Featured
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Article
| Open AccessGenome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities
Identifying the metabolic interactions that underlie microbial communities is challenging. Here, the authors combine Tara Oceans -omics data with co-activity networks and genome-scale metabolic models to predict biotic interactions among planktonic prokaryotes in the upper ocean.
- Nils Giordano
- , Marinna Gaudin
- & Samuel Chaffron
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Article
| Open AccessThe SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86
Due to the focus of vaccination on the SARS CoV-2 spike protein, spike has been associated with high levels of viral mutation and subsequent immune escape. Here the authors study a conserved epitope in SARS CoV-2 sub-domain-1 and characterise the neutralising antibody response and evasion in contemporary SARS COV-2 viral strains.
- Daming Zhou
- , Piyada Supasa
- & Gavin R. Screaton
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Article
| Open AccessAnaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution
Here, Pratt et al identify a community of deep-branching anaerobic fungi in tortoise feces. Multiple characteristics underpinning their success in tortoise, as opposed to scarcity in mammalian alimentary tracts, are presented.
- Carrie J. Pratt
- , Casey H. Meili
- & Noha H. Youssef
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Article
| Open AccessDirect observation of a crescent-shape chromosome in expanded Bacillus subtilis cells
The spatial structure of the bacterial chromosome is resolved in the absence of confinement by the cell boundary. Size-expanded cells reveal a crescent-shaped Bacillus subtilis chromosome and the effects of ParB and SMC proteins on chromosome shape.
- Miloš Tišma
- , Florian Patrick Bock
- & Cees Dekker
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Article
| Open AccessTrade-offs shaping transmission of sylvatic dengue and Zika viruses in monkey hosts
Hanley et al show that transmission of dengue and Zika virus from Old and New World monkeys is shaped by an immunologically-mediated trade-off between magnitude and duration of replication. Patterns of Zika transmission suggests high risk of spillback into neotropical monkeys.
- Kathryn A. Hanley
- , Hélène Cecilia
- & Shannan L. Rossi
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Article
| Open AccessReal-time monitoring of replication errors’ fate reveals the origin and dynamics of spontaneous mutations
An interdisciplinary approach following replication errors in Escherichia coli unveils that many spontaneous mutations originate from inefficient repair, and that repair capacity is variable between single cells within a bacterial population.
- Chiara Enrico Bena
- , Jean Ollion
- & Marina Elez
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Article
| Open AccessFibrinolytic-deficiencies predispose hosts to septicemia from a catheter-associated UTI
Catheter-associated urinary tract infections can often lead to secondary bloodstream infections, and catheter-induced bladder inflammation. In this work, authors utilise murine models to probe defective fibrinolysis drives extravascular fibrin formation, potentially predisposing hosts to severe CAUTI.
- Jonathan J. Molina
- , Kurt N. Kohler
- & Ana L. Flores-Mireles
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Article
| Open AccessInsights into the modulation of bacterial NADase activity by phage proteins
The defense-associated sirtuin 2 (DSR2) effector protects bacteria from phage infection by depleting NAD+. Here, the authors employ biochemical and structural approaches to reveal the inhibition and activation mechanisms of DSR2 by the phage anti-DSR2 protein (DSAD1) and tail tube protein (TTP).
- Hang Yin
- , Xuzichao Li
- & Heng Zhang
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Article
| Open AccessStructure of the intact tail machine of Anabaena myophage A-1(L)
The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Here, authors present the high-resolution cryo-EM structure of its intact tail machine, and identify multiple hydrolytic and binding modules.
- Rong-Cheng Yu
- , Feng Yang
- & Cong-Zhao Zhou
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Article
| Open AccessSynthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution.
- Pavel Dvořák
- , Barbora Burýšková
- & Martin Benešík
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Perspective
| Open AccessEcological countermeasures to prevent pathogen spillover and subsequent pandemics
In this Perspective, the authors discuss the importance of preventing zoonotic spillover to prevent pandemics. They highlight mechanisms by which environmental changes can enable spillover, identify ecological interventions for spillover prevention and suggest policy frameworks through which interventions can be implemented.
