Biological techniques articles within Nature Communications

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  • Article
    | Open Access

    Tracking single molecules on long stretches of single-stranded DNA poses technical challenges due to its propensity to form hairpin structures. To solve this problem, the authors combine TIRF microscopy with optical tweezers to stretch the DNA and capture the dynamics of DNA unwinding by UvrD DNA helicase.

    • Kyung Suk Lee
    • , Hamza Balci
    •  & Taekjip Ha

  • Article |

    Light-sensitive proteins are useful tools to control protein localization and gene expression, but are currently limited to excitation with red or blue light. Here Crefcoeur et al. present a novel optogenetic system to induce protein–protein interactions with ultraviolet-B light that does not require exogenous chromophores.

    • Remco P. Crefcoeur
    • , Ruohe Yin
    •  & Thanos D. Halazonetis

  • Article
    | Open Access

    Single-molecule force spectroscopy provides useful quantitative information about the properties of macromolecules. Otto and colleagues non-invasively inspect the tension dynamics in a taut strand of DNA, thereby extending the use of single-molecule force spectroscopy to the study of macromolecular dynamics.

    • Oliver Otto
    • , Sebastian Sturm
    •  & Klaus Kroy

  • Article |

    Optical tweezers based on focused laser beams are widely used for biophysical measurements of single molecules in vitro. Here Zhong et al. use infrared optical tweezers to trap and manipulate red blood cells within subdermal capillaries in living mice.

    • Min-Cheng Zhong
    • , Xun-Bin Wei
    •  & Yin-Mei Li

  • Article
    | Open Access

    Transcription activator-like effector nucleases (TALENs) are dimeric 'molecular scissors' that can be readily engineered for gene-targeting applications. Beurdeley et al. develop a single-chain TALEN architecture having significant in vivoactivity in yeast, plant and mammalian systems.

    • Marine Beurdeley
    • , Fabian Bietz
    •  & George H. Silva

  • Article |

    Directly comparing patterns of gene expression in matched normal and cancerous tissues provides a powerful tool to identify drivers of tumour progression. Here the authors discover genes that are recruited into mitotic signalling networks in lung adenocarcinoma.

    • Il-Jin Kim
    • , David Quigley
    •  & Allan Balmain

  • Article
    | Open Access

    Mouse models of arthritis generally do not result in both chronic disease and autoantibody production—two key features of the human disease. Here the authors obtain both features by combining two common protocols, and find that disease severity is associated with the presence of a previously unidentified lymph node.

    • Uta Baddack
    • , Sven Hartmann
    •  & Gerd Müller

  • Article |

    Transcription factor diffusion along DNA regulates many fundamental cellular and developmental processes. Kaur et al. combine photoactivation and fluorescence correlation spectroscopy to investigate transcription factor diffusion in mouse embryos and show that diffusion kinetics change during cell differentiation.

    • Gurpreet Kaur
    • , Mauro W. Costa
    •  & Nicolas Plachta

  • Article
    | Open Access

    HNF1B is overexpressed in the clear cell subtype and epigenetically silenced in the serous subtype of ovarian cancer. Pearce and colleagues now show that genetic variants in HNF1B are differentially associated with risks of developing these two cancer subtypes, possibly through an epigenetic mechanism.

    • Hui Shen
    • , Brooke L. Fridley
    •  & Celeste Leigh Pearce

  • Article |

    Bacterial type III secretion systems (T3SS) improve the delivery of vaccine antigens and antigen-specific immune responses but require the use of live vaccines. Carleton et al. report the assembly of a functional T3SS in replication-incompetent bacterial minicells that can deliver vaccine antigens in vitro and in vivo.

    • Heather A. Carleton
    • , María Lara-Tejero
    •  & Jorge E. Galán

  • Article
    | Open Access

    Flexible organic electronic devices have the potential to serve as biosensors in living animals. Khodagholy et al. show that organic transistors can be used to record brain activity in rats and demonstrate that they have a superior signal-to-noise ratio compared with electrodes due to local signal amplification.

