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Journal articleMolnar Z, Aumeeruddy-Thomas Y, Babai D, et al., 2024,
Towards richer knowledge partnerships between ecology and ethnoecology
, TRENDS IN ECOLOGY & EVOLUTION, Vol: 39, Pages: 109-115, ISSN: 0169-5347 -
Journal articleHatfield JH, Banks-Leite C, Barlow J, et al., 2024,
Constraints on avian seed dispersal reduce potential for resilience in degraded tropical forests
, FUNCTIONAL ECOLOGY, Vol: 38, Pages: 315-326, ISSN: 0269-8463 -
Journal articleCruz-Silva E, Harrion SP, Prentice IC, et al., 2024,
Holocene vegetation dynamics of the Eastern Mediterranean region: old controversies addressed by a new analysis
, Journal of Biogeography, Vol: 51, Pages: 294-310, ISSN: 0305-0270Aim:We reconstruct vegetation changes since 12 ky in the Eastern Mediterranean to examine four features of the regional vegetation history that are controversial: the extent of non-analogue vegetation assemblages in the transition from the Late Glacial to the early Holocene, the synchroneity of postglacial forest expansion, the geographical extent of temperate deciduous forest during the mid-Holocene and the timing and trigger for the re-establishment of drought-tolerant vegetation during the late Holocene.Location:The Eastern Mediterranean–Black Sea Caspian Corridor.Taxon:Vascular plants.Methods:We reconstruct vegetation changes for 122 fossil pollen records using a method that accounts for within-biome variability in pollen taxon abundance to determine the biome with which a sample has greatest affinity. Per-biome affinity threshold values were used to identify samples that do not belong to any modern biome. We apply time series analysis and mapping to examine space and time changes.Results:Sites with non-analogue vegetation were most common between 11.5 and 9.5 ky and mostly in the Carpathians. The transition from open vegetation to forest occurred at 10.64 ± 0.65 ky across the whole region. Temperate deciduous forest was not more extensive at 6 ky; maximum expansion occurred between 5.5 and 5 ky. Expansion of forest occurred between c. 4 and 2.8 k, followed by an abrupt decrease and a subsequent recovery. This pattern is not consistent with a systematic decline of forest towards more drought-tolerant vegetation in the late Holocene but is consistent with centennial-scale speleothem patterns linked to variations in moisture availability.Main Conclusions:We show the occurrence of non-analogue vegetation types peaked during early Holocene, forest expansion was synchronous across the region and there was an expansion of moisture-demanding temperate trees around 5.5 to 5 ky. There is no signal of a continuous late Holocene aridificat
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Journal articleCurrie D, Wong N, Zane I, et al., 2024,
A Potential Prognostic Gene Signature Associated with p53-Dependent NTRK1 Activation and Increased Survival of Neuroblastoma Patients
, CANCERS, Vol: 16 -
Journal articleLeung PB, Matanza XM, Roche B, et al., 2024,
<i>Shigella</i><i> sonnei</i> utilises colicins during inter- bacterial competition
, MICROBIOLOGY-SGM, Vol: 170, ISSN: 1350-0872 -
Journal articleSchuster M, Eisele S, Armas-Egas L, et al., 2024,
Enhanced late blight resistance by engineering an EpiC2B-insensitive immune protease
, Plant Biotechnology Journal, Vol: 22, Pages: 284-286, ISSN: 1467-7644Papain-like immune proteases (PLCPs) are promising engineering targets for crop protection, given their significant roles in plant immunity for key crops such as tomato, maize and citrus (Misas-Villamil et al., 2016). The wide range of pathogen-secreted PLCP inhibitors highlights the importance of these proteases in defending against various pathogens. Depletion of the apoplastic immune PLCP Phytophthora-inhibited protease 1 (Pip1) from tomato, for instance, causes hyper-susceptibility to bacterial, fungal and oomycete tomato pathogens (Ilyas et al., 2015). Immunity by Pip1 in wild-type tomato is, however, suboptimal since Pip1 is suppressed during infection by diverse pathogen-secreted inhibitors, such as the cystatin-like EpiC2B from the oomycete late blight pathogen Phytophthora infestans (Tian et al., 2007). Here, we tested whether we could increase Pip1-based immunity against late blight by engineering Pip1 into an EpiC2B-insensitive protease. To guide Pip1 mutagenesis, we generated a structural model of the EpiC2B-Pip1 complex using AlphaFold-Multimer (Evans et al., 2022). This structural model represents a classic interaction between the tripartite wedge of cystatin (EpiC2B) in the substrate binding groove of papain (Pip1). This model indicated that engineering Pip1 to prevent inhibition without affecting Pip1 substrate specificity is possible because the interaction surface of Pip1 with EpiC2B is larger than the substrate binding groove (Figure 1a).
