Biological techniques

  • Article
    | Open Access

    Mass spectrometry-based metabolomics is a powerful method for profiling large clinical cohorts but batch variations can obscure biologically meaningful differences. Here, the authors develop a computational workflow that removes unwanted data variation while preserving biologically relevant information.

    • Taiyun Kim
    • , Owen Tang
    •  & Jean Yee Hwa Yang
  • Article
    | Open Access

    Lineage tracing and snapshots of transcriptional state at the single-cell level are powerful, complementary tools for studying development. Here, the authors propose a mathematical method combining lineage tracing with trajectory inference to improve our understanding of development.

    • Aden Forrow
    •  & Geoffrey Schiebinger
  • Article
    | Open Access

    The only known animal polyketide-nonribosomal peptides, the nemamides, are biosynthesized by two megasynthetases in the canal-associated neurons (CANs) of C. elegans. Here, the authors map the biosynthetic roles of individual megasynthetase domains and identify additional enzymes in the CANs required for nemamide biosynthesis.

    • Likui Feng
    • , Matthew T. Gordon
    •  & Rebecca A. Butcher
  • Article
    | Open Access

    Analogues of α-ketoglutarate are used in many cellular studies but assumptions are made about cellular uptake. Here, the authors show that esterified analogues rapidly hydrolyse in aqueous medium resulting in an analogue which can be quickly taken up by many cell lines, contrary to prevailing assumptions.

    • Seth J. Parker
    • , Joel Encarnación-Rosado
    •  & Alec C. Kimmelman
  • Article
    | Open Access

    Mapping neuronal proteomes with genetic, subcellular, and temporal specificity is a challenging task. This study uncovers proteome dynamics in two classes of striatal spiny projection neurons in the mouse brain using a genetically targeted APEX2-based proximity labeling approach.

    • V. Dumrongprechachan
    • , R. B. Salisbury
    •  & Y. Kozorovitskiy
  • Article
    | Open Access

    The nature of the mitochondrial permeability transition pore (PTP) is still under debate. Here, through genetically modified F-ATP synthase, the authors show that PTP formation can be mediated by F-ATP synthase or by adenine nucleotide translocator, suggesting the existence of distinct but related permeability pathways.

    • Andrea Carrer
    • , Ludovica Tommasin
    •  & Paolo Bernardi
  • Article
    | Open Access

    The development of the coronal suture remains incompletely understood. Here the authors perform scRNA-seq and expression validation to uncover the cellular diversity within the murine embryonic coronal suture, thus revealing possible mechanisms for its loss in craniosynostosis.

    • D’Juan T. Farmer
    • , Hana Mlcochova
    •  & Stephen R. F. Twigg
  • Article
    | Open Access

    Label-free quantitative proteomics by data dependent acquisition offers high protein identification rates but is often limited by missing values. Here, the authors develop a quantification workflow that substantially reduces missing values while maintaining high identification rates and quantification accuracy.

    • Mathias Kalxdorf
    • , Torsten Müller
    •  & Jeroen Krijgsveld
  • Article
    | Open Access

    Coenzyme Q (CoQ) is a lipid made in the inner mitochondrial membrane with antioxidant roles throughout the cell, but regulation of its cellular distribution is unclear. Here the authors identify two proteins that have reciprocal CoQ trafficking functions to help coordinate CoQ localization in yeast.

    • Zachary A. Kemmerer
    • , Kyle P. Robinson
    •  & David J. Pagliarini
  • Article
    | Open Access

    Brain organoids derived from human pluripotent stem cells can model human brain development and disease, though current culture systems fail to ensure reliable production of high-quality organoids. Here the authors combine human brain extracellular matrix and culture in a microfluidic device to promote structural and functional maturation of human brain organoids.

    • Ann-Na Cho
    • , Yoonhee Jin
    •  & Seung-Woo Cho
  • Article
    | Open Access

    Single-pixel holography generates holographic images with a single-pixel detector making this relatively inexpensive. Here the authors report a high-throughput single-pixel compressive holography method for imaging biological tissue which can either provide a large field of view or high resolution.

    • Daixuan Wu
    • , Jiawei Luo
    •  & Zhaohui Li
  • Article
    | Open Access

    Lipins need to bind cell membranes before they can function as phosphatidic acid phosphatases. Here, the authors elucidate the structural basis of lipin membrane-association and identify a lipin domain with a novel protein fold that is critical for membrane binding and full functionality of lipins.

    • Weijing Gu
    • , Shujuan Gao
    •  & Michael V. Airola
  • Article
    | Open Access

    The authors have recently developed molecular force microscopy (MFM) which uses fluorescence polarisation to measure cell-surface receptor force orientation. Here they show that structured illumination microscopes, which inherently use fluorescence polarisation, can be used for MFM in a turn-key manner.

