Baobab Index

Although Rwanda has increasingly adopted DNA evidence in criminal investigations, paternity testing, and civil applications, comprehensive population-specific autosomal STR reference data remain limited. The first forensic STR study in Rwanda analyzed a relatively small cohort of unrelated individuals using a limited marker panel, and provided an initial allele frequency dataset with restricted population coverage. The present study provides nationally distributed allele frequency data and forensic efficiency parameters for 23 autosomal STR loci. This retrospective study collected 815 autosomal STR profiles generated between 2005 and 2015. The profiles were obtained through database sampling whereby all archived STR genotype data meeting the inclusion criteria were retrieved. Because the study comprised autosomal STR profiles generated over a 10-year period, laboratory records were reviewed to verify the extraction and quantification methods, amplification systems, capillary electrophoresis platforms, allele-calling software, and quality assurance procedures used during the study period. DNA extraction was performed using Chelex® 100 method, followed by Quantification using Quantifiler Duo DNA Quantification kit on the ABI 7500 Real-Time PCR System (only for casework samples), and STR amplification with PowerPlex 16 in combination with PowerPlex ESI 17 Pro and/or PowerPlex ESX 17 kits to obtain a combined panel of 23 autosomal STR loci. All 23 autosomal loci were polymorphic. The number of observed alleles per locus ranged from 7 (D16S539) to 50 (SE33). Forensic parameters indicated high informativeness across loci with very low combined match probability (CMP = 1.7239 × 10⁻³⁰). At most loci, one or two alleles predominated, while the remaining alleles occurred at relatively low frequencies. For example, allele 16 at D3S1358 (0.3392638), allele 7 at TH01 (0.37791411), allele 12 at D13S317 (0.36319018), allele 10 at D7S820 (0.40552147), allele 12 at D5S818 (0.36809816). The present findings strengthen the forensic genetic resources available for Rwanda. Compared with previous Rwandan studies, the expanded characterization of highly polymorphic loci and detection of rare alleles provide more comprehensive allele frequency estimates and strengthen the statistical basis of forensic DNA interpretation.

Manual expert gating remains common practice for defining specific cell populations in flow cytometry data, but increasing numbers of measured parameters and high inter-rater variability limit consistency across studies. Cluster-based approaches use the full marker space to define cell populations more consistently, but their outputs cannot be directly implemented on a cell sorter. Here we develop ConvexGating, an artificial intelligence tool to address this gap by automatically learning interpretable gating strategies for sorting in an unbiased, data-driven manner, generating low-contamination strategies for both known and previously unknown cell populations, including plasmacytoid dendritic cells identified solely as CD57-CD13-CD45RA+ CD123+ cells. We show that ConvexGating derives sorting strategies for CD8+ subtypes and adipose progenitor cell populations, which we validate experimentally by single-cell sequencing of sorted cells. We also demonstrate that the method transfers effectively to Cytometry by Time of Flight and Cellular Indexing of Transcriptomes and Epitopes by Sequencing data and improves marker panel design for cell sorting.

Urinary Tract Infections (UTIs) are among the most prevalent bacterial diseases associated with serious health complications, particularly those caused by antibiotic resistant Uropathogenic Escherichia coli (UPEC). Antibiotic resistant UPEC infections present significant treatment challenges due to multiple pathogenic factors and resistance mechanisms to various antibiotics. Consequently, bacteriophages have emerged as a promising alternative for controlling antibiotic resistant bacterial infection. In this study, a virulent phage (vB_Eco_ZCEC02) was isolated and characterized on both the physical and molecular aspects to combat Extensively Drug Resistant (XDR) UPEC isolate (EC-02). The vB_Eco_ZCEC02 phage, classified within the Autographiviridae family and Kayfunavrius genus, possesses a short non-contractile tail with a narrow host range (EC-02, EC-08, EC-23). The phage exhibits strong temperature stability (from -80 °C to 60 °C) and pH values (from 3 to 12). Also, the time-kill assay showed that vB_Eco_ZCEC02 phage has a potent lytic activity against its host (EC-08) at MOIs of 0.1, 1, and 10 for 8.5 hours. A whole-genome study of the 39,488 bp vB_Eco_ZCEC02 phage revealed 48 predicted Open Reading Frames (ORFs), with no lysogeny, antibiotic resistance, or bacterial virulence genes. Further, vB_Eco_ZCEC02 phage demonstrated high safety in the T-24 cell model at different MOIs (0.1, 1, 10 and100). However, the bacterial-phage dynamics on T-24 cells indicated that lower MOIs (such as 0.1) could induce bacterial reduction without affecting the cell viability, to higher MOIs (such as 100). In conclusion, this study suggests an in vitro, comprehensively characterized virulent phage that can be used to treat antibiotic resistant UPEC infections.

