Featured
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Article
| Open AccessGroup 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition
The differential effects of targeting individual domains of multidomain enzymatic proteins are generally poorly understood. Here, the authors demonstrate lineage-specific sensitivities to domain-specific inhibition of EP300/CBP proteins across cancer and link these effects in group 3 medulloblastoma to control of a transcriptional dependency network.
- Noha A. M. Shendy
- , Melissa Bikowitz
- & Adam D. Durbin
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Article
| Open AccessDietary L-Glu sensing by enteroendocrine cells adjusts food intake via modulating gut PYY/NPF secretion
Enteroendocrine cells in the gut sense food to regulate feeding behavior. Here, the authors show in Drosophila L-glutamate reduces the frequency of calcium oscillations in enteroendocrine cells and decreases the release of NPF, thereby reducing the activation of a pair of anorexic enteric neurons.
- Junjun Gao
- , Song Zhang
- & Zheng Guo
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Article
| Open AccessCross-species spill-over potential of the H9N2 bat influenza A virus
In this study, the authors report that a bat influenza A (H9N2) virus shows receptor binding features similar to avian influenza viruses, efficiently infects ex-vivo human respiratory cells and replicates in the lungs of mice and upper respiratory tract of ferrets following airborne transmission.
- Rabeh El-Shesheny
- , John Franks
- & Richard J. Webby
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Article
| Open AccessNMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity
DDX3X is a member of the RNA helicase family, which remodels RNA structures. Using solution NMR, here the authors show that DDX3X preferentially binds to single-stranded RNA, which underlies its unwinding activity toward various structured RNA substrates.
- Yuki Toyama
- & Ichio Shimada
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Article
| Open AccessThe antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes
The fibupeptide lugdunin has shown activity against antibiotic-resistant bacteria. Here, authors disclose its mechanism of action in lipid membranes and demonstrate that it assembles into nanotubes facilitating the translocation of monovalent cations.
- Dominik Ruppelt
- , Marius F. W. Trollmann
- & Claudia Steinem
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Article
| Open AccessBat-borne H9N2 influenza virus evades MxA restriction and exhibits efficient replication and transmission in ferrets
In this study, the authors report that bat H9N2 influenza A virus replicates and transmits in ferrets, efficiently infects human lung explant cultures, evades MxA antiviral activity in mice, and has low antigenic similarity to seasonal N2, meeting pre-pandemic criteria.
- Nico Joel Halwe
- , Lea Hamberger
- & Martin Beer
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Article
| Open AccessPurines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress
Root-associated microbiota confers benefits to plant in responding to environmental stress. Here, the authors show that wild soybean secretes purines under salt stress, reshapes the microbiota and recruits Pseudomonas.
- Yanfen Zheng
- , Xuwen Cao
- & Cheng-Sheng Zhang
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Article
| Open AccessNumb positively regulates Hedgehog signaling at the ciliary pocket
The precise regulatory mechanisms controlling ciliary Hedgehog signaling remain incomplete. Here, the authors use ciliary proteomics to reveal that Numb facilitates the endocytosis of the receptor Ptch1 from the ciliary pocket, thereby enabling activation of Hedgehog signaling.
- Xiaoliang Liu
- , Patricia T. Yam
- & Xuecai Ge
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Article
| Open AccessTravel surveillance uncovers dengue virus dynamics and introductions in the Caribbean
Dengue is a major public health concern in the Americas, and the Caribbean can be a source for reintroduction and spread. Here, the authors use travel surveillance data and genomic epidemiology to reconstruct Dengue epidemic dynamics in the Caribbean from 2009-2022.
- Emma Taylor-Salmon
- , Verity Hill
- & Nathan D. Grubaugh
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Article
| Open AccessDeep learning the cis-regulatory code for gene expression in selected model plants
This study explores the variation in gene regulation across plant species and genotypes using interpretable deep learning on DNA sequence and RNA-seq data, demonstrating the models’ utility in functional genomics and phenotypic trait prediction.
