Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma.

In this study, we find that Mif expression is associated with tumor growth and aggressiveness, specifically in tumors with low heterogeneity. These findings could facilitate the development of new strategies to treat patients with homogeneous, high MIF-expressing tumors that are unresponsive to immune checkpoint therapy.

When synthetic biology meets medicine.

In recent years, the world has faced significant challenges with the coronavirus disease 2019 (COVID-19) pandemic, as well as other infectious diseases such as Zika and Ebola. Furthermore, the rapid rise of non-communicable diseases such as diabetes, heart disease, and cancer has placed tremendous strain on healthcare resources and systems. Unfortunately, advancements in drug development, diagnostics, and therapeutics have struggled to keep pace with the emergence and progression of diseases, necessitating the exploration of new technologies for the discovery and development of biomedicines and biotherapies.

Downregulation of RhoA/ROCK1/YAP/F-actin causing decreased aortic smooth muscle cell stiffness promotes aortic dissection formation.

Downregulated RhoA/ROCK1/YAP/F-actin axis leads to decreased AoSMC stiffness and promotes AD formation.

HMOX1 as a potential drug target for upper and lower airway diseases: insights from multi-omics analysis.

Background: Oxidative stress is key in inflammatory airway diseases. Heme oxygenase 1 (HMOX1) regulates oxidative stress, but its role in airway diseases needs exploration.

Methods: Differentially expressed genes (DEGs) between healthy nasal mucosa and chronic rhinosinusitis with nasal polyps (CRSwNP) were identified from Gene Expression Omnibus (GEO).

The multi-omics signatures of telomere length in childhood.

Background: Telomere length is an important indicator of biological age and a complex multi-factor trait. To date, the telomere interactome for comprehending the high-dimensional biological aspects linked to telomere regulation during childhood remains unexplored. Here we describe the multi-omics signatures associated with childhood telomere length.

sp. nov., an acidotolerant sulphate-reducing bacterium isolated from moderately acidic fen soil.

An obligately anaerobic, spore-forming sulphate-reducing bacterium, strain SB140, was isolated from a long-term continuous enrichment culture that was inoculated with peat soil from an acidic fen. Cells were immotile, slightly curved rods that stained Gram-negative. The optimum temperature for growth was 28 °C.

Combining radio-telemetry and radar measurements to test optimal foraging in an aerial insectivore bird.

Optimal foraging theory posits that foragers adjust their movements based on prey abundance to optimize food intake. While extensively studied in terrestrial and marine environments, aerial foraging has remained relatively unexplored due to technological limitations. This study, uniquely combining BirdScan-MR1 radar and the Advanced Tracking and Localization of Animals in Real-Life Systems biotelemetry system, investigates the foraging dynamics of Little Swifts () in response to insect movements over Israel's Hula Valley.

Comparative Efficacy of Nonsteroid Immunosuppressive Medications in Childhood Nephrotic Syndrome.

Importance: Cyclophosphamide and calcineurin inhibitors are the most used nonsteroid immunosuppressive medications globally for children with various chronic inflammatory conditions. Their comparative effectiveness remains uncertain, leading to worldwide practice variation. Nephrotic syndrome is the most common kidney disease managed by pediatricians globally and suboptimal treatment is associated with high morbidity.

methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.

Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph.

Dynamic behavior of cell-cell adhesion factors in collective cell migration.

Collective cell migration is a fundamental process underlying various biological phenomena, including embryonic development and cancer cell invasion. The cohesive yet flexible movement of cell collectives largely depends on the coordinated regulation of cell-cell and cell-substrate adhesions. In this review, we summarize the regulation of key cell-cell junction components, such as cadherins and zonula occludens proteins during collective cell migration, with a particular focus on the recently discovered multifaceted roles of ZO-1 in both cell-cell and cell-substrate interactions.

HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells.

Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) techniques hold great value in evaluating the heterogeneity and spatial characteristics of hematopoietic cells within tissues. These two techniques are highly complementary, with scRNA-seq offering single-cell resolution and ST retaining spatial information. However, there is an urgent demand for well-organized and user-friendly toolkits capable of handling single-cell and spatial information.

Roles for Exosomes in the Pathogenesis, Drug Delivery and Therapy of Psoriasis.

Psoriasis is a chronic, recurrent and inflammatory skin disease. Although conventional immunosuppressants can ameliorate psoriatic symptoms, it tends to relapse over time. Previous studies have shown that exosomes from both immune and non-immune cells participate in psoriatic immunopathology.

Genomic Insight into Isolates from Fresh Raw Mussels and Ready-to-Eat Stuffed Mussels.

Consuming raw or undercooked mussels can lead to gastroenteritis and septicemia due to contamination. This study analyzed the prevalence, density, species diversity, and molecular traits of spp. in 48 fresh raw wild mussels (FRMs) and 48 ready-to-eat stuffed mussels (RTE-SMs) through genome analysis, assessing health risks.

Novel Assignment of Gene Markers to Hematological and Immune Cells Based on Single-Cell Transcriptomics.

