Biotechnology articles within Nature Communications

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  • Article
    | Open Access

    Bacteriophages have great potential in both medicine and biotechnology. Here the authors present PHEIGES, a cell-free method for phage genome engineering, synthesis and selection based on T7, which allows direct selection of engineered and mutant phages without compartmentalization.

    • Antoine Levrier
    • , Ioannis Karpathakis
    •  & Vincent Noireaux

  • Article
    | Open Access

    Inhibiting SARS-CoV-2 interaction with ACE2 is a promising antiviral strategy. Here, the authors show that exosomes derived from human lung spheroid cells expressing hACE2 accumulate in the lung following prophylactic inhalation to bind and neutralize SARS-CoV-2 and protect mice from SARS-CoV-2-induced disease.

    • Zhenzhen Wang
    • , Shiqi Hu
    •  & Ke Cheng

  • Article
    | Open Access

    Binning is an essential step in genome-resolved metagenomic analysis in which assembled contigs originating from the same source population are clustered. However it is challenging, especially for low abundance microbial species. Here the authors introduce a toolkit that integrates multiple prominent binning tools and AI for efficient and high-resolution recovery of non-redundant bins from short- and long-read metagenomic sequencing datasets.

    • Zhiguang Qiu
    • , Li Yuan
    •  & Ke Yu

  • Article
    | Open Access

    Current gene silencing tools can have drawbacks. Here the authors report CRISPRδ, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13): they also show that fusion of a translational repressor to dCas13 further improved the performance.

    • Antonios Apostolopoulos
    • , Naohiro Kawamoto
    •  & Shintaro Iwasaki

  • Article
    | Open Access

    The delivery of therapeutic payloads and living vectors to tumors remains a clinical challenge. Here the authors explore a spatially targeted control strategy applying torque density to magnetotactic bacteria, demonstrating feasibility in vitro and in vivo.

    • Nima Mirkhani
    • , Michael G. Christiansen
    •  & Simone Schuerle

  • Article
    | Open Access

    Activatable afterglow luminescence nanoprobes reduce unspecific signals and improve imaging fidelity, but their utility is limited by a requisition of donor-acceptor distance (>10 nm) in common biomarker-activatable designs. Here, the authors address this issue by developing organic afterglow luminescence cocktail nanoparticles for acid-activatable upconversion afterglow luminescence imaging.

    • Yue Jiang
    • , Min Zhao
    •  & Qingqing Miao

  • Article
    | Open Access

    Compared to traditional Cas9 nucleases prime editors (PEs) are less active. Here the authors use OrthoRep, a yeast-based platform for directed protein evolution to enhance the editing efficiency of PEs: they identify mutations that have a positive effect on kinetics and use this knowledge to generate an efficient in vivo PE.

    • Yanik Weber
    • , Desirée Böck
    •  & Gerald Schwank

  • Article
    | Open Access

    Engineered biosensing bacteria can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. Here the authors present a robust biocontainment assisted by Cas9 and an engineered gene expression control combined in a genetically engineered human commensal bacterium that successfully functioned in a mouse intestinal tract as well as cell culture condition.

    • Naoki Hayashi
    • , Yong Lai
    •  & Timothy K. Lu

  • Article
    | Open Access

    Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are currently extracted from low-yielding daffodils. Here, authors pair biosensor-assisted screening with machine learning-guided protein design to rapidly engineer an improved Amaryllidaceae enzyme in a microbial host.

    • Simon d’Oelsnitz
    • , Daniel J. Diaz
    •  & Andrew D. Ellington

  • Article
    | Open Access

    Bioresorbable neural implants offer a promising solution to the challenges of secondary surgeries required for the removal of implanted devices. Here, the authors introduce a fully bioresorbable flexible hybrid opto-electronic system for simultaneous electrophysiological recording and optogenetic stimulation.

