Biological techniques articles within Nature Communications

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  • Article
    | Open Access

    Sequencing of newly synthesised RNA can reveal the transcriptional dynamics in a population of cells. Here the authors develop NASC-seq to bring this sensitivity and temporal resolution to single-cell analysis.

    • Gert-Jan Hendriks
    • , Lisa A. Jung
    •  & Rickard Sandberg

  • Article
    | Open Access

    AsCpf1 is an alternative nuclease to Cas9 for CRISPR mediated genome engineering. Here the authors demonstrate functional genomic screens with AsCpf1 that minimize library size with no loss in gene targeting efficiency.

    • Jintan Liu
    • , Sanjana Srinivasan
    •  & Giulio Draetta

  • Article
    | Open Access

    Single cell RNA sequencing generates short reads from one end of a template, providing incomplete transcript coverage and limiting identification of diverse sequences such as antigen receptors. Here the authors combine long read nanopore sequencing with short read profiling of barcoded libraries to generate full-length antigen receptor sequences.

    • Mandeep Singh
    • , Ghamdan Al-Eryani
    •  & Alexander Swarbrick

  • Article
    | Open Access

    Bacillus subtilis has complex spatial and temporal gene expression patterns but currently lacks optogenetic tools to explore these processes. Here the authors import and debug a cyanobacterial green light sensor pathway and show that it enables precise optical control of gene expression.

    • Sebastian M. Castillo-Hair
    • , Elliot A. Baerman
    •  & Jeffrey J. Tabor

  • Article
    | Open Access

    Imaging sensory neurons in the dorsal root ganglion (DRG) in awake animals is challenging due to motion artefacts and other technical issues. Here the authors develop an intervertebral fusion procedure which minimizes spinal movement thereby enabling chronic imaging of DRG neurons in awake, behaving mice.

    • Chao Chen
    • , Jinhui Zhang
    •  & Guang Yang

  • Article
    | Open Access

    Photoswitchable nanoparticles can be used for selective imaging in biological systems but usually have only one color. Here the authors develop a two-color fluorescent emissive system that allows full on-off switching of one component color of the system while the other color is unaffected, which has implications for super-resolution imaging.

    • Dojin Kim
    • , Keunsoo Jeong
    •  & Soo Young Park

  • Article
    | Open Access

    Lamin A is critical for nuclear architecture but its structure and assembly are not fully understood. Here, the authors use quantitative cross-linking mass spectrometry to map intra- and intermolecular interactions within lamin homomers, providing insights into the molecular basis for lamin’s mechanical properties.

    • Alex A. Makarov
    • , Juan Zou
    •  & Eric C. Schirmer

  • Perspective
    | Open Access

    Lack of best practice guidelines currently limits the application of metabolomics in the regulatory sciences. Here, the MEtabolomics standaRds Initiative in Toxicology (MERIT) proposes methods and reporting standards for several important applications of metabolomics in regulatory toxicology.

    • Mark R. Viant
    • , Timothy M. D. Ebbels
    •  & Ralf J. M. Weber

  • Article
    | Open Access

    Monoallelic expression of variant surface glycoprotein genes (VSGs) is essential for immune evasion by Trypanosoma brucei. Here, Faria et al. show that the VEX protein complex controls VSG allelic exclusion, and that CAF‐1 sustains inheritance of the VEX‐complex in association with the active VSG.

    • Joana Faria
    • , Lucy Glover
    •  & David Horn

  • Article
    | Open Access

    Construction of yeast libraries is time-consuming, costly and limited to the genetic background of the chosen strain. Here the authors present CASTLING which uses CRISPR-Cas12a and oligonucleotide pools to rapidly generate pooled libraries with large insertions such as fluorescent protein tags.

    • Benjamin C. Buchmuller
    • , Konrad Herbst
    •  & Michael Knop

  • Article
    | Open Access

    Light-sheet microscopes are increasingly used for imaging cleared tissues, but have imposed constraints on sample geometries and protocols. Here the authors present a multi-immersion open-top light-sheet microscope to overcome these limitations and enable high-throughput imaging of samples processed with various clearing protocols.

    • Adam K. Glaser
    • , Nicholas P. Reder
    •  & Jonathan T. C. Liu

  • Article
    | Open Access

    Gene transcription is known to vary with age and sex, although the underlying mechanisms are unresolved. Here, the authors show that epigenetic enzymes known as HDACs, which regulate gene transcription, are increasingly expressed with age in the living human brain, with sex differences also observed.

    • Tonya M. Gilbert
    • , Nicole R. Zürcher
    •  & Jacob M. Hooker

  • Article
    | Open Access

    The ability to encapsulate living cells could lead to many applications. Here, the authors present a flexible method to graft DNA polymers onto bacteria, yeast and mammalian cells, polymerize them into DNA cocoons and use these to manipulate and select cells based on the encoded polymer sequences on DNA cocoons.

