Baobab Index

To evaluate the diagnostic yield of integrated molecular autopsy (IMA) by combining deep post-mortem phenotyping with exome (ES) and targeted genome sequencing (GS) for prenatally detected anomalies. This retrospective study evaluated 28 perinatal cases (22 fetuses, six neonates) with severe anomalies, normal first-tier genetics, and high consanguinity (42.9%). Deep phenotyping (radiography, macroscopy, histopathology) guided singleton ES (n = 28), supplemented by GS (n = 14) for exome-negative rescue or technical validation, and trio Sanger confirmation. The inter-method agreement between morphological hypotheses and molecular diagnoses was assessed using Cohen's Kappa. The IMA established a molecular diagnosis in 19 of 28 cases (67.9% yield), with system-specific yields of 100% in skeletal dysplasias (5/5), 62.5% in central nervous system defects (5/8), and 60% in cardiovascular malformations (3/5). Autosomal recessive inheritance accounted for 52.6% (10/19) of solved cases. The inter-method agreement was substantial (Cohen's Kappa = 0.81, p < 0.001). Phenotypic expansions occurred in six cases (21.4%), while nine cases (32.1%) remained unexplained. The IMA framework achieved a high diagnostic yield of 67.9% within a highly selected, consanguineous cohort. Although clinical yield and concordance are influenced by selection biases, comprehensive post-mortem phenotyping remains essential to resolve atypical presentations, guide variant prioritization, and optimize reproductive counseling.

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide and a public health concern, with 75% of cases considered preventable. Biannual liver ultrasound, with or without serum alpha-fetoprotein, is recommended as surveillance for patients at high risk of HCC. While the rationale for surveillance is strong and it continues to be recommended by all professional societies, there is ongoing debate about the strength and relevance of the evidence supporting surveillance for all populations with cirrhosis. European surveillance uptake is suboptimal, with high rates of late-stage diagnosis and subsequent poor prognosis. In this paper, we provide an overview of surveillance focusing on Europe and draw lessons from across the world. We discuss lessons learnt from the implementation of national and coordinated surveillance programmes in Asian countries and the global challenges resulting from the changing epidemiology of chronic liver disease, particularly the rise of MASLD. We consider the patient perspective, including stigma and inequalities in access and delivery. We explore emerging approaches to surveillance, including biomarkers, abbreviated MRI and risk-stratification, which may improve early diagnosis. Finally, we address the lack of funding and political willpower arising from an insufficient evidence base.

The nuclear, internal transcribed spacer (ITS) and mitochondrial cox1 markers are widely used to differentiate Schistosoma haematobium from its livestock counterparts, S. bovis and S. curassoni. Schistosoma isolated from humans with ITS and cox1 alleles from livestock parasites are typically inferred to be zoonotic infections and those with heterozygous ITS alleles (suggesting mixed species ancestry) are classified as recent hybrids. These classifications assume that the ITS and cox1 markers accurately reflect genome-wide ancestry. Here, we evaluated the reliability of this classification scheme by genotyping ITS and cox1 from 132 parasites isolated from human urine, and from 37 adult schistosomes collected from cattle at 14 Nigerian locations. We also genome sequenced each sample to empirically determine livestock schistosome ancestry. ITS/cox1 genotyping suggested extensive recent hybridization and zoonotic infection. Among parasites from humans, 10.1% carried both S. curassoni and S. haematobium ITS, consistent with F1 or early generation hybrids, 21% had livestock schistosome markers at both cox1 and ITS suggesting zoonotic infection, while 13.7% carried S. bovis cox1 alongside mixed S. curassoni and S. haematobium ITS, suggesting more complex ancestry. Genome sequencing revealed a very different picture. All parasites from humans formed a tight cluster regardless of ITS or cox1 genotype, while all worms from cattle were well differentiated. We found no schistosomes containing 50% livestock parasite ancestry consistent with F1s. Instead, we observed regionally varying levels of S. bovis introgression, with modest levels in southern Nigeria (mean = 4.9%) and low levels in northern Nigeria (mean = 0.06%). These results demonstrate that: (i) two-locus genotyping is uninformative for detecting zoonotic infection or recent hybridization between S. haematobium and livestock schistosomes and (ii) previous data generated using this approach requires reinterpretation. These findings reveal the limitations of widely-used approaches for documenting zoonotic infection and hybridization between S. haematobium and livestock schistosome species.

