Biotechnology articles within Nature Communications

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  • Article
    | Open Access

    Suppression of gene expression due to aberrant promoter methylation contributes to organ fibrosis. Here, the authors couple a deactivated Cas9 to the TET3 catalytic domain to induce expression of four antifibrotic genes, and show that lentiviral-mediated delivery is effective in reducing kidney fibrosis in mouse models.

    • Xingbo Xu
    • , Xiaoying Tan
    •  & Michael Zeisberg

  • Article
    | Open Access

    Regulated secretion is an essential process that requires packing and maturation of cargo proteins in membranous secretory granules. Here, authors identify a gene, pgant9, that influences the glycosylation status of the secretory cargo as well as the structure of secretory granules within the Drosophila salivary gland.

    • Suena Ji
    • , Nadine L. Samara
    •  & Kelly G. Ten Hagen

  • Article
    | Open Access

    Bacterial microcompartments (BMCs) are protein-bound organelles encapsulating segments of metabolic pathways. Here the authors utilize specific de novo coiled-coil protein-protein interactions to display proteins on the outer or inner surface of BMCs.

    • Matthew J. Lee
    • , Judith Mantell
    •  & Martin J. Warren

  • Article
    | Open Access

    There is interest in the development of mussel inspired materials; however, this requires an understanding of the materials. Here, the authors report on an investigation into the properties of mussel cuticle from different species that challenges conventional wisdom about particle filled composites.

    • Christophe A. Monnier
    • , Daniel G. DeMartini
    •  & J. Herbert Waite

  • Article
    | Open Access

    Several therapeutics are glycosylated proteins, yet the analysis of their specific glycosylation patterns remains challenging. Here the authors demonstrate an approach for the detailed characterization of glycosylated biopharmaceuticals applied to the determination of the glycoproteoform profile of glycoengineered variants of erythropoietin.

    • Tomislav Čaval
    • , Weihua Tian
    •  & Albert J. R. Heck

  • Article
    | Open Access

    Plasmacytoid dendritic cells (pDC) are a pivotal component of the immune system. Here, the authors utilize single-cell microfluidics to interrogate the human pDC compartment and reveal a subset of type I IFN secreting pDCs that is regulated by stochastic gene expression and amplified by microenvironmental cues.

    • Florian Wimmers
    • , Nikita Subedi
    •  & Jurjen Tel

  • Article
    | Open Access

    Optimization of the recently discovered Class 2 CRISPR protein Cpf1 has the potential to promote its applications in gene editing and therapeutics. Here, the authors find that extending the 5′ end of the crRNA can increase both the editing efficiency and delivery of Cpf1 in vitro and in vivo.

    • Hyo Min Park
    • , Hui Liu
    •  & Kunwoo Lee

  • Article
    | Open Access

    Isolation of circulating tumor cells (CTCs) allows for non-invasive disease monitoring and characterization. Here the authors describe an alternative CTC isolation method based on the ability of the malaria rVAR2 protein to specifically bind oncofetal chondroitin sulfate, which is expressed by all cancer cells

    • Mette Ø. Agerbæk
    • , Sara R. Bang-Christensen
    •  & Ali Salanti

  • Article
    | Open Access

    The promise of stem cell therapy for treating central nervous system disease is limited by low stem cell transplantation survival rates and poorly controlled cell fate. Here, the authors develop a biodegradable nanoscaffold for spinal cord injury that enhances transplantation and differentiation of neural stem cells and delivers drugs.

    • Letao Yang
    • , Sy-Tsong Dean Chueng
    •  & Ki-Bum Lee

  • Article
    | Open Access

    The synthetic biology era has seen a rapidly growing number of engineered DNA sequences. Here, the authors develop a deep learning method to predict the lab-of-origin of a DNA sequence based on hidden design signatures.

    • Alec A. K. Nielsen
    •  & Christopher A. Voigt

  • Article
    | Open Access

    Surface enhanced Raman scattering is a bio-analytical tool and the development and optimisation of probes is an active area of investigation. Here, the authors report on the development and testing of biocompatible semiconductor zinc oxide quantum probes on a platform for cell adhesion and analysis.

    • Rupa Haldavnekar
    • , Krishnan Venkatakrishnan
    •  & Bo Tan

  • Article
    | Open Access

    Reducing aerobic ethanol production, a phenomenon referred to as the Crabtree effect, may open up new perspectives for using yeast as a cell factory. Here, the authors turn the Crabtree-positive yeast into Crabtree negative by combined engineering of cytosolic acetyl-CoA metabolism and mutating the RNA polymerase II mediator complex.