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Journal articleMajumdar A, Moulick D, Srivastava S, 2024,
Editorial: ‘Save Soil' by managing soil nutrient losses, agronomic practices and crop-microbial interaction: World Soil Day 2022
, Frontiers in Sustainable Food Systems, Vol: 8 -
Journal articleCantwell-Jones A, Tylianakis J, Larson K, et al., 2024,
Using individual-based trait frequency distributions to forecast plant-pollinator network responses to environmental change
, Ecology Letters, Vol: 27, ISSN: 1461-023XDetermining how and why organisms interact is fundamental to understanding ecosystem responses to future environmental change. To assess the impact on plant-pollinator interactions, recent studies have examined how the effects of environmental change on individual interactions accumulate to generate species-level responses. Here, we review recent developments in using plant-pollinator networks of interacting individuals along with their functional traits, where individuals are nested within species nodes. We highlight how these individual-level, trait-based networks connect intraspecific trait variation (as frequency distributions of multiple traits) with dynamic responses within plant-pollinator communities. This approach can better explain interaction plasticity, and changes to interaction probabilities and network structure over spatiotemporal or other environmental gradients. We argue that only through appreciating such trait-based interaction plasticity can we accurately forecast the potential vulnerability of interactions to future environmental change. We follow this with general guidance on how future studies can collect and analyse high-resolution interaction and trait data, with the hope of improving predictions of future plant-pollinator network responses for targeted and effective conservation.
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Journal articleAnderson MAE, Gonzalez E, Edgington MP, et al., 2024,
A multiplexed, confinable CRISPR/Cas9 gene drive can propagate in caged Aedes aegypti populations.
, Nat Commun, Vol: 15Aedes aegypti is the main vector of several major pathogens including dengue, Zika and chikungunya viruses. Classical mosquito control strategies utilizing insecticides are threatened by rising resistance. This has stimulated interest in new genetic systems such as gene drivesHere, we test the regulatory sequences from the Ae. aegypti benign gonial cell neoplasm (bgcn) homolog to express Cas9 and a separate multiplexing sgRNA-expressing cassette inserted into the Ae. aegypti kynurenine 3-monooxygenase (kmo) gene. When combined, these two elements provide highly effective germline cutting at the kmo locus and act as a gene drive. Our target genetic element drives through a cage trial population such that carrier frequency of the element increases from 50% to up to 89% of the population despite significant fitness costs to kmo insertions. Deep sequencing suggests that the multiplexing design could mitigate resistance allele formation in our gene drive system.
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ReportWaring BG, 2024,
The potential for enhanced soil carbon sequestration to mitigate climate change
This briefing note assesses the potential for soil carbon sequestration to mitigate climate change, summarising the basic science and providing an overview of best practices for measuring and modifying soil carbon stocks. We also set out recommendations for policy makers, examining UK land use policies as a case study.
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Journal articleLi S, Waring B, Powers J, et al., 2024,
Tropical dry forest response to nutrient fertilization: a model validation and sensitivity analysis
, BIOGEOSCIENCES, Vol: 21, Pages: 455-471, ISSN: 1726-4170 -
Journal articleMoulick D, Mukherjee A, Das A, et al., 2024,
Selenium - An environmentally friendly micronutrient in agroecosystem in the modern era: An overview of 50-year findings.