- Raina K. Plowright
- , Aliyu N. Ahmed
- & Annika T. H. Keeley
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Article
| Open AccessProfiling the colonic mucosal response to fecal microbiota transplantation identifies a role for GBP5 in colitis in humans and mice
Faecal microbiota transplantation (FMT) can be used to treat established colitis. Here the authors profile transcriptional changes in humans after FMT and how this relates to colitis remission identifying a role for GBP5, and this protein is validated in a loss-of-function mouse model.
- Laurence D. W. Luu
- , Abhimanu Pandey
- & Nadeem O. Kaakoush
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Article
| Open AccessMulti-omic integration of microbiome data for identifying disease-associated modules
Here, Muller et al. introduce MintTea, a method for analyzing multi-omic microbiome data and identifying disease-associated modules comprising mixed sets of features that collectively shift in disease, offering insights into microbiome-disease interactions.
- Efrat Muller
- , Itamar Shiryan
- & Elhanan Borenstein
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Article
| Open AccessPlasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria
In this work, authors combine computational models with single-cell and population-level data showing the variability in plasmid copy number within bacterial populations leads to phenotypic diversity. They reveal how multicopy plasmids contribute to bacterial transient antibiotic resistance.
- J. Carlos R. Hernandez-Beltran
- , Jerónimo Rodríguez-Beltrán
- & Rafael Peña-Miller
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Article
| Open AccessPrior infection with unrelated neurotropic virus exacerbates influenza disease and impairs lung T cell responses
Co-infections are much less studied than single pathogen infections. Here, the authors show that co-infection with two unrelated viruses, neurotropic Semliki Forest virus and influenza A virus, exacerbates influenza-related lung pathology and prolongs lung virus replication in a mouse model.
- Isabelle Jia-Hui Foo
- , Brendon Y. Chua
- & Lukasz Kedzierski
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Article
| Open AccessBidirectional ATP-driven transport of cobalamin by the mycobacterial ABC transporter BacA
ABC transporters are generally considered to be unidirectional. Here, the authors develop a fluorescence-based transport assay and show that the mycobacterial ABC transporter BacA instead acts as a bidirectional transporter for cobalamin.
- Mark Nijland
- , Solène N. Lefebvre
- & Dirk J. Slotboom
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Article
| Open AccessMutations in the efflux pump regulator MexZ shift tissue colonization by Pseudomonas aeruginosa to a state of antibiotic tolerance
Mutations in mexZ, encoding a negative regulator of efflux pump genes, are frequently acquired by Pseudomonas aeruginosa during early lung infection, but do not confer high antibiotic resistance as measured in lab tests. Here, Laborda et al. show that mexZ mutations affect quorum sensing pathways, thus promoting tissue invasiveness and protecting bacteria from the action of antibiotics within tissues.
- Pablo Laborda
- , Signe Lolle
- & Helle Krogh Johansen
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Article
| Open AccessA fungal core effector exploits the OsPUX8B.2–OsCDC48-6 module to suppress plant immunity
Plant ubiquitin regulatory domain-containing proteins (PUX) play vital roles in CDC48-mediated protein quality control processes. Here Shi et al. show that a conserved core Magnaporthe oryzae effector (MoNLE1) can specially target the rice PUX protein OsPUX8B.2 and interfere with host immune responses.
- Xuetao Shi
- , Xin Xie
- & Wende Liu
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Article
| Open AccessStructural basis for peroxidase encapsulation inside the encapsulin from the Gram-negative pathogen Klebsiella pneumoniae
Peroxidase encapsulins are self-assembling protein compartments involved in oxidative stress response found in many pathogens. Here, the authors characterize the structural basis of peroxidase encapsulation inside the Klebsiella pneumoniae encapsulin.
- Jesse A. Jones
- , Michael P. Andreas
- & Tobias W. Giessen
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Article
| Open AccessNiche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions
Bioremediation via microbial inoculation often performs poorly in real-world conditions. Here, the authors show that bacterial inoculants may fail to establish in complex soil microbiomes because they open new niches that facilitate growth of resident microbes.
