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| Open AccessImmunoglobulin G N-glycan markers of accelerated biological aging during chronic HIV infection
In this study, Giron et al. find that people living with chronic HIV experience accelerated aging-associated alterations in antibody glycans. These alterations, attributed to senescence enzymes, predict comorbidities and reduce the antiviral function of antibodies.
- Leila B. Giron
- , Qin Liu
- & Mohamed Abdel-Mohsen
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Article
| Open AccessPrey killing without invasion by Bdellovibrio bacteriovorus defective for a MIDAS-family adhesin
The bacterium Bdellovibrio bacteriovorus is a predator of other bacteria, invading the prey’s periplasm and forming a rounded killed cell where it replicates. Here, Tyson et al. identify a B. bacteriovorus protein that is important for successful invasion of prey, and show that prey killing can occur without invasion.
- Jess Tyson
- , Paul Radford
- & R. Elizabeth Sockett
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Article
| Open AccessMetabolic plasticity, essentiality and therapeutic potential of ribose-5-phosphate synthesis in Toxoplasma gondii
Ribose-5-phosphate (R5P) is a precursor for nucleic acid biogenesis. Here, Guo and Ji et al. show that multiple routes can flexibly supply R5P to enable Toxoplasma gondii growth.
- Xuefang Guo
- , Nuo Ji
- & Ningbo Xia
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Article
| Open AccessComparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach
Here, the authors employ multi-omics on a cohort comprising three generations of family members, showing that fecal microbiota populations, functions, and metabolome of infants vary greatly from their maternal lineage, exhibiting a less diverse microbiota and differences in various metabolite classes including short- and branched-chain fatty acids.
- Tomás Clive Barker-Tejeda
- , Elisa Zubeldia-Varela
- & Alma Villaseñor
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Article
| Open AccessThe assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili
Type 1 pili are crucial cell surface bacterial virulence factors. Here, the authors show that FimD is required to assemble the most stable quaternary pilus structure by ensuring that the resulting protein polymer is free of structural defects.
- Dawid S. Zyla
- , Thomas Wiegand
- & Rudi Glockshuber
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Article
| Open AccessDermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice
The microbial community in the intestine can affect other organs such as the skin but it is not clear if the opposite can occur. Here the authors show that skin wounding affects the microbial composition of the intestinal flora which then enhances DSS induced colitis and intestinal inflammation.
- Tatsuya Dokoshi
- , Yang Chen
- & Richard L. Gallo
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Article
| Open AccessA live attenuated vaccine to prevent severe neonatal Escherichia coli K1 infections
Authors utilise a murine model of Escherichia coli infection to immunologically characterise the properties of their live attenuated vaccine candidate. They also demonstrate protection of newborn mice following maternal immunisation.
- Youssouf Sereme
- , Cécile Schrimp
- & David Skurnik
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Article
| Open AccessPhage-specific immunity impairs efficacy of bacteriophage targeting Vancomycin Resistant Enterococcus in a murine model
Bacteriophage can be used to target bacterial infection and used as a therapeutic approach for antibiotic resistant bacteria. Here the authors show that the use of bacteriophage to target antibiotic resistant bacteria in a mouse model of infection can induce phage specific immune responses and may impair their therapeutic efficacy.
- Julia D. Berkson
- , Claire E. Wate
- & Paul E. Carlson Jr.
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Article
| Open AccessDifferentiation granules, a dynamic regulator of T. brucei development
The African trypanosome Trypanosoma brucei has been shown to form stress granules in vitro that might be repurposed to enable differentiation and facilitate parasite transmission. Here, Cayla et al. show that differentiation between slender and stumpy forms does involve membrane-less granules that are different from nutritional stress granules.
- Mathieu Cayla
- , Christos Spanos
- & Keith R. Matthews
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Article
| Open AccessPotent human neutralizing antibodies against Nipah virus derived from two ancestral antibody heavy chains
Nipah virus is a WHO priority pathogen, and there is currently no approved drug for clinical therapy. Here, the authors identified potent human neutralizing antibodies that block receptor binding and provide protection against NiV infection in vivo.
