Biological techniques

  • Article
    | Open Access

    Minimizing toxicity of herpes simplex virus 1 (HSV) based tools for anterograde tracing is important for functional studies. Here the authors generate an anterograde monosynaptic tracer system based on HSV amplicon, which shows fast tracing, bright labeling, low toxicity, input-defined postsynaptic neurons’ anterograde monosynaptic tracing feature, and has potential for functional mapping.

    • Feng Xiong
    • , Hong Yang
    •  & Wen-Bo Zeng
  • Article
    | Open Access

    Despite the importance of DNA methylation, accessible and high-throughput methods to profile methylation at the single-cell level are lacking. Here, the authors present sciMETv2, a high-throughput workflow that provides high-quality single-cell methylomes in a robust and simple workflow.

    • Ruth V. Nichols
    • , Brendan L. O’Connell
    •  & Andrew C. Adey
  • Article
    | Open Access

    Genetically encoded sensors have been developed and become versatile tools for imaging serotonin dynamics. Here, authors developed a family of serotonin (5-HT) sensors (sDarken), three variants with different affinities for 5-HT enable high spatiotemporal resolution of 5-HT dynamics.

    • Martin Kubitschke
    • , Monika Müller
    •  & Olivia Andrea Masseck
  • Article
    | Open Access

    Methods for jointly analysing the different spatial data modalities in 3D are lacking. Here the authors report the computational framework STACI (Spatial Transcriptomic data using over-parameterized graph-based Autoencoders with Chromatin Imaging data) which they apply to an Alzheimer’s disease mouse model.

    • Xinyi Zhang
    • , Xiao Wang
    •  & Caroline Uhler
  • Article
    | Open Access

    The presented Mean-Shift Super Resolution (MSSR) algorithm can extend spatial resolution within a single microscopy image. Its applicability extends across a wide range of experimental and instrumental configurations and it is compatible with other super-resolution microscopy approaches.

    • Esley Torres-García
    • , Raúl Pinto-Cámara
    •  & Adán Guerrero
  • Article
    | Open Access

    Metabolic labeling is often used to measure protein turnover. Here the authors show that for interconvertible protein species like phosphoforms metabolic labeling does not provide information on turnover differences, but that the relative order of modification can determine the observed dynamics.

    • Henrik M. Hammarén
    • , Eva-Maria Geissen
    •  & Mikhail M. Savitski
  • Article
    | Open Access

    The translational states of eukaryotic ribosomes have so far been only investigated in vitro. Here, authors obtained the 3.8 Å in situ 80S ribosome structure, the distribution of translational states and unique arrangement of rRNA expansion segments.

    • Patrick C. Hoffmann
    • , Jan Philipp Kreysing
    •  & Martin Beck
  • Article
    | Open Access

    Metabolic dynamics within the small intestine are difficult to study due to the lack of in situ access. Here, the authors report an ingestible, self-powered, and wireless biosensing system, demonstrating proof-of-principle real-time glucose monitoring in the small intestines of pigs.

    • Ernesto De la Paz
    • , Nikhil Harsha Maganti
    •  & Patrick P. Mercier
  • Article
    | Open Access

    Spatially resolved proteomics is an emerging approach for mapping proteome heterogeneity. Here, the authors report a method based on the combination of hydrogel-based tissue transformation with mass spectrometry-based proteomics, that enables proteome profiling with a lateral resolution of 160 µm.

    • Lu Li
    • , Cuiji Sun
    •  & Kiryl D. Piatkevich
  • Article
    | Open Access

    Macrophage is located in different tissue to serve diverse functions. Here the authors use mass spectrometry and bulk RNA-sequencing to profile 11 mouse macrophage populations from 8 tissues, and combine their de novo data with public datasets to report an integrated proteomic and transcriptomic landscape of mouse macrophage as a valuable resource.

    • Jingbo Qie
    • , Yang Liu
    •  & Chen Ding
  • Article
    | Open Access

    Traditional methods for cell stiffness measurements are limited by long processing times and unsuitability for multiple cell analysis. Here, the authors demonstrate a fast technique based on acoustic stimulation and holographic imaging to reconstruct whole-cell stiffness maps of individual and multiple cells.

    • Rahmetullah Varol
    • , Zeynep Karavelioglu
    •  & Huseyin Uvet
  • Article
    | Open Access

    Artificial receptors targeted to the secretory pathway often fail to exhibit the expected activity due to post-translational modifications and/or improper folding. Here, the authors engineer diverse synthetic receptors that reside in the cytoplasm, inside the endoplasmic reticulum, or on the plasma membrane through orientation adjustment of the receptor parts and by elimination of dysfunctional PTMs sites.