    • Aaron Blanchard
    • , J. Dale Combs
    •  & Khalid Salaita
  • Article
    | Open Access

    Existing methods for non-invasively monitoring water flow in plants have limited spatial/temporal resolution. Here, the authors report that Raman microspectroscopy, complemented by hydrodynamic modelling, can monitor hydrodynamics within living root tissues at cell- and sub-second-scale resolutions.

    • Flavius C. Pascut
    • , Valentin Couvreur
    •  & Kevin F. Webb
  • Article
    | Open Access

    Placenta accreta spectrum (PAS) is a high-risk obstetrical complication associated with significant morbidity and mortality. Here the authors discover a uniquely high prevalence of circulating trophoblasts clusters in PAS and explore their diagnostic potential to augment current diagnostic modalities for the early detection of PAS.

    • Yalda Afshar
    • , Jiantong Dong
    •  & Yazhen Zhu
  • Article
    | Open Access

    The authors demonstrate efficient excitation of nanodiamonds by a focused beam of helium ions, resulting in ionoluminescence. They use this for quantification and correlative localization of single particles within a whole cell at sub-30 nm resolution, and investigate nanodiamond radiosensitisation effects.

    • Zhaohong Mi
    • , Ce-Belle Chen
    •  & Andrew A. Bettiol
  • Article
    | Open Access

    Metastatic and locally-advanced neuroendocrine neoplasms (aNEN) display heterogeneous clinical and genetic characteristics. Here, the authors investigate the mutational landscape of 85 aNEN by whole genome sequencing and identify distinct subpopulations, tumour mutational burden patterns, drivers and actionable somatic alterations.

    • Job van Riet
    • , Harmen J. G. van de Werken
    •  & Bianca Mostert
  • Article
    | Open Access

    UBE2W catalyzes the ubiquitination of protein N-termini but its substrate spectrum is largely unknown. Here, the authors discover mAbs selective for peptides derived from N-terminally ubiquitinated proteins, solve the structure of a peptide-bound mAb and apply the mAbs to map endogenous UBE2W substrates by proteomics.

    • Christopher W. Davies
    • , Simon E. Vidal
    •  & James T. Koerber
  • Article
    | Open Access

    Multifocal imaging suffers from a number of limitations. Here the authors report an open-source 3D reconstruction algorithm to enable label-free tracking of spherical and filamentous structures which they use to characterise fluid flow and flagellar beating of human and sea urchin sperm.

    • Jan N. Hansen
    • , An Gong
    •  & Luis Alvarez
  • Article
    | Open Access

    Many current immunoassays require multiple washing, incubation and optimization steps. Here the authors present Ratiometric Plug-and-Play Immunodiagnostics (RAPPID), a generic assay platform that uses ratiometric bioluminescent detection to allow sandwich immunoassays to be performed directly in solution.

    • Yan Ni
    • , Bas J. H. M. Rosier
    •  & Maarten Merkx
  • Article
    | Open Access

    Mitochondrial transport toward both the plus- and minus-ends of microtubules is mediated by motor proteins linked to mitochondria by TRAK adaptor proteins. Here the authors investigate the role of TRAK2 as a bidirectional motor adaptor, and propose a model where TRAK2 coordinates the activities of opposing kinesin-1 and cytoplasmic dynein motors as a single interdependent motor complex.

    • Adam R. Fenton
    • , Thomas A. Jongens
    •  & Erika L. F. Holzbaur
  • Article
    | Open Access

    Differentiation of hPSCs to cardiomyocytes suffers from high variability. Here the authors report a label-free live cell imaging platform based on autofluorescence imaging to enable the prediction of cardiomyocyte differentiation efficiency from hPSCs.

    • Tongcheng Qian
    • , Tiffany M. Heaster
    •  & Melissa C. Skala
  • Article
    | Open Access

    Imaging rates in single-pixel imaging has been limited by the dependence on configurable spatial light modulators. Here, the authors use cyclic Hadamard patterns coded onto a spinning mask to demonstrate dynamic imaging with rates up to 72 frames per second and real time reconstruction capabilities.

    • Evgeny Hahamovich
    • , Sagi Monin
    •  & Amir Rosenthal
  • Article
    | Open Access

    The authors develop a method to build Manhattan Raman Scattering (MARS) probes based on different core atoms, conjugation ring numbers, and stable isotope substitutions. A quantitative model predicts vibrational frequencies of MARS dyes from structures, which are used in supermultiplexed vibrational imaging.

    • Yupeng Miao
    • , Naixin Qian
    •  & Wei Min
  • Article
    | Open Access

    Currently, bidirectional control of activity in the same neurons in the same experiment is difficult. Here the authors report a Bidirectional Pair of Opsins for Light-induced Excitation and Silencing, BiPOLES, which they use in a range of organisms including worms, fruit flies, mice and ferrets.

