M. Jones

Mapping fibrotic microenvironments: single-cell and spatial profiling of Schistosoma mansoni-induced tissue fibrosis

This study uses single-cell spatial transcriptomics to map fibrotic microenvironments in Schistosoma mansoni-infected mice, revealing organ-specific fibrosis architecture and shared signaling pairs for potential therapeutic targets.

BRCA1 secondary splice-site mutations drive exon-skipping and PARP inhibitor resistance

This study identifies secondary splice-site mutations in BRCA1 that drive exon skipping and PARP inhibitor resistance in ovarian and breast cancer.

Classification of dinosaur footprints using machine learning

The paper trains machine learning models to classify dinosaur footprints as ornithopods or theropods using 20 landmark features, finding that MLP performs best with class imbalance.

Non-disruptive inducible labeling of ER-membrane contact sites using the Lamin B Receptor

The paper introduces LaBeRling, a non-disruptive method for inducible labeling of ER-MCSs, and demonstrates its use in studying mitotic changes and ER-Golgi contacts.

RESOLVING BIOLOGY'S DARK MATTER: SPECIES RICHNESS, SPATIOTEMPORAL DISTRIBUTION, AND COMMUNITY COMPOSITION OF A DARK TAXON

The paper uses DNA barcoding to study scuttle flies in Sweden, revealing high diversity and showing that climate factors strongly influence their distribution.

Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses

The paper documents reduced seabird and sea duck mortalities in eastern Canada during the 2023 breeding season compared to 2022 following HPAI introduction, with more diverse species affected in 2023.

Spatial proteomic analysis of a lung cancer model reveals regulatory T cells attenuate KRAS-G12C inhibitor-induced immune responses

The paper identifies regulatory T cells as mediators of resistance to KRAS-G12C inhibitors and anti-PD-1 therapy through spatial proteomic analysis of lung cancer models.

Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers

The paper links geochemistry and microbial functional potential to organic matter development across seven rivers using DOM characterization, geochemical analyses, and shotgun metagenomics.

Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022

The paper estimates 40,966 wild bird mortalities in eastern Canada due to H5N1 avian influenza in 2022, highlighting potential population-level impacts on Northern Gannets and American Common Eiders.

Decoding mTOR signalling heterogeneity in the tumour microenvironment using multiplexed imaging and graph convolutional networks

The paper uses multiplexed imaging and graph convolutional networks to analyze mTOR signaling heterogeneity in colorectal tumors and its correlation with patient prognosis.

High pathogenicity avian influenza (H5N1) in Northern Gannets: Global spread, clinical signs, and demographic consequences

This study tracks the global spread of HPAI H5N1 in Northern Gannets, documenting high mortality rates and demographic impacts across multiple colonies.

Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

This paper uses whole-genome sequencing and coalescent methods to show that Galapagos giant tortoises form a species complex with at least 9 species, challenging previous single-species classifications.

Rare germline genetic variation in PAX8 transcription factor binding sites and susceptibility to epithelial ovarian cancer

This study investigates rare germline variation in PAX8 binding sites for ovarian cancer risk using burden testing but finds no significant association.

Extensive hybridisation between multiple differently adapted species may aid persistence in a changing climate

This study shows extensive hybridisation between five wood ant species in Finland, with hybrids occupying warmer habitats than cold-adapted parents, suggesting potential for increased hybridisation with climate change.

An alpaca-derived nanobody neutralizes the SARS-CoV-2 omicron variant

This paper identifies a nanobody that effectively neutralizes the SARS-CoV-2 Omicron variants BA.1 and BA.2, showing high affinity and pre-clinical promise.

A histone methylation-MAPK signaling axis drives durable epithelial-mesenchymal transition in hypoxic pancreas cancer

This study identifies a hypoxia-driven histone methylation-MAPK feedback loop that sustains EMT in pancreatic cancer, with potential therapeutic implications.

FBXL4 suppresses mitophagy by restricting the accumulation of NIX and BNIP3 mitophagy receptors

This study identifies FBXL4 as a suppressor of basal mitophagy by ubiquitylating and degrading NIX and BNIP3, and shows pathogenic variants disrupt this function leading to mtDNA depletion syndrome.

The Ecosystem Integrity Index: a novel measure of terrestrial ecosystem integrity

This paper introduces the Ecosystem Integrity Index (EII), a global measure of terrestrial ecosystem integrity, finding that one fifth of ecosystems and one quarter of ecoregions have lost over half their integrity.

Post-vaccination Omicron infections induce broader immunity across antigenic space than prototype mRNA COVID-19 booster vaccination or primary infection

The paper compares antibody responses to different SARS-CoV-2 variants after vaccination and infection, finding that post-vaccination Omicron infection induces broader immunity than triple vaccination alone.

CRISPR metabolic screen identifies ATM and KEAP1 as targetable genetic vulnerabilities in solid tumors.

The paper identifies ATM and KEAP1 as targetable vulnerabilities in solid tumors through a CRISPR metabolic screen revealing their synthetic lethality.

Single Nucleus RNA Sequencing of Pre-Malignant Liver Reveals Disease-Associated Hepatocyte State with HCC Prognostic Potential

The paper uses snRNA-seq to identify a disease-associated hepatocyte state in pre-malignant livers that correlates with HCC risk in mice and humans.

Cell-surface PD-L1 expression identifies a sub-population of distal epithelial cells enriched in idiopathic pulmonary fibrosis

The paper identifies CD274-expressing cells in human lungs that are expanded in IPF and show progenitor-like behavior in ex vivo assays.

Bacterial colonisation dynamics of household plastics in a coastal environment

The paper tracks bacterial colonisation of household plastics in a coastal environment, finding rapid colonisation by diverse bacteria, including pathogens, regardless of polymer type.

Identification of a new family of "megaphages" that are abundant in the marine environment

The paper identifies a new family of marine megaphages with large genomes and novel metabolic genes.

Pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis

This study shows that pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis by promoting bone-type cross-linking and increasing tissue stiffness.

INfrastructure for a PHAge REference Database: Identification of large-scale biases in the current collection of phage genomes

The paper develops a tool to extract phage genomes and identifies biases in their representation, such as overrepresentation of lytic phages and limited host diversity.

Hydroxycarboxylic acid receptor 2 (HCAR2/GPR109A) expression and signaling promotes the maintenance of an immunoinhibitory retinal environment

This study shows that HCAR2/GPR109A maintains an immunoinhibitory retinal environment by regulating immune cell responses and preventing inflammation in retinal diseases.

Phagocytosed polyhedrin-cytokine co-crystal nanoparticles provide sustained secretion of bioactive cytokines from macrophages

This paper demonstrates that PODS nanoparticles can be phagocytosed by macrophages and sustain cytokine secretion, enabling potential therapeutic applications in immunotherapy.

Expression of type I interferon-associated genes at antiretroviral therapy interruption predicts HIV virological rebound

The paper identifies type I interferon-associated gene expression in CD4 T cells as a predictor of delayed HIV viral rebound after antiretroviral therapy interruption.

Flower Power: Floral reversion as a viable alternative to nodal micropropagation in Cannabis sativa.

This study develops a floral reversion method for Cannabis sativa micropropagation, showing it can produce up to eight times more explants per cycle than nodal methods.