, Ecotoxicol Environ Saf, Vol: 270Agricultural productivity is constantly being forced to maintain yield stability to feed the enormously growing world population. However, shrinking arable and nutrient-deprived soil and abiotic and biotic stressor (s) in different magnitudes put additional challenges to achieving global food security. Though well-defined, the concept of macro, micronutrients, and beneficial elements is from a plant nutritional perspective. Among various micronutrients, selenium (Se) is essential in small amounts for the life cycle of organisms, including crops. Selenium has the potential to improve soil health, leading to the improvement of productivity and crop quality. However, Se possesses an immense encouraging phenomenon when supplied within the threshold limit, also having wide variations. The supplementation of Se has exhibited promising outcomes in lessening biotic and abiotic stress in various crops. Besides, bulk form, nano-Se, and biogenic-Se also revealed some merits and limitations. Literature suggests that the possibilities of biogenic-Se in stress alleviation and fortifying foods are encouraging. In this article, apart from adopting a combination of a conventional extensive review of the literature and bibliometric analysis, the authors have assessed the journey of Se in the "soil to spoon" perspective in a diverse agroecosystem to highlight the research gap area. There is no doubt that the time has come to seriously consider the tag of beneficial elements associated with Se, especially in the drastic global climate change era.
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Journal articleWorboys JD, Davis DM, 2024,
Do inhibitory receptors need to be proximal to stimulatory receptors to function?
, GENES AND IMMUNITY, ISSN: 1466-4879 -
Journal articleHersperger F, Meyring T, Weber P, et al., 2024,
DNA damage signaling in Drosophila macrophages modulates systemic cytokine levels in response to oxidative stress
, eLife, Vol: 12<jats:p>Environmental factors, infection, or injury can cause oxidative stress in diverse tissues and loss of tissue homeostasis. Effective stress response cascades, conserved from invertebrates to mammals, ensure reestablishment of homeostasis and tissue repair. Hemocytes, the <jats:italic>Drosophila</jats:italic> blood-like cells, rapidly respond to oxidative stress by immune activation. However, the precise signals how they sense oxidative stress and integrate these signals to modulate and balance the response to oxidative stress in the adult fly are ill-defined. Furthermore, hemocyte diversification was not explored yet on oxidative stress. Here, we employed high-throughput single nuclei RNA-sequencing to explore hemocytes and other cell types, such as fat body, during oxidative stress in the adult fly. We identified distinct cellular responder states in plasmatocytes, the <jats:italic>Drosophila</jats:italic> macrophages, associated with immune response and metabolic activation upon oxidative stress. We further define oxidative stress-induced DNA damage signaling as a key sensor and a rate-limiting step in immune-activated plasmatocytes controlling JNK-mediated release of the pro-inflammatory cytokine <jats:italic>unpaired-3</jats:italic>. We subsequently tested the role of this specific immune activated cell stage during oxidative stress and found that inhibition of DNA damage signaling in plasmatocytes, as well as JNK or upd3 overactivation, result in a higher susceptibility to oxidative stress. Our findings uncover that a balanced composition and response of hemocyte subclusters is essential for the survival of adult <jats:italic>Drosophila</jats:italic> on oxidative stress by regulating systemic cytokine levels and cross-talk to other organs, such as the fat body, to control energy mobilization.</jats:p>
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Journal articleMeccariello A, 2024,
Gene drive and genetic sex conversion in theglobal agricultural pest Ceratitis capitata
, Nature Communications, Vol: 15, ISSN: 2041-1723Homing-based gene drives are recently proposed interventions promising the area-wide, species-specific genetic control of harmful insect populations. Here we characterise a first set of gene drives in a tephritid agricultural pest species, the Mediterranean fruit fly Ceratitis capitata (medfly). Our results show that the medfly is highly amenable to homing-based gene drive strategies. By targeting the medfly transformer gene, we also demonstrate how CRISPR-Cas9 gene drive can be coupled to sex conversion, whereby genetic females are transformed into fertile and harmless XX males. Given this unique malleability of sex determination, we modelled gene drive interventions that couple sex conversion and female sterility and found that such approaches could be effective and tolerant of resistant allele selection in the target population. Our results open the door for developing gene drive strains for the population suppression of the medfly and related tephritid pests by co-targeting female reproduction and shifting the reproductive sex ratio towards males. They demonstrate the untapped potential for gene drives to tackle agricultural pests in an environmentally friendly and economical way.
