Biotechnology articles within Nature Communications

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  • Article |

    Analyses of genome and transcriptome data are unable to accurately predict protein levels and function in tumour samples. Here, the authors carry out a comprehensive protein analysis in 3,467 samples from the cancer genome atlas, providing a resource to study the prognostic and therapeutic potential of tumour proteins.

    • Rehan Akbani
    • , Patrick Kwok Shing Ng
    •  & Gordon B. Mills

  • Article |

    Model-based part design is a key step in synthetic biology. Here, the authors report a method for tuning nucleosome architecture in order to strengthen native promoters and facilitate synthetic promoter design in yeast.

    • Kathleen A. Curran
    • , Nathan C. Crook
    •  & Hal S. Alper

  • Article |

    Infrared fluorescent proteins offer advantages for deep in vivo imaging thanks to the tissue-penetrating properties of infrared light. Here, Yu et al. design a monomeric infrared fluorescent protein that, when combined with expression of haeme oxygenase in cells, shows improved performance for in vivoimaging of neurons and brain tumours.

    • Dan Yu
    • , William Clay Gustafson
    •  & Xiaokun Shu

  • Article |

    Macromolecular complexes hold promise for future generations of drug delivery carriers, but probing their structures with high resolution is challenging. Here, the authors combine X-ray free-electron laser and synchrotron approaches to reveal the core-shell structure of RNA interference microsponges.

    • Marcus Gallagher-Jones
    • , Yoshitaka Bessho
    •  & Changyong Song

  • Article
    | Open Access

    Patients with oesophageal diseases may require surgical removal and replacement of the oesophagus. Here the authors seed mesenchymal stromal cells on a decellularized rat oesophagus and show that this bioengineered tissue construct restores swallowing function after transplantation into rats.

    • Sebastian Sjöqvist
    • , Philipp Jungebluth
    •  & Paolo Macchiarini

  • Article
    | Open Access

    The (seco)iridoids and their monoterpenoid indole alkaloid (MIA) derivatives are plant-derived compounds with pharmaceutical applications. Here, the authors identify the last four missing steps of the (seco)iridoid pathway, which they reconstitute in an alternative plant host to produce the complex MIA, strictosidine.

    • Karel Miettinen
    • , Lemeng Dong
    •  & Danièle Werck-Reichhart

  • Article
    | Open Access

    Ionic liquids (ILs) are important solvents in the microbial production of biofuels, but can inhibit microbial growth. Here, the authors transfer newly discovered IL-resistance genes from rain forest soil bacteria to E. coliand report growth and biofuel production at IL levels that are otherwise toxic to native strains.

    • Thomas L. Ruegg
    • , Eun-Mi Kim
    •  & Michael P. Thelen

  • Article |

    Cellular heterogeneity is a feature of diverse disease processes, yet is masked in typical biochemical assays. Sarkar et al.develop a microfluidic device to access the contents of single cells in adherent culture, allowing biochemical measurements to be connected with phenotypic information.

    • Aniruddh Sarkar
    • , Sarah Kolitz
    •  & Jongyoon Han

  • Article |

    MicroRNA has been identified to play a role in cancer development, thus its detection at low concentrations would be a highly beneficial diagnostic tool. Here, the authors develop a gel-based bio-barcode assay for microRNA detection using DNA-modified gold nanoparticles, with aM limits of detection.

    • Hyojin Lee
    • , Jeong-Eun Park
    •  & Jwa-Min Nam

  • Article
    | Open Access

    Pheromones can be used as an environmentally friendly alternative to traditional pesticides. Here, the authors produce moth sex pheromones in Nicotiana benthamianaby transient expression and demonstrate that these pheromones are able to trap male moths as efficiently as their synthetic counterparts.

    • Bao-Jian Ding
    • , Per Hofvander
    •  & Christer Löfstedt

  • Article |

    Traditional methods for forming hydrogel particles are limited by geometry and lack of addressability after synthesis. Here the authors use digital microfluidics to form individually addressable gels with customisable shapes and compositions.

    • Irwin A. Eydelnant
    • , Bingyu Betty Li
    •  & Aaron R. Wheeler

  • Article |

    Brain–machine interfaces are being investigated for recovery of motor function after paralysis. Shanechi et al.present a neural prosthesis that decodes premotor neuronal activity in an alert monkey to activate spinal neurons and muscles that produce target-directed movements in a sedated monkey or avatar.

