Bovine ocular squamous cell carcinoma (BOSCC) is a common epithelial tumor in Hereford cattle, particularly affecting those with non-pigmented ocular areas. Given its genetic susceptibility, this exploratory study aimed to identify genes and pathways involved in BOSCC development. Ocular tumor samples from five purebreed Hereford cattle and control samples from three healthy animals were obtained. Histopathological analyses and whole transcriptome sequencing were performed. Altered pathways were analyzed with Gene Ontology and KEGG. Histopathological analysis confirmed BOSCC characteristics like keratin pearls, lymphocytic infiltration, and increased mitosis and vascularization. Transcriptome sequencing identified 836 underexpressed and 845 overexpressed genes in tumor tissue compared to healthy controls. Key overexpressed genes included TRPV3, KRT6A, KLK6, MMP13, PROKR2, IL31RA, DHRS9, and MMP9, all linked to keratinocyte proliferation, tumor progression, invasion, and metastasis. Underexpressed genes such as GPHA2, TNN, EMILIN3, BGLAP, TGFB1, MATN4, CHAD, and CLEC3A are involved in maintaining limbal stem cells, cell adhesion, and tumor suppression. These findings provide important insights into the genetic underpinnings of BOSCC, revealing immune response alterations, transcriptional misregulation in cancer, and viral protein interactions that align with tumor development. These preliminary results can guide future genomic studies, aiding in the development of selective breeding programs designed to decrease disease susceptibility in Hereford cattle.
Permanent cover crops offer multiple benefits, including improved soil and plant health and reduced use of agrochemicals. This study examined the impact of under-vine soil management—herbicide weeding (HW) vs. permanent cover crop (PCC) with Festuca arundinacea—on Botrytis Bunch Rot (BBR) caused by Botrytis cinerea, and potential plant defense mechanisms involved. The experiment was conducted in an irrigated experimental vineyard of Tannat grapevines grafted onto SO4, where HW and PCC treatments had been established for more than 10 years. During the 2020/2021 season, BBR incidence and severity, disease progression in inoculated leaves, levels of phytoalexins and antioxidant activity in leaves and berries, berry skin anatomy and rhizosphere microbial communities were evaluated. PCC was associated with lower BBR incidence (p = 0.001) and intensity (p < 0.001) for visible symptoms and latent infections (p = 0.002), and reduced disease progression in inoculated leaves (p < 0.001). Berries from PCC exhibited thicker cuticle (p < 0.001) and epidermis (p = 0.008), higher total polyphenol content in leaves (p = 0.01) and increased ascorbate peroxidase activity in berry skin (p < 0.001). Distinct microbial community compositions were observed at harvest, with differential taxa identified as indicators of each soil management, with a higher abundance of potentially beneficial bacteria in PCC. The enhanced response of grapevines to BBR under PCC management likely results from the combined effect of multiple factors.
Trypanosoma cruzi, the causative agent of Chagas disease, exhibits remarkable genomic variability and possesses an expanded genome rich in multigene families. However, its precise chromosomal composition has remained elusive due to the challenges posed by extensive repetitive regions. In this work, we determined the complete molecular karyotype of the T. cruzi Dm28c strain, which comprises 32 chromosomes. Comparison with two independently isolated Clade A (TcI) strains revealed clear chromosomal homology, indicating that the 32-chromosome karyotype is stable, at least among this clade. T. cruzi is diploid for all chromosomes, except chromosome 16, which is consistently tetrasomic in all strains analyzed. This tetrasomic chromosome is homologous to chromosome 31 of Leishmania major, which is also tetrasomic. Through a comprehensive annotation pipeline, we refined gene content and resolved haplotypes. Comparative analysis of chromosomal architecture revealed that all chromosomes exhibit a conserved distribution of core and disruptive compartments, along with notable conservation in GC content transitions. These findings demonstrate a high degree of structural conservation, challenging the prevailing paradigm of extensive chromosomal rearrangements and high genomic plasticity in T. cruzi. Subtelomeres—enriched in RHS, DGF-1, and TS genes, and depleted in MASP and mucins—constitute a distinct third genomic compartment that is transcriptionally active and represents the primary source of interstrain genomic variability. Furthermore, a reclassification of the TS gene family revealed differential distribution patterns across subtelomeric and disruptive compartments. Altogether, this work defines the complete chromosomal complement of T. cruzi, establishing a robust framework for comparative genomics and enabling detailed investigations into genome organization, antigenic variability, and evolutionary dynamics across strains and clades, opening new avenues for exploring T. cruzi biology, pathogenic diversity, and adaptive mechanisms.
Maintaining thiol redox homeostasis is key for cell viability and development. Therefore, all organisms are equipped with redox systems conformed by redox-active proteins and low-molecular-weight thiols that facilitate target-specific delivery of electrons from NADPH to different (macro)molecules. Trypanosomatids are early branching single-cell eukaryotes harboring a unique thiol-redox system centered on the use of trypanothione (bis-glutathionylspermidine) as a low-molecular-weight thiol-redox cofactor. The irruption of trypanothione in these organisms acted as a major and positive selective pressure that shaped their redox biochemistry. The most radical changes involved the loss of otherwise highly conserved and indispensable glutathione reductase and thioredoxin reductase genes and the concomitant assignment of secondary roles to the related redoxins (glutaredoxins and thioredoxins). Here, we revise the state-of-the-art on the field and provide new research perspectives based on the identification of novel members of the thioredoxin-fold family.
Abstract Physical virology investigates viral particles by focusing on their assembly, stability, mechanics, and interactions with host cells, neutralizing antibodies, and surfaces. Within this field, computational virology is becoming an indispensable pillar, serving as a “computational microscope” that bridges the spatio-temporal scales of viral processes, from individual protein dynamics to capsid assembly and cellular entry. This perspective article offers a critical overview of the current state, challenges, and future directions of computational approaches in physical virology. Our vision is anchored in the research presented at the 2025 EMBO/FEBS Lecture Course on Physical Virology held in Sant Feliu de Guixols, Spain, and complemented by a targeted survey among attendees. We survey the principal methodological frameworks in use, from all-atom to multiscale molecular simulations, mesoscale simulations, and growing integration of artificial intelligence (AI) tools. We also critically examine the central obstacles impeding the field’s progress, including the computational-experimental gap, limited accessibility to simulation data, reproducibility concerns, and systemic gender and geographic inequities. Finally, we outline future perspectives, proposing that integrating physics-aware AI with multiscale simulation frameworks, combined with community-driven data-sharing initiatives, will transform the computational microscope from a descriptive tool into a predictive engine for antiviral therapies, rational vaccine design, and biotechnological innovation.
