Biotechnology articles within Nature Communications

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  • Article
    | Open Access

    A pan-genome can reduce bias in genetic diversity analysis inherent in using a single reference genome. Here, the authors assemble genomes of 10 diverse apple accessions, conduct pan-genome analysis together with three existing genomes, and reveal the role of mitogen-activated protein kinase homolog MMK2 in fruit coloration.

    • Ting Wang
    • , Shiyao Duan
    •  & Ting Wu

  • Article
    | Open Access

    Current techniques for visualizing cell generated forces suffer from throughput limitations. Here, Gu et al. introduced photonic crystal cellular force microscopy, inspired by chameleons, enabling visualization and quantification of vertically directed cell forces, well-suited for drug screening.

    • Qiwei Li
    • , Zaozao Chen
    •  & Zhongze Gu

  • Article
    | Open Access

    Among all wheat rust resistance genes, SR9 has the largest number of alleles. Here, the authors use gene cloning, complementation and comparative genetics to resolve the relationship among Sr9 alleles, confirm their allelic identities, and show that a single amino acid change leads to resistance to Ug99.

    • Jianping Zhang
    • , Jayaveeramuthu Nirmala
    •  & Evans Lagudah

  • Article
    | Open Access

    Cell therapy is a promising treatment for brain injury, but it is unclear if transplanted neurons demonstrate population dynamics. By monitoring transplanted neurons in injured mice, here the authors show the emergence of dynamics resembling intact networks.

    • Harman Ghuman
    • , Kyungsoo Kim
    •  & Karunesh Ganguly

  • Article
    | Open Access

    Enveloped viruses encased within a lipid bilayer membrane are highly contagious and cause diseases like influenza and COVID-19, so strategies for their prevention and inactivation are needed. Here, the authors develop a diatomic iron nanozyme with lipoxidase-like activity for the inactivation of enveloped viruses, where the diatomic iron sites destroy the viral envelope via lipid peroxidation.

    • Beibei Li
    • , Ruonan Ma
    •  & Yadong Li

  • Article
    | Open Access

    Despite promising advantages, bioresorbable electronics face practical limitations due to unpredictable device lifetimes. Here, the authors introduce an on-demand bioresorbable neurostimulator powered by biosafe ultrasound to treat peripheral nerve injury and neuropathies.

    • Dong-Min Lee
    • , Minki Kang
    •  & Sang-Woo Kim

  • Article
    | Open Access

    Roughly 10% of Cystic Fibrosis (CF) patients still have no effective medicine to take. Lung Selective Organ Targeting (SORT) Lipid Nanoparticles can efficiently deliver Cas9 mRNA, sgRNA, and donor ssDNA templates for precise homology-directed repair-mediated gene correction in ex vivo and in vivo CF models.

    • Tuo Wei
    • , Yehui Sun
    •  & Daniel J. Siegwart

  • Article
    | Open Access

    Sufficient supply of sulfonate group donor is critical to biomanufacturing of the sulfate containing compounds. Here, the authors engineer two sulfonate group donor regeneration systems, including 3'-phosphoadenosine-5'-phosphosulfate and the newly discovered 5'-phosphosulfate, to boost biosynthesis of sulfated compounds.

    • Ruirui Xu
    • , Weijao Zhang
    •  & Zhen Kang

  • Article
    | Open Access

    Pseudotime analysis is prevalent in single-cell RNA-seq, but it remains challenging to perform it across multiple samples and experimental conditions. Here, the authors develop Lamian, a computational framework for multi-sample pseudotime analysis that adjusts for biological and technical variation to detect gene program changes along cell trajectories and across conditions.

    • Wenpin Hou
    • , Zhicheng Ji
    •  & Hongkai Ji

  • Article
    | Open Access

    Unlocking the blood proteome requires exquisite sensitivity and multiplexing to detect low and high abundance proteins simultaneously. Here the authors describe a 200-plex immunoassay with attomolar sensitivity to detect important low abundance proteins in inflammatory diseases and COVID-19.

    • Wei Feng
    • , Joanne C. Beer
    •  & Xiao-Jun Ma

  • Article
    | Open Access

    Epacadostat is a selective IDO1 inhibitor shown to promote anti-tumor immune responses in preclinical models, however it has failed in a Phase III clinical trial for treating metastatic melanoma. Here the authors design a sphingomyelin-derived nanovesicle system for epacadostat delivery with improved pharmacokinetics and anti-tumor activity when combined with a PD-1 inhibitor in melanoma preclinical models.

    • Zhiren Wang
    • , Wenpan Li
    •  & Jianqin Lu

  • Article
    | Open Access

    Oxygen is the most limiting factor in cell transplantation. Here, the authors present an on-site oxygen production platform for implantable cell therapeutics via electrocatalytic water electrolysis, demonstrating the maintenance of high cell loading in hypoxic incubation and a rat model.