- Li Chen
- , Mengmeng Sun
- & Sandra Chiu
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Article
| Open AccessThe secreted protein Amuc_1409 from Akkermansia muciniphila improves gut health through intestinal stem cell regulation
Microbiome-secreted proteins act as key modulators of host-microbiome crosstalk. Here, the authors show that Amuc_1409 protein, secreted from Akkermansia muciniphila, plays a key role in intestinal homeostasis by regulating intestinal stem cells through interaction with E-cadherin, indicating its potential as a biomolecule for improving gut health.
- Eun-Jung Kang
- , Jae-Hoon Kim
- & Chul-Ho Lee
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Article
| Open AccessProbing altered receptor specificities of antigenically drifting human H3N2 viruses by chemoenzymatic synthesis, NMR, and modeling
Binding modes of antigenically drifted hemagglutinins of human influenza A viruses have been determined by NMR using synthetic N-glycans having 13C-labeled monosaccharides to pinpoint which monosaccharides of extended LacNAc chains engage with the HAs.
- Luca Unione
- , Augustinus N. A. Ammerlaan
- & Geert-Jan Boons
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Article
| Open AccessOrigin and dispersal history of Hepatitis B virus in Eastern Eurasia
Hepatitis B virus is an ancient human pathogen that dates back more than 10,000 years. Here, the authors investigate the evolutionary history of the virus in Eastern Eurasia by sequencing 34 genomes dating from approximately 400–5,000 years ago and comparing them with other contemporary sequences.
- Bing Sun
- , Aida Andrades Valtueña
- & Yinqiu Cui
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Article
| Open AccessA genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience
This study provides insights into the functional roles of microbial symbionts within the reef-building coral Acropora kenti. The findings reveal molecular mechanisms underpinning coral health and adaptation to local environmental stressors, which may support host resilience in the face of anthropogenic climate change and pollution.
- Lauren F. Messer
- , David G. Bourne
- & Gene W. Tyson
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Article
| Open AccessLegume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification
Sustainability in agriculture can be improved harnessing biological N2 fixation in legumes. Here, the authors combine different crops with peanut plants finding that maize and oilseed rape are the most successful combinations which have potential to enhance rhizosphere microbiota N2 fixation.
- Mengjie Qiao
- , Ruibo Sun
- & Yan Chen
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Article
| Open AccessMonoclonal antibodies targeting sites in respiratory syncytial virus attachment G protein provide protection against RSV-A and RSV-B in mice
Effective antibodies targeting various respiratory syncytial virus (RSV) proteins are needed to address public health burden of RSV. Here the authors shows that in addition to the currently approved F-targeting monoclonal antibodies, anti-G cross-reactive monoclonal antibodies to RSV-A and RSV-B strains can provide cross-protection and prevent from RSV disease.
- Youri Lee
- , Laura Klenow
- & Surender Khurana
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Article
| Open AccessGenomic language model predicts protein co-regulation and function
A gene’s function is governed by its sequence, structure and context. Here, the authors develop a genomic language model that learns contextualized functional representations from diverse and large-scale metagenomic datasets.
- Yunha Hwang
- , Andre L. Cornman
- & Peter R. Girguis
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Article
| Open AccessA commensal protozoan attenuates Clostridioides difficile pathogenesis in mice via arginine-ornithine metabolism and host intestinal immune response
Faecal microbiome transplant has been shown to be able to reduce Clostridioides difficile infection. Here the authors show that an intestinal commensal protozoan reduces C. difficile infection by inhibiting neutrophil recruitment and affecting arginine-ornithine metabolism.
- Huan Yang
- , Xiaoxiao Wu
- & Bing Gu
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Article
| Open AccessHidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages
Soil viruses could have a disproportionate role in ecosystem functioning. Here, the authors combine multiple data and approaches to explore diversity and distribution of P-acquisition genes encoded by soil bacteriophages, suggesting the importance of viral auxiliary metabolism for nutrient cycling.
- Jie-Liang Liang
- , Shi-wei Feng
- & Jin-tian Li
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Article
| Open AccessPatchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery
Regulatory arrest peptides interact with the bacterial ribosome to halt their own translation. Here, Fujiwara et al. analyse thousands of bacterial genome sequences and identify additional arrest peptides, revealing sequence diversity and patchy, but widespread, distribution across the bacterial domain.