- Fritz Forbang Peleke
- , Simon Maria Zumkeller
- & Jędrzej Szymański
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Article
| Open AccessDenaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions
Choosing best chemical cross-linking (XL) reagents and conditions for studying protein-protein interactions in structural biology is laborious and lacks in accuracy. The authors develop here an accurate, fast, robust and quantiative denaturing mass photometry approach for screening of XL conditions.
- Hugo Gizardin-Fredon
- , Paulo E. Santo
- & Sarah Cianférani
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Article
| Open AccessPersistent TFIIH binding to non-excised DNA damage causes cell and developmental failure
Hereditary nucleotide excision repair deficiencies cause different cancerous and progeroid disorders of which the exact etiology is not understood. This study finds that prolonged binding of DNA repair factor TFIIH to DNA damage contributes to a more severe phenotype caused by DNA repair deficiency.
- Alba Muniesa-Vargas
- , Carlota Davó-Martínez
- & Hannes Lans
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Article
| Open AccessThe gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids
Here, the authors show that elevating fiber intake in humans alters their gut microbiota, which, upon transplantation into mice, enhances intestinal mucus function, and identify a crucial role played by the commensal bacterium Blautia and its fermentation products.
- Sandra M. Holmberg
- , Rachel H. Feeney
- & Bjoern O. Schroeder
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Article
| Open AccessFunctional connectivity development along the sensorimotor-association axis enhances the cortical hierarchy
Human cortical maturation is organized along the sensorimotor-association axis. Here, the authors investigate in multiple cohorts if the development of functional connectivity during adolescence conforms to this hierarchy.
- Audrey C. Luo
- , Valerie J. Sydnor
- & Theodore D. Satterthwaite
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Article
| Open AccessDynamic corticothalamic modulation of the somatosensory thalamocortical circuit during wakefulness
Layer 6 corticothalamic (L6CT) neurons provide feedback that shapes signaling in sensory pathways. Here, authors show that L6CT neurons are bi-directional modulators of thalamocortical signaling, in a manner dependent upon both L6CT magnitude and synchronization
- Elaida D. Dimwamwa
- , Aurélie Pala
- & Garrett B. Stanley
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Article
| Open AccessPhotobody formation spatially segregates two opposing phytochrome B signaling actions of PIF5 degradation and stabilization
Photobodies are plant nuclear bodies containing the photoreceptor phytochrome B. Here, the authors reveal that photobody formation segregates opposing phytochrome B-mediated light-signaling actions into two phase-separated subnuclear compartments
- Ruth Jean Ae Kim
- , De Fan
- & Meng Chen
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Article
| Open AccessBIN1 knockdown rescues systolic dysfunction in aging male mouse hearts
Cardiac dysfunction is a hallmark of aging in humans and mice. Here, the authors show that by restoring youthful Bridging Integrator 1 (BIN1) protein levels in the hearts of 24-month-old mice in vivo cardiac systolic function is rejuvenated, and the aging phenotype partially reversed within two weeks.
- Maartje Westhoff
- , Silvia G. del Villar
- & Rose E. Dixon
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Article
| Open AccessCortex-wide transcranial localization microscopy with fluorescently labeled red blood cells
Existing neuroimaging tools are still hampered by restricted field-of-view, slow imaging speed or suboptimal spatial resolution. Here, the authors present a fluorescence localization imaging approach aided by sparsely-labeled red blood cells for cortex-wide morphological and functional cerebral angiography with high spatiotemporal resolution.
- Quanyu Zhou
- , Chaim Glück
- & Zhenyue Chen
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Article
| Open AccessAmbient carbon dioxide concentration correlates with SARS-CoV-2 aerostability and infection risk
Carbon dioxide concentration has previously been used as a proxy for overall ventilation efficiency to indirectly estimate the risk of indoor SARS-CoV-2 transmission. Here, authors investigate whether the concentration of carbon dioxide also has a direct mechanistic role in improving transmission efficiency.
- Allen Haddrell
- , Henry Oswin
- & Jonathan P. Reid
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Article
| Open AccessCross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections
Omics data’s diversity and high-dimensionality challenge integration across technologies and with imaging. Here, authors introduce mapping method xIV-LDDMM that estimates geometric and feature transformations to integrate tissue-scale atlases with molecular and cellular-scale data.