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Journal articleSavolainen V, Bailey NW, Diamond L, et al., 2024,
A broader cultural view is necessary to study the evolution of sexual orientation
, Nature Ecology and Evolution, Vol: 8, Pages: 181-183, ISSN: 2397-334XThe causation of sexual orientation is likely to be complex and influenced by multiple factors1. We advocate incorporating a broader cultural view into evolutionary andgenetic studies to account for differences in how sexual orientation is experienced, expressed, and understood in both human and non-human animals.
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Journal articleWaring BG, 2024,
Grand challenges in ecosystem restoration
, FRONTIERS IN ENVIRONMENTAL SCIENCE, Vol: 11 -
Journal articleZhang X, Gao F, Ye F, et al., 2024,
Structural basis of s54 displacement and promoter escape in bacterial transcription
, Proceedings of the National Academy of Sciences of USA, ISSN: 0027-8424Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated and in bacteria, transcription initiation is mediated by sigma (σ) factors. σ recruits RNAP to the promoter DNA region, located upstream oftranscription start site (TSS), and facilitates open complex formation, where double stranded DNA is opened up into a transcription bubble and template strand DNA is positioned inside RNAP for initial RNA synthesis. During initial transcription, RNAP remains bound to sigma andupstream DNA, presumably with an enlarging transcription bubble. The release of RNAP fromupstream DNA is required for promoter escape and processive transcription elongation. Bacteria sigma factors can be broadly separated into two classes with the majority belonging to the σ70 class, represented by the σ70 that regulates housekeeping genes. σ54 forms a class on its own and regulates stress response genes. Extensive studies on σ70 have revealed the molecularmechanisms of σ70 dependent process while how σ54 transitions from initial transcription to elongation is currently unknown. Here we present a series of cryo electron microscopy structures of the RNAP-σ54 initial transcribing complexes with progressively longer RNA, which reveal structural changes that lead to promoter escape. Our data show that initially, the transcription bubble enlarges, DNA strands scrunch, reducing the interactions between σ54 and DNA strands in the transcription bubble. RNA extension and further DNA scrunching help to release RNAP from σ54 and upstream DNA, enabling the transition to elongation.
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Journal articleGrob A, Enrico Bena C, Di Blasi R, et al., 2024,
Mammalian cell growth characterisation by a non-invasive plate reader assay
, Nature Communications, Vol: 15, ISSN: 2041-1723Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here, we report the development of a high throughput non-invasive method for tracking mammalian cell growth and performance based on plate reader measurements. We show the method to be suitable for both suspension and adhesion cell lines, and we demonstrate it can be adopted when cells are grown under different environmental conditions. We establish that the method is suitable to inform on effective drug treatments to be used depending on the cell line considered, and that it can support characterisation of engineered mammalian cells over time. This work provides the scientific community with an innovative approach to mammalian cell screening, also contributing to the current efforts towards high throughput and automated mammalian cell engineering.