- Senka Čaušević
- , Manupriyam Dubey
- & Jan Roelof van der Meer
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Comment
| Open AccessAn OLD protein teaches us new tricks: prokaryotic antiviral defense
Reporting in Nature Communications, Huo and colleagues provide three-dimensional structures of a bacterial immune defense system called Gabija. This work builds on recently published structural and functional studies and contributes strong evidence that protein assembly formation is essential for antiviral function.
- Eirene Marie Q. Ednacot
- & Benjamin R. Morehouse
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Article
| Open AccessParechovirus infection in human brain organoids: host innate inflammatory response and not neuro-infectivity correlates to neurologic disease
In comparison to PeV-A1, infection with PeV-A3 is associated with neurological illness in infants. Here, using brain organoids, the authors suggest that the innate inflammatory response as the underlying reason, and not replication kinetics.
- Pamela E. Capendale
- , Inés García-Rodríguez
- & Katja C. Wolthers
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Article
| Open AccessWidespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE
How do cells put electrons to rest? Using a minimal pathway to get rid of excess metabolic electrons, diverse environmentally important microbes overcome large spatial, kinetic, and thermodynamic barriers in order to survive in extreme anoxic conditions.
- Pilar C. Portela
- , Catharine C. Shipps
- & Nikhil S. Malvankar
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Article
| Open AccessLegionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain
The pathogen Legionella pneumophila mediates NAD+-dependent ubiquitination pathways upon infection. Here, the authors show the Legionella effector MavL reverses ubiquitin ADP-ribosylation to regulate these pathways. MavL represents a new macrodomain class specific for reversal of arginine ADP-ribosylation with distinct ADP-ribose binding features.
- Zhengrui Zhang
- , Jiaqi Fu
- & Chittaranjan Das
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Article
| Open AccessLong-term effects of Omicron BA.2 breakthrough infection on immunity-metabolism balance: a 6-month prospective study
Here the authors study recovery from mild to moderate Omicron breakthrough infection at six months post infection. Serum proteomics, PBMC single-cell transcriptomics and clinical parameters indicate slow recovery with coagulation abnormalities and an imbalance of the immune response and metabolism remaining.
- Yanhua Li
- , Shijie Qin
- & George Fu Gao
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Article
| Open AccessStructure of orthoreovirus RNA chaperone σNS, a component of viral replication factories
Orthoreovirus σNS, essential for forming viral replication factories, has RNA chaperone activity that requires the association of σNS dimers into filamentous structures stabilized by domain-swapping interactions of the flexible N-terminal arms.
- Boyang Zhao
- , Liya Hu
- & B. V. Venkataram Prasad
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Article
| Open AccessAccurate and rapid antibiotic susceptibility testing using a machine learning-assisted nanomotion technology platform
Sturm et. al developed a 2 to 4 h antibiotic susceptibility test based on bacterial vibrations. This diagnostic test applies to the most frequently found gram-negative bacteria in bloodstream infections and demonstrates its potential in contributing to faster treatment decisions.
- Alexander Sturm
- , Grzegorz Jóźwiak
- & Danuta Cichocka
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Article
| Open AccessCryo-EM structures of type IV pili complexed with nanobodies reveal immune escape mechanisms
Bacterial type IV pili are filamentous cell surface structures and candidate targets for vaccine development. Here, authors determine how antibodies interact with pili at the structural level providing insight into immune escape mechanisms and potential countermeasures.
- David Fernandez-Martinez
- , Youxin Kong
- & Guillaume Duménil
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Article
| Open AccessRapid evolution of an adaptive multicellular morphology of Candida auris during systemic infection
Bing et al. report that Candida auris undergoes rapid evolution via de novo genetic mutations and forms multicellular aggregates that exhibit a survival advantage over the single-celled yeast-form phenotype during host infection.
- Jian Bing
- , Zhangyue Guan
- & Guanghua Huang
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Article
| Open AccessTargeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus
The impact of other pathogens on disease outcome was studied in European infants with RSV infection. Additional viruses were commonly co-detected during infection but were weakly linked to severity. However, presence of Haemophilus bacteria strongly associated with severe cases.