    • Dion Khodagholy
    • , Thomas Doublet
    •  & George G. Malliaras

  • Article |

    Current pharmacokinetic models describe the distribution of drugs within tissues but usually lack single-cell resolution. Here Weissleder and colleagues visualize the subcellular distribution of an anticancer drug in real time in living animals and develop a model to extrapolate these findings to humans.

    • Greg M. Thurber
    • , Katy S. Yang
    •  & Ralph Weissleder

  • Article |

    RNA detection is important in biomedical research and largely relies on the reverse transcription–PCR reaction. Zhao et al.report an isothermal reaction, which involves cleavage by a DNAzyme and signal amplification, to simultaneously amplify and detect RNA.

    • Yongyun Zhao
    • , Li Zhou
    •  & Zhuo Tang

  • Article |

    Large-scale screening of animal phenotypes requires automated detection and analysis of complex morphological information. Here, Yanik and colleagues present an imaging system based on optical projection tomography that generates micrometre-resolution 3D images of zebrafish larvae with within tens of seconds per animal.

    • Carlos Pardo-Martin
    • , Amin Allalou
    •  & Mehmet Fatih Yanik

  • Article
    | Open Access

    Temporal lobe epilepsy in adults does not always respond to treatment. Krook-Magnuson and colleagues use optogenetics to inhibit and activate excitatory and inhibitory neurons, respectively, in a mouse model of temporal lobe epilepsy, and find that they can stop seizures on a moment-to-moment basis.

    • Esther Krook-Magnuson
    • , Caren Armstrong
    •  & Ivan Soltesz

  • Article |

    In vitro, retroviruses spread between cells via structures resembling synapses. Sewaldet al. now demonstrate that virological synapses can also be observed in living mice by intravital microscopy, validating this concept in vivo.

    • Xaver Sewald
    • , David G. Gonzalez
    •  & Walther Mothes

  • Article
    | Open Access

    Diagnostic microfluidic devices often require complicated optical systems and computers to quantify results. Here, Qin and colleagues link enzymatic biomarker detection with the displacement of ink, resulting in a device that displays quantitative results as bar graphs directly on the device.

    • Yujun Song
    • , Yuanqing Zhang
    •  & Lidong Qin

  • Article |

    Reading requires accurate and rapid distinction between similar visual stimuli. Thesen and colleagues use human intracranial electrophysiology and brain imaging to show that letter-selective responses, in an area of the brain immediately posterior to the visual word-form area, occur before word selection.

    • Thomas Thesen
    • , Carrie R. McDonald
    •  & Eric Halgren

  • Article
    | Open Access

    Luminescent proteins are important tools for biomedical imaging but tend to emit fairly little light. Saito et al.. describe a brighter version of a bioluminescent protein that can visualize intracellular dynamics of various signalling molecules with high spatial and temporal resolution.

    • Kenta Saito
    • , Y-F Chang
    •  & Takeharu Nagai

  • Article
    | Open Access

    The use of animal products as culture substrates for human embryonic stem cell and induced pluripotent stem cell culture raises numerous safety concerns in a therapeutic setting. Miyazaki et al.. show that minimal fragments of human laminins provide a more effective support for the culture of these cell types.

    • Takamichi Miyazaki
    • , Sugiko Futaki
    •  & Eihachiro Kawase

  • Article |

    Species coexistence can be explained by the competition–colonization trade-off theory. Here, Livingston et al. illustrate this theory in a metacommunity experiment using two bacterial strains, finding a negative correlation between diversity and productivity when scaled to full metacommunities.

    • George Livingston
    • , Miguel Matias
    •  & Nicolas Mouquet

  • Article
    | Open Access

    Abnormal human embryo development is implicated in the embryo arrest observed during in vitrofertilization. Chavez and colleagues perform time-lapse imaging on human embryos and find that chromosomally abnormal embryos exhibit diverse cell cycle parameters that may contribute to arrest.

