Biology subjects

Coelho, J.

Publications and source records attributed to Coelho, J..

9 recordsLinked to original sources

bioRxiv2026

Diversity of penicillin-binding protein 2x in Streptococcus pyogenes from England and Wales, 2001 to 2015

Streptococcus pyogenes remains clinically susceptible to {beta}-lactam antibiotics, its first-line treatment. Yet recent reports from the US, Iceland, and Japan have identified isolates with PBP2x (a primary {beta}-lactam target) substitutions that reduced antibiotic susceptibility. To determine whether these PBP2x substitutions occurred in S. pyogenes from England and Wales, we re-analysed 2,970 invasive genomes from 2001 to 2015. We found 42 PBP2x sequence mutants in 34% (996/2,970) of the genomes, revealing an unexpected diversity in this antibiotic target. Nine emm12 isolates carried a novel double substitution, PBP2x G600A_P601H, that co-occurred with macrolide resistance genes. Experimentally, these isolates showed 2- to 4-fold elevated minimum inhibitory concentrations for four {beta}-lactam antibiotics, alongside erythromycin resistance. Other PBP2x substitutions, found across seven emm types without reduced antibiotic susceptibility, appeared driven by emm lineage expansion rather than antibiotic pressure. These findings establish a baseline for pbp2x variation, reinforcing the case for sustained genomic surveillance globally.

microbiology↗

bioRxiv2026

Tissue lamination state switches neuronal translocation from active to passive in the vertebrate retina

Neuronal migration is essential for establishing functional tissue architecture in the developing central nervous system. While cell-intrinsic mechanisms driving neuronal movement have been identified, how migratory strategies adapt to dynamic developmental tissue changes remains less understood. Here, we address this question using retinal bipolar cells generated across unlaminated and laminated stages. This enables direct comparison of neuronal translocation across tissue states. Combining quantitative live imaging with targeted perturbations, we show that the migration mode of bipolar cells switches depending on tissue lamination state. Bipolar cells born before photoreceptor layer formation undergo directed, microtubule-dependent somal translocation. In contrast, later-born cells exhibit passive, non-directed displacement driven by collective tissue movements. Interference with tissue-wide movements impairs this displacement, while disrupting photoreceptor layer formation restores directed translocation. Independent of strategy, cells achieve accurate laminar positioning, indicating that tissue context determines neuronal migration mode, a principle likely relevant across the developing neural and other tissues.

developmental biology↗

bioRxiv2025

eDNA enables proof-of-origin of samples from reservoirs with rich and abundant biodiversity

Environmental DNA (eDNA) is increasingly used for biodiversity monitoring, but its application in verifying the geographic origin of samples remains limited. Here, we evaluated whether eDNA profiles from water samples can indicate sample provenance across three large Brazilian reservoirs. Using multi-marker metabarcoding (COI, 12S, 16S), we showed that biodiversity signatures enable spatial attribution. To ensure traceability, each report was encoded in a machine-readable format, hashed, and registered on the blockchain. This framework demonstrates a novel approach to independently verifying sample origin through molecular and cryptographic evidence.

ecology↗

bioRxiv2024

Nuclear deformability facilitates apical nuclear migration in the developing zebrafish retina

Nuclear positioning is an important aspect of cell and developmental biology. One example is the apical positioning of nuclei in retinal and other neuroepithelia. Here, apical nuclear migration is crucial for correct tissue formation. Cytoskeletal mechanisms that drive nuclei to the apical side have been explored. Yet, whether also nuclear properties influence apical nuclear migration remained comparatively less understood. Lamin A/C expression levels have been shown to be directly related to nuclear deformability. Further, it was shown that many nuclei in early development, including neuroepithelial nuclei, express only low levels of Lamin A/C. Thus, we asked whether increased expression of Lamin A in the densely packed zebrafish retinal neuroepithelium affects nuclear migration phenomena. We find that overexpressing Lamin A in retinal nuclei of single cells or in the whole tissue increased nuclear stiffness and consequently impaired apical positioning. Interestingly, also nuclei of control cells embedded in a Lamin A overexpressing environment displayed impaired apical nuclear migration. When Lamin A is overexpressed at the tissue level this further leads to a delay in mitotic entry. Thus, nuclear material properties, within cells but also in the surrounding environment, can influence nuclear and cell behavior in densely packed neuroepithelia. Overall, this work quantitatively shows a relevance of low Lamin A/C levels in early neuroepithelial development. These findings are most likely also applicable for other developing tissues which feature nuclear and cell motion through crowded environments.

developmental biology↗

bioRxiv2023

Tricontinental detection of Streptococcus pyogenes M1UK: A call for wider research and active surveillance.