- Gu-Lung Lin
- , Simon B. Drysdale
- & Andrew J. Pollard
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Article
| Open AccessBeyond the microcirculation: sequestration of infected red blood cells and reduced flow in large draining veins in experimental cerebral malaria
Cerebral malaria can lead to fatal brain swelling. Oelschlegel et al. find infected red blood cells and reduced flow in large draining cerebral veins in mouse model of cerebral malaria, suggesting that impaired venous efflux could cause the swelling.
- A. M. Oelschlegel
- , R. Bhattacharjee
- & G. Nishanth
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Article
| Open AccessData-driven prediction of colonization outcomes for complex microbial communities
Predicting the colonization of exogenous species in complex communities is a challenge in ecology. Here, the authors propose a data-driven approach to predict colonization outcomes and perform validation experiments in human gut microbial communities.
- Lu Wu
- , Xu-Wen Wang
- & Lei Dai
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Article
| Open AccessUptake of COVID-19 vaccinations amongst 3,433,483 children and young people: meta-analysis of UK prospective cohorts
COVID-19 vaccination has been recommended for children and young people (aged 5–17) in the UK since 2021/2022. In this study, the authors use linked health and administrative data to estimate vaccine uptake in this age group and show that age and adult household vaccination status are associated with uptake.
- Sarah J. Aldridge
- , Utkarsh Agrawal
- & Rhiannon K. Owen
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Article
| Open AccessClearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation
There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.
- Farina Karim
- , Catherine Riou
- & Alex Sigal
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Article
| Open AccessA citric acid cycle-deficient Escherichia coli as an efficient chassis for aerobic fermentations
While tricarboxylic acid cycle (TCA cycle) is required for heterotrophic microbes, it reduces carbon yield of industrial products due to the release of excess CO2. Here, the authors construct an E. coli strain without a functional TCA cycle and demonstrate its feasibility as a chassis strain for production of four separate compounds.
- Hang Zhou
- , Yiwen Zhang
- & Baixue Lin
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Article
| Open AccessBacteria can compensate the fitness costs of amplified resistance genes via a bypass mechanism
Antibiotic heteroresistance, in which a susceptible bacterial population includes a small resistant subpopulation, can arise by tandem amplification of resistance genes, which often carry fitness costs. Here, Pal and Andersson show that these fitness costs can be ameliorated by the acquisition of compensatory mutations and a reduction in copy number of the resistance genes.
- Ankita Pal
- & Dan I. Andersson
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Article
| Open AccessCharacterisation of colistin resistance in Gram-negative microbiota of pregnant women and neonates in Nigeria
Here, the authors report the results of a BARNARDS sub-study identifying a 1% mobile colistin resistance gene (mcr) carriage rate in around 5000 rectal swabs from mothers and neonates across Nigeria, of which 90% were mcr-10 (mostly Enterobacter spp.) and 10% were mcr-1 and mcr9.
- E. A. R. Portal
- , K. Sands
- & O. B. Spiller
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Article
| Open AccessEngineered dityrosine-bonding of the RSV prefusion F protein imparts stability and potency advantages
Here the authors describe a stabilization technology that engineers crosslinks between tyrosine sidechains into a natively folded vaccine immunogen and show that immunogenicity is improved in small animal models by locking the most potently neutralizing epitopes.
- Sonal V. Gidwani
- , Devarshi Brahmbhatt
- & Mark A. Yondola
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Article
| Open AccessEdible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit
Fungi have the potential to produce sustainable foods for a growing population, but current products are based on a small number of strains with inherent limitations. Here, the authors develop genetic tools for an edible fungus and engineer its nutritional value and sensory appeal for alternative meat applications.
- Vayu Maini Rekdal
- , Casper R. B. van der Luijt
- & Jay D. Keasling
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Article
| Open AccessInter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection closely related to Streptococcus pyogenes. Here the authors investigate the degree of genomic similarity between the two species and assess implications for development of vaccines.