    • Maryam M. Shanechi
    • , Rollin C. Hu
    •  & Ziv M. Williams

  • Article |

    Serial femtosecond X-ray crystallography permits the use of very small protein crystals; however, a continuous flow of sample is required. Weierstall et al. design and demonstrate an injector system that can supply microcrystals in the lipidic cubic phase, dramatically reducing the quantities of protein required.

    • Uwe Weierstall
    • , Daniel James
    •  & Vadim Cherezov

  • Article |

    Benzylisoquinoline alkaloids are a group of plant secondary metabolites with important pharmaceutical applications. Here, the authors have reconstituted a 10-gene alkaloid pathway in Saccharomyces cerevisiae, demonstrating the feasibility of producing commercially important alkaloids in microbial systems.

    • Elena Fossati
    • , Andrew Ekins
    •  & Vincent J. J. Martin

  • Article |

    Eukaryotic algae and cyanobacteria can produce hydrogen in the presence of little or no oxygen. Here, the authors show that two microalgal strains are capable of producing hydrogen under aerobic conditions, and provide new insights into the natural evolution of oxygen-tolerant hydrogenase.

    • Jae-Hoon Hwang
    • , Hyun-Chul Kim
    •  & Byong-Hun Jeon

  • Article |

    The hair follicle bulge contains epithelial stem cells that contribute to follicle formation during each hair cycle. Here the authors differentiate human induced pluripotent stem cells into folliculogenic epithelial stem cells, which can produce all hair follicle lineages including a stem cell population.

    • Ruifeng Yang
    • , Ying Zheng
    •  & Xiaowei Xu

  • Article |

    Colour changes in response to external stimuli are common in nature, from turkey skin to butterfly wings. Here, inspired by this behaviour, the authors have developed a sensor capable of providing an individual colour response to specific target chemicals using genetically engineered viruses.

    • Jin-Woo Oh
    • , Woo-Jae Chung
    •  & Seung-Wuk Lee

  • Article |

    Cas9 RNA-guided engineered nucleases (RGENs) induce site-specific DNA cleavages in cultured cells and organisms and are used widely as genome-editing tools. Here, the authors develop an RGEN-based technology to genotype both RGEN-induced mutations and cancer-associated mutations in human cell lines.

    • Jong Min Kim
    • , Daesik Kim
    •  & Jin-Soo Kim

  • Article |

    Self-propelled biological microswimmers in viscous fluids are common in nature, but their synthetic counterparts are not available to date. Williams et al.develop a hybrid swimmer to emulate flagellar propulsion, which provides a platform to add engineered functionality to complex motile devices.

    • Brian J. Williams
    • , Sandeep V. Anand
    •  & M. Taher A. Saif

  • Article |

    Despite their clinical potential, cytokines can often be highly toxic in patients, due to their systemic activity. Here, the authors present a strategy to engineer immunocytokines with very high targeting efficacies using mutant cytokines linked to nanobodies that only become active when bound to a specific cell marker.

    • Geneviève Garcin
    • , Franciane Paul
    •  & Gilles Uzé

  • Article
    | Open Access

    Nanopore sensors are a promising tool for the controlled detection of a range of possible substrates. Here the authors describe a nanopore sensor based on short single-walled carbon nanotubes inserted into a lipid bilayer, with modified sensing properties compared to longer nanotubes.

    • Lei Liu
    • , Chun Yang
    •  & Hai-Chen Wu

  • Article
    | Open Access

    The topographical features of insect wings result in some interesting surface properties, including hydrophobicity and antibacterial activity. Here the authors identify the surface of black silicon as a mimic of dragonfly wings and show that it too possesses antibacterial activity.

    • Elena P. Ivanova
    • , Jafar Hasan
    •  & Russell J. Crawford

  • Article
    | Open Access

    Designer gene circuits allow the controlled expression of proteins in response to specific stimuli. Here, Rössger et al.use synthetic biology approaches to create a fatty-acid biosensor that controls the production of a satiety hormone and use it to control diet-induced obesity in mice.