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Journal articleLiu Y, Blanco-Toral C, Larrouy-Maumus G, 2024,
The role of cyclic nucleotides in bacterial antimicrobial resistance and tolerance
, Trends in Microbiology, ISSN: 0966-842XNucleotide signalling molecules – mainly cyclic 3′,5′-adenosine phosphate (cAMP), bis-(3′,5′)-cyclic diguanosine monophosphate (c-di-GMP), and bis-(3′,5′)-cyclic diadenosine monophosphate (c-di-AMP) – contribute to the regulation of cellular pathways. Numerous recent works have focused on the involvement of these cyclic nucleotide phosphates (cNPs) in bacterial resistance and tolerance to antimicrobial treatment. Indeed, the rise of antimicrobial resistance (AMR) is a rising global threat to human health, while the rise of antimicrobial tolerance underlies the development of AMR and long-term infections, placing an additional burden on this problem. Here, we summarise the current understanding of cNP signalling in bacterial physiology with a focus on our understanding of how cNP signalling affects AMR and antimicrobial tolerance in different bacterial species. We also discuss additional cNP-related drug targets in bacterial pathogens that may have therapeutic potential.
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Journal articleSugiura M, Kimura M, Shimamoto N, et al., 2024,
Tuning of the ChlD1 and ChlD2 properties in photosystem II by site-directed mutagenesis of neighbouring amino acids
, BBA: Bioenergetics, Vol: 1865, ISSN: 0005-2728Photosystem II is the water/plastoquinone photo-oxidoreductase of photosynthesis. The photochemistry and catalysis occur in a quasi-symmetrical heterodimer, D1D2, that evolved from a homodimeric ancestor. Here, we studied site-directed mutants in PSII from the thermophilic cyanobacterium Thermosynechoccocus elongatus, focusing on the primary electron donor chlorophyll a in D1, ChlD1, and on its symmetrical counterpart in D2, ChlD2, which does not play a direct photochemical role. The main conserved amino acid specific to ChlD1 is D1/T179, which H-bonds the water ligand to its Mg2+, while its counterpart near ChlD2 is the non-H-bonding D2/I178. The symmetrical-swapped mutants, D1/T179I and D2/I178T, and a second ChlD2 mutant, D2/I178H, were studied. The D1 mutations affected the 686 nm absorption attributed to ChlD1, while the D2 mutations affected a 663 nm feature, tentatively attributed to ChlD2. The mutations had little effect on enzyme activity and forward electron transfer, reflecting the robustness of the overall enzyme function. In contrast, the mutations significantly affected photodamage and protective mechanisms, reflecting the importance of redox tuning in these processes. In D1/T179I, the radical pair recombination triplet on ChlD1 was shared onto a pheophytin, presumably PheD1 and the detection of 3PheD1 supports the proposed mechanism for the anomalously short lifetime of 3ChlD1; e.g. electron transfer quenching by QA− of 3PheD1 after triplet transfer from 3ChlD1. In D2/I178T, a charge separation could occur between ChlD2 and PheD2, a reaction that is thought to occur in ancestral precursors of PSII. These mutants help understand the evolution of asymmetry in PSII.
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Journal articleSeddon C, Frankel G, Beis K, 2024,
Structure of the outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae
, Acta Crystallographica Section F: Structural Biology and Crystallization Communications Online, Vol: 80, Pages: 22-27, ISSN: 1744-3091Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraNα in the donor and OmpW in the recipient. Here, the crystal structure of K. pneumoniae OmpW (OmpWKP) is reported at 3.2 Å resolution. OmpWKP forms an eight-stranded β-barrel flanked by extracellular loops. The structures of E. coli OmpW (OmpWEC) and OmpWKP show high conservation despite sequence variability in the extracellular loops.
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Book chapterPrentice IC, Cowling SA, 2024,
Dynamic Global Vegetation Models
, Encyclopedia of Biodiversity, Third Edition: Volume 1-7Dynamic global vegetation models encapsulate our knowledge of plant and ecosystem function. They have many potential applications but not all of these are well developed, and large differences among model predictions are a concern. Fields of application include analysis of land–atmosphere biophysical interactions, carbon and water cycling, climate impacts on vegetation structure, fire, atmospheric trace gas composition, Quaternary vegetation and environmental changes, and ecosystem structure and function through Earth history. There is scope to improve models using a wider range of information from plant functional ecology, ecophysiology, environmental remote sensing, and atmospheric measurement, Quaternary paleoecology, and paleobotany.