- Ouli Xie
- , Jacqueline M. Morris
- & Mark R. Davies
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Article
| Open AccessBacteriophage DNA induces an interrupted immune response during phage therapy in a chicken model
Bacteriophage are potential therapeutics to target bacterial infections, but recent studies suggest that bacteriophage may induce immune responses in eukaryotic cells. Here the authors show that bacteriophage DNA induces interrupted host immunity in a chicken infection model.
- Magdalena Podlacha
- , Lidia Gaffke
- & Alicja Węgrzyn
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Article
| Open AccessCryo-EM structures of Banna virus in multiple states reveal stepwise detachment of viral spikes
Here, Li et al. provide the cryo-EM structures of Banna virus (BAV) in four configurations. VP10 functions as a unique cementing protein to stabilize the capsid shells and spikes in the full particles and during cell entry. Structural transition from BAV virions to cores is a stepwise process of dissociation of receptor binding protein VP9 and membrane penetration protein VP4.
- Zhiqiang Li
- , Han Xia
- & Sheng Cao
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Article
| Open AccessDistinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion
SARS-CoV-2 evolved into several sublineages harboring different mutations in spike. Here, the authors isolate and characterize nine SARS-CoV-2 variants and show that EG.5.1.3 has highest fitness in nasal epithelial cells, while JN.1 shows lower affinity to ACE2 and higher immune evasion compared to BA.2.86.1.
- Delphine Planas
- , Isabelle Staropoli
- & Olivier Schwartz
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Article
| Open AccessInhalation of ACE2-expressing lung exosomes provides prophylactic protection against SARS-CoV-2
Inhibiting SARS-CoV-2 interaction with ACE2 is a promising antiviral strategy. Here, the authors show that exosomes derived from human lung spheroid cells expressing hACE2 accumulate in the lung following prophylactic inhalation to bind and neutralize SARS-CoV-2 and protect mice from SARS-CoV-2-induced disease.
- Zhenzhen Wang
- , Shiqi Hu
- & Ke Cheng
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Article
| Open AccessTheileria parasites sequester host eIF5A to escape elimination by host-mediated autophagy
Theileria parasites have evolved mechanisms to evade host cell defenses. Here, Villares et al use an anti-parasite drug to show how intracellular parasites sequester host eIF5A to escape elimination by autophagy pathways.
- Marie Villares
- , Nelly Lourenço
- & Jonathan B. Weitzman
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Article
| Open AccessPHEIGES: all-cell-free phage synthesis and selection from engineered genomes
Bacteriophages have great potential in both medicine and biotechnology. Here the authors present PHEIGES, a cell-free method for phage genome engineering, synthesis and selection based on T7, which allows direct selection of engineered and mutant phages without compartmentalization.
- Antoine Levrier
- , Ioannis Karpathakis
- & Vincent Noireaux
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Article
| Open AccessLipoarabinomannan mediates localized cell wall integrity during division in mycobacteria
Mycobacteria have a unique cell envelope that includes characteristic lipoglycans, such as lipoarabinomannan. Here, Sparks et al. show that this lipoglycan plays roles in maintenance of local cell envelope integrity and septal placement during cell division.
- Ian L. Sparks
- , Takehiro Kado
- & Yasu S. Morita
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Article
| Open AccessN6-methyladenosine modification is not a general trait of viral RNA genomes
A comprehensive analysis found no evidence of m6A modifications in the genome of the cytoplasmic RNA viruses CHIKV and DENV, challenging the current notion that m6A modification is a general feature of cytoplasmic RNA viruses.
- Belinda Baquero-Pérez
- , Ivaylo D. Yonchev
- & Juana Díez
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Article
| Open AccessImpact of vaccination on the association of COVID-19 with cardiovascular diseases: An OpenSAFELY cohort study
SARS-CoV-2 infection is associated with an increased risk of arterial and venous thrombotic events. Here, the authors investigate the degree to which this association is modified by virus variant and vaccination using electronic health record data for ~18 million adults in England.
- Genevieve I. Cezard
- , Rachel E. Denholm
- & Venexia Walker
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