Biological techniques articles within Nature Communications

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  • Article |

    Magneto-fluorescent nanoparticles hold promise for bioimaging applications, but synthesizing uniform particles with tunable sizes remains challenging. Chen et al. propose an approach for co-assembling magnetic particles with fluorescent quantum dots, leading to well-defined core-shell structures.

    • Ou Chen
    • , Lars Riedemann
    •  & Moungi G. Bawendi

  • Article
    | Open Access

    Next-generation sequencing technology has made the generation of huge amounts of genetic data possible, but phenotype characterization remains slow and difficult. Here the authors develop a high-throughput phenotyping facility for rice that is able to accurately identify and characterize traits related to morphology, biomass and yield.

    • Wanneng Yang
    • , Zilong Guo
    •  & Lizhong Xiong

  • Article |

    Respiratory syncytial virus (RSV) causes severe respiratory disease in young children. Here, Rameix-Welti et al. create fluorescent and bioluminescent RSV strains that allow real-time analysis of viral replication and screening of antiviral compounds in cultured cells and in live animals.

    • Marie-Anne Rameix-Welti
    • , Ronan Le Goffic
    •  & Jean-François Eléouët

  • Article |

    The essential nature of replicative polymerases has hampered the study of polymerase-δ mutations found in colorectal cancer cells. Here, using polymerase-δ mutations as a proof of principle, the authors present an inducible single vector system that replaces any endogenous gene with an RNAi-resistant mutant version.

    • Medini Manohar Ghodgaonkar
    • , Patrick Kehl
    •  & Josef Jiricny

  • Article |

    Protein–protein interactions are fundamental to nearly all molecular and cellular processes. Here Taslimi et al.describe a versatile new optogenetic module that can be used to visualize protein–protein interactions, as well as reversibly control them with light with spatiotemporal resolution.

    • Amir Taslimi
    • , Justin D. Vrana
    •  & Chandra L. Tucker

  • Article
    | Open Access

    Single molecule fluorescence microscopy is a powerful technique to study protein dynamics in cells, but it has not been applied to adult animals. The authors use complementation-activated light microscopy in C. elegansto discover that dystrophin regulates the diffusion properties of voltage-dependent calcium ion channels at the surface of body-wall muscle cells.

    • Hong Zhan
    • , Ramunas Stanciauskas
    •  & Fabien Pinaud

  • Article |

    1H magnetic resonance can detect endogenous metabolites at physiological concentrations but its application in animal models is challenged by low sensitivity. Here the authors focus ultrahigh magnetic fields on metabolites whose spectral signatures are selectively excited, and achieve microarchitectural insight of rat brains after a stroke.

    • Noam Shemesh
    • , Jens T. Rosenberg
    •  & Lucio Frydman

  • Article |

    The non-invasive detection and imaging of bacterial infection in living organisms is increasingly important. Here, the authors demonstrate the use of labelled carbon nanotubes as bacterial probes in living hosts, and are able to image deep tissue infections with higher signal amplification than dye imaging.

    • Neelkanth M. Bardhan
    • , Debadyuti Ghosh
    •  & Angela M. Belcher

  • Article
    | Open Access

    Microtubule dynamics in neurons play critical roles in physiology, injury and disease. Here the authors develop a transgenic mouse line expressing a fluorescently tagged version of the microtubule binding protein EB3, and using a range of imaging techniques, study microtubule dynamics under normal and injury conditions in living mice.

    • Tatjana Kleele
    • , Petar Marinković
    •  & Thomas Misgeld

  • Article |

    During cell division, a single chromosome that lacks attachment to microtubules is sufficient to delay chromosome segregation. Chen and Liu construct a model demonstrating that the transport of regulators along microtubules may explain the remarkable sensitivity and robustness of this checkpoint.

    • Jing Chen
    •  & Jian Liu

  • Article
    | Open Access

    Deubiquitylases (DUBs) remove ubiquitin chains from proteins. Here the authors develop a mass spectrometry-based DUB activity screen using unmodified diubiquitin isomers to characterize substrate specificity for 42 human DUBs, and assess the potency and selectivity of 11 DUB inhibitors.

    • Maria Stella Ritorto
    • , Richard Ewan
    •  & Matthias Trost

  • Article
    | Open Access

    Intracellular calcium waves are key signalling elements during the fertilization process of animals, involved in egg activation. Here the authors image calcium oscillations during the fertilization process in flowering plants, revealing specific signatures involved in the success of this process.

    • Yuki Hamamura
    • , Moe Nishimaki
    •  & Tetsuya Higashiyama

  • Article
    | Open Access

    RNA sequencing has enabled the global analysis of both gene expression levels and splicing events. Here, the authors develop a multivariate approach that is able to identify SNPs that influence splicing, and investigate the overlap of these with functional domains across the genome, including previously identified GWAS signals.

    • Jean Monlong
    • , Miquel Calvo
    •  & Roderic Guigó

  • 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
    | Open Access

    Identifying miRNA response elements (MREs) within target mRNAs can be done computationally but the functional validation of putative MREs remains challenging. Here, Bassett et al. describe applications of genome engineering to target and assess the functional significance of MREs in different organisms and stages of development.