    • Zongjie Dai
    • , Mingtao Huang
    •  & Jens Nielsen

  • Article
    | Open Access

    Human pluripotent stem cell-derived intestinal organoids (hIOs) are a useful model with which to study intestinal development and disease, but they require in vivo maturation to resemble adult tissue. Here, the authors show that T lymphocyte-derived IL-2 induces hIO maturation in vitro through the activation of STAT3.

    • Kwang Bo Jung
    • , Hana Lee
    •  & Mi-Young Son

  • Article
    | Open Access

    Designer organelles with new biochemical functionalities are of great interest in synthetic biology and cellular engineering. Here the authors present a single-protein-based platform for generating synthetic membraneless compartments that is capable of enzymatically-triggered alterations to phase behavior and of recruiting and concentrating cargo proteins.

    • Benjamin S. Schuster
    • , Ellen H. Reed
    •  & Daniel A. Hammer

  • Perspective
    | Open Access

    Synthetic biology often views the organism as a chassis into which a circuit can be inserted. Here the authors explore the idea of the organism as a core aspect of design, aiding researchers in navigating the genetic space opened up by SCRaMbLE.

    • Erika Szymanski
    •  & Jane Calvert

  • Article
    | Open Access

    Single-cell RNA-barcoding and sequencing is an efficient, genome-wide method to characterize cellular identities. Here the authors systematically evaluate the protocol and develop molecular crowding SCRB-seq with improved sensitivity and cost-efficiency.

    • Johannes W. Bagnoli
    • , Christoph Ziegenhain
    •  & Wolfgang Enard

  • Article
    | Open Access

    Gut microbial dysbiosis has been implicated in the pathogenesis of inflammatory bowel disease. Here, the authors examine host-microbiota protein interactions that occur in inflammatory bowel disease; they show an upregulation in proteins related to antimicrobial activities, and alterations in intestinal extracellular vesicles that are associated with aberrant microbiota-interactions.

    • Xu Zhang
    • , Shelley A. Deeke
    •  & Daniel Figeys

  • Article
    | Open Access

    While ChIP-exo is low noise and highly informative regarding genome-wide binding proteins, libraries are difficult to construct. Here the authors present a simplified ChIP-exo method for high-resolution detection of interactions.

    • Matthew J. Rossi
    • , William K. M. Lai
    •  & B. Franklin Pugh

  • Article
    | Open Access

    To improve trauma survival and surgical outcomes, hemostatic agents are needed. Here, the authors report on the development of injectable, biocompatible carbon nanotube reinforced quaternized chitosan cryogels with shape memory, conductivity and antibacterial properties for hemostatic control.

    • Xin Zhao
    • , Baolin Guo
    •  & Peter X. Ma

  • Article
    | Open Access

    X-ray radiation has excellent tissue penetration depth, making it a useful trigger for deep tissue cancer therapy. Here, the authors design X-ray triggered drug/gene-loaded liposomes by embedding photosensitizers and gold nanoparticles in the liposome bilayer, and demonstrate their efficacy in cancer and gene therapy.

    • Wei Deng
    • , Wenjie Chen
    •  & Ewa M. Goldys

  • Article
    | Open Access

    The ability to produce homogeneous glycoproteins is expected to advance fundamental understanding in glycoscience, but current in vivo-based production systems have several limitations. Here, the authors develop an E. coli extract-based one-pot system for customized production of N-linked glycoproteins.

    • Thapakorn Jaroentomeechai
    • , Jessica C. Stark
    •  & Matthew P. DeLisa

  • Article
    | Open Access

    The engineering of synthetic microbial communities necessitates the use of synthetic, orthogonal cell-to-cell communication channels. Here the authors present a library of characterised AHL-receiver devices and a software tool for the automatic identification of non-interfering chemical communication channels.

    • Nicolas Kylilis
    • , Zoltan A. Tuza
    •  & Karen M. Polizzi

  • Article
    | Open Access

    In vivo reprogramming of somatic cells is hampered by the need for vectors to express the OKSM factors in selected organs. Here the authors report new AAV-based vectors capable of in vivo reprogramming at low doses.

    • Elena Senís
    • , Lluc Mosteiro
    •  & Dirk Grimm

  • Article
    | Open Access

    Resistance of gRNA to ubiquitous ribonucleases is required for CRISPR-Cas9-based therapeutics. Here, the authors explore chemical modifications at all positions of the crRNA guide and tracrRNA cofactor, and identify modified versions that are more potent and stable than their unmodified counterparts in editing human cells.

