Biology subjects

Alawi, M.

Publications and source records attributed to Alawi, M..

8 recordsLinked to original sources

bioRxiv2026

RnR-ExM: Robust Non-rigid Registration Challenge for Expansion Microscopy Volumes

Expansion Microscopy (ExM) enables nanoscale imaging of biological samples while preserving structural and molecular details. The Robust Non-rigid Registration Challenge for ExM (RnR-ExM) was launched to benchmark 3D registration algorithms on real-world ExM datasets. The challenge released 24 pairs of high-resolution 3D volumes from zebrafish, mouse, and C.~elegans, deliberately selected for their difficulty with standard alignment methods. To evaluate performance, we provided curated segmentation masks of nuclei and blood vessels as landmarks for half of the dataset. To encourage learning-based approaches, we released code for generating synthetic training data reflecting the deformation and appearance of the unlabeled pairs. By submission, 168 participants registered, with six teams submitting results by the deadline; the top three were invited to present at ISBI 2023. Accurate registration of ExM volumes is essential for downstream biological analyses such as multiplexed molecular mapping and cell-type-specific structural profiling. In this paper, we detail the methods and results of these top teams, highlighting current capabilities and future directions for 3D registration in ExM. All datasets and code are available at https://rnr-exm.grand-challenge.org/

neuroscience↗

bioRxiv2026

A Novel Plasmid-Encoded Mobile Colistin Resistance Gene mcr-13.1 Detected in Escherichia coli Isolated from Grassland.

Plasmid-encoded mobile colistin resistance (mcr) genes have raised concern due to dissemination potential. While mcr variants are reported across One Health compartments, they remain unreported in grass. This study characterises a novel mcr variant (mcr-13.1), detected in Escherichia coli isolated from the grass phylosphere within an agricultural grassland. The two mcr-positive isolates were clonal copies isolated at timepoints eight weeks apart. They belonged to the serotype O17:H18 and were of the sequence type ST394. The E. coli were phenotypically susceptible to {beta}-lactams, aminoglycosides, quinolones, sulphonamides, phenicols, tetracyclines, diaminopyrimidine and colistin (Minimum Inhibitory Concentration (MIC) = 0.5 {micro}g/mL). The mcr-13.1 gene was encoded on an IncFIB plasmid. This plasmid was transferable by conjugation but the colistin MIC of the E. coli J53 transconjugant did not change (0.5 {micro}g/mL). Further, cloned pUC19::mcr-13.1 did not alter the colistin MIC for E. coli DH5 (0.25 {micro}g/mL). The translated amino acid sequence showed highest homology (82 %) to MCR-10.2 and MCR-10.4. Our findings identify grass as a previously unrecognised reservoir for E. coli carrying mobile mcr genes, reports the identification of the novel mcr-13.1 variant from this niche and demonstrates the importance of genomic screening in identifying mcr genes that would otherwise remain undetected.

microbiology↗

bioRxiv2026

CD73-derived adenosine at the blood-brain barrier confers protection in a mouse model of ischemic stroke

Ischemic stroke remains a leading cause of death and disability, and current reperfusion therapies do not address the secondary neuroinflammatory response following blood-brain barrier (BBB) disruption. Purinergic signaling critically regulates this process: extracellular ATP promotes inflammation, whereas its enzymatic conversion into adenosine exerts tissue-protective effects. Notably, the ectonucleotidase CD73 (NT5E), which catalyzes AMP-to-adenosine conversion, is highly expressed by human but not murine brain endothelial cells (BECs). Here, we investigated the role of endothelial CD73 in ischemic stroke using an AAV vector engineered for selective transduction of murine BECs to induce BBB-specific CD73 expression. Endothelial CD73 enhanced extracellular ATP degradation toward adenosine generation and established a purine metabolism profile resembling that of human BECs. In the transient middle cerebral artery occlusion (tMCAO) mouse model, BBB-targeted CD73 expression reduced infarct volume by 40% and prevented early mortality within 48 h after reperfusion. Transcriptomic and flow cytometric analyses revealed altered leukocyte responses, including increased recruitment of monocytes/macrophages whose gene expression signatures were consistent with inflammation-resolving programs. These findings identify endothelial CD73 as an important regulator of post-ischemic neuroinflammation and highlight species-specific differences in BBB purine metabolism with implications for translational stroke research.

