Pathways to Recovery: Genomics and Resistance Assays for Tree Species Devastated by the Myrtle Rust Pathogen.

Myrtle rust is a plant disease caused by the invasive fungal pathogen Austropuccinia psidii (G. Winter) Beenken, which has a global host list of 480 species. It was detected in Australia in 2010 and has caused the rapid decline of native Myrtaceae species, including rainforest trees Rhodamnia rubescens (Benth.

Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq.

Microscopy and omics are complementary approaches to probe cellular molecular states in health and disease, combining granularity with scalability. However, integrating both imaging- and sequencing-based assays on the same cell has proven challenging. This study demonstrates a new approach called SpectralSeq that combines hyperspectral autofluorescence imaging with transcriptomics on the same cell.

PI(4)P recruits CIDE proteins to promote the formation of unilocular lipid droplets during adipogenesis and hepatic steatosis.

Lipid droplets (LDs) are evolutionarily conserved organelles that play important roles in metabolism. Each LD is enclosed by a monolayer of phospholipids, distinct from bilayer membranes. The composition of LD surface phospholipids and their impact on LD growth and function remain to be defined.

Ameliorates Metabolic Dysfunction-Associated Steatotic Liver Disease in Rats via Gut Microbiota Remodeling and Inflammatory Suppression.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a highly prevalent chronic liver condition linked to obesity and metabolic imbalance. Alterations in the gut microbiota are increasingly recognized as contributors to its progression. , a core member of the human gut microbiota, has been linked with metabolic health, but its functional role in MASLD remains unclear.

Eubacterium limosum modulates tumor microenvironments and produces antitumor metabolites active against colorectal cancer.

None declared.Conflicts of interestGut microbiota play a key role in ameliorating colorectal cancer (CRC). Eubacterium limosum is a potential probiotic with anti-CRC functions.

What makes a small RNA work?

Bacterial small RNAs (sRNAs) are key regulators of gene expression, interacting with target messenger RNAs (mRNAs) through imperfect base pairing. Unlike other non-coding RNAs such as microRNAs and PIWI-interacting RNAs, bacterial sRNAs exhibit significant sequence and structural diversity, complicating functional predictions. Recent high-throughput profiling of the sRNA interactome has accentuated this problem by revealing a highly complex network of sRNA interactions.

Guidelines for preventing and reporting contamination in low-biomass microbiome studies.

Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples.

Population genomics of a sailing siphonophore reveals genetic structure in the open ocean.

The open ocean is a vast, highly connected environment, and the organisms found there have been hypothesized to represent massive, well-mixed populations. Of these, the man-o'-war or bluebottle (Physalia) is uniquely suited to long-distance travel, using its gas-filled float and muscular crest to catch the wind and sail the sea surface. We tested the hypothesis of a global, panmictic Physalia population by sequencing whole genomes of 151 samples and found five distinct lineages, with multiple lines of evidence indicating strong reproductive isolation, despite range overlap.

Long read sequencing reveals transgene concatemerization and vector sequences integration following AAV-driven electroporation of CRISPR RNP complexes in mouse zygotes.

Over the last decade CRISPR gene editing has been successfully used to streamline the generation of animal models for biomedical research purposes. However, one limitation to its use is the potential occurrence of on-target mutations that may be detrimental or otherwise unintended. These bystander mutations are often undetected using conventional genotyping methods.

Lipoic Acid Based Redox-Responsive Degradable Antimicrobial Polymers.

The rise of multidrug-resistant (MDR) pathogens poses a critical threat to global health, exacerbated by the overuse of antibiotics and the lack of effective alternatives. Antimicrobial peptides (AMPs) have emerged as promising candidates due to their broad-spectrum activity and unique mechanisms of action. However, several challenges such as enzymatic degradation, high production costs, and potential cytotoxicity have hindered their clinical translation.

Mapping the loss of flagellar motility across the tree of life.

Bacterial swimming is mostly powered by the bacterial flagellar motor and the number of proteins involved in the flagellar motor can vary. Quantifying the proteins present in flagellar motors from a range of species delivers insight into how motility has changed throughout history and provides a platform for estimating from its genome whether a species is likely to be motile. We conducted sequence and structural homology searches for 54 flagellar pathway proteins across 11 365 bacterial genomes and developed a classifier with up to 95% accuracy that could predict whether a strain was motile or not.

Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution.

Understanding viral evolutionary dynamics is crucial to pandemic responses, prediction of virus adaptation over time, and virus surveillance for public health strategies. Whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has enabled fine-grained studies of virus evolution in the human population. Serial passaging offers a complementary controlled environment to investigate the emergence and persistence of genetic variants that may confer selective advantage.

Comparative genome analysis investigation of nosocomial and community-acquired cases of Legionnaires' disease caused by ST2858 and ST378.

Eight cases of Legionnaires' disease caused by serogroup 1 sequence type (ST) ST2858 were detected within 4 years in Montréal, Canada. Most cases were associated with a single healthcare facility, and one of them presented with a co-infection, from which ST378 was isolated as well. The source of ST2858 was not identified, despite extensive environmental sampling.