The Streptococcus pyogenes M1UK lineage, characterised by an intrinsic ability to express SpeA toxin and defined by 27 single nucleotide polymorphisms in the core genome, dominates the population of emm1 S. pyogenes isolates throughout Europe, Canada, South America, Japan and Oceania. While not the sole deterministic factor, enhanced SpeA expression is likely to have contributed to M1UK lineage expansion, but was not sufficient to support expansion of intermediate lineage M123SNP, that expresses SpeA at a similar level to M1UK. A single nucleotide polymorphism (SNP) in the ssrA leader sequence upstream of speA is one of a limited number of SNPs that distinguish intermediate sublineages that differ in SpeA production. It was recently shown that this SNP leads to increased ssrA terminator read-through, and consequent increased transcription of speA, which lies downstream of ssrA. In this work, introduction of the ssrA SNP into representative isolates of the widely disseminated M1global clone and the intermediate M113SNP lineage, that cannot otherwise produce readily-detectable SpeA in culture, resulted in SpeA expression, confirming the importance of the ssrA SNP to SpeA phenotype. Consistent with this, correction of the ssrA SNP in M1UK abrogated SpeA expression. However, RNAseq analysis of 8 emm1 clinical pharyngitis strains showed that presence of the SNP was not invariably linked to read-through from the ssrA leader sequence or SpeA expression. Read-through was observed in isolates that did not possess the ssrA SNP. Critical review of existing data suggests that speA mRNA transcript length may be impacted by the two-component regulator CovRS, pointing to a complex regulatory network interaction between the bacterial chromosome and phage-encoded superantigens.

microbiology↗

bioRxiv2022

Characterisation of emergent toxigenic M1UK Streptococcus pyogenes and associated sublineages

Emm1 Streptococcus pyogenes is a successful, globally-distributed epidemic clone that is regarded as inherently invasive. An emm1 sublineage, M1UK, that expresses increased SpeA toxin, was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1UK is now dominant in England. To more fully characterise M1UK, we undertook comparative transcriptomic and proteomic analyses of M1UK and contemporary non-M1UK emm1 strains (M1global). Just seven genes were differentially expressed by M1UK compared with contemporary M1global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1UK (gldA, mipB/talC, pflD, and pts system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1UK strains have a stop codon in gldA. Deletion of the gldA gene in M1global abrogated glycerol dehydrogenase activity, and recapitulated upregulation of gene expression within the operon that includes gldA, consistent with a feedback effect. Phylogenetic analysis identified two intermediate emm1 sublineages in England comprising 13/27 (M113SNPs) and 23/27 SNPs (M123SNPs) respectively, that had failed to expand in the population. Proteomic analysis of these four major phylogenetic emm1 groups highlighted sublineage-specific changes in carbohydrate metabolism, protein synthesis and protein processing; upregulation of SpeA was not observed in chemically-defined medium. In rich broth however, transcription and secretion of SpeA was upregulated ~10-fold in both M123SNPs and M1UK sublineages, compared with M113SNPs and M1global. We conclude that stepwise accumulation of SNPs led to the emergence of M1UK. While increased expression of SpeA is a key indicator of M1UK and undoubtedly important, M1UK strains have outcompeted M123SNPs and other emm types that produce similar or more superantigen toxin. We speculate that an accumulation of adaptive SNPs has contributed to a wider fitness advantage in M1UK on an inherently successful emm1 streptococcal background. Data availabilityRNAseq. All new RNAseq data are uploaded to the European Nucleotide Archive under project reference PRJEB58303 Genomic data. All genomes listed are available on the European Nucleotide Archive using accession numbers as listed in the appendix, Proteomes. Proteomic data are available on FigShare 10.6084/m9.figshare.21777809 and will be uploaded to PRIDE Impact SummaryAlthough the major Streptococcus pyogenes reservoir is in children with pharyngitis and skin infections, S. pyogenes can lead to rarer, invasive infections that are rapidly progressive and associated with high mortality and morbidity. Emm1 S. pyogenes strains are the single most frequent genotype to cause invasive infections in high income countries and are established worldwide as an epidemic clone. The M1UK S. pyogenes emm1 sublineage which is defined by 27 new SNPs in the core genome, and characterised by increased scarlet fever toxin SpeA production, emerged and rose to dominance over a period of 5-6 years since initial recognition, outcompeting other emm1 strains in England. Increased dominance of emm1 among invasive infections this winter, on a background of already-increased numbers of S. pyogenes infections, points to a key shift in host-pathogen interaction. We hypothesize that a combination of pathogen fitness, virulence, and host susceptibility have coalesced to account for the excess of circulating S. pyogenes and emm1 invasive infections. In this paper we undertake a systems-based evaluation of M1UK in comparison to older non-M1UK emm1 strains, and identify a number of pathways that are altered in addition to the previously-reported increased SpeA expression. The emergence of a new sublineage within an already virulent clone requires ongoing surveillance, and more detailed investigation of the likely mechanisms leading to increased fitness. The capacity of S. pyogenes to cause outbreaks at national scale highlights a potential need to consider strain-specific public health guidance, underlining the inherent virulence of this exclusively human pathogen.