neuroscience↗

bioRxiv2025

Polyethylene terephthalate (PET) primary degradation products affect c-di-GMP-, cAMP-signaling and quorum sensing (QS) in Vibrio gazogenes DSM 21264

Global plastic pollution in oceans and estuaries is increasing rapidly and its well known that bacteria colonize plastic particles of all sizes. Vibrio spp. are frequently found as part of the plastisphere. We recently showed that Vibrio gazogenes DSM 21264 harbors a promiscuous esterase designated PET6. We now provide evidence that the pet6 gene is expressed under a wide range of environmental conditions in its native host. However, in PET- and PE-grown biofilms the pet6 gene expression was not affected by the type of surface. The pet6 transcription was sufficient to allow enzyme production and release of {micro}M amounts of mono-(2-hydroxyethyl) terephthalate (MHET) and terephthalic acid (TPA) already after 24 hours of incubation on PET foil. Notably, the highest pet6 gene transcription was observed in planktonic lifestyle in the presence of bis(2-hydroxyethyl) terephthalate (BHET) one of the primary degradation products of PET. BHET was further hydrolyzed by PET6 and UlaG, a lactonase that had not been known to be involved in BHET degradation. Elevated concentrations of BHET affected the major signaling circuits involved in bacterial quorum sensing (QS), c-di-GMP and cAMP-CRP signaling. This resulted in failure to form biofilms, synthesis of the red pigment prodigiosin and altered colony morphologies. While BHET had a very wide impact, TPA interfered mainly with the bacterial QS by attenuating the expression of the CAI-I autoinducer synthase gene. These observations imply a potential role of BHET and TPA as nutritional signals in Vibrio gazogenes and that may affect its growth and survival in the plastisphere. IMPORTANCEThis study provides first evidence that Vibrio gazogenes DSM 21264 secretes an active PET hydrolase and degrades the polymer using PET6 when growing in biofilms on foils and microplastic particles. The study further provides evidence that the primary PET degradation products BHET and TPA may have a profound impact on the global QS, c-di-GMP and cAMP-CRP signaling of V. gazogenes and its capability to colonize plastic particles in the marine environment.

microbiology↗

bioRxiv2021

Multiplexed mRNA analysis of brain-derived extracellular vesicles upon experimental stroke in mice reveals increased mRNA content related to inflammation and recovery processes

Extracellular vesicles (EVs) are lipid bilayer enclosed structures that not only represent a newly discovered means for cell-to-cell communication but may also serve as promising disease biomarkers and therapeutic tools. Apart from proteins, lipids, and metabolites, EVs can deliver genetic information such as mRNA eliciting a response in the recipient cells. In the present study, we have analyzed the mRNA content of brain-derived EVs (BDEVs) isolated 72 hours after experimental stroke in mice and compared them to controls (shams) using the nCounter(R) Nanostring panels, with or without prior RNA isolation from BDEVs. We found that both panels show similar results when comparing upregulated mRNA in stroke. Notably, the higher upregulated mRNAs were related to processes of stress and immune system responses, but also to anatomical structure development, cell differentiation, and extracellular matrix organization, indicating that regenerative mechanisms are already taking place at this time-point. The five top overexpressed mRNAs in stroke mice compared to shams were confirmed by RT-qPCR and, interestingly, were found to be present as full-length open-reading frame in BDEVs. We could reveal that the majority of the mRNA cargo in BDEVs was of microglial origin and probably predominantly present in small BDEVs ([≤] 200 nm in diameter). However, the EV population with the highest increase in the total BDEVs pool at 72 h after stroke was of oligodendrocytic origin. Our study shows that nCounter(R) panels are a good tool to study mRNA content in tissue-derived EVs as they can be carried out even without previous mRNA isolation and that the mRNA cargo of BDEVs indicates their participation in inflammatory but also recovery processes after stroke.