    • Mohamed Mahameed
    • , Pengli Wang
    •  & Martin Fussenegger
  • Article
    | Open Access

    Gene activation methods are valuable for studying gene functions and may have potential applications in bioengineering and medicine. Here the authors developed Narta technology to achieve gene activation by recruiting artificial transcription factors to transcription sites through nascent RNAs of the target gene.

    • Ying Liang
    • , Haiyue Xu
    •  & Baohui Chen
  • Article
    | Open Access

    Low-dose interleukin-2 is showing promise in the treatment of several autoimmune inflammatory diseases. Here authors map the trajectory of cellular and transcriptional changes in type 1 diabetes patients receiving an interval dosing interleukin-2 regimen, which shows an anti-inflammatory gene expression signature shared by all immune cell types analysed, persisting for at least a month after ending treatment.

    • Jia-Yuan Zhang
    • , Fiona Hamey
    •  & Ricardo C. Ferreira
  • Article
    | Open Access

    Plasma cells are terminally differentiated B cells that are specialized for antibody secretion. Authors show here that genomic deletion of the p38α mitogen activated protein kinase specifically in the B cell lineage leads to diminished plasma cell differentiation via impairment of a transcriptional regulatory program by BLIMP1.

    • Jianfeng Wu
    • , Kang Yang
    •  & Jiahuai Han
  • Article
    | Open Access

    The bacterial ABC transporter MsbA is essential for lipopolysaccharide biogenesis. Here, the authors apply native mass spectrometry, X-ray crystallography, cryo-EM and biochemical approaches to characterize the structural basis and functional roles of MsbA binding to copper and specific lipids.

    • Jixing Lyu
    • , Chang Liu
    •  & Arthur Laganowsky
  • Article
    | Open Access

    Engineering enzymes to accept noncanonical cofactor biomimetics is difficult. Here, the authors establish a self-sufficient growth selection method and demonstrate its application in engineering the Lactobacillus pentosus NADH oxidase to efficiently recycle reduced nicotinamide mononucleotide (NMNH).

    • Edward King
    • , Sarah Maxel
    •  & Han Li
  • Article
    | Open Access

    The mode of cytokine receptor activation is diverse. Here, the authors find that the marine-sponge derived lectin ThC, a bivalent sugar binding protein, activates human cytokine receptor MPL. This mode of action resembles the pathogenic activation of MPL by mutant molecular chaperon calreticulin in hematologic malignancies.

    • Hiromi Watari
    • , Hiromu Kageyama
    •  & Ryuichi Sakai
  • Article
    | Open Access

    In anaphase, any unresolved DNA entanglements between the segregating sister chromatids can give rise to chromatin bridges. Here, the authors present an in vitro single-molecule assay that mimics chromatin under tension, to show that PICH is a tension- and ATP-dependent nucleosome remodeler.

    • Dian Spakman
    • , Tinka V. M. Clement
    •  & Gijs J. L. Wuite
  • Article
    | Open Access

    Channelrhodopsin photoreceptors are responsible for phototaxis in C. reinhardtii. Here, authors introduce point mutations in the channel which modify photocycle kinetics and ion selectivity, resulting in a deeper understanding of phototaxis in low light conditions.

    • Olga Baidukova
    • , Johannes Oppermann
    •  & Peter Hegemann
  • Article
    | Open Access

    Single-cell proteomics is an emerging approach to study cellular heterogeneity but its coverage is still limited. Here, the authors develop a single-cell proteomics approach with improved protein sequence coverage, allowing them to quantify PTMs and characterize effects of inhibitor treatment in single human cells.

    • Benjamin C. Orsburn
    • , Yuting Yuan
    •  & Namandjé N. Bumpus
  • Article
    | Open Access

    Adipose tissue is an important secretory organ, but less is known about the secretory activity of perivascular fat. Here the authors use proteomics analysis on secretomes from perivascular fat to identify neuronal growth regulator 1 as an adipocyte-derived neurotrophic factor, whose decreased secretion in obesity results in a loss of sympathetic innervation of adipose depots in mice.

    • Elisa Duregotti
    • , Christina M. Reumiller
    •  & Manuel Mayr
  • Article
    | Open Access

    Idiopathic multicentric Castleman disease (iMCD) is a life-threatening inflammatory disease requiring immediate intervention, for which the recommended first-line therapy is the Interleukin-6 pathway inhibitor siltuximab. Authors here show that the change in levels of the chemokine CXCL13 shortly following the start of siltuximab treatment is predictive of response.

