Biological techniques

  • Article
    | Open Access

    Label-free trapping of nanoparticles via dielectophoretic forces is traditionally done with electrodes in a horizontal gap layout. Here, the authors present a vertical nanogap architecture, which allows for precise capture and spatiotemporal manipulation of nanoparticles and molecular assemblies.

    • Eui-Sang Yu
    • , Hyojin Lee
    • , Sun-Mi Lee
    • , Jiwon Kim
    • , Taehyun Kim
    • , Jongsu Lee
    • , Chulki Kim
    • , Minah Seo
    • , Jae Hun Kim
    • , Young Tae Byun
    • , Seung-Chul Park
    • , Seung-Yeol Lee
    • , Sin-Doo Lee
    •  & Yong-Sang Ryu
  • Article
    | Open Access

    In Parkinson’s disease (PD) the monomeric protein alpha-synuclein (aSyn) misfolds and aggregates into insoluble fibrils. Here the authors use NMR measurements and hydrogen–deuterium exchange mass spectrometry and find that the more solvent exposed the N-terminus of aSyn is, the more aggregation prone its conformation becomes, and further show how PD mutations and post translational modifications influence the extent of the N-terminus solvent exposure.

    • Amberley D. Stephens
    • , Maria Zacharopoulou
    • , Rani Moons
    • , Giuliana Fusco
    • , Neeleema Seetaloo
    • , Anass Chiki
    • , Philippa J. Woodhams
    • , Ioanna Mela
    • , Hilal A. Lashuel
    • , Jonathan J. Phillips
    • , Alfonso De Simone
    • , Frank Sobott
    •  & Gabriele S. Kaminski Schierle
  • Article
    | Open Access

    Conventional co-culture systems often lack physiological complexity of the tumor microenvironment. Here, the authors report an organotypic skin melanoma culture and use this model to investigate the tumor induced suppression on dendritic cells.

    • S. Di Blasio
    • , G. F. van Wigcheren
    • , A. Becker
    • , A. van Duffelen
    • , M. Gorris
    • , K. Verrijp
    • , I. Stefanini
    • , G. J. Bakker
    • , M. Bloemendal
    • , A. Halilovic
    • , A. Vasaturo
    • , G. Bakdash
    • , S. V. Hato
    • , J. H. W. de Wilt
    • , J. Schalkwijk
    • , I. J. M. de Vries
    • , J. C. Textor
    • , E. H. van den Bogaard
    • , M. Tazzari
    •  & C. G. Figdor
  • Article
    | Open Access

    Extracellular vesicles (EVs) in plasma can affect pathogenesis of parasites, but details remain unclear. Here, Toda et al. characterize plasma-derived EVs from Plasmodium vivax patients and show that PvEVs are preferentially taken up by human spleen fibroblasts, facilitating parasite cytoadherence.

    • Haruka Toda
    • , Miriam Diaz-Varela
    • , Joan Segui-Barber
    • , Wanlapa Roobsoong
    • , Barbara Baro
    • , Susana Garcia-Silva
    • , Alicia Galiano
    • , Melisa Gualdrón-López
    • , Anne C. G. Almeida
    • , Marcelo A. M. Brito
    • , Gisely Cardoso de Melo
    • , Iris Aparici-Herraiz
    • , Carlos Castro-Cavadía
    • , Wuelton Marcelo Monteiro
    • , Eva Borràs
    • , Eduard Sabidó
    • , Igor C. Almeida
    • , Jakub Chojnacki
    • , Javier Martinez-Picado
    • , Maria Calvo
    • , Pilar Armengol
    • , Jaime Carmona-Fonseca
    • , Maria Fernanda Yasnot
    • , Ricardo Lauzurica
    • , Antonio Marcilla
    • , Hector Peinado
    • , Mary R. Galinski
    • , Marcus V. G. Lacerda
    • , Jetsumon Sattabongkot
    • , Carmen Fernandez-Becerra
    •  & Hernando A. del Portillo
  • Article
    | Open Access

    Immunopeptidomics allows identifying the cellular repertoire of MHC-bound peptides, but quantifying them remains challenging. Here, the authors present a method to efficiently generate internal peptide MHC standards and calibration curves, facilitating relative and absolute quantitative immunopeptidomics.