    • Myeongki Cho
    • , Jeong-Kyu Han
    •  & Ki Jun Yu

  • Article
    | Open Access

    Rational antibody engineering can greatly improve the clinical value of therapeutic antibodies. Here authors describe ISB 1442, a fully human bispecific antibody, consisting of two targeting modules against two different epitopes on CD38, combined with a targeting module blocking CD47 and engineered effector properties, to enhance complement dependent cytotoxicity, antibody dependent cells cytotoxicity and antibody dependent cell phagocytosis to combat multiple myeloma.

    • C. Grandclément
    • , C. Estoppey
    •  & S. Sammicheli

  • Article
    | Open Access

    Fruits contain a large variety of cis-diols but their rapid and direct analysis without complex sample pretreatment was not achieved. Here, the authors report a Mycobacterium smegmatis porin A nanopore modified with a phenylboronic acid adapter for recognition of 1,2-diphenols, alditols, α-hydroxy acids and saccharides in fruits.

    • Pingping Fan
    • , Zhenyuan Cao
    •  & Shuo Huang

  • Article
    | Open Access

    All natural AAV serotypes transduce murine hepatocytes more efficiently than their human counterparts in human liver chimeric mouse models. Here the authors developed a novel humanized mouse were human transduction of AAV can be studied.

    • Mercedes Barzi
    • , Tong Chen
    •  & Karl-Dimiter Bissig

  • Article
    | Open Access

    Artificial biomolecular condensates are valuable tools to study the design principles of phase separation. Here, the authors demonstrate and characterize a model system of artificial DNA condensates whose kinetic formation and dissolution depends on DNA inputs that activate or deactivate the phase separating DNA subunits.

    • Siddharth Agarwal
    • , Dino Osmanovic
    •  & Elisa Franco

  • Article
    | Open Access

    Winged bean is a tropical legume that can produce similar level of seed protein to soybean. Here, the authors report the genome assembly, population genetics, QTL mapping of the plant architecture, protein content and phytonutrients for this species.

    • Wai Kuan Ho
    • , Alberto Stefano Tanzi
    •  & Sean Mayes

  • Article
    | Open Access

    Identifying pulmonary delivery of lipid libraries poses an obstacle for mRNA drugs. Here, the authors use a barcoded screening system to identify lung-targeting of cationic, degradable lipid-like materials for mRNA delivery and gene editing in female preclinical models.

    • Lulu Xue
    • , Alex G. Hamilton
    •  & Michael J. Mitchell

  • Perspective
    | Open Access

    The development of human cellular models of aging that surpass the limitations of animal models of aging is urgent. Here, the authors explore the opportunities and limitations of cellular reprogramming to create reliable aging in vitro models and their potential for the discovery of anti-aging compounds.

    • Patricia R. Pitrez
    • , Luis M. Monteiro
    •  & Lino Ferreira

  • 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

    Manual processes to produce ocular prostheses are time-consuming and yield varying quality. Here, authors present an automatic digital end-to-end process for custom ocular prostheses. It creates shape and appearance from image data of an OCT device and produces them using a full-colour 3D printer.

    • Johann Reinhard
    • , Philipp Urban
    •  & Mandeep S. Sagoo

  • 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

    Branched ionizable lipids have aroused great interest for mRNA delivery. Here, the authors devise an in situ construction method for combinatorial synthesis of degradable branched ionizable lipids and summarize key design criteria to enable potent delivery of mRNA therapeutics and gene editors.

    • Xuexiang Han
    • , Junchao Xu
    •  & Michael J. Mitchell

  • Article
    | Open Access

    The delivery of CRISPR RNPs has potential advantages over other genome editing approaches, including reduced off-target editing and reduced immunogenicity. Here the authors report self-deliverable Cas9 RNPs capable of robustly editing cultured cells in vitro and the mouse brain upon direct injections.

    • Kai Chen
    • , Elizabeth C. Stahl
    •  & Jennifer A. Doudna

  • Article
    | Open Access

    A key aim in the development of diagnostic assays is improving diagnostic speed while maintaining sensitivity. Here the authors report an approach for the rapid and accurate analysis of lateral flow tests, which integrates time-series deep learning and AI verification, achieving a diagnostic time of 1-2 minutes.