microbiology↗

bioRxiv2022

Ongoing emergence of M1UK lineage among invasive group A streptococcus isolates in 2020 and use of allele-specific PCR

BackgroundAn increasing burden of invasive group A streptococcal infections is reported in multiple countries, notably England, where scarlet fever cases are also abundant. In England, increased scarlet fever and invasive infections have been associated with emergence of a sublineage of emm1 Streptococcus pyogenes that expresses increased SpeA scarlet fever erythrogenic toxin. Wider surveillance for toxigenic Streptococcus pyogenes lineage M1UK is much needed however, to date, lineage assignment has required genome sequencing limiting surveillance to those centres with access to such facilities. MethodsTo circumvent the requirement for genome sequencing, an allele-specific PCR was developed to distinguish M1UK from other emm1 strains. Additional PCR assays were developed to distinguish M1UK from two intermediate lineages that were detected previously. The assay was evaluated using DNA from genome-sequenced upper respiratory tract emm1 S. pyogenes strains and a further set of 16 genome-sequenced invasive S. pyogenes isolates that included the two intermediate lineages. The assay was then applied to DNA from all 305 invasive emm1 isolates that had been submitted to the reference laboratory in the one pear period Jan 1-Dec 31 2020, in order to assign lineage. ResultsThe allele specific PCR was 100% accurate when compared with genome sequencing, correctly identifying M1UK, two intermediate sublineages, and other emm1 strains. The assay demonstrated the M1UK lineage to be dominant among emm1 invasive isolates in England, representing 278/305 (91%) of invasive emm1 isolates by end of 2020. ImplicationsEmm1 S. pyogenes have a prominent role in invasive infections; any emm1 lineage that demonstrates enhanced fitness within the population is of public health concern. The allele specific PCR provides a readily available method to subtype emm1 isolates and does not require access to complex sequencing facilities. The data confirm that the M1UK lineage has persisted and further expanded in England underlining the importance of wider global surveillance.

microbiology↗

bioRxiv2022

An SNF2 helicase-like protein links mitotic transcription termination to sister chromatid resolution

AO_SCPLOWBSTRACTC_SCPLOWMitotic chromatin is largely assumed incompatible with transcription due to changes in the transcription machinery and chromosome architecture. However, the mechanisms of mitotic transcriptional inactivation and their interplay with chromosome assembly remain largely unknown. By monitoring ongoing transcription in Drosophila early embryos, we reveal that eviction of nascent mRNAs from mitotic chromatin occurs after substantial chromosome compaction and is not promoted by condensin I. Instead, we show that the timely removal of transcripts from mitotic chromatin is driven by the SNF2 helicase-like protein Lodestar (Lds), identified here as a modulator of sister chromatid cohesion defects. In addition to transcriptional termination, we uncovered that Lds cooperates with Topoisomerase 2 to ensure efficient sister chromatid resolution and mitotic fidelity. We conclude that mitotic transcriptional termination is not a passive consequence of cell cycle progression and/or chromosome compaction but occurs via dedicated mechanisms with functional parallelisms to sister chromatid resolution.

cell biology↗

bioRxiv2018

The study of hormonal metabolism of Trincadeira and Syrah cultivars indicates new roles of salicylic acid, jasmonates, ABA and IAA during grape ripening and upon infection with Botrytis cinerea

Hormones play an important role in fruit ripening and in response to biotic stress. Nevertheless, analyses of hormonal profiling during plant development and defense are scarce. In this work, changes in hormonal metabolism in grapevine (Vitis vinifera) were compared between a susceptible (Trincadeira) and a tolerant (Syrah) variety during grape ripening and upon infection with Botrytis cinerea. Infection of grapes with the necrotrophic pathogen Botrytis cinerea leads to significant economic losses worldwide.\n\nPeppercorn-sized fruits were infected in the field and mock-treated and infected berries were collected at green, veraison and harvest stages for hormone analysis and targeted qPCR analysis of genes involved in hormonal metabolism and signaling. Results indicate a substantial reprogramming of hormonal metabolism during grape ripening and in response to fungal attack. Syrah and Trincadeira presented differences in the metabolism of abscisic acid (ABA), indole-3-acetic acid (IAA) and jasmonates during grape ripening that may be connected to fruit quality. On the other hand, high basal levels of salicylic acid (SA), jasmonates and IAA at an early stage of ripening, together with activated SA, jasmonates and IAA signaling, likely enable a fast defense response leading to grape resistance/ tolerance towards B. cinerea.\n\nThe balance among the different phytohormones seems to depend on the ripening stage and on the intra-specific genetic background and may be fundamental in providing resistance or susceptibility. In addition, this study indicated the involvement of SA and IAA in defense against necrotrophic pathogens and gains insights into possible strategies for conventional breeding and/or gene editing aiming at improving grape quality and grape resistance against Botrytis cinerea.

plant biology↗