    • Inkyu Lee
    • , Abhijith Surendran
    •  & Tzahi Cohen-Karni

  • Article
    | Open Access

    Deep learning holds a great promise for the discovery and design of bioactive peptides, but experimental approaches to validate candidates in high throughput and at low cost are needed. Here, the authors combine deep learning and cell free biosynthesis for antimicrobial peptide (AMP) development and identify 30 functional AMPs, of which six with broad-spectrum activity against drug-resistant pathogens.

    • Amir Pandi
    • , David Adam
    •  & Tobias J. Erb

  • Article
    | Open Access

    Reperfusion is a main strategy for restoring blood supply after ischemic stroke, but it induces neuroinflammation that undergoes dynamic progression, hindering the treatment of ischemic stroke. Here, the authors report a pathogenesis-adaptive nanosystem for sequential and on-demand regulation of reperfusion-induced dynamic neuroinflammation for ischemic stroke therapy.

    • Di Wu
    • , Jing Zhou
    •  & Zhong Chen

  • Article
    | Open Access

    It is needed yet difficult to achieve a strategy for synthesizing single-atom nanozymes that integrate atomic metal dispersion, elevated mass transport and tailorable coordination environment. Here, the authors address this issue by developing a biomimetic synthetic strategy and demonstrate the application of the resultant single-atom Fe nanozymes for tumor visual identification.

    • Da Chen
    • , Zhaoming Xia
    •  & Yongquan Qu

  • Article
    | Open Access

    Overexpression of human antigen R (HuR) correlates with high grade tumours and poor patient prognosis. Here, the authors engineer a TRIM21 biological PROTAC to demonstrate the benefit of a targeted protein degradation approach to deplete HuR, resulting in tumour growth inhibition in pre-clinical cancer models by altering the HuR-regulated proteome.

    • Alice Fletcher
    • , Dean Clift
    •  & James Hunt

  • Article
    | Open Access

    Therapeutic modulation of Janus kinase family enzymes is an established approach for inflammatory and autoimmune skin diseases. Here the authors rationally design small interfering RNAs to enable single Janus kinase targeting and test this new therapeutic approach in a skin disease model for maintaining efficacy and improving selectivity.

    • Qi Tang
    • , Hassan H. Fakih
    •  & John E. Harris

  • Article
    | Open Access

    The meninges protect the central nervous system at the brain border, and its dysfunction can lead to neural inflammation and cell damage. Here, the authors uncover the gene signatures of diverse cell types in the aged human leptomeninges and highlight their changes in Alzheimer’s Disease.

    • Nicola A. Kearns
    • , Artemis Iatrou
    •  & Yanling Wang

  • 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

    Despite delivering gene-specific silencing, the use of deoxyribozymes (DNAzymes) for cancer therapy is limited by toxicity due to off-target effects. Here, the authors develop a multi-component DNAzyme, targeting both miRNA21 and HSP70, to induce tumour-specific sensitisation to photothermal therapy in preclinical models of pancreatic cancer.

    • Jiaqi Yan
    • , Xiaodong Ma
    •  & Hongbo Zhang

  • Article
    | Open Access

    l-Lactate is increasingly recognized as a key metabolite and signalling molecule in mammals, but the methods to investigate it in vivo have been limited. Here, authors report a pair of improved biosensors—one green and one red—for visualizing l-lactate both inside and outside of cells.

    • Yusuke Nasu
    • , Abhi Aggarwal
    •  & Robert E. Campbell

  • Article
    | Open Access

    Microbial communication has significant implications for industrial applications, but constructing communication systems which support coordinated behaviors is challenging. Here, the authors report an electron transfer triggered redox communication network and demonstrate its ability to coordinate microbial metabolism.

    • Na Chen
    • , Na Du
    •  & Quan Yuan

  • Article
    | Open Access

    Many diseases are driven by the insufficient expression of critical genes, but few technologies are capable of rescuing these endogenous protein levels. Here, Cao et al. present an RNA-based technology that boosts protein production from endogenous mRNAs by upregulating their translation.

    • Yang Cao
    • , Huachun Liu
    •  & Bryan C. Dickinson

  • Article
    | Open Access

    Unnatural base pairing xenonucleic acids (XNAs) can be used to expand life’s alphabet beyond ATGC. Here, authors show strategies for enzymatic synthesis and next-generation nanopore sequencing of XNA base pairs for reading and writing 12-letter DNA (ATGCBSPZXKJV).