    • Seungmin Lee 
    • , Jeong Soo Park
    •  & Jeong Hoon Lee

  • Article
    | Open Access

    Spatial imaging methods in lipid research can disrupt tissue integrity and can have limited spatial and spectral resolution. Here, the authors present an SRS-based hyperspectral imaging platform to visualise lipids and lipoproteins in a variety of tissues and animal species.

    • Wenxu Zhang
    • , Yajuan Li
    •  & Lingyan Shi

  • 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

    Profiling antibody responses to vast antigenic spaces has been challenging using programmable phage display (PhIP-Seq). Here, authors develop a methodology for compressing large proteomic spaces and have discovered human antibodies targeting gut bacteria-infecting phages.

    • Anna-Maria Liebhoff
    • , Thiagarajan Venkataraman
    •  & H. Benjamin Larman

  • Article
    | Open Access

    Limited tumor cell delivery is a major challenge for the efficacious delivery of siRNAs to silence traditionally undruggable oncogenes. Here the authors optimize siRNAs for in situ binding to albumin through C18 lipid modifications and show the application of the lead conjugate structure for targeting MCL1 in orthotopic breast tumors in mice.

    • Ella N. Hoogenboezem
    • , Shrusti S. Patel
    •  & Craig L. Duvall

  • Article
    | Open Access

    The assembly of oligopeptide and polypeptide molecules can reconstruct various ordered advanced structures. Here the authors develop a “molecular velcro”-inspired amphiphilic supramolecular co-assembly strategy, which improves the mechanical strength and cartilaginous regeneration efficiency through conformation transition.

    • Chengkun Zhao
    • , Xing Li
    •  & Yong Sun

  • Article
    | Open Access

    Vascularization remains a significant challenge in organoid technology. Here, the authors develop a microfluidic platform that enhances organoid growth, function and maturation, by establishing functional perfusable vascular networks.

    • Clément Quintard
    • , Emily Tubbs
    •  & Xavier Gidrol

  • Article
    | Open Access

    Conditional degradation of proteins is instrumental to advance our knowledge of cell biology but has been lacking for organelles like mitochondria. Here, the authors develop a proteolysis system based on the mycoplasma Lon protease that functions selectively within mitochondria in yeast and human cells.

    • Swastika Sanyal
    • , Anna Kouznetsova
    •  & Camilla Björkegren

  • Article
    | Open Access

    The Tibetan Plateau is the largest plateau in the world and hosts a variety of aquatic ecosystems. Here, the authors present a gene and genome catalogue of Tibetan Plateau aquatic microbiomes, greatly expanding known taxonomic and functional diversity for the region and giving insights into its microbial biogeography.

    • Mingyue Cheng
    • , Shuai Luo
    •  & Kang Ning

  • Comment
    | Open Access

    Selecting omic biomarkers using both their effect size and their differential status significance (i.e., selecting the “volcano-plot outer spray”) has long been equally biologically relevant and statistically troublesome. However, recent proposals are paving the way to resolving this dilemma.

    • Thomas Burger

  • Article
    | Open Access

    The most recent class of base editors utilize DddAtox, a deaminase domain that can act upon double-stranded DNA. Here the authors target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers; they also identify a variety of DddAtox orthologues.

    • Friedrich Fauser
    • , Bhakti N. Kadam
    •  & Jeffrey C. Miller

  • Article
    | Open Access

    Most RNA velocity models extract dynamics from the phase delay between unspliced and spliced mRNA for each gene. Here, authors propose TFvelo, broadening RNA velocity beyond splicing information to include gene regulation. TFvelo accurately models genes dynamics and infers cell pseudo-time from RNA abundance data.

    • Jiachen Li
    • , Xiaoyong Pan
    •  & Hong-Bin Shen

  • Article
    | Open Access

    Injectable pro-regenerative biomaterials are vital for developing minimally invasive regenerative treatment, but impeded by brittleness and lack of biological functions. Here the authors address these issues by engineering injectable functionalized composites that facilitate the sequential release of IL-4 and IGF-1 to regulate macrophages and stem cell behavior for enhanced in situ regeneration.

    • Yi Li
    • , Siyang Liu
    •  & Meifeng Zhu

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