    • Shawn L. Chavez
    • , Kevin E. Loewke
    •  & Renee A. Reijo Pera

  • Article |

    Enzymes are traditionally viewed as being highly specific for their substrates. Tokuriki et al.follow the accumulation of mutations during the laboratory evolution of a phosphotriesterase into an arylesterase, and postulate that many naturally occurring enzymes may not be optimal for their substrates.

    • Nobuhiko Tokuriki
    • , Colin J. Jackson
    •  & Dan S. Tawfik

  • Article |

    Fluorescent proteins are widely used to image cellular structures. Here, Shemiakina and colleagues develop an enhanced version of a red fluorescent protein that is monomeric and less cytotoxic, thereby improving the quality of images that can be obtained in the red part of the visible spectrum.

    • I.I. Shemiakina
    • , G.V. Ermakova
    •  & D. Shcherbo

  • Article |

    Sequence-specific DNA endonucleases have found numerous applications in biology, but similar manipulations of RNA have been limited by the lack of suitable enzymes. These authors combine a cleavage domain with a designable binding domain and demonstrate the resulting RNA endonuclease's utilityin vitroand in cells.

    • Rajarshi Choudhury
    • , Yihsuan S. Tsai
    •  & Zefeng Wang

  • Article |

    Rapid synaptic transmission requires efficient recycling of synaptic vesicle membrane proteins. Sochackiet al.use live cell, electron and super-resolution microscopy to visualize exocytosis of vesicular transporters and their rapid recapture in clathrin-rich microdomains in the plasma membrane.

    • Kem A. Sochacki
    • , Ben T. Larson
    •  & Justin W. Taraska

  • Article |

    Protein encapsulation in molecular cages has the potential to alter protein function and aid crystallization. Here, ubiquitin is encapsulated within a giant coordination cage; the protein is attached to a bidentate ligand, and the cage self-assembles upon addition of capping ligands and Pd(II) ions.

    • Daishi Fujita
    • , Kosuke Suzuki
    •  & Makoto Fujita

  • Article
    | Open Access

    The efficiency of reprogramming somatic cells to induced pluripotent stem cells is low. To enhance reprogramming efficiency, Li and Rana used a chemical screen and identified several kinase inhibitors that enhance reprogramming, and show that blocking Aurora A, p38 and inositiol triphosphate 3-kinase signalling is important for this process.

    • Zhonghan Li
    •  & Tariq M. Rana

  • Article
    | Open Access

    Seizure activity in the brain is characterized by the recruitment of cortical neuronal activity. Schevon and colleagues study seizure activity in human subjects and find that the recruitment of neurons is hypersynchronous and that there is an intrinsic restraint on the propagation of this activity.

    • Catherine A. Schevon
    • , Shennan A. Weiss
    •  & Andrew J. Trevelyan

  • Article |

    Microscopic imaging techniques have a high spatio-temporal resolution but, in living animals, are hampered by cardiac and respiratory motion. This paper describes a microscopic setup that allows fluorescent confocal imaging of the beating mouse heart over a period of several hours.

    • Sungon Lee
    • , Claudio Vinegoni
    •  & Ralph Weissleder

  • Article |

    Calcium-sensing fluorescent proteins such as TN-XXL are valuable tools for studying cellular function but, when expressed in mice, may affect animal physiology and behaviour. The authors of this paper create transgenic mice expressing TN-XXL and show that long-term expression of TN-XXL is tolerated well.

    • Stephan Direnberger
    • , Marsilius Mues
    •  & Oliver Griesbeck

  • Article |

    Supramolecular interactions allow some small molecules to self-assemble into nanofibres and hydrogels in aqueous environments. Gaoet al.report a hydrogelator that forms fluorescent nanofibres within cells, leading to the visualization of their self-assembly at the endoplasmic reticulum.

    • Yuan Gao
    • , Junfeng Shi
    •  & Bing Xu

  • Article
    | Open Access

    Semi-automated imaging systems help with the task of classifying large numbers of biological images. This study presents a novel framework—CARTA—with an active learning algorithm combined with a genetic algorithm, whose applications include the classification of magnetic resonance imaging of cancer cells.

