Biological techniques articles within Nature Communications

Featured

  • 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

  • Article
    | Open Access

    Pulsed infrared laser light can directly stimulate nerves and muscles, but the underlying biophysical mechanism has remained enigmatic. This study reveals that infrared pulses depolarize target cells by reversibly altering the electrical capacitance of the plasma membrane.

    • Mikhail G. Shapiro
    • , Kazuaki Homma
    •  & Francisco Bezanilla

  • Article
    | Open Access

    Intracellular temperature mapping has not previously been achieved. Now, a fluorescent polymeric thermometer has been developed that can be used in combination with fluorescence-lifetime imaging microscopy to allow thermometry with spatial and temperature resolutions of 200 nm and 0.18–0.58 ° C.

    • Kohki Okabe
    • , Noriko Inada
    •  & Seiichi Uchiyama

  • Article
    | Open Access

    Algae show much promise in the production of biofuels owing to their high photoautotrophic biomass and lipid production rates. In this study, the draft genome ofNannochloropsis gaditanaCCMP526 and a method for the transformation of this alga are reported, facilitating the investigation of lipid synthesis and biofuel production.

    • Randor Radakovits
    • , Robert E. Jinkerson
    •  & Matthew C. Posewitz

  • Article
    | Open Access

    The influenza A virus genome consists of eight RNA segments, which permits genetic reassortment and contributes to the emergence of novel strains with pandemic potential. Here, electron tomography is used to study the three-dimensional structure of ribonucleoprotein complexes within progeny virions.

    • Takeshi Noda
    • , Yukihiko Sugita
    •  & Yoshihiro Kawaoka

  • Article |

    A dual-contrast agent has been developed for combined ultrasound and photoacoustic imaging. This agent uses vaporization for ultrasound contrast enhancement and photoacoustic signal generation, providing significantly higher signals than thermal expansion, the most commonly used photoacoustic mechanism.

    • Katheryne Wilson
    • , Kimberly Homan
    •  & Stanislav Emelianov

  • Article |

    Multivalent display of integrin antagonists enhances their efficacy, but current synthetic scaffolds used to display ligands are limited in range and precision. Englundet al. develop a new scaffold to study the multivalent effects of integrin antagonists across wide ranges of ligand number, density, and 3D arrangement.

    • Ethan A. Englund
    • , Deyun Wang
    •  & Daniel H. Appella

  • Article
    | Open Access

    Albumin transport proteins circulate in the blood and are protected from degradation by interaction with the neonatal Fc receptor. Andersenet al. investigate the albumin binding site of the neonatal Fc receptor and find pH sensitive ionic networks at the binding interface.

    • Jan Terje Andersen
    • , Bjørn Dalhus
    •  & Inger Sandlie

  • Article |

    Surface characterization of soft materialsin situis challenging due to the importance of non-covalent interactions. Now, a new chemical imaging method is reported that generates images of surface interactions by combining many molecular probe trajectories.

    • Robert Walder
    • , Nathaniel Nelson
    •  & Daniel K. Schwartz

  • Article |

    Ampullary organs are involved in electroreception, but whether these are derived from placodes, thickened ectoderm, is unclear. In this study, the ampullary organs of the primitive ray-finned fish,Polyodon spathula, are shown to develop from lateral line placodes, suggesting that this is the ancestral state in bony fishes.

    • Melinda S. Modrell
    • , William E. Bemis
    •  & Clare V.H. Baker

  • Article |

    The generation of human cell lines using somatic cell nuclear transfer has been difficult to achieve. In this study, Egliet al. show that while mouse eggs reprogram somatic cells within hours, human eggs arrest after nuclear transfer which may be due to a lack of genome transcription.

    • Dieter Egli
    • , Alice E. Chen
    •  & Kevin Eggan

  • Article
    | Open Access

    Understanding the genetics and physiology of domesticated species is important for crop improvement. By studying natural variation and the phenotypic traits of 413 diverse accessions of rice, Zhao et al. identify many common genetic variants that influence quantitative traits such as seed size and flowering time.

    • Keyan Zhao
    • , Chih-Wei Tung
    •  & Susan R. McCouch

  • Article
    | Open Access

    The appearance of a new intron that splits an exon without disrupting the corresponding peptide sequence is a rare event in vertebrate genomes. Hellstenet al.demonstrate that, under certain circumstances, a functional intron can be produced in a single step by segmental genomic duplication.

    • Uffe Hellsten
    • , Julie L. Aspden
    •  & Daniel S. Rokhsar

  • Article |

    Modern female horses are genetically diverse but male horses are relatively homogenous. Lippoldet al. sequence the Y chromosome of nine ancient horses and detect diversity in the ancestral paternal lineage, demonstrating ancient Y-chromosomal DNA sequencing can provide insights into evolution.

    • Sebastian Lippold
    • , Michael Knapp
    •  & Michael Hofreiter

  • Article
    | Open Access

    Polo-like kinase 1 is a key regulator of mitosis and is a candidate for drug development to treat cancer. Here, reduced expression of polo-like kinase 1 in adult mice has a minor impact on animal physiology, suggesting that polo-like kinase 1 inhibitors may be useful in the killing of tumour cells while sparing normal cells.

    • Monika Raab
    • , Sven Kappel
    •  & Klaus Strebhardt

  • Article |

    Soluble cytosolic proteins can be degraded in lysosomes by chaperone-mediated autophagy, however, the current method to measure this process requires isolation of lysosomes. Now, a fluorescent reporter is described that can measure this type of autophagy in intact cells.

    • Hiroshi Koga
    • , Marta Martinez-Vicente
    •  & Ana Maria Cuervo

  • Article |

    Encapsulating molecules within supramolecular frameworks for potential biological application is challenging. Bhatiaet al. incorporate a fluorescent polymer within an icosahedral DNA nanocapsule, and show that it can be used to target specific cells in vivoand map pH spatially and temporally.

    • Dhiraj Bhatia
    • , Sunaina Surana
    •  & Yamuna Krishnan

  • Article
    | Open Access

    ADAR enzymes edit double-stranded RNA, converting adenosines to inosines, and are essential for neuronal function. Eggingtonet al. quantify edit sites in RNA using a Sanger sequencing protocol and use the resulting data to develop algorithms to predict RNA edit sites.

    • Julie M. Eggington
    • , Tom Greene
    •  & Brenda L. Bass

Browse broader subjects

Browse narrower subjects

Browse Biological techniques across other nature.com journals