    • Lauren E. Stopfer
    • , Joshua M. Mesfin
    • , Brian A. Joughin
    • , Douglas A. Lauffenburger
    •  & Forest M. White
  • Article
    | Open Access

    Cryo-electron microscopy is widely employed in structural biology and uses phase contrast imaging. Here, the authors employ electron ptychography, a quantitative phase retrieval method for high-contrast, low-dose phase imaging of cryo-state rotavirus and immature HIV-1 virus-like particles, and show that electron ptychography is more efficient for phase recovery than conventional phase contrast imaging.

    • Liqi Zhou
    • , Jingdong Song
    • , Judy S. Kim
    • , Xudong Pei
    • , Chen Huang
    • , Mark Boyce
    • , Luiza Mendonça
    • , Daniel Clare
    • , Alistair Siebert
    • , Christopher S. Allen
    • , Emanuela Liberti
    • , David Stuart
    • , Xiaoqing Pan
    • , Peter D. Nellist
    • , Peijun Zhang
    • , Angus I. Kirkland
    •  & Peng Wang
  • Article
    | Open Access

    While organisms like squid can adaptively modulate the optical properties of their tissues, human cells lack analogous abilities. Here the authors engineer human cells to produce protein architectures with tunable light scattering functionalities.

    • Atrouli Chatterjee
    • , Juana Alejandra Cerna Sanchez
    • , Toyohiko Yamauchi
    • , Vanessa Taupin
    • , Justin Couvrette
    •  & Alon A. Gorodetsky
  • Article
    | Open Access

    Numerous strategies exist to limit the off-target activity of CRISPR-Cas9 nucleases. Here the authors co-administer truncated gRNAs that block both Cas9 and high-fidelity Cas9 variants from cleaving at off-target sites.

    • John C. Rose
    • , Nicholas A. Popp
    • , Christopher D. Richardson
    • , Jason J. Stephany
    • , Julie Mathieu
    • , Cindy T. Wei
    • , Jacob E. Corn
    • , Dustin J. Maly
    •  & Douglas M. Fowler
  • Article
    | Open Access

    α-Syn in CSF is a biomarker of neurodegenerative diseases; however, the detection of clinically relevant species is difficult. Here, the authors create a nanobody biosensor that reveals the presence of α-Syn in cells, which allow the detection of transmittable forms of α-Syn present in human CSF.

    • Christoph Gerdes
    • , Natalia Waal
    • , Thomas Offner
    • , Eugenio F. Fornasiero
    • , Nora Wender
    • , Hannes Verbarg
    • , Ivan Manzini
    • , Claudia Trenkwalder
    • , Brit Mollenhauer
    • , Timo Strohäker
    • , Markus Zweckstetter
    • , Stefan Becker
    • , Silvio O. Rizzoli
    • , Fitnat Buket Basmanav
    •  & Felipe Opazo
  • Article
    | Open Access

    The relative contribution of fallopian tube (FT) or ovarian surface epithelium (OSE) to high-grade serous ovarian cancer (HG-SOC) development is unclear. Here, the authors establish organoid models from murine oviductal and OSE tissues that allow cancer modeling via CRISPR-Cas9 genome editing, and report a dual origin of murine HG-SOC.

    • Kadi Lõhmussaar
    • , Oded Kopper
    • , Jeroen Korving
    • , Harry Begthel
    • , Celien P. H. Vreuls
    • , Johan H. van Es
    •  & Hans Clevers
  • Article
    | Open Access

    Until now, the transcriptome of preimplantation mouse embryos has only been analysed by short-read sequencing. Here, the authors perform long-read sequencing to provide a more detailed transcriptome of the preimplantation mouse embryo, identifying various novel transcripts, for example Kdm4dl.

    • Yunbo Qiao
    • , Chao Ren
    • , Shisheng Huang
    • , Jie Yuan
    • , Xingchen Liu
    • , Jiao Fan
    • , Jianxiang Lin
    • , Susu Wu
    • , Qiuzhen Chen
    • , Xiaochen Bo
    • , Xiangyang Li
    • , Xingxu Huang
    • , Zhen Liu
    •  & Wenjie Shu
  • Review Article
    | Open Access

    Between 2014 and 2023, 100,000 UK Biobank participants are undergoing brain, heart and abdominal MRI, as well as DXA and carotid ultrasound scans. In this review, authors provide a detailed overview of the rationale for the collection of these imaging data, the procedures of data collection and management, and the future directions of the UK biobank imaging enhancement.