    • Tao Gao
    • , Tianshu Chen
    •  & Genxi Li

  • Article
    | Open Access

    Single-nucleus RNA-seq enables interrogation of complex tissues but is limited due to batch effects and processing costs. Here the authors use barcoded antibodies against the nuclear pore complex to label nuclei from distinct samples, and develop a computational tool to assign the sample of origin.

    • Jellert T. Gaublomme
    • , Bo Li
    •  & Aviv Regev

  • Article
    | Open Access

    Stimuli affecting migration of filaria in host tissues are unclear. Using in situ imaging, Kilarski et al. here show that universal adaptations of nematodes allow Litomosoides sigmodontis infective larvae to mechanically break into pre-collecting lymphatics and follow the direction of flow towards the lymph node.

    • Witold W. Kilarski
    • , Coralie Martin
    •  & Melody A. Swartz

  • Article
    | Open Access

    Synthetic promoters can be superior to native ones but the design is challenging without knowledge of gene regulation. Here the authors develop a pipeline that allows for screening a synthetic promoter library to identify high performance promoters in potentially any given cell state of interest.

    • Ming-Ru Wu
    • , Lior Nissim
    •  & Timothy K. Lu

  • Article
    | Open Access

    Correct spindle positioning is critical for cell division but the full set of proteins regulating this is unclear. Here, with a live imaging siRNA-based screen in human cells, the authors identify 16 candidates required for this process, 11 of which were previously unassociated with such a function, including TYRO3 and GAK.

    • Benita Wolf
    • , Coralie Busso
    •  & Pierre Gönczy

  • Article
    | Open Access

    The sinus node generates rhythmic heartbeat but the molecular basis of pacemaking is still under debate. Here, the authors combine quantitative proteomics and single-nucleus transcriptomics to characterize the molecular composition of the sinus node and provide insights into the underpinnings of pacemaking.

    • Nora Linscheid
    • , Sunil Jit R. J. Logantha
    •  & Alicia Lundby

  • Article
    | Open Access

    Single-cell studies in solid tissues remain challenging and have benefited from the development of single-nuclei RNA sequencing strategies. Here Lake et al. apply single-nucleus RNA sequencing to human kidney tissues to provide a comprehensive molecular and cellular atlas of the human kidney, with potential implications for the understanding of kidney physiology and disease.

    • Blue B. Lake
    • , Song Chen
    •  & Sanjay Jain

  • Article
    | Open Access

    Optogenetic stimulation of damaged peripheral nerves has advantages over electrical stimulation but it’s limited to single-site stimulation. Here the authors develop a spiral-shaped LED implant for precise optogenetic stimulation of peripheral nerve bundles at multiple sites and use it to induce distinct limb movements in mice.

    • Hao Zheng
    • , Zhitao Zhang
    •  & Jiayi Zhang

  • Article
    | Open Access

    During wound induced hair follicle neogenesis (WIHN), stem cells regenerate hair follicles but how this arises is unclear. Here, the authors show that self-noncoding dsRNA activates the antiviral receptor TLR3 to induce intrinsic retinoic acid, which stimulates WIHN in mice, and in isolated human keratinocyte cells.

    • Dongwon Kim
    • , Ruosi Chen
    •  & Luis A. Garza

  • Article
    | Open Access

    The transcriptional signature of embryonic lethality has not been defined. Here, the authors, as part of the Deciphering the Mechanisms of Developmental Disorders programme, define genes causing murine embryonic lethality around E9.5 and identify developmental delay transcriptional signatures.

    • John E. Collins
    • , Richard J. White
    •  & Elisabeth M. Busch-Nentwich

  • Article
    | Open Access

    The left hemisphere of the brain is especially involved in processing social vocalizations and (in humans) language, but the mechanisms of this lateralization of function are unclear. Here, the authors compared left and right auditory cortex in mice and show lateralized, experience-dependent circuit-motifs.

    • Robert B. Levy
    • , Tiemo Marquarding
    •  & Hysell V. Oviedo

  • Article
    | Open Access

    Existing methods for protein polymer engineering suffer from low efficiency especially for synthesis large size polyproteins. Here, Deng et al. construct homo-polymer and co-polymer up to decamer by stepwise ligation and cleavage validated by atomic force microscopy-based single-molecule force spectroscopy.

    • Yibing Deng
    • , Tao Wu
    •  & Peng Zheng

  • Article
    | Open Access

    Obesity is associated with leptin resistance and rising blood leptin levels while central leptin exposure may be limited. Here, the authors show that brain leptin infusion reduces hepatic lipid content in rats by increasing hepatic VLDL secretion and lowering liver de novo lipogenesis via a vagal mechanism.

    • Martina Theresa Hackl
    • , Clemens Fürnsinn
    •  & Thomas Scherer

  • Article
    | Open Access

    The dopamine transporter is responsible for termination of neurotransmission through Na+-driven reuptake of neurotransmitter from the extracellular space. Here authors use hydrogen-deuterium exchange mass spectrometry to monitor Na+- and dopamine-induced conformational dynamics of the dopamine transporter.