    • Sheila K. Pierson
    • , Laura Katz
    •  & David C. Fajgenbaum
  • Article
    | Open Access

    Here, combining diagnostic imaging modalities and in vivo assays, Windfelder and colleagues established tobacco hornworm larvae Manduca sexta as an alternative high-throughput platform to study the innate immunity of the gut and host-pathogen interactions. Using the platform, the authors identify mediators of gut inflammation, differentiate pathogens from gut mutualist bacteria, and demonstrate pharmacological interventions.

    • Anton G. Windfelder
    • , Frank H. H. Müller
    •  & Ulrich Flögel
  • Article
    | Open Access

    Zinc finger (ZF) arrays are programmable DNA-binding proteins. Here the authors report ZF-DddA-derived cytosine base editors (DdCBEs) and optimise their architectures to improve targeting; they apply these variants in vitro and in vivo to mitochondrial base editing and show higher editing than ZF deaminases.

    • Julian C. W. Willis
    • , Pedro Silva-Pinheiro
    •  & David R. Liu
  • Article
    | Open Access

    Single-molecule localization microscopy relies on stochastic blinking events, treated as independent events without assignment to a particular emitter. Here, BaGoL takes low precision localizations generated from multiple emitter blinkings during DNAPAINT and dSTORM and finds the underlying emitter positions with high precision.

    • Mohamadreza Fazel
    • , Michael J. Wester
    •  & Keith A. Lidke
  • Article
    | Open Access

    Recovering dropout-affected gene expression values is a challenging problem in bioinformatics. Here, the authors propose a data-driven framework, that first learns the underlying data distribution and then recovers the expression values by imposing a self-consistency on the expression matrix.

    • Md Tauhidul Islam
    • , Jen-Yeu Wang
    •  & Lei Xing
  • Article
    | Open Access

    Biosensors using ligand-receptor binding tend to operate under equilibrium conditions, but this can make real-time monitoring challenging. Here the authors provide a theoretical foundation for biosensing where ligand concentrations can be continuously measured without needing to reach equilibrium.

    • Nicolò Maganzini
    • , Ian Thompson
    •  & Hyongsok Tom Soh
  • Article
    | Open Access

    Reductive stress, reflected by the elevated intracellular NADH/NAD+ ratio, is associated with multiple human diseases. Here, the authors develop a genetic tool to manipulate the ratios of cellular NADH/NAD+ and NADPH/NADP+, and identify purine biosynthesis as an NADH-sensing pathway to mediate reductive stress.

    • Ronghui Yang
    • , Chuanzhen Yang
    •  & Binghui Li
  • Article
    | Open Access

    RNA viruses have been responsible for large-scale epidemics and pandemics throughout the last few centuries. Here, the authors show the design, synthesis and screening of artificial RNA endonuclease XNAzymes capable of cleaving genomic SARS-CoV-2 RNA and self-assembling into enzymatic nanostructures inhibiting cellular viral replication.

    • Pehuén Pereyra Gerber
    • , Maria J. Donde
    •  & Alexander I. Taylor
  • Article
    | Open Access

    Previously, peptide selectivity in the VPAC receptor family of GPCRs was poorly understood. Here, authors combine cryo-EM and MD data to understand binding and selectivity of VPAC1R and PAC1R peptide agonists that can guide future drug development.

    • Sarah J. Piper
    • , Giuseppe Deganutti
    •  & Denise Wootten
  • Article
    | Open Access

    Here, the authors discover that ligandability of BTB domains correlates with the presence of μs-ms time scale dynamics. This finding suggests that protein dynamics may be a broadly applicable tool in drug discovery to assess the ligandability of novel and challenging targets.

    • Vladlena Kharchenko
    • , Brian M. Linhares
    •  & Łukasz Jaremko
  • Article
    | Open Access

    It is currently difficult to perform accurate single-cell assays in 384-well plates. Here the authors report Dye Drop which uses sequential density displacement and microscopy for multi-step assays on cells, and use this to collect single-cell dose-response data for small molecules in breast cancer cells.

    • Caitlin E. Mills
    • , Kartik Subramanian
    •  & Peter K. Sorger
  • Article
    | Open Access

    Retrieval of a new starting active compound with a novel scaffold during early drug development is an important but challenging task. Here, the authors propose a generative deep learning model and by applying this model they discover a potent and highly selective RIPK1 inhibitor with a previously unreported scaffold.

    • Yueshan Li
    • , Liting Zhang
    •  & Shengyong Yang