    • Thomas J. Littlejohns
    • , Jo Holliday
    • , Lorna M. Gibson
    • , Steve Garratt
    • , Niels Oesingmann
    • , Fidel Alfaro-Almagro
    • , Jimmy D. Bell
    • , Chris Boultwood
    • , Rory Collins
    • , Megan C. Conroy
    • , Nicola Crabtree
    • , Nicola Doherty
    • , Alejandro F. Frangi
    • , Nicholas C. Harvey
    • , Paul Leeson
    • , Karla L. Miller
    • , Stefan Neubauer
    • , Steffen E. Petersen
    • , Jonathan Sellors
    • , Simon Sheard
    • , Stephen M. Smith
    • , Cathie L. M. Sudlow
    • , Paul M. Matthews
    •  & Naomi E. Allen
  • Article
    | Open Access

    Changes in microbial taxa are commonly derived from estimations of relative abundance, which inherently limits the depth of the analysis. Here, the authors present an absolute quantification method based on digital PCR anchoring and 16S rRNA gene sequencing and show how a ketogenic diet affects individual taxon’s absolute abundance in stool and small-intestine mucosa samples in mice

    • Jacob T. Barlow
    • , Said R. Bogatyrev
    •  & Rustem F. Ismagilov
  • Article
    | Open Access

    Type 1 diabetes is associated with autoimmune destruction of pancreatic beta-cells. Here the authors compose a large-scale electron microscopy image data base of pancreatic organ donor tissue to enable data mining and further understanding of the disease.

    • Pascal de Boer
    • , Nicole M. Pirozzi
    • , Anouk H. G. Wolters
    • , Jeroen Kuipers
    • , Irina Kusmartseva
    • , Mark A. Atkinson
    • , Martha Campbell-Thompson
    •  & Ben N. G. Giepmans
  • Article
    | Open Access

    Protein-protein interactions are fundamental to the regulation of protein activity and cellular phyisology. Here the authors present Split Intein-Mediated Protein Ligation, which uses bait and prey proteins fused to intein fragments to generate single intact proteins upon interaction.

    • Zhong Yao
    • , Farzaneh Aboualizadeh
    • , Jason Kroll
    • , Indira Akula
    • , Jamie Snider
    • , Anna Lyakisheva
    • , Priscilla Tang
    • , Max Kotlyar
    • , Igor Jurisica
    • , Mike Boxem
    •  & Igor Stagljar
  • Article
    | Open Access

    The type III secretion system (T3SS) of bacteria can be used to inject cargo into eukaryotic cells but its lack of target specificity is a disadvantage. Here the authors place the T3SS under the regulation of light by engineering optogenetic switches into the dynamic cytosolic T3SS component SctQ.

    • Florian Lindner
    • , Bailey Milne-Davies
    • , Katja Langenfeld
    • , Thorsten Stiewe
    •  & Andreas Diepold
  • Article
    | Open Access

    Neutrophils mobilize rapidly and travel through the vasculature and microcirculation en masse in response to inflammatory stimuli. Here the authors use a microfluidic device and intravital microscopy to show neutrophils move through tissues in a highly ordered pattern, taking turns to file into alternate branches at bifurcations.

    • Xiao Wang
    • , Mokarram Hossain
    • , Ania Bogoslowski
    • , Paul Kubes
    •  & Daniel Irimia
  • Article
    | Open Access

    Noninvasive detection of molecular targets in living subjects could provide valuable insights into healthy function and disease. Here, the authors develop vasoactive imaging probes which allow wide-field in vivo mapping of nanomolar-level molecular species in rat brain.

    • Robert Ohlendorf
    • , Agata Wiśniowska
    • , Mitul Desai
    • , Ali Barandov
    • , Adrian L. Slusarczyk
    • , Nan Li
    •  & Alan Jasanoff
  • Article
    | Open Access

    Due to the polygenic nature of most diseases, simultaneous correction or introduction of single nucleotide variants is needed. Here, the authors demonstrated the feasibility of multiplex base editing for polygenes disease modeling in cynomolgus monkey embryos with high specificity.

    • Wenhui Zhang
    • , Tomomi Aida
    • , Ricardo C. H. del Rosario
    • , Jonathan J. Wilde
    • , Chenhui Ding
    • , Xiaohui Zhang
    • , Zulqurain Baloch
    • , Yan Huang
    • , Yu Tang
    • , Duanduan Li
    • , Hongyu Lu
    • , Yang Zhou
    • , Minqing Jiang
    • , Dongdong Xu
    • , Zhihao Fang
    • , Zhanhong Zheng
    • , Qunshan Huang
    • , Guoping Feng
    •  & Shihua Yang
  • Article
    | Open Access

    Detailed understanding of how cancer cells transition from a drug sensitive to a tolerant state is lacking. Here, using single cell proteomic and metabolic data the authors uncover that isogenic BRAF mutant melanoma cells can take two distinct paths to become tolerant to BRAF inhibition.

