Biotechnology articles within Nature Communications

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  • Article |

    Bacterial cells use a self-generated extracellular matrix of various biomolecules in order to form biofilms and promote their stability. Here, the authors present a method for genetically controlling the composition of this extracellular matrix to yield more functional biofilms.

    • Peter Q. Nguyen
    • , Zsofia Botyanszki
    •  & Neel S. Joshi

  • Article
    | Open Access

    Cell therapy requires sufficient amounts of therapeutic cells to be delivered to the injured tissue. Here the authors use magnetic iron nanoparticles conjugated with antibodies that bind therapeutic cells and cardiomyocytes to treat myocardial ischemia/reperfusion injury in rats and show that targeting to the heart is enhanced upon local application of a magnetic field.

    • Ke Cheng
    • , Deliang Shen
    •  & Eduardo Marbán

  • Article
    | Open Access

    Protein unfolding and translocation through membrane pores occurs in several biological processes and has implications in nanopore technologies. Here, the authors show that the kinetics of unfolding differ depending on which end of the chain enters the pore first.

    • David Rodriguez-Larrea
    •  & Hagan Bayley

  • Article |

    Current leukocyte migration assays usually report bulk attractive behaviour of cells within a chemokine gradient. Here, the authors develop a microfluidic device to simultaneously measure several migration responses on exposure to commonly used leukocyte chemokines, and report previously unrecognized cell behaviour.

    • Leo Boneschansker
    • , Jun Yan
    •  & Daniel Irimia

  • Article
    | Open Access

    Propane is the main component of liquid petroleum gas and has a wide variety of commercial applications. Here, the authors engineer a synthetic metabolic pathway in E. coli, and demonstrate for the first time the renewable production of propane.

    • Pauli Kallio
    • , András Pásztor
    •  & Patrik R. Jones

  • Article
    | Open Access

    Common methods to detect adenosine-to-inosine RNA editing sites rely on mapping short RNA reads to the genome while allowing only a limited number of mismatches. Here, Porath et al. present a novel RNA-seq based approach to identify hyper-edited reads that significantly expands the RNA editome.

    • Hagit T. Porath
    • , Shai Carmi
    •  & Erez Y. Levanon

  • Article |

    Nanoparticles can be used for therapeutic and diagnostic purposes. Here, the authors report that nanoparticles made of a single chemical building block, called nanoporphyrins, incorporate eight different functionalities, including various types of imaging, drug delivery and cancer therapy.

    • Yuanpei Li
    • , Tzu-yin Lin
    •  & Kit S. Lam

  • Article |

    Optimizing cell-surface biological reactions is an important goal of biotechnology and industrial processes. Here the authors use macromolecular crowding to enhance the enzymatic conversion of red blood cells to the universal type O blood type, using orders of magnitude less enzyme than was previously required.

    • Rafi Chapanian
    • , David H. Kwan
    •  & Jayachandran N Kizhakkedathu

  • Article |

    Current CRISPR-mediated genome-editing methods are limited by the requirement for a specific +1 nucleotide when using the U6 promoter to drive guide RNA synthesis. Now, Ranganathan et al.report a modification of the CRISPR–Cas9 system that more than doubles the number of targetable CRISPR sites within the human genome.

    • Vinod Ranganathan
    • , Karl Wahlin
    •  & Donald J. Zack

  • Article |

    The amino acid, L-arginine, has important applications in the food, pharmaceutical and cosmetics industries. Here the authors systematically engineer a Corynebacterium glutamicum strain for the production of L-arginine, and show that their metabolic engineering approach can be used for the industrial production of valuable chemicals.

    • Seok Hyun Park
    • , Hyun Uk Kim
    •  & Sang Yup Lee

  • Article
    | Open Access

    The advancement of sensitive, accurate and non-invasive methods to identify the allergen that drives allergic disease in an individual remains a challenge. Here, the authors develop a synthetic biology approach using human designer cells to profile allergic reactions against an array of allergens measuring histamine release from whole blood.

    • David Ausländer
    • , Benjamin Eggerschwiler
    •  & Martin Fussenegger

  • Article
    | Open Access

    The ability to control antibody binding could have important medical implications. Here, the authors present a method to engineer phosphatase-controllable antibodies that bind to a specific recognition site in the presence of two biomarker inputs.

    • Smita B. Gunnoo
    • , Helene M. Finney
    •  & Benjamin G. Davis

  • Article |

    The incorporation of foreign objects into cells can be used in various avenues of biological research, although crossing the cell membrane can be challenging. Here, the authors use a diamond nanoneedle array for enhanced delivery of various particles into cells, including neurons.

    • Ying Wang
    • , Yang Yang
    •  & Peng Shi

  • Article |

    Antibody–antigen recognition is one of the important aspects of immunity, but the nanomechanical process of this recognition is not fully understood. Here, using high-speed atomic force microscopy, the authors observe that on membranes containing a high density of immobile antigens antibodies move in a ‘random walking’ motion.