    • Katrin Rössger
    • , Ghislaine Charpin-El-Hamri
    •  & Martin Fussenegger

  • Article |

    Microbial fuels cells present a way of generating electricity using the natural metabolism of microorganisms. Here the authors carry out single-cell current measurements ofGeobacter sulfurreducensDL-1 to determine the upper limits of microbial fuel cell performance.

    • Xiaocheng Jiang
    • , Jinsong Hu
    •  & Justin C. Biffinger

  • Article |

    Semiconductor-based, non-optical DNA sequencing technologies such as Ion Torrent sequencing offer speed and cost advantages compared with alternative techniques. Cheng et al. demonstrate a protocol allowing the use of Ion Torrent technology to sequence DNA from chromatin immunoprecipitation experiments.

    • Christine S. Cheng
    • , Kunal Rai
    •  & Ido Amit

  • Article |

    Cells can adapt rapidly to survive and efficiently exploit constantly changing environments by varying their mutation rate. Here the authors construct an in silicosystem to modulate mutation rate, and demonstrate that this method can be used in the laboratory to create specific phenotypes.

    • Howard H. Chou
    •  & Jay D. Keasling

  • Article |

    4-hydroxycoumarin (4HC), a precursor for anticoagulant drugs such as warfarin, has a major role in the treatment of thromboembolic diseases. Here, the authors present an artificial biosynthetic pathway for 4HC production in E. coliand demonstrate its potential for large-scale microbial production.

    • Yuheng Lin
    • , Xiaolin Shen
    •  & Yajun Yan

  • Article |

    Graphene nanopores hold great potential for single-molecule DNA screening; however, pore clogging due to hydrophobic interactions is a severe problem. Schneider et al. show that this can be prevented by non-covalently coating graphene with an ultrathin hydrophilic self-assembled monolayer.

    • Grégory F. Schneider
    • , Qiang Xu
    •  & Cees Dekker

  • Article
    | Open Access

    Transport of colloidal cargoes to target sites can be done by controlling active carriers, like self-propelled bacteria, under external stimuli. Koumakis et al.show that bacteria can autonomously achieve the same goal when moving over pre-designed asymmetric microstructures.

    • N. Koumakis
    • , A. Lepore
    •  & R. Di Leonardo

  • Article
    | Open Access

    Lacrimal glands maintain a healthy corneal epithelium but are dysfunctional for example in dry-eye disease. Here, the authors transplant bioengineered lacrimal and harderian gland germs into mice, where they connect to the host duct and nervous system and restore lacrimal gland function.

    • Masatoshi Hirayama
    • , Miho Ogawa
    •  & Takashi Tsuji

  • Article
    | Open Access

    Salivary gland dysfunction as a result of diseases or ageing reduces the quality of life and causes various oral health problems. Here the authors show that the salivary gland function of mice can be recovered by orthotopic transplantation of a bioengineered salivary gland germ.

    • Miho Ogawa
    • , Masamitsu Oshima
    •  & Takashi Tsuji

  • Article |

    Cre recombinase is widely used to precisely manipulate genes and chromosomes, but it often displays off-target activity. Here, the authors improve the accuracy of Cre-mediated recombination by introducing specific mutations in the enzyme’s dimerization surface.

    • Nikolai Eroshenko
    •  & George M. Church

  • Article
    | Open Access

    Transport of DNA molecules across lipid membranes requires protein conduits such as the nuclear pore complex. Franceschiniet al.engineer an artificial sequence-selective DNA transporter by attaching gating oligonucleotides to a bacterial nanopore.

    • Lorenzo Franceschini
    • , Misha Soskine
    •  & Giovanni Maglia

  • Article |

    Tissue engineering relies on the vascular compatibility of the synthesised constructs with target tissues. Here, the authors fabricate a prevascularised tissue construct of cell-laden hydrogel fibres as a framework that allows the formation of vascularised adipose and hepatic tissues.

    • Meng Fatt Leong
    • , Jerry K. C. Toh
    •  & Jackie Y. Ying

  • Article |

    The potential tumorigenicity of human pluripotent stem cells (hPSCs) limits their application in cell therapies. Ben-David et al.identify the tight-junction protein Claudin-6 as a cell-surface marker of hPSCs, and demonstrate three Claudin-6-based strategies to remove tumorigenic hPSCs from mixed cell cultures.

    • Uri Ben-David
    • , Neta Nudel
    •  & Nissim Benvenisty

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