    • Yapeng Su
    • , Melissa E. Ko
    • , Hanjun Cheng
    • , Ronghui Zhu
    • , Min Xue
    • , Jessica Wang
    • , Jihoon W. Lee
    • , Luke Frankiw
    • , Alexander Xu
    • , Stephanie Wong
    • , Lidia Robert
    • , Kaitlyn Takata
    • , Dan Yuan
    • , Yue Lu
    • , Sui Huang
    • , Antoni Ribas
    • , Raphael Levine
    • , Garry P. Nolan
    • , Wei Wei
    • , Sylvia K. Plevritis
    • , Guideng Li
    • , David Baltimore
    •  & James R. Heath
  • Article
    | Open Access

    Increasingly large scRNA-seq datasets demand better and more scalable analysis tools. Here, the authors introduce a scalable unsupervised deep embedding algorithm that clusters scRNA-seq data by iteratively optimizing a clustering objective function and enables removal of batch effects.

    • Xiangjie Li
    • , Kui Wang
    • , Yafei Lyu
    • , Huize Pan
    • , Jingxiao Zhang
    • , Dwight Stambolian
    • , Katalin Susztak
    • , Muredach P. Reilly
    • , Gang Hu
    •  & Mingyao Li
  • Article
    | Open Access

    Chemical modification of proteins can be used to decipher function or use that function for therapeutic purposes. Here, the authors insert synthetic peptides via tandem protein trans-splicing to add post-translational modifications or non-canonical amino acids.

    • K. K. Khoo
    • , I. Galleano
    • , F. Gasparri
    • , R. Wieneke
    • , H. Harms
    • , M. H. Poulsen
    • , H. C. Chua
    • , M. Wulf
    • , R. Tampé
    •  & S. A. Pless
  • Article
    | Open Access

    Early life exposure to environmental stressors, including endocrine disrupting chemicals (EDCs), can impact health later in life. Here, the authors show that neonatal EDC exposure in rats causes epigenetic reprogramming in the liver, which is transcriptionally silent until animals are placed on a Western-style diet.

    • Lindsey S. Treviño
    • , Jianrong Dong
    • , Ahkilesh Kaushal
    • , Tiffany A. Katz
    • , Rahul Kumar Jangid
    • , Matthew J. Robertson
    • , Sandra L. Grimm
    • , Chandra Shekar R. Ambati
    • , Vasanta Putluri
    • , Aaron R. Cox
    • , Kang Ho Kim
    • , Thaddeus D. May
    • , Morgan R. Gallo
    • , David D. Moore
    • , Sean M. Hartig
    • , Charles E. Foulds
    • , Nagireddy Putluri
    • , Cristian Coarfa
    •  & Cheryl Lyn Walker
  • Article
    | Open Access

    Deriving functional pancreatic cell types from human stem cells may have important clinical applications. Building on previous work, here the authors generate stem cell-derived alpha cells via a polyhormonal intermediate, which have a gene expression pattern similar to human islet alpha cells and behave as such when transplanted into mice.

    • Quinn P. Peterson
    • , Adrian Veres
    • , Lihua Chen
    • , Michael Q. Slama
    • , Jennifer H. R. Kenty
    • , Shaimaa Hassoun
    • , Matthew R. Brown
    • , Haiqiang Dou
    • , Caden D. Duffy
    • , Quan Zhou
    • , Aleksey V. Matveyenko
    • , Björn Tyrberg
    • , Maria Sörhede-Winzell
    • , Patrik Rorsman
    •  & Douglas A. Melton
  • Article
    | Open Access

    High-throughput rheological measurements of cells and cell clusters by microfluidics is limited by fixed channel dimensions. Here the authors create virtual fluidic channels inside the cuvette of commercial flow cytometers to dynamically tune channel cross section to enable rheological measurements from cells and cell clusters.

    • Muzaffar H. Panhwar
    • , Fabian Czerwinski
    • , Venkata A. S. Dabbiru
    • , Yesaswini Komaragiri
    • , Bob Fregin
    • , Doreen Biedenweg
    • , Peter Nestler
    • , Ricardo H. Pires
    •  & Oliver Otto
  • Article
    | Open Access

    Though DNA framework-based scaffolds for biomolecular assembly are attractive for bioimaging applications, realizing super-multiplex fluorescent amplifiers remains a challenge. Here, the authors report a topological engineering approach to designing fractal DNA frameworks for multiplexed amplifiers.