    • Anne Kathrine Nielsen
    • , Ingvar R. Möller
    •  & Claus J. Loland

  • Article
    | Open Access

    The activity of the membrane-bound enzyme pMMO depends on copper but the location of the copper centers is still under debate. Here, the authors reconstitute pMMO in nanodiscs and use native top-down MS to localize its copper centers, providing insights into which sites are essential for activity.

    • Soo Y. Ro
    • , Luis F. Schachner
    •  & Amy C. Rosenzweig

  • Article
    | Open Access

    Transcranial Magnetic Stimulation (TMS) can modulate human brain activity, but the extent of the cortical area activated by TMS is unclear. Here, the authors show that TMS affects monkey single neuron activity in an area less than 2 mm diameter, while TMS-induced activity and task-related activity do not summate.

    • Maria C. Romero
    • , Marco Davare
    •  & Peter Janssen

  • Article
    | Open Access

    Metabolic engineering requires the balancing of gene expression to obtain optimal output. Here the authors present COMPASS – COMbinatorial Pathway ASSembly – which uses plant-derived artificial transcription factors and cloning of thousands of DNA constructs in parallel to rapidly optimise pathways.

    • Gita Naseri
    • , Jessica Behrend
    •  & Bernd Mueller-Roeber

  • Article
    | Open Access

    In vitro blood-brain barrier (BBB) models do not fully recapitulate the in vivo barrier function. Here the authors develop an organ-on-a-chip BBB model using iPS-derived human brain endothelial cells differentiated under hypoxia, primary human pericytes and astrocytes, which maintains in vivo-like BBB barrier and shuttling functions for a week.

    • Tae-Eun Park
    • , Nur Mustafaoglu
    •  & Donald E. Ingber

  • Article
    | Open Access

    Type VI secretion systems (T6SS) are important for bacterial interaction, competition and virulence, but the abundance and assembly of their components is still not well understood. Here, the authors apply targeted proteomics to measure the abundance of T6SS components across different species and conditions.

    • Lin Lin
    • , Emmanuelle Lezan
    •  & Marek Basler

  • Article
    | Open Access

    Transcranial alternating current stimulation (TACS) of the brain is widely used in neuroscience, but the electric fields produced when multiple stimulation electrodes are used are not well understood. Here, the authors directly record electric fields in primate brains during multi-electrode TACS.

    • Ivan Alekseichuk
    • , Arnaud Y. Falchier
    •  & Alexander Opitz

  • Article
    | Open Access

    Fiber optic implantation in deep areas of the rodent’s brain for MRI combined with optogenetics is challenging. Here the authors use an MRI-guided robotic arm as the navigation method for accurate fiber optic placement and precise microinjection during multi-modal fMRI, optogenetics and calcium recordings.

    • Yi Chen
    • , Patricia Pais-Roldan
    •  & Xin Yu

  • Article
    | Open Access

    Brown macroalgae is a good candidate feedstock for biorefinery, but the major carbohydrate alginate cannot be digested by current industrial microbes. Here, the authors isolate Vibrio sp. dhg and engineer it to produce value-added biochemicals from alginate using newly developed genetic tools.

    • Hyun Gyu Lim
    • , Dong Hun Kwak
    •  & Gyoo Yeol Jung

  • Article
    | Open Access

    Amyloid-β (Aβ) deposition occurs in Alzheimer's disease but its relation to disease features such as local brain hypometabolism or cognitive decline is unclear. Here, the authors show that Aβ aggregation in the brain’s default mode network leads to hypometabolism in distant but functionally connected areas.

    • Tharick A. Pascoal
    • , Sulantha Mathotaarachchi
    •  & Pedro Rosa-Neto

  • Article
    | Open Access

    Different sensory experiences can affect longevity in Drosophila. Here the authors find that exposure of Drosophila directly to dead conspecifics affects longevity via a serotonergic mechanism, and that Drosophila exposed to dead conspecifics also become an aversive stimulus to naïve choosers.

    • Tuhin S. Chakraborty
    • , Christi M. Gendron
    •  & Scott D. Pletcher

  • Article
    | Open Access

    Acyl carrier proteins (ACPs), a universal and highly conserved carrier of acyl intermediates during fatty acid and polyketide synthesis, are difficult to visualise. Here, the authors developed a facile, Raman spectroscopy-based method to detect ACP-substrate interactions.

    • Samuel C. Epstein
    • , Adam R. Huff
    •  & Louise K. Charkoudian

  • Article
    | Open Access

    Single-cell CRISPR screening combines pooled CRISPR screening with scRNA-seq analysis to expand the resolution power of genetic screening. Here, the authors develop MUSIC, a computational pipeline for analyzing single-cell CRISPR screening data.

    • Bin Duan
    • , Chi Zhou
    •  & Qi Liu

  • Article
    | Open Access

    Here the authors fuse hRad51 and variants thereof to Cas9 nickase to facilitate homology-directed repair without generating double strand breaks, minimizing indel formation and off-target editing. This tool represents progress towards the goal of performing HDR without an excess of undesired side products.

    • Holly A. Rees
    • , Wei-Hsi Yeh
    •  & David R. Liu

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