria is vital for effective treatment and to avoid antibiotic misuse. Here authors report a paper-based sensor which utilises chromogenic carbapenem and cephalosporin substrates for the identification and discrimination of β-lactamase subtypes.

    • Wenshuai Li
    • , Jingqi Li
    •  & Dingbin Liu

  • Article
    | Open Access

    No consensus exists on the computationally tractable use of dynamic models for strain design. To tackle this, the authors report a framework, nonlinear-dynamic-model-assisted rational metabolic engineering design, for efficiently designing robust, artificially engineered cellular organisms.

    • Bharath Narayanan
    • , Daniel Weilandt
    •  & Vassily Hatzimanikatis

  • Article
    | Open Access

    The mechanical dysregulation of cells is associated with several diseases and strategies to deliver drugs based on the “mechanical phenotype” of a cell are desirable. Here, the authors design and characterize DNA mechanocapsules comprised of DNA tetrahedrons that are force responsive, and showed they can encapsulate macromolecular cargo and release it upon application of force.

    • Arventh Velusamy
    • , Radhika Sharma
    •  & Khalid Salaita

  • Article
    | Open Access

    Cas13 systems suffer from a lack of spatiotemporal control. Here the authors report paCas13, a light-inducible Cas13 system created by fusing Magnet with fragment pairs; they also report padCas13, a light-inducible base-editing system by fusing ADAR2 to catalytically inactive paCas13 fragments.

    • Jeonghye Yu
    • , Jongpil Shin
    •  & Won Do Heo

  • Comment
    | Open Access

    While the research community continues to develop novel proposals for intrinsic biocontainment of genetically engineered organisms, translation to real-world deployment faces several challenges.

    • Dalton R. George
    • , Mark Danciu
    •  & Emma K. Frow

  • Article
    | Open Access

    The in-depth study on the sweat–blood partitioning mechanisms of amino acids is promising for noninvasive metabolic monitoring. Here, the authors develop a wearable biochip for sweat phenylalanine multimodal analysis aimed at tracking exercise metabolic risk and exploring the sweat–blood correlation.

    • Bowen Zhong
    • , Xiaokun Qin
    •  & Lili Wang

  • 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

    There is an unmet medical need for the detection and treatment of early adenomas to prevent their progression to malignant disease. Here the authors show that orally administered E. coli Nissle 1917 can selectively colonize adenomas in mouse models and in patients as a detection tool, as well as deliver immunotherapeutics for colorectal neoplasia treatment.

    • Candice R. Gurbatri
    • , Georgette A. Radford
    •  & Tal Danino

  • Article
    | Open Access

    Electrical signals with characteristic parameters for reconstructing neural circuits remain incompletely understood, limiting the therapeutic potential of electrical neuromodulation techniques. Here, the authors demonstrate that dual electrical stimulation at 10–20 Hz rebuilds the spinal sensorimotor neural circuit after spinal cord injury, indicating the characteristic signals of circuit remodeling.

    • Kai Zhou
    • , Wei Wei
    •  & Yaobo Liu

  • Article
    | Open Access

    The Notch receptor is known to be activated by a pulling force, but whether it is strictly required remains to be clarified. Here, the authors demonstrate activation of Notch through soluble multivalent DNA origami constructs, showing effects in neuroepithelial-like stem cells.

    • Ioanna Smyrlaki
    • , Ferenc Fördős
    •  & Björn Högberg

  • Article
    | Open Access

    Here the authors screen different lipid nanoparticle (LNP) formulations for intramuscular delivery of plasmid DNA and uptake by antigen-presenting cells. The lead LNP exhibits immunogenicity and protection in small animal models that is comparable to approved SARS-CoV-2 mRNA vaccine formulations.

    • Lays Cordeiro Guimaraes
    • , Pedro Augusto Carvalho Costa
    •  & Pedro Pires Goulart Guimaraes

  • Article
    | Open Access

    The recent emergence of monoclonal antibodies able to neutralize snake toxins have revolutionized the approach of developing novel therapies to treat snakebite envenoming, at least in animal models. Here, the authors show antibody-dependent enhancement of toxicity (ADET) for a toxin derived from snake venom and highlight the importance of this phenomenon when testing therapeutic antibodies against snake venoms in animal models.

    • Christoffer V. Sørensen
    • , Julián Fernández
    •  & Andreas H. Laustsen

  • Article
    | Open Access

    Organic neural implants hold considerable promise for biocompatible neural interfaces. Here, the authors employ polymer-based organic electrochemical diodes and transistors to develop neuron-sized complex circuits, enabling multiplexing without crosstalk and demonstrate that, when integrated onto ultra-thin plastic, these circuits achieve high performance while maintaining minimal invasiveness.

    • Ilke Uguz
    • , David Ohayon
    •  & Kenneth L. Shepard

  • Article
    | Open Access

    Harvesting biomechanical energy from cardiac motion is an attractive power source for implantable bioelectronic devices. Here, the authors report a battery-free, transcatheter, self-powered intracardiac pacemaker for the treatment of arrhythmia in large animal models.

    • Zhuo Liu
    • , Yiran Hu
    •  & Zhong Lin Wang

  • Article
    | Open Access

    Microneedle patches that can actively address individual needles are challenging to realize. Here, the authors introduce a spatiotemporal on-demand patch for precise and personalized drug delivery, utilizing electrically triggered control with drug-loaded microneedles and biocompatible metallic membranes.

    • Yihang Wang
    • , Zeka Chen
    •  & Wubin Bai

  • Article
    | Open Access

    Ajmaline is an antiarrhythmic monoterpenoid indole alkaloid produced by the root of Rauwolfia serpentina. Here, the authors complete the ajmaline biosynthetic pathway by identifying two reductases and two esterases, and achieve the de novo ajmaline biosynthesis by engineering Baker’s yeast.

    • Jun Guo
    • , Di Gao
    •  & Yang Qu

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