    • Jiang Li
    • , Jiangbing Dai
    • , Shuoxing Jiang
    • , Mo Xie
    • , Tingting Zhai
    • , Linjie Guo
    • , Shuting Cao
    • , Shu Xing
    • , Zhibei Qu
    • , Yan Zhao
    • , Fei Wang
    • , Yang Yang
    • , Lei Liu
    • , Xiaolei Zuo
    • , Lihua Wang
    • , Hao Yan
    •  & Chunhai Fan
  • Article
    | Open Access

    The contribution of central and peripheral channels of nuclear pores to transport of transmembrane proteins is unclear. Here the authors show that most inner nuclear membrane proteins use only peripheral channels, but some extend nuclear localization signals into the central channel for directed nuclear transport.

    • Krishna C. Mudumbi
    • , Rafal Czapiewski
    • , Andrew Ruba
    • , Samuel L. Junod
    • , Yichen Li
    • , Wangxi Luo
    • , Christina Ngo
    • , Valentina Ospina
    • , Eric C. Schirmer
    •  & Weidong Yang
  • Article
    | Open Access

    The genome is folded in 3-dimensions, though the lack of robust ultra-resolution imaging makes this difficult to visualise. Here, the authors present 3D-EMISH that combines serial block-face scanning electron microscopy with in situ hybridization.

    • Paweł Trzaskoma
    • , Błażej Ruszczycki
    • , Byoungkoo Lee
    • , Katarzyna K. Pels
    • , Katarzyna Krawczyk
    • , Grzegorz Bokota
    • , Andrzej A. Szczepankiewicz
    • , Jesse Aaron
    • , Agnieszka Walczak
    • , Małgorzata A. Śliwińska
    • , Adriana Magalska
    • , Michal Kadlof
    • , Artur Wolny
    • , Zofia Parteka
    • , Sebastian Arabasz
    • , Magdalena Kiss-Arabasz
    • , Dariusz Plewczyński
    • , Yijun Ruan
    •  & Grzegorz M. Wilczyński
  • Article
    | Open Access

    Previous versions of photoactivatable Cre recombinase (PA-Cre) suffered from unintentional recombination in dark conditions. Here, the authors develop an improved version of PA-Cre, called PA-Cre 3.0, which shows reduced leakiness and improved efficiency upon activation, and make mouse lines that express PA-Cre 3.0 conditionally.

    • Kumi Morikawa
    • , Kazuhiro Furuhashi
    • , Carmen de Sena-Tomas
    • , Alvaro L. Garcia-Garcia
    • , Ramsey Bekdash
    • , Alison D. Klein
    • , Nicholas Gallerani
    • , Hannah E. Yamamoto
    • , Seon-Hye E. Park
    • , Grant S. Collins
    • , Fuun Kawano
    • , Moritoshi Sato
    • , Chyuan-Sheng Lin
    • , Kimara L. Targoff
    • , Edmund Au
    • , Michael C. Salling
    •  & Masayuki Yazawa
  • Article
    | Open Access

    The chaperone SurA is involved in outer membrane protein (OMP) biogenesis in Gram-negative bacteria, but its mechanism of action is not fully understood. Combining mass spectrometric, biophysical and computational approaches, the authors here show how the conformational dynamics of SurA facilitate OMP binding.

    • Antonio N. Calabrese
    • , Bob Schiffrin
    • , Matthew Watson
    • , Theodoros K. Karamanos
    • , Martin Walko
    • , Julia R. Humes
    • , Jim E. Horne
    • , Paul White
    • , Andrew J. Wilson
    • , Antreas C. Kalli
    • , Roman Tuma
    • , Alison E. Ashcroft
    • , David J. Brockwell
    •  & Sheena E. Radford
  • Article
    | Open Access

    The mechanism of PARP1-dependent poly-ADP-ribosylation in response to DNA damage is still under debate. Here, the authors use ATR-FTIR spectroscopy to provide time-resolved insights into the molecular details of this process under near physiological conditions.

    • Annika Krüger
    • , Alexander Bürkle
    • , Karin Hauser
    •  & Aswin Mangerich
  • Article
    | Open Access

    Cellular markers of endothelial cell proliferation help identify the vasculature of tumours in homeostasis. Here, the authors report Apelin-based synthetic Notch (synNotch) receptors that can target Apj expressed on endothelium and stimulate the synNotch pathways upon Apj binding, and suggest this as a strategy to treat solid tumours.