PIWI-associated RNAs (piRNAs) are a diverse and abundant class of small regulatory non-coding RNAs that play central roles in genome regulation and transposon silencing. First identified in germline cells, piRNAs are now also implicated in somatic cell function, stem cell maintenance, immunity, and human disease, particularly cancer and neurodegeneration. This review follows the evolution of piRNA research, highlighting advances in their biogenesis, molecular mechanisms, and multifaceted roles in gene regulation. It also outlines how recent computational developments, especially deep learning and network-based models, together with dedicated databases and web tools, have improved functional and disease-association prediction, and discusses emerging clinical applications of piRNAs as diagnostic biomarkers and therapeutic targets at the frontiers of RNA-based precision medicine.

CBS-B5, isolated from sugar beet rhizosphere, was characterized using an integrated multi-omics approach combining phenotypic assays, whole-genome sequencing, phylogenomic and comparative genomic analyses, and metabolomic profiling. CBS-B5 exhibited visible growth under elevated salinity conditions, demonstrated recovery following heat stress exposure, and strong biofilm formation, but no detectable phosphate solubilization. Whole-genome sequencing revealed a 5.02 Mb genome with 35% GC content, 100% completeness, and 0.03% contamination. Phylogenomic analysis placed CBS-B5 within the Overall, CBS-B5 combines genomic stability, metabolic flexibility, and ecological adaptability. From a One Health perspective, the genomic analyses suggest a limited potential for horizontal dissemination of antimicrobial resistance and virulence determinants. However, the presence of chromosomally encoded toxin-associated genes and β-hemolytic activity indicates that additional biosafety evaluation is required before agricultural application.

SARS-CoV-2 has been deprioritized post-pandemic, especially in Africa. Vaccination in Kenya was conducted using the Wuhan-based vaccines only, which showed reduced neutralization efficacy against Omicron and its sublineages. We performed SARS-CoV-2 immune surveillance in five health facilities within the Kilifi Health Demographic and Surveillance System from November 2024 to March 2026. Patients in the facilities presenting acute respiratory symptoms were recruited and nasopharyngeal/oropharyngeal swabs taken for SARS-CoV-2 RT-PCR. Convalescent plasma from 30 patients with confirmed SARS-CoV-2 RT-PCR positive tests and genome sequences were taken for sero-neutralization assays against the infecting variants LF.7, MV.1, and globally predominant strains, XEC.4, LP.8.1 and XFG. In total 5115 patients were tested and 171 patients (3.4%) were positive for SARS-CoV-2. Cough (91.7%), nasal discharge (74.5%) and fever (55.4%) were the most common symptoms while wheezing (2%) and crackles (2.8%) were rarest. Sequencing revealed circulation of JN.1 omicron sub-lineages, LF.7, MV.1 and XEF. Sera from majority of individuals infected by the dominant variants, LF.7 and MV.1 were able to neutralize infecting variants but not the recently circulating XFG variant 23% (7/30) suggesting that infection with a JN.1 lineage virus alone is not sufficient to prevent re-infection with XFG. Overlapping titer distributions was observed between vaccinated and unvaccinated sera, with no statistically significant difference observed for any variant. Our study demonstrates that SARS-CoV-2 continues to circulate in coastal Kenya causing predominantly mild upper respiratory illness while evolution enabling immune escape. These findings emphasize the importance of integrated genomic and immunological surveillance to track emerging variants, evaluate population-level protection, and inform future vaccine update strategies and public health preparedness efforts.

Prader-Willi syndrome (PWS) is a rare genetic disorder caused by loss of paternal genes on chromosome 15. It is characterised by hyperphagia, obesity, endocrine deficiencies and neurodevelopmental challenges. We report on a boy in his early teens presenting with short stature, early-onset obesity and clinical features consistent with PWS. Genetic testing confirmed maternal uniparental disomy of chromosome 15. Management included food restriction and increased physical activity, resulting in modest improvement. This case highlights the diagnostic and management challenges of PWS in resource-limited settings and underscores the value of comprehensive genetic testing in clarifying phenotypic variations.

Chiari I malformation (CM1), the most common structural hindbrain disorder in humans, is traditionally characterized by the downward displacement of the cerebellar tonsils through the foramen magnum. However, this definition does not reflect the variability in clinical presentation, natural history and treatment response of this disorder. Some individuals with minimal tonsillar descent have severe neurological symptoms and syringomyelia, whereas others with extensive descent remain asymptomatic. Emerging evidence from neuroimaging, developmental biology and human genetics indicates that CM1 is not a single anatomical entity but a spectrum of disorders resulting from disruptions in coordinated growth and homeostasis across the cerebellum, posterior fossa, craniocervical junction, cerebrospinal fluid and neurovascular systems. CM1 may be best understood as a disorder of disrupted developmental scaling, in which the tightly regulated relationships between cerebellar growth and cranial accommodation are altered within a dynamic neurovascular and cerebrospinal fluid environment. In this context, tonsillar herniation is a geometric consequence rather than the primary disease process. This Primer synthesizes current knowledge on the epidemiology, mechanisms, diagnosis and management of CM1 across the lifespan. We highlight advances in neuroimaging, genomics and phenomics that support a shift from anatomy-based definitions towards an integrated genomic-phenomic classification.