- Keigo Fujiwara
- , Naoko Tsuji
- & Shinobu Chiba
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Article
| Open AccessMaternal hybrid immunity and risk of infant COVID-19 hospitalizations: national case-control study in Israel
Maternal anti-SARS-CoV-2 antibodies can provide protection against severe COVID-19 in infants, but the relative protection conferred by maternal infection, vaccination, and hybrid immunity is unknown. Here, the authors use data from Israel and show that infants born to mothers with hybrid immunity had lowest rates of COVID-19 hospitalisation.
- Joshua Guedalia
- , Michal Lipschuetz
- & Ofer Beharier
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Article
| Open AccessIncident allergic diseases in post-COVID-19 condition: multinational cohort studies from South Korea, Japan and the UK
SARS-CoV-2 infection has been linked to various persistent or new-onset health consequences, including disruption of the immune system. Here, the authors investigate the risk of new-onset allergic diseases following SARS-CoV-2 infection using data from South Korea, Japan, and the UK.
- Jiyeon Oh
- , Myeongcheol Lee
- & Dong Keon Yon
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Article
| Open AccessMitochondrial injury induced by a Salmonella genotoxin triggers the proinflammatory senescence-associated secretory phenotype
Chen et al. probe the role of a genotoxin of Salmonella typhi in triggering a senescence-associated secretory phenotype, via mitochondrial DNA damage.
- Han-Yi Chen
- , Wan-Chen Hsieh
- & Shu-Jung Chang
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Article
| Open AccessColitis reduces active social engagement in mice and is ameliorated by supplementation with human microbiota members
Past intestinal distress is associated with diminished social behavior in mice. Here, the authors show that treatment with microbiota members that are enriched in neurotypical people versus people with ASD can ameliorate colitis severity and associated sociability deficits.
- D. Garrett Brown
- , Michaela Murphy
- & June L. Round
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Article
| Open AccessStructural basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system
The bacterial DSR2 defense system counters phage invasion by depleting NAD+. Here, Zhang et al. reveal molecular mechanisms underlying phage-mediated activation and repression of DSR2, enhancing our understanding of the bacterial-phage arms race.
- Jun-Tao Zhang
- , Xiao-Yu Liu
- & Ning Jia
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Article
| Open AccessTranscription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin
Proteins compacting the bacterial chromosome obstruct transcription and must be transiently displaced to allow gene expression. Here, the authors show that the bacterial nucleoid structuring protein H-NS can be dislodged, from a distance, by the twisting in the DNA generated ahead of approaching RNA polymerase.
- Nara Figueroa-Bossi
- , Rocío Fernández-Fernández
- & Lionello Bossi
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Article
| Open AccessColonisation of hospital surfaces from low- and middle-income countries by extended spectrum β-lactamase- and carbapenemase-producing bacteria
In hospitals, surfaces present as a reservoir for bacteria pathogens, potentially leading to nosocomial infections. In this work, authors aim to profile extended-spectrum β lactamase- and carbapenemase-carrying bacterial species colonising neonatal hospital wards and causing neonatal sepsis.
- Maria Nieto-Rosado
- , Kirsty Sands
- & Timothy R. Walsh
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Article
| Open AccessStructural basis of Acinetobacter type IV pili targeting by an RNA virus
Here, the authors structurally characterise the interaction between Acinetobacter phage AP205 and the type IV Acinetobacter pili using cryo-electron microscopy, uncovering the mechanistic determinants of this interaction.
- Ran Meng
- , Zhongliang Xing
- & Junjie Zhang
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Article
| Open AccessMicroevolution, reinfection and highly complex genomic diversity in patients with sequential isolates of Mycobacterium abscessus
Mycobacterium abscessus is considered an emerging pathogen, given its prevalence in patients with pulmonary diseases, such as cystic fibrosis. Here, authors perform a genomic analysis on sequential isolates obtained from patients with persistent infections of M. abscessus.
- Sergio Buenestado-Serrano
- , Miguel Martínez-Lirola
- & Darío García de Viedma
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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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