    • Zhifu Wang
    • , Fan Wang
    • , Junjie Zhong
    • , Tongming Zhu
    • , Yongtao Zheng
    • , Tong Zhao
    • , Qiang Xie
    • , Fukai Ma
    • , Ronggang Li
    • , Qisheng Tang
    • , Feng Xu
    • , Xueying Tian
    •  & Jianhong Zhu
  • Article
    | Open Access

    Real-time monitoring human motions normally demands connecting a large number of sensors in a complicated network. To make it simpler, Kim et al. decode the motion of fingers using a flexible sensor attached on wrist that measures skin deformation with the help of a deep-learning architecture.

    • Kyun Kyu Kim
    • , InHo Ha
    • , Min Kim
    • , Joonhwa Choi
    • , Phillip Won
    • , Sungho Jo
    •  & Seung Hwan Ko
  • Article
    | Open Access

    Adeno-associated viruses (AAVs) can be targeted in a tissue-specific manner, but their tissue accumulation cannot be assessed in a non-invasive manner. Here the authors conjugate a multivalent chelator labelled with Cu-64 to the surface of AAVs and image the brain accumulation of the PHB.eB capsid by PET.

    • Jai Woong Seo
    • , Elizabeth S. Ingham
    • , Lisa Mahakian
    • , Spencer Tumbale
    • , Bo Wu
    • , Sadaf Aghevlian
    • , Shahin Shams
    • , Mo Baikoghli
    • , Poorva Jain
    • , Xiaozhe Ding
    • , Nick Goeden
    • , Tatyana Dobreva
    • , Nicholas C. Flytzanis
    • , Michael Chavez
    • , Kratika Singhal
    • , Ryan Leib
    • , Michelle L. James
    • , David J. Segal
    • , R. Holland Cheng
    • , Eduardo A. Silva
    • , Viviana Gradinaru
    •  & Katherine W. Ferrara
  • Article
    | Open Access

    Single-cell RNA-seq can reveal accurate and precise cell types and states. Here the authors present an scRNA-seq platform, Paired-seq, which uses differential flow resistance to achieve 95% cell utilisation efficiency for improved cell-free RNA removal and gene detection.

    • Mingxia Zhang
    • , Yuan Zou
    • , Xing Xu
    • , Xuebing Zhang
    • , Mingxuan Gao
    • , Jia Song
    • , Peifeng Huang
    • , Qin Chen
    • , Zhi Zhu
    • , Wei Lin
    • , Richard N. Zare
    •  & Chaoyong Yang
  • Article
    | Open Access

    Altering cellular responses to double-strand breaks in DNA could rebalance CRISPRediting outcomes. Here, the authors use a pooled CRISPR screen to identify inhibition of CDC7 as a strategy to improve HDR outcomes.

    • Beeke Wienert
    • , David N. Nguyen
    • , Alexis Guenther
    • , Sharon J. Feng
    • , Melissa N. Locke
    • , Stacia K. Wyman
    • , Jiyung Shin
    • , Katelynn R. Kazane
    • , Georgia L. Gregory
    • , Matthew A. M. Carter
    • , Francis Wright
    • , Bruce R. Conklin
    • , Alex Marson
    • , Chris D. Richardson
    •  & Jacob E. Corn
  • Article
    | Open Access

    A prior live-cell exosome reporter showed dim fluorescence and could not be expressed stably, limiting its usefulness. Here the authors stabilise the reporter to allow long-term tracking of exosomes, and incorporate a second fluorophore to visualise the entire exosome lifecycle.

    • Bong Hwan Sung
    • , Ariana von Lersner
    • , Jorge Guerrero
    • , Evan S. Krystofiak
    • , David Inman
    • , Roxanne Pelletier
    • , Andries Zijlstra
    • , Suzanne M. Ponik
    •  & Alissa M. Weaver
  • Article
    | Open Access

    Testing mechanical forces on native molecules in natural environments remains a challenge. Here the authors engineer titin to carry a HaloTag-TEV insertion to allow analysis of dynamics under force in muscle fibers.