    • Johannes Vierock
    • , Silvia Rodriguez-Rozada
    •  & J. Simon Wiegert
  • Article
    | Open Access

    Quantitative methods to assess the quality of hPSC-derived organoids have not been developed. Here they present a prediction algorithm to assess the transcriptomic similarity between hPSC-derived organoids and the corresponding human target organs and perform validation on lung bud organoids, antral gastric organoids, and cardiomyocytes.

    • Mi-Ok Lee
    • , Su-gi Lee
    •  & Hyun-Soo Cho
  • Article
    | Open Access

    Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and reconstruct strain genomes from single-sample low-complexity microbiomes.

    • Riccardo Vicedomini
    • , Christopher Quince
    •  & Rayan Chikhi
  • Article
    | Open Access

    Pannexin 1 (PANX1) is a membrane channel mediating release of signaling molecules to the extracellular space. PANX1 can be activated by GPCRs. Here, the authors elucidate a non-canonical channel activation pathway by α1-adrenergic receptor that involves HDAC6- mediated lysine deacetylation of PANX1.

    • Yu-Hsin Chiu
    • , Christopher B. Medina
    •  & Douglas A. Bayliss
  • Article
    | Open Access

    Scintillators emit visible luminescence when irradiated with X-rays and may enable remote optogenetic control of neurons deep in the brain. The authors inject an inorganic scintillator to activate and inhibit midbrain dopamine neurons in freely moving mice by X-ray irradiation to modulate place preference behavior.

    • Takanori Matsubara
    • , Takayuki Yanagida
    •  & Takayuki Yamashita
  • Article
    | Open Access

    Currently many of the time resolved serial femtosecond (SFX) crystallography experiments are done with light driven protein systems, whereas the reaction initiation for non-light triggered enzymes remains a major bottle neck. Here, the authors present an expanded Drop-on-Tape system, where picoliter-sized droplets of a substrate or inhibitor are turbulently mixed with nanoliter sized droplets of microcrystal slurries, and they use it for time-resolved SFX measurements of inhibitor binding to lysozyme and secondly, binding of a β-lactam antibiotic to a bacterial serine β-lactamase.

    • Agata Butryn
    • , Philipp S. Simon
    •  & Allen M. Orville
  • Article
    | Open Access

    Spatial analysis of RNAseq data is important. Here the authors report a method for transcriptome profiling combined with photo-isolation chemistry to allow determination of expression profiles specifically from photo-irradiated regions of interest which they use in mouse brains and embryonic tissues.

    • Mizuki Honda
    • , Shinya Oki
    •  & Yasuyuki Ohkawa
  • Article
    | Open Access

    High-speed atomic force microscopy height spectroscopy and single channel electrophysiology recordings are used to correlate conformational and functional dynamics of the model membrane protein, outer membrane protein G (OmpG). These techniques show that both states coexist and rapidly interchange in all conditions supported by molecular dynamics simulations.

    • Raghavendar Reddy Sanganna Gari
    • , Joel José Montalvo‐Acosta
    •  & Simon Scheuring
  • Article
    | Open Access

    Wavefront shaping is used to overcome scattering in biological tissues during imaging, but determining the compensation is slow. Here, the authors use holographic phase stepping interferometry, where new phase information is updated after each measurement, enabling fast improvement of the wavefront correction.

    • Molly A. May
    • , Nicolas Barré
    •  & Alexander Jesacher
  • Article
    | Open Access

    Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs) but only few specific interactions are known. Using TIRF microscopy based assays, functional studies and an experimentally validated prediction algorithm, the authors show that specific PIP binding is widespread among human PH domains.

    • Nilmani Singh
    • , Adriana Reyes-Ordoñez
    •  & Jie Chen
  • Article
    | Open Access

    Current methods to estimate energy expenditure are either infeasible for everyday use or associated with significant errors. Here the authors present a Wearable System using inertial measurement units worn on the shank and thigh that estimates metabolic energy expenditure in real-time during common steady-state and time-varying activities.

    • Patrick Slade
    • , Mykel J. Kochenderfer
    •  & Steven H. Collins
  • Article
    | Open Access

    Single-cell RNA-seq reveals the cellular heterogeneity in development and disease. Here the authors present a single-nucleus RNA-seq2 that allows deep characterization of nuclei isolated from frozen archived tissues, apply it for transcriptional profiling of individual hepatocytes, and determine a functional crosstalk between liver zonation and ploidy.

    • M. L. Richter
    • , I. K. Deligiannis
    •  & C. P. Martinez-Jimenez
  • Article
    | Open Access

    The epithelial-mesenchymal transition (EMT) has been implicated in stem cell properties and therapeutic resistance in cancer. Here, the authors show organoids derived from mesenchymal breast cancers exhibit a spikey structure which can be reverted and exploited for screening drugs that reverse EMT.

    • Na Zhao
    • , Reid T. Powell
    •  & Jeffrey M. Rosen