There are many different cells that perform highly specialized functions in the human hematological and immune systems. Due to the relevance of their activity, in this work we investigated the cell types and subtypes that form this complex system, using single-cell RNA sequencing (scRNA-seq) to dissect and assess the markers that best define each cell population. We first developed an optimized computational workflow for analyzing large scRNA-seq datasets.

Exploring the Pharmacogenomic Map of Croatia: PGx Clustering of 522-Patient Cohort Based on UMAP + HDBSCAN Algorithm.

Pharmacogenetics is a branch of genomic medicine aiming to personalize drug prescription guidelines based on individual genetic information. This concept might lead to a reduction in adverse drug reactions, which place a heavy burden on individual patients' health and the economy of the healthcare system. The aim of this study was to present insights gained from the pharmacogenetics-based clustering of over 500 patients from the Croatian population.

A Multi-Omics Analysis of a Mitophagy-Related Signature in Pan-Cancer.

Mitophagy, an essential process within cellular autophagy, has a critical role in regulating key cellular functions such as reproduction, metabolism, and apoptosis. Its involvement in tumor development is complex and influenced by the cellular environment. Here, we conduct a comprehensive analysis of a mitophagy-related gene signature, composed of , , , , , , and , across various cancer types, revealing significant differential expression patterns associated with molecular subtypes, stages, and patient outcomes.

Identification of Biomarkers of Arrhythmogenic Cardiomyopathy (ACM) by Plasma Proteomics.

The pathophysiology of arrhythmogenic cardiomyopathy (ACM), previously known as arrhythmogenic right ventricular cardiomyopathy (ARVC), and its specific biological features remain poorly understood. High-throughput plasma proteomic profiling, a powerful tool for gaining insights into disease pathophysiology at the systems biology level, has not been used to study ACM. This study aimed at characterizing plasmatic protein changes in patients with ACM, which were compared with those of healthy controls, and at exploring the potential role of the identified proteins as biomarkers for diagnosis and monitoring.

Developing a Versatile Arsenal: Novel Antimicrobials as Offensive Tools Against Pathogenic Bacteria.

The pervasive and often indiscriminate use of antibiotics has accelerated the emergence of drug-resistant bacterial strains, thus presenting an acute threat to global public health. Despite a growing acknowledgment of the severity of this crisis, the current suite of strategies to mitigate antimicrobial resistance remains markedly inadequate. This paper asserts the paramount need for the swift development of groundbreaking antimicrobial strategies and provides a comprehensive review of an array of innovative techniques currently under scrutiny.

MicroRNAs Expression Profile in MN1-Altered Astroblastoma.

Background/objectives: Astroblastoma is a rare glial neoplasm more frequent in young female patients, with unclear clinical behaviors and outcomes. The diagnostic molecular alteration is a rearrangement of the Meningioma 1 () gene. MicroRNAs (miRNAs) are important gene expression regulators with strong implications in biological processes.

Effects of socioeconomic and human-modified landscape variables on medicinal species richness at a macroscale: the case of the Caatinga, Brazil.

Background: Ethnobiological studies at local scales have shown that knowledge of medicinal species tends to decrease as socioeconomic status and the extent of human-modified landscapes increase. However, it remains largely unknown whether these same factors can predict knowledge of useful species at broader scales and whether their interaction might create scenarios that enhance knowledge of medicinal species.

Methods: To address this, we tested whether knowledge of woody medicinal species-measured as the number of species known-is influenced by socioeconomic status, human-modified landscapes, and their interaction.

TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states.

Mutations in cancer risk genes increase susceptibility, but not all carriers develop cancer. Indeed, while DNA mutations are necessary drivers of cancer, only a small subset of mutated cells go on to cause the disease. To date, the mechanisms underlying individual cancer susceptibility remain unclear.

Integrative proteogenomic analysis identifies COL6A3-derived endotrophin as a mediator of the effect of obesity on coronary artery disease.

Obesity strongly increases the risk of cardiometabolic diseases, yet the underlying mediators of this relationship are not fully understood. Given that obesity strongly influences circulating protein levels, we investigated proteins mediating the effects of obesity on coronary artery disease, stroke and type 2 diabetes. By integrating two-step proteome-wide Mendelian randomization, colocalization, epigenomics and single-cell RNA sequencing, we identified five mediators and prioritized collagen type VI α3 (COL6A3).

A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology.

A major goal of cancer biology is to understand the mechanisms driven by somatically acquired mutations. Two distinct methodologies-one analyzing mutation clustering within protein sequences and 3D structures, the other leveraging protein-protein interaction network topology-offer complementary strengths. We present NetFlow3D, a unified, end-to-end 3D structurally-informed protein interaction network propagation framework that maps the multiscale mechanistic effects of mutations.

Plant secondary metabolites against biotic stresses for sustainable crop protection.

Sustainable agriculture practices are indispensable for achieving a hunger-free world, especially as the global population continues to expand. Biotic stresses, such as pathogens, insects, and pests, severely threaten global food security and crop productivity. Traditional chemical pesticides, while effective, can lead to environmental degradation and increase pest resistance over time.