    • Johannes Preiner
    • , Noriyuki Kodera
    •  & Peter Hinterdorfer

  • Article
    | Open Access

    Graphene’s properties are well known, but turning this atomically thin material into three-dimensional devices remains a challenge. Here, the authors report an assembly process for chemically modified graphene into three-dimensional cellular networks, with control over the physical properties of the resulting materials.

    • Suelen Barg
    • , Felipe Macul Perez
    •  & Eduardo Saiz

  • Article |

    Nucleic acids possess a number of properties that can be beneficial for the fabrication of nanomaterials. Here, the authors present an enzymatically synthesised RNA membrane, and show how its physical properties can be controlled by changes to base-pairing.

    • Daehoon Han
    • , Yongkuk Park
    •  & Jong Bum Lee

  • Article |

    The study of cell membrane proteins can be simplified by incorporating them into lipid bilayers, but doing this for multiple proteins can be challenging. Here, the authors present a technique to achieve this, and show reconstitution of a bacterial respiratory chain from individual components.

    • Gustav Nordlund
    • , Peter Brzezinski
    •  & Christoph von Ballmoos

  • Article |

    Many tissues can be grown as 3D spheroid models in hanging drops of media. Here, Frey et al. develop a microfluidic, interconnected hanging drop network to facilitate inter-drop communication, and demonstrate that pro-drug conversion by liver spheroids can limit the growth of cancer spheroids in adjacent drops.

    • Olivier Frey
    • , Patrick M. Misun
    •  & Andreas Hierlemann

  • Article |

    Robust and reliable structure–function relationships are valuable for the development of potent drug delivery systems. Here, the authors use a library of lipid-like materials to predict in vivosiRNA delivery efficacy without any biological testing.

    • Kathryn A. Whitehead
    • , J. Robert Dorkin
    •  & Daniel G. Anderson

  • Article |

    Gramicidin A pores are important natural structures for the transport of ions through biological membranes. Here, the authors show that this functionality can be mimicked using an artificial transmembrane channel formed of synthetic pore-forming compounds.

    • Mihail Barboiu
    • , Yann Le Duc
    •  & Thomas Fyles

  • Article |

    Ganglioside GM3, a cellular lipid included in the envelope of HIV-1 viral particles, interacts with cellular receptor CD169. Here, the authors develop artificial nanoparticles, consisting of a golden core and a GM3-containing synthetic membrane, that recapitulate the CD169-dependent uptake of viral particles.

    • Xinwei Yu
    • , Amin Feizpour
    •  & Björn M. Reinhard

  • Article
    | Open Access

    Vanilla is derived from vanillin isolated from a vanillin-producing orchid, but the process is laborious, costly and results in a small yield. Here, the authors identified an enzyme from the orchid, Vanilla planifolia, that is able to catalyse the formation of vanillin and vanillin glucoside from ferulic acid and its glucoside in vitro, respectively.

    • Nethaji J. Gallage
    • , Esben H. Hansen
    •  & Birger Lindberg Møller

  • Article
    | Open Access

    Extreme reproductive sex ratios could result in the suppression or elimination of pest populations. Here, the authors design a synthetic sex distortion system in Anopheles gambiaethat gives rise to fertile mosquito strains that produce over 95% male offsprings and could therefore be used to suppress mosquito populations.

    • Roberto Galizi
    • , Lindsey A. Doyle
    •  & Andrea Crisanti

  • Article |

    Oxygen is vital for all multicellular organisms and oxygen deprivation, hypoxia, influences cellular functions. Here, the authors develop an oxygen-controlling hydrogel that can be used as a three-dimensional hypoxic microenvironment, and may aid the study of hypoxia-related biological conditions.

    • Kyung Min Park
    •  & Sharon Gerecht

  • Article |

    Optogenetic tools allow fine spatial control of signalling pathways using light. Chang et al. present a strategy for constructing light-sensitive receptor tyrosine kinases and demonstrate that optogenetic stimulation of Trk receptors in neurons promotes neurite outgrowth.

    • Ki-Young Chang
    • , Doyeon Woo
    •  & Won Do Heo

  • Article
    | Open Access

    Non-invasive monitoring of solid tumour growth in mice is difficult. In this study, the authors develop a system for monitoring the secretion of luciferase either from Gaussia princeps or Cypridina noctiluca in the blood of mice harbouring luciferase-labelled tumour cells, thus providing a system to monitor two different cell populations in vivo.

    • Joël P. Charles
    • , Jeannette Fuchs
    •  & Thorsten Stiewe

  • Article |

    Diatoms are photosynthetic microalgae with underutilized biotechnological potential. Here, the authors carry out targeted gene modifications of lipid metabolism genes in the diatom, Phaeodactylum tricornutum, resulting in a strain that exhibits a 45-fold increase in triacylglycerol accumulation.

    • Fayza Daboussi
    • , Sophie Leduc
    •  & Philippe Duchateau

  • 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

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