Baobab Index

The Lancet Oncology Commission on cancer genomics and precision oncology identified workforce capability, education, and training as major constraints to equitable implementation. As genomic and multi-omic technologies become integrated into cancer care, structured approaches are needed to define competencies across the multidisciplinary workforce. The Core Competency Framework for Precision Oncology was developed using a narrative review and iterative expert-informed framework development process. Competency frameworks, professional standards, policy guidance, organisational reports, and educational literature relevant to genomic medicine, precision oncology, and workforce development were identified through purposive searches of organisational repositories, peer-reviewed literature, and reference list screening between January 2025 and March 2026. Search terms included combinations of "precision oncology", "cancer genomics", "genomic medicine", "competenc∗", "education", "training", and "workforce". Competency domains, role functions, progression structures, and implementation concepts were extracted, compared, and synthesised into shared and role-specific competencies mapped across foundational, intermediate, and advanced levels. The framework was refined through iterative multidisciplinary expert consultation involving contributors to the Lancet Oncology Commission. The framework defines three components; shared core competencies applicable across professional groups; role-specific competencies aligned with functions across the precision oncology pathway; and a progression model reflecting increasing interpretive complexity, autonomy, accountability, and leadership. An associated tiered workforce model links competencies to service contexts and levels of practice, supporting distribution of genomic responsibilities while preserving escalation pathways and governance structures. The framework is designed to be adaptable across professions, health systems, and resource settings. This framework provides an implementation-oriented structure to support workforce development, curriculum design, continuing professional education, role mapping, competency assessment, and service planning in precision oncology. Its application may support scalable, equitable, and sustainable integration of genomics into routine cancer care. No specific funding was received for this work.

Carbapenem non-susceptible Here, we used long-read whole-genome sequencing to characterize 20 clinical Of these isolates, 18 (90%) were resistant or intermediate resistant to imipenem and/or meropenem. Resistance determinants, mobile genetic elements, and virulence factors were strongly lineage structured. In the high-risk ST233 lineage, resistance was marked by extensive duplication of antimicrobial resistance genes across non-contiguous chromosomal loci. Genes including Together, these findings show that carbapenem non-susceptible in South African

Species conservation assessments evaluate extinction risk, and recovery potential, advancing species persistence through guiding resource prioritization and planning. Assessment frameworks, including the International Union for Conservation of Nature Red List and Green Status of Species, typically focus on species as a whole. Importantly, they do not routinely account for genetically distinct units or do not have standardized methods of unit delineation. This limits the representation of genetically distinct components, including adaptive genetic diversity that underpins long-term resilience and recovery. Incorporating standardized within-species units like subpopulations and Evolutionarily Significant Units (ESUs) into species assessments could help address this oversight. However, identifying and delineating such units remain challenging, particularly when molecular data are limited. Here, we propose a flexible framework that integrates molecular and non-molecular evidence to identify both subpopulations and ESUs across taxa, providing a practical tool to incorporate within-species diversity into conservation assessments.

HIV remains among the world's most serious healthcare challenges, with adolescent girls and young women in sub-Saharan Africa at particularly high risk of infection. Bacterial vaginosis (BV) is a key risk factor for HIV acquisition; however, current treatment strategies are limited. Optimal vaginal lactobacilli protect against BV and HIV, largely through immunoregulatory and antimicrobial activities mediated in part by lactic acid. Toward the development of a live biotherapeutic for African women, we sampled 181 isolates of vaginal lactobacilli from 25 BV-negative South African women. Fifty isolates were selected for evaluation of inflammatory responses using vaginal epithelial cells, D- and L-lactate, lactic acid production, and culture acidification. Aside from a single

DNA methylation (DNAm)-based tools are predominantly developed in European ancestry, high-income populations, raising questions on their applicability in diverse and rural settings. To evaluate these tools in a sub-Saharan African low-income context, we analyzed genome-wide DNAm data from 49 dried blood spot samples from adults aged 45+ years in the Malawi Longitudinal Study of Families and Health (MLSFH). Leveraging varying field and storage conditions inherent to this rural setting, we examined their impact on DNAm and found no significant contribution to genome-wide DNAm or predictive sites used in these tools. DNAm-derived estimates of epigenetic clocks and lifestyle biomarkers showed modest to high correlations with self-reported measures. Known associations of epigenetic age acceleration with adverse health behaviors were validated. DNAm-based immune cell type proportions aligned with expected cell-type changes in aging and human immunodeficiency virus. Our findings lay the groundwork for broader use of DNAm-based tools in sub-Saharan African populations.