    • Jaime Andrés Rivas-Pardo
    • , Yong Li
    • , Zsolt Mártonfalvi
    • , Rafael Tapia-Rojo
    • , Andreas Unger
    • , Ángel Fernández-Trasancos
    • , Elías Herrero-Galán
    • , Diana Velázquez-Carreras
    • , Julio M. Fernández
    • , Wolfgang A. Linke
    •  & Jorge Alegre-Cebollada
  • Article
    | Open Access

    Targeted mass spectrometry enables reproducible and accurate lipid quantification but dedicated software tools to develop targeted lipidomics assays are lacking. Here, the authors develop a targeted lipidomics workbench and lipid knowledgebase for the streamlined generation of targeted assays.

    • Bing Peng
    • , Dominik Kopczynski
    • , Brian S. Pratt
    • , Christer S. Ejsing
    • , Bo Burla
    • , Martin Hermansson
    • , Peter Imre Benke
    • , Sock Hwee Tan
    • , Mark Y. Chan
    • , Federico Torta
    • , Dominik Schwudke
    • , Sven W. Meckelmann
    • , Cristina Coman
    • , Oliver J. Schmitz
    • , Brendan MacLean
    • , Mailin-Christin Manke
    • , Oliver Borst
    • , Markus R. Wenk
    • , Nils Hoffmann
    •  & Robert Ahrends
  • Article
    | Open Access

    Tissue clearing has revolutionised histology, but limited penetration of antibodies and stains into thick tissue segments is still a bottleneck. Here, the authors characterise optically cleared tissue as an electrolyte gel and apply this knowledge to stain the entirety of thick tissue samples.

    • Etsuo A. Susaki
    • , Chika Shimizu
    • , Akihiro Kuno
    • , Kazuki Tainaka
    • , Xiang Li
    • , Kengo Nishi
    • , Ken Morishima
    • , Hiroaki Ono
    • , Koji L. Ode
    • , Yuki Saeki
    • , Kazunari Miyamichi
    • , Kaoru Isa
    • , Chihiro Yokoyama
    • , Hiroki Kitaura
    • , Masako Ikemura
    • , Tetsuo Ushiku
    • , Yoshihiro Shimizu
    • , Takashi Saito
    • , Takaomi C. Saido
    • , Masashi Fukayama
    • , Hirotaka Onoe
    • , Kazushige Touhara
    • , Tadashi Isa
    • , Akiyoshi Kakita
    • , Mitsuhiro Shibayama
    •  & Hiroki R. Ueda
  • Article
    | Open Access

    Regulating polyadenylation is important for mRNA stability, which can in turn affect B cell maturation and humoral immune responses. Here the authors use Nanopore poly(A) sequencing to explore the importance of the cytoplasmic poly(A) polymerase TENT5C, particularly in the production of immunoglobulins.

    • Aleksandra Bilska
    • , Monika Kusio-Kobiałka
    • , Paweł S. Krawczyk
    • , Olga Gewartowska
    • , Bartosz Tarkowski
    • , Kamil Kobyłecki
    • , Dominika Nowis
    • , Jakub Golab
    • , Jakub Gruchota
    • , Ewa Borsuk
    • , Andrzej Dziembowski
    •  & Seweryn Mroczek
  • Article
    | Open Access

    Enteric pathogens such as Salmonella depend on propanediol-utilising microcompartments (Pdu MCP), which self-assemble from cytosolic proteins. Using mass spectrometry-based absolute quantification, the authors here define the protein stoichiometry and propose an organizational model of a Salmonella Pdu MCP.

    • Mengru Yang
    • , Deborah M. Simpson
    • , Nicolas Wenner
    • , Philip Brownridge
    • , Victoria M. Harman
    • , Jay C. D. Hinton
    • , Robert J. Beynon
    •  & Lu-Ning Liu
  • Article
    | Open Access

    Malate dehydrogenase (MDH) is one of the key enzymes for succinic acid (SA) bioproduction. Here, the authors report biochemical and structural analyses of various MDHs to reveal amino acids influencing the specific activity and susceptibility to substrate inhibition, and achieve industrial-level SA production.

    • Jung Ho Ahn
    • , Hogyun Seo
    • , Woojin Park
    • , Jihye Seok
    • , Jong An Lee
    • , Won Jun Kim
    • , Gi Bae Kim
    • , Kyung-Jin Kim
    •  & Sang Yup Lee
  • Article
    | Open Access

    DMSP is a ubiquitous organosulfur compound in the ocean that, once degraded by bacteria, plays key roles in global biogeochemical cycles and climate regulation. Here, the authors use single-cell measurements of transcription to investigate the intricate dynamics of bacterial DMSP degradation.

