Biotechnology articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Here the authors develop perfusable inner blood-retinal barrier-specific microvascular networks with human primary retinal microvascular cells. They show that chronic diabetic stimulation leads to the generation of early hallmarks of diabetic retinopathy, including pericyte and capillary dropout, ghost vessels, and inflammation.

    • Thomas L. Maurissen
    • , Alena J. Spielmann
    •  & Héloïse Ragelle

  • Article
    | Open Access

    Evolution of SARS-CoV-2 and emergence of other sarbecoviruses are of potential concern. Here, the authors designed a trivalent spike-protein-nanoparticle vaccine that elicits neutralizing antibodies and protects female hamsters against challenges with SARS-CoV-2-like and SARS-CoV-1-like coronaviruses.

    • Peter J. Halfmann
    • , Kathryn Loeffler
    •  & Ravi S. Kane

  • Article
    | Open Access

    Tissue adhesives have received significant interest for their clinical utility but are typically incompatible with advanced manufacturing methods. Here, the authors introduce a 3D printable tissue adhesive for the fabrication of patches and devices for diverse biomedical applications.

    • Sarah J. Wu
    • , Jingjing Wu
    •  & Xuanhe Zhao

  • Article
    | Open Access

    The contribution of rare variants to complex traits has not been well studied. Here, the authors present RARity, a method to assess rare variant heritability without assuming a particular genetic architecture and enabling both gene-level and exome-wide heritability estimation of continuous traits.

    • Nazia Pathan
    • , Wei Q. Deng
    •  & Guillaume Paré

  • Article
    | Open Access

    Polyamides (PAs) or nylons are types of plastics with wide applications, but due to their accumulation in the environment, strategies for their deconstruction are of interest. Here, the authors screen 40 potential nylon-hydrolyzing enzymes (nylonases) using a mass spectrometry-based approach and identify a thermostabilized N-terminal nucleophile hydrolase as the most promising for further development, as well as crucial targets for progressing PA6 enzymatic depolymerization.

    • Elizabeth L. Bell
    • , Gloria Rosetto
    •  & Gregg T. Beckham

  • Article
    | Open Access

    It is vital but challenging to develop coating technologies for addressing reliability and durability issues of electrochemical sensors when exposed to diverse and complex biological environments. Here, the authors report a micrometer-thick, porous and robust nanocomposite coating that enables highly sensitive and stable electrochemical sensors.

    • Jeong-Chan Lee
    • , Su Yeong Kim
    •  & Donald E. Ingber

  • Article
    | Open Access

    Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Here the authors develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation.

    • Charlotte Cautereels
    • , Jolien Smets
    •  & Kevin J. Verstrepen

  • Article
    | Open Access

    Transcriptional cell states can drive treatment resistance in cancer. Here, the authors develop ReSisTrace to predict cell states that are primed to resist ovarian cancer treatment and validate their findings using small molecule inhibitors.

    • Jun Dai
    • , Shuyu Zheng
    •  & Anna Vähärautio

  • Article
    | Open Access

    In this work, the authors report the use of a computationally and rationally designed self-assembling peptide that has robust antiviral capability with demonstrated specificity in binding to SARS-CoV-2 and inhibition of viral entry into human cells.

    • Joseph Dodd-o
    • , Abhishek Roy
    •  & Vivek Kumar

  • Article
    | Open Access

    Chemosensory tissues are remarkably variable between species but the cause of this diversity is unclear. Here, the authors conduct transcriptomic analyses of chemosensory tissues from diverse Drosophila species, revealing evidence of stabilizing selection and recent species- and sex-specific changes.

    • Gwénaëlle Bontonou
    • , Bastien Saint-Leandre
    •  & J. Roman Arguello

  • Article
    | Open Access

    The Bioconductor project aims to develop R packages for analysis of genomic datasets. Here the authors show the HiCExperiment package suite and its companion online book (https://bioconductor.org/books/OHCA/) which present data structures, computational methods and visualization tools available in Bioconductor to investigate chromatin conformation capture (3C) data in R.

    • Jacques Serizay
    • , Cyril Matthey-Doret
    •  & Romain Koszul

  • 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

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