Mixed-strain We conducted an exploratory whole-genome sequencing (WGS) analysis of 28 drug-resistant Lineage 4 (46%) and Lineage 2 (43%) predominated, with 10.7% of isolates classified as probable mixed-strain candidates. Heteroallelic variants were most frequently observed in This pilot study provides preliminary genomic evidence of mixed-strain infection and heteroresistance in a high-burden rural setting. While these findings highlight the potential role of subclonal diversity in shaping resistance patterns, their clinical and epidemiological relevance remains uncertain due to the absence of patient-level data and limited sample size. Future studies integrating genomic, clinical, and epidemiological data in larger cohorts and incorporating benchmarking against established tools are required to validate these findings and clarify their implications for tuberculosis control.

Many natural products can selectively modulate biological processes, making them prime candidates for drug discovery. However, the complexity of biological samples makes clear attribution of activity to molecules challenging, thereby hampering hypothesis-driven prioritization, with liquid chromatography-tandem mass spectrometry routinely detecting hundreds of molecules per sample. Existing biochemometric tools typically focus on facilitating data-driven exploration to support manual interpretation, rather than more objective, data-driven prioritization and hypothesis generation. Here, we introduce FERMO, a free online dashboard interface for biochemometrics-based prioritization of molecular features and samples. FERMO accepts qualitative and quantitative bioactivity assay data and further integrates group metadata and results from genome mining. FERMO performs automated data processing, organization, and annotation, supporting prioritization with the calculation of custom scores. FERMO supports both exploratory and targeted analysis through efficient interactive visualization, reproducible prioritization, and data filtering. We demonstrate FERMO's utility in benchmarking studies prioritizing bioactive natural products from complex biological matrices. FERMO is freely available at https://fermo.bioinformatics.nl/.

Advanced proteome extraction and characterization techniques for Diuraphis noxia (Russian Wheat Aphid: RWA) enable precise biochemical profiling, where high-quality proteome extraction is critical. This chapter introduces an optimized proteome extraction method for comprehensive profiling of D. noxia, enabling analysis of whole-body and saliva proteomes to advance biochemical and functional characterization. The efficacy of two optimized proteome extraction methods was compared: a nondestructive artificial saliva extraction and a destructive whole-body extraction. The proteome extract concentration was quantified, and Carbohydrate-Active Enzymes (CAZymes) assays were performed to identify and quantify soluble sugar-degrading enzymes and cell wall-degrading enzymes. RWA is a phloem feeder, and this chapter demonstrates that it utilizes an enzyme cocktail consisting of invertase, trehalase, amyloglucosidase, and amylase during feeding. RWA is also equipped with cell wall-degrading enzymes in its proteome, such as cellulases and hemicellulases, which break down the cell wall, allowing the stylet to access the photoassimilates in phloem.

Impacts of alien fungal and fungus-like plant pathogens depend on host interactions, including novel associations with native plants and co-xenic associations with alien plants that do not share the same area of origin, both largely unquantified globally. Combining global distribution and association data, we characterised associations across pathogens' introduced regions, calculated host species richness (SR) and phylogenetic divergence, and examined predictors of novel/co-xenic associations. Novel/co-xenic alien pathogen-plant association records were common (53%) and dominated by widespread generalists. They were found in about one-third of alien pathogens examined, mostly within their known phylogenetic host range. However, 46% of associations remained unclassified due to limited knowledge of pathogen biogeography. Novel/co-xenic associations were more likely for pathogens with larger introduced ranges, wider phylogenetic host range, economically used hosts co-occurring in the region, and host communities phylogenetically similar to the recipient regions' plant community. They were also more likely for host plants with no economic use and restricted native ranges, and in regions with higher plant SR. Novel/co-xenic associations are common and shaped by contact opportunity, phylogenetic host range, and regional community composition. Unravelling fungal and fungus-like pathogen biogeography is key to assessing their full magnitude.