- Kaitlin M. Stouffer
- , Alain Trouvé
- & Michael I. Miller
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Article
| Open AccessControl of polymers’ amorphous-crystalline transition enables miniaturization and multifunctional integration for hydrogel bioelectronics
Soft elastic materials could be useful in the fabrication of brain-machine interfaces, but achieving the desirable material properties can be challenging. Here, the authors report control of the amorphous-crystalline transition of polymers to alter hydrogel properties and monitor mouse behaviour.
- Sizhe Huang
- , Xinyue Liu
- & Siyuan Rao
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Article
| Open AccessVegetation dieback in the Mississippi River Delta triggered by acute drought and chronic relative sea-level rise
Coastal wetlands are vulnerable to sea-level rise. Here, the authors use 16 years of data to correlate vegetation dieback in the Mississippi River Delta to drought-induced salt water intrusion in the summer of 2012.
- Tracy Elsey-Quirk
- , Austin Lynn
- & Dubravko Justic
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Article
| Open AccessLoss of TRIM29 mitigates viral myocarditis by attenuating PERK-driven ER stress response in male mice
Knowledge of pathogenesis mechanisms and effective treatments for viral myocarditis is lacking. Here, Wang et al show that loss of TRIM29 and PERK inhibitor mitigate viral myocarditis by attenuating PERK-driven ER stress and ROS responses in male mice.
- Junying Wang
- , Wenting Lu
- & Junji Xing
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Article
| Open AccessIFT cargo and motors associate sequentially with IFT trains to enter cilia of C. elegans
Intraflagellar transport is essential for the formation and function of cilia. Here, the authors use single-molecule imaging in live C. elegans to show that transport trains are formed by the sequential attachment of proteins before departing into the cilium.
- Aniruddha Mitra
- , Elizaveta Loseva
- & Erwin J. G. Peterman
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Article
| Open AccessHigh clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue
It remains challenging to characterise somatic copy number alterations (SCNAs) in tumors and the surrounding tissues with spatial and single-cell resolution. Here, the authors develop the scCUTseq approach to characterise SCNAs from single cells in multi-region prostate cancer samples and identify pseudo-diploid cells and subclones.
- Ning Zhang
- , Luuk Harbers
- & Nicola Crosetto
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Article
| Open AccessEmergence of enhancers at late DNA replicating regions
Here the authors report that enhancers appear more often in late-replicating DNA regions and are enriched for mutations affecting TF binding. This relationship with DNA replication time is seen in species evolution and cancer, suggesting a fundamental principle of genome evolution.
- Paola Cornejo-Páramo
- , Veronika Petrova
- & Emily S. Wong
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Perspective
| Open AccessAutomated in vivo enzyme engineering accelerates biocatalyst optimization
Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. In this Perspective, the authors propose an integrated solution combining growth-coupled selection with machine learning and automated workflows to accelerate development pipelines.
- Enrico Orsi
- , Lennart Schada von Borzyskowski
- & Steffen N. Lindner
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Article
| Open AccessPatrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck
Prior work has identified a male-only effective population size bottleneck 3-5000 years ago. While violent competition has been proposed as a cause, the authors here show that a segmentary patrilineal system with lineal fission provides a peaceful alternative explanation.
- Léa Guyon
- , Jérémy Guez
- & Raphaëlle Chaix
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Article
| Open AccessChromosome organization shapes replisome dynamics in Caulobacter crescentus
Whether bacterial replisome progression follows a “factory” or “track” model remains a long-standing controversy. Here, the authors find that cells can switch between the two models, in a process governed by dynamic chromosome organization processes.
- Chen Zhang
- , Asha Mary Joseph
- & Suliana Manley
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Article
| Open AccessFunctional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development
Cell metabolism has emerged as a major factor implicated in human brain evolution. Here, the authors show that an ape-specific enzyme enhances the ability of a human-specific enzyme to increase glutaminolysis and therefore expand the size of the human neocortex.