    • Cherry Gao
    • , Vicente I. Fernandez
    • , Kang Soo Lee
    • , Simona Fenizia
    • , Georg Pohnert
    • , Justin R. Seymour
    • , Jean-Baptiste Raina
    •  & Roman Stocker
  • Article
    | Open Access

    The mechanisms of action of proteasome inhibitors (PI) in multiple myeloma (MM) treatment are not fully elucidated. Here, the authors use unbiased phosphoproteomics in PI-treated MM and show increased phosphorylation of splicing-associated proteins, ultimately revealing splicing interference as a mode of PI action as well as demonstrating the spliceosome as a specific therapeutic vulnerability in this disease.

    • Hector H. Huang
    • , Ian D. Ferguson
    • , Alexis M. Thornton
    • , Prabhakar Bastola
    • , Christine Lam
    • , Yu-Hsiu T. Lin
    • , Priya Choudhry
    • , Margarette C. Mariano
    • , Makeba D. Marcoulis
    • , Chin Fen Teo
    • , Julia Malato
    • , Paul J. Phojanakong
    • , Thomas G. Martin III
    • , Jeffrey L. Wolf
    • , Sandy W. Wong
    • , Nina Shah
    • , Byron Hann
    • , Angela N. Brooks
    •  & Arun P. Wiita
  • Article
    | Open Access

    Sample contamination has been reported in high throughput RNA sequencing. Here the authors analyze the RNA sequencing data from the Genotype-Tissue Expression project and describe how highly expressed, tissue specific genes contaminate across samples, which is corroborated in other data sets.

    • Tim O. Nieuwenhuis
    • , Stephanie Y. Yang
    • , Rohan X. Verma
    • , Vamsee Pillalamarri
    • , Dan E. Arking
    • , Avi Z. Rosenberg
    • , Matthew N. McCall
    •  & Marc K. Halushka
  • Article
    | Open Access

    Collagen production by lung cells is critical to maintain organ architecture but can also drive pathological scarring. Here the authors perform single cell RNA sequencing of collagen-producing lung cells identifying a subset of pathologic fibroblasts characterized by Cthrc1 expression which are concentrated within fibroblastic foci in fibrotic lungs and show a pro-fibrotic phenotype.

    • Tatsuya Tsukui
    • , Kai-Hui Sun
    • , Joseph B. Wetter
    • , John R. Wilson-Kanamori
    • , Lisa A. Hazelwood
    • , Neil C. Henderson
    • , Taylor S. Adams
    • , Jonas C. Schupp
    • , Sergio D. Poli
    • , Ivan O. Rosas
    • , Naftali Kaminski
    • , Michael A. Matthay
    • , Paul J. Wolters
    •  & Dean Sheppard
  • Article
    | Open Access

    During development, organs undergo large scale forces driven by the cytoskeleton but the precise molecular regulation of cytoskeletal networks remains unclear. Here, the authors report a Cdc42-dependent supracellular cytoskeletal network integrates local actomyosin contraction at tissue scale and drives global tissue elongation.

    • Anna Popkova
    • , Orrin J. Stone
    • , Lin Chen
    • , Xiang Qin
    • , Chang Liu
    • , Jiaying Liu
    • , Karine Belguise
    • , Denise J. Montell
    • , Klaus M. Hahn
    • , Matteo Rauzi
    •  & Xiaobo Wang
  • Article
    | Open Access

    The initial mutational processes and how these lead to progression in multiple myeloma (MM) are unclear. Here, the authors identify mutational signatures that occur over time in a large cohort of MM patients and suggest features that may help in early diagnosis.

    • Even H. Rustad
    • , Venkata Yellapantula
    • , Daniel Leongamornlert
    • , Niccolò Bolli
    • , Guy Ledergor
    • , Ferran Nadeu
    • , Nicos Angelopoulos
    • , Kevin J. Dawson
    • , Thomas J. Mitchell
    • , Robert J. Osborne
    • , Bachisio Ziccheddu
    • , Cristiana Carniti
    • , Vittorio Montefusco
    • , Paolo Corradini
    • , Kenneth C. Anderson
    • , Philippe Moreau
    • , Elli Papaemmanuil
    • , Ludmil B. Alexandrov
    • , Xose S. Puente
    • , Elias Campo
    • , Reiner Siebert
    • , Herve Avet-Loiseau
    • , Ola Landgren
    • , Nikhil Munshi
    • , Peter J. Campbell
    •  & Francesco Maura