neuroscience↗

bioRxiv2020

High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms

Merkel Cell Polyomavirus (MCPyV) is the etiological agent of the majority of Merkel Cell Carcinomas (MCC). MCPyV positive MCCs harbor integrated, defective viral genomes that constitutively express viral oncogenes. Which molecular mechanisms promote viral integration, if distinct integration patterns exist, and if integration occurs preferentially at loci with specific chromatin states is unknown. We here combined short and long-read (nanopore) next-generation sequencing and present the first high-resolution analysis of integration site structure in MCC cell lines as well as primary tumor material. We find two main types of integration site structure: Linear patterns with chromosomal breakpoints that map closely together, and complex integration loci that exhibit local amplification of genomic sequences flanking the viral DNA. Sequence analysis suggests that linear patterns are produced during viral replication by integration of defective/linear genomes into host DNA double strand breaks via non-homologous end joining, NHEJ. In contrast, our data strongly suggest that complex integration patterns are mediated by microhomology-mediated break-induced replication, MMBIR. Furthermore, we show by ChIP-Seq and RNA-Seq analysis that MCPyV preferably integrates in open chromatin and provide evidence that viral oncogene expression is driven by the viral promoter region, rather than transcription from juxtaposed host promoters. Taken together, our data explain the characteristics of MCPyV integration and may also provide a model for integration of other oncogenic DNA viruses such as papillomaviruses. Author summaryIntegration of viral DNA into the host genome is a key event in the pathogenesis of many virus-induced cancers. One such cancer is Merkel cell carcinoma (MCC), a highly malignant tumor that harbors monoclonally integrated and replication-defective Merkel cell polyomavirus (MCPyV) genomes. Although MCPyV integration sites have been analyzed before, there is very little knowledge of the mechanisms that lead to mutagenesis and integration of viral genomes. We used multiple sequencing technologies and interrogation of chromatin states to perform a comprehensive characterization of MCPyV integration loci. This analysis allowed us to deduce the events that likely precede viral integration. We provide evidence that the mutations which result in the replication defective phenotype are acquired prior to integration and propose that the cellular DNA repair pathways non-homologous end joining (NHEJ) and microhomology-mediated break-induced replication (MMBIR) produce two principal MCPyV integration patterns (simple and complex, respectively). We show that, although MCPyV integrates predominantly in open chromatin regions, viral oncogene expression is independent of host promoters and driven by the viral promotor region. Our findings are important since they can explain the mechanisms of MCPyV integration. Furthermore, our model may also apply to papillomaviruses, another clinically important family of oncogenic DNA viruses.

molecular biology↗

bioRxiv2018

The landscape of viral associations in human cancers

Potential viral pathogens were systematically investigated in the whole-genome and transcriptome sequencing of 2,656 donors as part of the Pan-Cancer Analysis of Whole Genomes using a consensus approach integrating three independent pathogen detection pipelines. Viruses were detected in 382 genomic and 68 transcriptome data sets. We extensively searched and characterized numerous features of virus-positive cancers integrating various PCAWG datasets. We show the high prevalence of known tumor associated viruses such as EBV, HBV and several HPV types. Our systematic analysis revealed that HPV presence was significantly exclusive with well-known driver mutations in head/neck cancer. A strong association was observed between HPV infection and the APOBEC mutational signatures, suggesting the role of impaired mechanism of antiviral cellular defense as a driving force in the development of cervical, bladder and head neck carcinoma. Viral integration into the host genome was observed for HBV, HPV16, HPV18 and AAV2 and associated with a local increase in copy number variations. The recurrent viral integrations at the TERT promoter were coupled to high telomerase expression uncovering a further mechanism to activate this tumor driving process. High levels of endogenous retrovirus ERV1 expression is linked to worse survival outcome in kidney cancer.

cancer biology↗

bioRxiv2018

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-α7 mediated nuclear import pathway

Influenza A viruses are able to adapt to restrictive conditions due to their high mutation rates. Here, we addressed the question by which mechanisms influenza A viruses may escape restriction by the cellular importin-7 protein, a component of the nuclear import machinery required for avian-mammalian adaptation and replicative fitness in human cells. Therefore, we assessed viral evolution in mice lacking the importin-7 gene. Here, we show that particularly three mutations occur with high frequency in the viral NP protein (G102R, M105K and D375N) in a specific structural area upon in vivo adaptation. Moreover, our findings suggest that the adaptive NP mutations mediate viral escape from importin-7 requirement likely due to the utilization of alternative interaction sites in NP beyond the classical nuclear localization signal and importin- isoforms. However, viral escape from importin-7 is, at least in part, associated with reduced replicative fitness in human cells.

molecular biology↗