    • Hinako Kawabe
    • , Christopher A. Thomas
    •  & Jorge A. Marchand

  • Article
    | Open Access

    The multiplex CRISPR system is the tool of choice for creating targeted tandemly arrayed genes (TAGs) deletions in plants. Here, the authors show that up to 80% of CRISPR-mediated TAG knockout alleles in Arabidopsis and rice are deletion-inversion bi-alleles, an unwanted products of targeted TAG deletions.

    • Jiuer Liu
    • , Feng-Zhu Wang
    •  & Jian-Feng Li

  • Article
    | Open Access

    Regulated cholesterol transport is essential for the maintenance of cellular cholesterol distribution and homeostasis, but tools to monitor this process are limited. Here, the authors develop a genetically encoded cholesterol biosensor and demonstrate its use for visualising cellular cholesterol distribution in various live cells in real time.

    • Dylan Hong Zheng Koh
    • , Tomoki Naito
    •  & Yasunori Saheki

  • Article
    | Open Access

    Cost, scalability, and durability are critical factors determining the application of artificial photosynthesis systems. Here, the authors address these problems by inserting a carbon nanofiber into the chloroplast of green algae to transfer of electrons for photosynthesis and demonstrate H2 production up to 50 days.

    • Hyo Jin Gwon
    • , Geonwoo Park
    •  & Hyun S. Ahn

  • Article
    | Open Access

    KRASG12D mutations frequently co-occur with mutated TP53 tumour suppressor in patients with pancreatic ductal adenocarcinoma (PDAC). Here the authors report the design of dual targeted therapeutic extracellular vesicles containing high copy numbers of TP53 mRNA and siKRASG12D, showing anti-tumor activity in PDAC preclinical models.

    • Chi-Ling Chiang
    • , Yifan Ma
    •  & L. James Lee

  • Article
    | Open Access

    Current methods to generate spheroids are associated with low production throughputs, limiting clinical and industrial translation. Here the authors present a clean ultra-high-throughput in-air microfluidic platform for mass production of lumenogenic embryoid bodies and functional cardiospheres.

    • Bas van Loo
    • , Simone A. ten Den
    •  & Jeroen Leijten

  • 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

    Synthetic gene networks in mammalian cells are currently limited to either transcription factors or RNA regulators. Here, the authors develop a regulatory approach based on circular single-stranded DNA, which can be used as a conformationally switchable genetic vector in mammalian cells.

    • Linlin Tang
    • , Zhijin Tian
    •  & Jie Song

  • Article
    | Open Access

    Endo-lysosomal escape is a highly inefficient process. Here the authors present a lipid-based nanoscale molecular machine that achieves efficient cytosolic transport of biologics by destabilizing endo-lysosomal compartments through nanomechanical action upon light irradiation.

    • Yu Zhao
    • , Zhongfeng Ye
    •  & Qiaobing Xu

  • Article
    | Open Access

    The development of liposome-based drug delivery systems has been hindered by the systemic toxicity and limited duration of effect due to insufficient drug loading and leakage of payload. Here the authors address these issues by designing aromatized liposomes that feature increased drug loading and slowed release compared to conventional liposomes.

    • Yang Li
    • , Tianjiao Ji
    •  & Daniel S. Kohane

  • Article
    | Open Access

    There is an emerging interest in the use of mRNA therapeutics in cancer treatment, but their precise in vivo delivery remains a challenge. Here the authors develop IFN-γ mRNA-loaded small extracellular vesicles (sEVs) with CD64 overexpressed on their surface and demonstrate its efficacy in glioblastoma mouse models resistant to immunotherapy.

    • Shiyan Dong
    • , Xuan Liu
    •  & Wen Jiang

  • Article
    | Open Access

    Nonribosomal peptides have diverse bioactivities and can possess unusual moieties at their C-terminus, such as polyamines. In this study, the authors identify a class of dodecapeptides glidonins that feature diverse N-terminal modifications and a uniform putrescine moiety at the C-terminus, elucidate their biosynthesis, and introduce the putrescine into the C-terminus of other nonribosomal peptides.

    • Hanna Chen
    • , Lin Zhong
    •  & Xiaoying Bian

  • Article
    | Open Access

    Large genes require dual adeno-associated viral (AAV) vectors for in vivo delivery/expression, but current methods have limitations. Here the authors develop and functionally evaluate REVeRT, an efficient and flexible dual AAV vector technology based on reconstitution via mRNA trans-splicing.

    • Lisa Maria Riedmayr
    • , Klara Sonnie Hinrichsmeyer
    •  & Elvir Becirovic

  • Article
    | Open Access

    Exogenous control of genes in vivo is important. Here the authors report a system that can be inducibly activated through thermal energy produced by ultrasound absorption and use this to control induction of gene activation and base editing: they apply this in cell lines and in a mouse model.

    • Pei Liu
    • , Josquin Foiret
    •  & Lei S. Qi

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