    • Andrew R. Bassett
    • , Ghows Azzam
    •  & Tudor A. Fulga

  • Article
    | Open Access

    Complex molecular interactions occur in the active zone cytomatrix (CAZ) within the presynaptic terminal to regulate synaptic plasticity. Here, the authors use imaging techniques to show that the CAZ is composed of units containing on average 137 Bruchpilot proteins, many of which are arranged into clusters.

    • Nadine Ehmann
    • , Sebastian van de Linde
    •  & Robert J. Kittel

  • Article |

    Genetically encoded voltage sensors are useful tools for the analysis of membrane potential and its influence on cell function. Here, the authors present a range of these sensors with varying colours for rapid and sensitive neuronal voltage imaging.

    • Peng Zou
    • , Yongxin Zhao
    •  & Adam E. Cohen

  • 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
    | Open Access

    Alarmins are locally released during inflammation and are early amplifiers of inflammation. Here Vogl et al.show that the alarmin S100A8/S100A9 can be used as a sensitive marker to detect subclinical inflammation and follow disease progression in a variety of disease models.

    • Thomas Vogl
    • , Michel Eisenblätter
    •  & Johannes Roth

  • Article
    | Open Access

    Feeding is an important behaviour, but its quantification remains challenging, particularly in small animal models like Drosophila melanogaster. Here the authors describe a method which uses capacitive sensing for automated high-resolution measuring of feeding behaviour in individual flies.

    • Pavel M. Itskov
    • , José-Maria Moreira
    •  & Carlos Ribeiro

  • 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
    | Open Access

    Numerous obstacles posed by cellular subcompartments and structures constrain protein transport in the cell. Here, Baum et al.map the intracellular topology from a diffusing protein’s point of view by measuring the diffusive movements of fluorescently labelled reporter proteins in living cells on multiple time and length scales.

    • Michael Baum
    • , Fabian Erdel
    •  & Karsten Rippe

  • Article |

    PTEN is a prominent tumour suppressor and monitoring its conformation and activity are key to developing targeted therapies. Here, the authors develop a bioluminescence resonance energy transfer biosensor for PTEN conformation and identify novel G protein-coupled receptor regulation and therapeutic activation.

    • Evelyne Lima-Fernandes
    • , Stanislas Misticone
    •  & Mark G.H. Scott

  • Article
    | Open Access

    3D cell culture matrices more closely resemble the natural microenvironments of stem cells than 2D systems. Here, the authors present a 3D cell culture approach to screen for the influence of environmental parameters on self-renewal and differentiation of single mouse embryonic stem cells.

    • A. Ranga
    • , S. Gobaa
    •  & M. P. Lutolf

  • Article |

    Epigenetic alterations alter chromatin structure and gene expression and are known contributors to cancer development. Here, Muratani et al.profile multiple epigenetic chromatin marks in primary gastric cancers and identify hundreds of altered promoters and enhancers that drive the gene expression program in these malignancies.

    • Masafumi Muratani
    • , Niantao Deng
    •  & Patrick Tan

  • 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 |

    The activity of heat shock proteins (Hsp) is modified by binding to cochaperones. Here, the authors develop a four-colour FRET system to show that cochaperone p23 binding to Hsp90 strengthens the ATP-dependent directionality, thus validating their approach for the study of other multicomponent protein machines.

    • C. Ratzke
    • , B. Hellenkamp
    •  & T. Hugel

  • Article
    | Open Access

    The use of intracellular calcium sensors provides important information about the dynamics of calcium signalling in cells. Here Suzuki et al. develop organelle-targeted sensors to simultaneously measure calcium concentrations in ER and mitochondria, and uncover novel insights into calcium flux in mitochondria.

    • Junji Suzuki
    • , Kazunori Kanemaru
    •  & Masamitsu Iino

  • Article
    | Open Access

    The three germ layers are formed from the inner cell mass of the mammalian embryo during gastrulation. Here, the authors present a method by which a single mouse embryonic stem cell, derived from inner cell mass, differentiates into the three germ layers in a self-organized manner when cultured in soft fibrin gel.

    • Yeh-Chuin Poh
    • , Junwei Chen
    •  & Ning Wang

  • Article
    | Open Access

    The control of cellular behaviour largely relies on genetic engineering, but artificial cells could be designed to control cell processes through chemical communication. Here, the authors develop an artificial cell that is able to translate a chemical message into a signal that can be sensed by E. coliand activate a cellular response.

    • Roberta Lentini
    • , Silvia Perez Santero
    •  & Sheref S. Mansy

  • 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
    | Open Access

    NAD and NADP play fundamentally different roles in cellular metabolism, and yet these pyridine nucleotides cannot be distinguished spectroscopically in living cells. Blacker et al.demonstrate that fluorescence lifetime imaging can be used to quantify NADPH/NADH balance in cultured cells and in the mammalian cochlea.

    • Thomas S. Blacker
    • , Zoe F. Mann
    •  & Michael R. Duchen

  • 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

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