- Lei Xing
- , Vasiliki Gkini
- & Takashi Namba
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Article
| Open AccessCell Painting-based bioactivity prediction boosts high-throughput screening hit-rates and compound diversity
Identifying active compounds for a target is time- and resource-intensive. Here, the authors show that deep learning models trained on Cell Painting and single-point activity data, can reliably predict compound activity across diverse targets while maintaining high hit rates and scaffold diversity.
- Johan Fredin Haslum
- , Charles-Hugues Lardeau
- & Erik Müllers
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Article
| Open AccessGoal-directed and flexible modulation of syllable sequence within birdsong
Birdsong contains strings of syllables and is essential for their communication. Using a new song decoder to annotates song in a quasi-real-time manner, and rewarding specific syllable sequences, this study shows Bengalese finches can flexibly modify the content of their song in a goal-directed way.
- Takuto Kawaji
- , Mizuki Fujibayashi
- & Kentaro Abe
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Article
| Open AccessFlexible TAM requirement of TnpB enables efficient single-nucleotide editing with expanded targeting scope
Here the authors report that a thermophilic archaeal TnpB enables efficient gene editing in the natural host: they see that the TnpB has different TAM requirements for eliciting cell death and for facilitating gene editing. They show that TnpB can be harnessed for flexible single-nucleotide editing with templated repair.
- Xu Feng
- , Ruyi Xu
- & Qunxin She
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Article
| Open AccessCoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing
Cas9 nucleases hold clinical significance for genome editing therapies. Here the authors characterize CoCas9, a compact, efficient and precise Cas9 from the human microbiome, and show that delivery via AAV vectors enables efficient editing in the mouse retina, expanding the genome editing toolbox.
- Eleonora Pedrazzoli
- , Michele Demozzi
- & Anna Cereseto
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Article
| Open AccessThe phosphorylation of carboxyl-terminal eIF2α by SPA kinases contributes to enhanced translation efficiency during photomorphogenesis
The non-canonical C-term-phosphorylation of eIF2α mediated by SPA protein kinases plays a significant positive role in eIF2 ternary complex formation and light-induced translation during photomorphogenesis.
- Hui-Hsien Chang
- , Lin-Chen Huang
- & Mei-Chun Cheng
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Article
| Open AccessMYADM binds human parechovirus 1 and is essential for viral entry
Host factors required for parechovirus entry are not well understood. Here, the authors identify MYADM as an essential host entry factor that directly binds human parechovirus 1 and that is required for PeV-A infection in cell lines and human gastrointestinal epithelial organoids.
- Wenjie Qiao
- , Christopher M. Richards
- & Jan E. Carette
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Article
| Open AccessSingle cell tracing of Pomc neurons reveals recruitment of ‘Ghost’ subtypes with atypical identity in a mouse model of obesity
Whether and how hypothalamic neurons can lose or change their identity in adulthood has remained elusive. Here, the authors show that mature pro-opiomelanocortin (Pomc) neurons contain invisible ‘Ghost’ subsets with atypical identities that are recruited in response to obesogenic stimuli.
- Stéphane Leon
- , Vincent Simon
- & Carmelo Quarta
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Article
| Open AccessKalium channelrhodopsins effectively inhibit neurons
Kalium channelrhodopsins (KCRs) are promising tools for optogenetic silencing. Here, the authors show that KCRs inhibit cellular excitability in flies, worms, and fish, establishing them as first-line tools for inhibiting diverse types of excitable cells.
- Stanislav Ott
- , Sangyu Xu
- & Adam Claridge-Chang
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Article
| Open AccessWild-type IDH2 is a therapeutic target for triple-negative breast cancer
Isocitrate dehydrogenase (IDH) mutations are associated with cancer development and IDH-mutant inhibitors are approved to treat IDH-mutant cancer. Here, the authors show in preclinical murine models that wild-type IDH2 is a potential therapeutic target for triple-negative breast cancer.
- Jiang-jiang Li
- , Tiantian Yu
- & Peng Huang
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Article
| Open AccessEZH2 mutations in follicular lymphoma distort H3K27me3 profiles and alter transcriptional responses to PRC2 inhibition
Cells carrying EZH2 mutations found in lymphoma show a specific transcriptional response to PRC2 inhibition. A longitudinal study reveals unexpected genetic heterogeneity in follicular lymphomas, with implications for therapeutic strategies.