    • Natsumaro Kutsuna
    • , Takumi Higaki
    •  & Seiichiro Hasezawa

  • Article
    | Open Access

    Hemimetabolous insects comprise many pests but introducing targeted mutations into these species has been difficult. This paper reports efficient targeted mutagenesis, and the generation of homozygous knockouts, in crickets based on zinc finger nucleases or transcription activator-like effector nucleases.

    • Takahito Watanabe
    • , Hiroshi Ochiai
    •  & Taro Mito

  • Article
    | Open Access

    Fbw7 is a ubiquitin-ligase, which targets several oncoproteins for proteolysis, and is therefore important for the control and prevention of tumorigenesis. In this study, Arabi and colleagues carry out a proteomic screen of the targets of Fbw7, and identify Nuclear Factor of κ-B2 as a substrate.

    • Azadeh Arabi
    • , Karim Ullah
    •  & Olle Sangfelt

  • Article
    | Open Access

    In uteroelectroporation allows the labelling of specific populations of neurons in the developing mouse brain. The authors of this paper present a simple modification of this method that increases labelling efficiency and allows, for the first time, transfection of Purkinje cells in the rat cerebellum.

    • Marco dal Maschio
    • , Diego Ghezzi
    •  & Laura Cancedda

  • Article
    | Open Access

    The motor protein myosin-V transports cargo along actin filaments, but the biophysical mechanisms by which myosin-V generates force are unclear. Here, optical tweezers and a DNA handle are used to study the forces generated by myosin-V: the mechanism of force generation is found to depend on the load applied.

    • Keisuke Fujita
    • , Mitsuhiro Iwaki
    •  & Toshio Yanagida

  • Article
    | Open Access

    Fluorescence imaging is important for biomedical research and applications, but the turbidity of biological material prohibits deep tissue study. By combining ultrasound-encoding with digital time-reversal, Wanget al.perform focussed fluorescence imaging at a tissue depth of 2.5mm.

    • Ying Min Wang
    • , Benjamin Judkewitz
    •  & Changhuei Yang

  • Article
    | Open Access

    Electrical stimulation is used to treat a range of neurological diseases, but there are limitations that reduce its benefits. Bonmassar and colleagues show that magnetic stimulation delivered by small coils, close to the targeted neural tissue, can also be used to activate neurons and with fewer limitations.

    • Giorgio Bonmassar
    • , Seung Woo Lee
    •  & John T. Gale

  • Article |

    The detection of subclonal variants in heterogeneous cancer specimens is a challenge due to errors that occur during sequencing. In this study, a statistical algorithm and a sequencing strategy are reported that circumvent this issue and can accurately detect variants at a frequency as low as 1/10,000.

    • Moritz Gerstung
    • , Christian Beisel
    •  & Niko Beerenwinkel

  • Article
    | Open Access

    Phage display screening can unravel protein–protein interactions, but its application has been mainly restricted to the cell surface. Here, a phage-based reagent is introduced that allows the targeting of combinatorial peptides to cell organelles, providing a tool for the discovery of intracellular ligand-receptors.

    • Roberto Rangel
    • , Liliana Guzman-Rojas
    •  & Wadih Arap

  • Article |

    Calcium nanodomains arise from the cytoplasmic mouth of calcium channels but have not been directly visualized. In this study, the nanodomain of the CaV2.2 calcium channel is imaged using total internal reflection fluorescence microscopy and a genetically encoded calcium sensor attached to the carboxy terminus.

    • Lai Hock Tay
    • , Ivy E. Dick
    •  & David T. Yue

  • Article
    | Open Access

    Jurors can be influenced by mitigating circumstances when deciding on sentences for committed crimes. Yamadaet al. show that feelings of sympathy created by mitigating circumstances activate moral conflict regions of the brain that predict individual differences in the severity of the sentence.

    • Makiko Yamada
    • , Colin F. Camerer
    •  & Hidehiko Takahashi

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