    • Aamir Mir
    • , Julia F. Alterman
    •  & Erik J. Sontheimer

  • Article
    | Open Access

    CRISPRa is an attractive tool for cellular reprogramming due to its multiplexing capacity and direct targeting of genomic loci. Here the authors demonstrate the reprogramming of human fibroblasts into iPSCs, which is enhanced by targeting a conserved Alu-motif.

    • Jere Weltner
    • , Diego Balboa
    •  & Timo Otonkoski

  • Article
    | Open Access

    The C-X-C chemokine receptor type 4 (CXCR4) pathway is a key regulator of cancer metastasis. Here, the authors present a method to block CXCR4 and thereby inhibit breast cancer metastasis by developing a liposome that presents CXCR4-binding peptides in a multivalent fashion.

    • Daxing Liu
    • , Peng Guo
    •  & Debra Auguste

  • Article
    | Open Access

    Therapeutic peptide nucleic acids can be delivered into cells by conjugation to cell penetrating peptides (CPPs), but efficiency is usually low. Here the authors use synthetic molecular evolution and a luciferase-based library screen to generate new CPPs with improved efficiency and lower toxicity.

    • W. Berkeley Kauffman
    • , Shantanu Guha
    •  & William C. Wimley

  • Article
    | Open Access

    The absence of effective gene activators in bacteria limits regulated expression programs. Here the authors design synthetic bacterial CRISPR-Cas transcriptional activators that can be used to construct multi-gene programs of activation and repression.

    • Chen Dong
    • , Jason Fontana
    •  & Jesse G. Zalatan

  • Article
    | Open Access

    The correction of genetic defects in utero could allow for improved outcomes of gene therapy. Here, the authors demonstrate safe delivery of nanoparticles to fetal mouse tissues, and show that nanoparticles containing peptide nucleic acids to edit the beta-globin gene are effective in a mouse model of beta-thalassemia.

    • Adele S. Ricciardi
    • , Raman Bahal
    •  & W. Mark Saltzman

  • Article
    | Open Access

    Depletion of the splicing factors MBNL 1 and 2 causes myotonic dystrophy. Here, the authors show that miR-23b and miR-218 target MBNL proteins, and that antagonists to these miRNAs rescue mis-splicing events in myoblasts and boost MBNL expression and rescue pathology in mouse models.

    • Estefania Cerro-Herreros
    • , Maria Sabater-Arcis
    •  & Ruben Artero

  • Article
    | Open Access

    Active matter composed of filaments and molecular motors can contract. Here, the authors report the spontaneous out-of-plane buckling of reconstituted contracting poroelastic actomyosin sheets in the absence of external cues.

    • Y. Ideses
    • , V. Erukhimovitch
    •  & A. Bernheim-Groswasser

  • Article
    | Open Access

    Cancer patients exhibit specific sensitivities toward drug combinations that cannot be easily predicted. Here the authors setup a microfluidic platform that allows testing of multiple drug combinations correctly predicting sensitivity in vivo and they use it on patients biopsies to define effective drugs.

    • Federica Eduati
    • , Ramesh Utharala
    •  & Christoph A. Merten

  • Article
    | Open Access

    Urinary tract infections are one of the most common infections in humans. Here, the authors use urinary cell-free DNA (cfDNA) to comprehensively monitor host and pathogen dynamics in bacterial and viral urinary tract infections, and show that it is a versatile analyte for monitoring urinary tract infections.

    • Philip Burnham
    • , Darshana Dadhania
    •  & Iwijn De Vlaminck

  • Article
    | Open Access

    In silico models of cells can provide insight into the causes and effects of disease states and reduce the need for in vivo studies. Here, the authors present a kinetic model of hepatocyte metabolism including energy, carbohydrate, lipid and nitrogen metabolism and hormonal and allosteric regulation of enzymatic activity.

    • Nikolaus Berndt
    • , Sascha Bulik
    •  & Hermann-Georg Holzhütter

  • Article
    | Open Access

    Engineering E. coli for metabolization of methanol to produce fuels and chemicals has not been fully achieved. Here, the authors combine metabolic engineering and chemical inhibition to improve methanol assimilation and distinguish the role of kinetics and thermodynamics under various culture conditions.

    • Benjamin M. Woolston
    • , Jason R. King
    •  & Gregory Stephanopoulos

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