- Pierre Romero
- , Laia Richart
- & Raphaël Margueron
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Article
| Open AccessTANGO1 inhibitors reduce collagen secretion and limit tissue scarring
Uncontrolled secretion of ECM proteins, such as collagen, can lead to excessive scarring. Here the authors describe membrane permeable peptides that target the interface of TANGO1 and cTAGE5, inhibit secretion of ECM components and could be of therapeutic benefit during wound healing and fibrotic processes.
- Ishier Raote
- , Ann-Helen Rosendahl
- & Vivek Malhotra
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Article
| Open AccessF-actin architecture determines the conversion of chemical energy into mechanical work
F-actin architecture modulates transmission and generation of stresses in cells, yet its impact on myosin ATP hydrolysis remains unknown. The authors perform experiments measuring myosin ATP hydrolysis rates, showing that F-actin architecture can control myosin energy consumption.
- Ryota Sakamoto
- & Michael P. Murrell
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Article
| Open AccessSynergism between two BLA-to-BNST pathways for appropriate expression of anxiety-like behaviors in male mice
How distinct circuits get coordinated to allow individuals to express appropriate level of anxiety is unclear. Here, authors show there are two functionally opposing BLA-BNST pathways interacting via the local inhibitory networks to enable anxiety expression with environmental needs.
- Ren-Wen Han
- , Zi-Yi Zhang
- & Bing-Xing Pan
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Article
| Open AccessAltered grid-like coding in early blind people
The contribution of visual experience to the formation of cognitive maps in humans is not well understood. Here, the authors show using fMRI and an imagined navigation paradigm, that sighted people display hexagonal grid-like neural coding, while blind people show neural representations consistent with a square grid.
- Federica Sigismondi
- , Yangwen Xu
- & Roberto Bottini
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Article
| Open AccessOverlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange
Streptococcus dysgalactiae subsp. equisimilis is closely related to Streptococcus pyogenes and colonises the same sites in humans. This study examines cross-species transmission interactions and genetic exchange in a high disease burden setting.
- Ouli Xie
- , Cameron Zachreson
- & Steven Y. C. Tong
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Article
| Open AccessA giant virus infecting the amoeboflagellate Naegleria
This is the first report on a virus infecting the amoeboflagellate Naegleria, including the lethal human pathogen N. fowleri. The new virus isolate, Catovirus naegleriensis (Naegleriavirus, NiV), shows hallmarks of giant viruses (Nucleocytoviricota) and unique adaptations to its protist host.
- Patrick Arthofer
- , Florian Panhölzl
- & Matthias Horn
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Article
| Open AccessLarge-scale cross-ancestry genome-wide meta-analysis of serum urate
This large-scale cross-ancestry genome-wide association study reveals the genetic architecture of serum urate across ancestries and identifies urate-associated diseases and potential targets of urate-lowering drugs.
- Chamlee Cho
- , Beomsu Kim
- & Hong-Hee Won
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Article
| Open AccessLong-term monitoring of SARS-CoV-2 seroprevalence and variants in Ethiopia provides prediction for immunity and cross-immunity
Detailed data on SARS-CoV-2 dynamics in Africa remain limited. Here, the authors use longitudinal serology and SARS-CoV-2 sequencing data from Ethiopia between August 2020 and July 2022 to characterise circulating variants, identify infection pathways, and explore cross-immunity properties.
- Simon Merkt
- , Solomon Ali
- & Andreas Wieser
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Article
| Open AccessA comprehensive synthetic library of poly-N-acetyl glucosamines enabled vaccine against lethal challenges of Staphylococcus aureus
Poly-β-(1–6)-N-acetylglucosamine (PNAG) is an important vaccine target, but the impact of the number and position of free amine vs N-acetylation on its antigenicity is not well understood. Here, the authors report a divergent strategy to synthesize a comprehensive library of PNAG pentasaccharides, enabling the identification of enhanced epitopes for vaccines against Staphylococcus aureus including drug resistant strains.
- Zibin Tan
- , Weizhun Yang
- & Xuefei Huang
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