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Book chapterMcArthur HCW, Bajur AT, Spillane KM, 2024,
Quantifying force-mediated antigen extraction in the B cell immune synapse using DNA-based tension sensors
, Methods in Cell BiologyB cells exert pulling forces against antigen-presenting cells (APCs) to extract antigens for internalization. The application of tugging forces on B cell receptor (BCR)-antigen bonds promotes discrimination of antigen affinities and sensing of APC physical properties. Here, we describe a protocol for preparing antigen-functionalized DNA tension sensors for quantifying force-mediated antigen extraction in the B cell immune synapse. We describe how to attach the sensors to planar lipid bilayers, quantify their surface density, use them to stimulate B cell activation, and analyze the efficiency of antigen extraction in fixed cells by fluorescence microscopy and image analysis. These techniques should be broadly applicable to studies of force-mediated transfer of molecules in cell-cell contacts.
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Journal articleGonzalez A, Vihervaara P, Balvanera P, et al., 2024,
A global biodiversity observing system to unite monitoring and guide action (AUG, 10.1038/s41559-023-02171-0, 2023)
, NATURE ECOLOGY & EVOLUTION, Vol: 8, Pages: 175-175, ISSN: 2397-334X -
Journal articleRen Y, Wang H, Harrison SP, et al., 2024,
Reduced global plant respiration due to the acclimation of leaf dark respiration coupled to photosynthesis
, New Phytologist, Vol: 241, Pages: 578-591, ISSN: 0028-646XLeaf dark respiration (Rd) acclimates to environmental changes. However, the magnitude, controls and time scales of acclimation remain unclear and are inconsistently treated in ecosystem models. We hypothesized that Rd and Rubisco carboxylation capacity (Vcmax) at 25°C (Rd,25, Vcmax,25) are coordinated so that Rd,25 variations support Vcmax,25 at a level allowing full light use, with Vcmax,25 reflecting daytime conditions (for photosynthesis), and Rd,25/Vcmax,25 reflecting night-time conditions (for starch degradation and sucrose export). We tested this hypothesis temporally using a 5-yr warming experiment, and spatially using an extensive field-measurement data set. We compared the results to three published alternatives: Rd,25 declines linearly with daily average prior temperature; Rd at average prior night temperatures tends towards a constant value; and Rd,25/Vcmax,25 is constant. Our hypothesis accounted for more variation in observed Rd,25 over time (R2 = 0.74) and space (R2 = 0.68) than the alternatives. Night-time temperature dominated the seasonal time-course of Rd, with an apparent response time scale of c. 2 wk. Vcmax dominated the spatial patterns. Our acclimation hypothesis results in a smaller increase in global Rd in response to rising CO2 and warming than is projected by the two of three alternative hypotheses, and by current models.
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Journal articleKawaguchi S, Atkinson A, Bahlburg D, et al., 2024,
Climate change impacts on Antarctic krill behaviour and population dynamics
, NATURE REVIEWS EARTH & ENVIRONMENT, Vol: 5, Pages: 43-58 -
Conference paperDavid A, Hanna G, Pennica C, et al., 2024,
Missense3D suite: harnessing the power of 3D protein structures to predict the effect of missense variants
, 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Publisher: SPRINGERNATURE, Pages: 297-297, ISSN: 1018-4813 -
Journal articleMoriel DG, Piccioli D, Raso MM, et al., 2024,
The overlooked bacterial pandemic
, SEMINARS IN IMMUNOPATHOLOGY, Vol: 45, Pages: 481-491, ISSN: 1863-2297 -
Journal articleDi Pilato V, Codda G, Niccolai C, et al., 2024,
Functional features of KPC-109, a novel 270-loop KPC-3 mutant mediating resistance to avibactam-based ,B-lactamase inhibitor combinations and cefiderocol
, INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS, Vol: 63, ISSN: 0924-8579
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