Uncovering the antifungal potential of Cannabidiol and Cannabidivarin.

Fungal infections pose a major threat to human health with increasing incidence of antifungal resistance globally. Despite the need for novel antifungal drugs, few are currently in clinical development. Here we evaluate the antifungal activity of five phytocannabinoids against several clinically relevant fungal pathogens, with a focus on the priority pathogen Cryptococcus neoformans.

Influenza epidemiology and co-infections within New South Wales-based multicentre health districts between 2018 and 2023.

Influenza epidemiology spanning pre-COVID-19 pandemic to post-COVID-19 pandemic periods in Australia is insufficiently described. This study reviewed influenza epidemiology in two metropolitan New South Wales (NSW) health districts between 2018 and 2023 and investigated influenza virus (IFV) co-infections with other respiratory viruses (ORVs). A retrospective analysis of diagnostic polymerase chain reaction data from patients requiring testing for IFV and/or ORVs was conducted.

Extensible Immunofluorescence (ExIF) accessibly generates high-plexity datasets by integrating standard 4-plex imaging data.

Standard immunofluorescence imaging captures just ~4 molecular markers (4-plex) per cell, limiting dissection of complex biology. Inspired by multimodal omics-based data integration approaches, we propose an Extensible Immunofluorescence (ExIF) framework that transforms carefully designed but easily produced panels of 4-plex immunofluorescence into a unified dataset with theoretically unlimited marker plexity, using generative deep learning-based virtual labelling. ExIF enables integrated analyses of complex cell biology, exemplified here through interrogation of the epithelial-mesenchymal transition (EMT), driving significant improvements in downstream quantitative analyses usually reserved for omics data, including: classification of cell phenotypes; manifold learning of cell phenotype heterogeneity; and pseudotemporal inference of molecular marker dynamics.

Design, Synthesis, and Biological Evaluation of Naphthoquinone Salts as Anticancer Agents.

The Warburg effect, a unique glycolytic phenomenon in cancer cells, presents a promising target for developing selective anticancer agents. Previously, , a hit compound disrupting glycolytic metabolism, was identified via phenotypic screening, with Kelch-like ECH-associated protein 1 (Keap1) proposed as a potential target. To enhance its potency and selectivity, a library of -derived salt compounds was synthesized.

Attenuates Hepatic Injury, Oxidative Stress, and Inflammation in a Rat Model of High-Fat Diet-Induced MASLD.

Metabolic-dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disorder globally. Probiotic supplementation has shown promise in its prevention and treatment. Although , a lactic acid bacterium with immunomodulatory effects, has antibacterial and anti-inflammatory activities, there is a lack of direct evidence for its role in alleviating MASLD.

Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs.

Hypomethylating agents are frontline therapies for myelodysplastic neoplasms (MDS), yet clinical responses remain unpredictable. We conducted a phase 2 trial comparing injectable and oral azacitidine (AZA) administered over one or three weeks per four-week cycle, with the primary objective of investigating whether response is linked to in vivo drug incorporation or DNA hypomethylation. Our findings show that injection results in higher drug incorporation, but lower DNA demethylation per cycle, while global DNA methylation levels in mononuclear cells are comparable between responders and non-responders.

alleviates experimental colitis in mice by regulating inflammatory pathways and gut microbiota.

Background: Inflammatory bowel disease (IBD) is a chronic condition with no cure. Probiotics may offer a new strategy for the treatment of IBD. has been shown to have antibacterial, anti-inflammatory, and antioxidant beneficial effects in animal models.

Predicting Motif-Mediated Interactions Based on Viral Genomic Composition.

Viruses manipulate host cellular machinery to propagate their life cycle, with one key strategy being the mimicry of short linear motifs (SLiMs) found in host proteins. While databases continue to expand with virus-host protein-protein interaction (vhPPI) data, accurately predicting viral mimicry remains challenging due to the inherent degeneracy of SLiMs. In this study, we investigate how viral genomic composition influences motif mimicry and the mechanisms through which viruses hijack host cellular functions.

Hydroxyurea reduces the levels of the fetal gene repressors ZBTB7A/LRF and BCL11A in erythroid cells .

Objectives: Hydroxyurea (HU) is the most widely used therapy for adults and children with sickle cell disease (SCD). It is believed to act largely by inducing the transcription of fetal genes to generate fetal hemoglobin (HbF), which inhibits the pathological polymerization of sickle hemoglobin (HbS). The mechanisms by which hydroxyurea elevates HbF are unclear.

Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis.

Non-coding RNAs (ncRNAs) are RNA molecules that are transcribed from DNA but are not translated into proteins. Studies over the past decades have revealed that ncRNAs can be classified into small RNAs, long non-coding RNAs and circular RNAs by genomic size and structure. Accumulated evidences have eludicated the critical roles of these non-coding transcripts in regulating gene expression through transcription and translation, thereby shaping cellular function and disease pathogenesis.