Drug-resistant tuberculosis (TB) hinders global TB control. Rifampicin-resistant TB (RR-TB) prevalence, in Côte d'Ivoire, was 4.6% (95% confidence interval [95% CI]: 2.4-6.7) for new cases and 22% (95% CI: 13.7-30.3) with retreatment cases in 2016. The TB drug resistance survey (DRS) conducted in 2023 aimed to determine the updated prevalence of resistance among new, previously treated TB cases and to characterize the genotypes of circulating Mycobacterium tuberculosis strains. A nationwide, cluster-based cross-sectional DRS was conducted in a 6-month timeframe in 44 health facilities across the country, grouped into 45 clusters according to the World Health Organization guidance. Bacteriologically confirmed pulmonary TB cases were recruited after giving informed consent. Xpert ® MTB/RIF Ultra, Hain MTBDR plus and MTBDR sl were carried out on sputum samples. All samples with resistance detected and 10% of rifampicin (RIF) susceptible TB cases were cultured in liquid medium with Mycobacterium growth incubator tube (MGIT) (MGIT 960). Phenotypic drug susceptibility testing was performed for isoniazid (INH), RIF, amikacin (AMK), moxifloxacin, levofloxacin, clofazimine, bedaquiline, and linezolid. Whole-genome or targeted next-generation sequencing was conducted on 120 selected drug-resistant and susceptible strains. KoboCollect v2013.1.2 was used for data collection and storage. For statistical and cluster analysis, STATA 19.5 and core genome multilocus sequence typing in Ridom SeqSphere + were used, respectively. 1024 participants were enrolled, 947 (92.5%) were new cases. INH monoresistant TB prevalence was 4.8% (95% CI: 3.6-6.4) in new cases and 5.6% (95% CI: 1.5-18.8) in retreatment cases. Multidrug-resistant TB (MDR-TB) prevalence was 2.5% (95% CI: 1.7%-3.8%) in new and 14.1% (95% CI: 7.0%-26.5%) in previous treated cases. Among RR-TB, MDR-TB prevalence was 89.5% (95% CI: 73.8-96.3), of whom 2 pre-extensively drug-resistant (XDR) TB and 1 XDR-TB were detected. Sequencing revealed a predominant circulation of lineage 4.6.2.2 and 4.1 (28% each) following by lineage 6 (11%). Progress has been made in combating TB drug resistance in Côte d'Ivoire compared to the previous DRS. Molecular tools have permitted to detect heteroresistance or mixed infection and the existence of circulating virulent strains associated with alarming rates of drug resistance.

Repeated freeze-thaw cycles represent a critical stress factor in frozen food processing, leading to a significant decline in the survival and fermentation performance of lactic acid bacteria. This study investigated the tolerance mechanism of The results showed after freeze-thaw treatment, QZW5 retained an 85.20%survival rate with a 14.80% reduction in growth rate, accompanied by gradual fermentation pH decline. Its antibacterial activity decreased markedly; for example, the inhibition zone against

Zebu cattle (Bos indicus) represent a critical livestock resource in the arid and semi-arid regions, known for their disease resistance, heat tolerance and physiological hardiness. Despite their agricultural importance, the precise matrilineal evolutionary history, genetic diversity and demographic trajectory remain incompletely resolved within the broader context of South Asian cattle domestication. This study explores the phylogeographic patterns and maternal lineage diversity of zebu cattle through complete mitochondrial genomes (mtDNA), the D-loop, and hypervariable regions from 50 individuals of 10 indigenous Pakistani breeds. These breeds were classified into three regions: North Pakistan, Central Pakistan/Punjab (Indus Valley region) and South Pakistan (the site of Mohenjo-Daro). Our data include 183 newly generated sequences and are supplemented with comparative datasets from 19 countries. Analysis reveals South Pakistan, especially the Mehrgarh area, as a key potential domestication epicentre, exhibiting highest nucleotide diversity (π = 0.01480) across Asian zebu populations, accompanied by ancient maternal lineages estimated to date back approximately 2.17 million years. Highest haplotype diversity was observed in Punjab (0.901 ± 0.014) followed by Southern Pakistan (0.893 ± 0.026). Phylogenetic and demographic analyses (mismatch distribution, Fu's Fs) further support an early dispersal scenario (I1 haplogroup) originating in Mehrgarh and radiating through the Indus Valley into broader Asian lineages. These findings enhance our understanding of the domestication origins of Bos indicus, its implications for breed conservation and sustainable livestock management.

The monkeypox virus (MPXV) has become a global health threat, with rising cases reported globally. Since its re-emergence in 2017, Nigeria has experienced a sustained outbreak, underscoring the critical need for robust surveillance mechanisms to identify transmission dynamics. Despite this urgency, data regarding MPXV seroprevalence among patients seeking medical care in Nigeria remains scarce. MPXV may be underreported because its clinical symptoms overlap with those of other common causes of fever. We assess MPXV seroprevalence among febrile patients across multiple Nigerian healthcare facilities using A35R and A29L antigens in a Luminex bead-based immunoassay. The study enrolled 245 febrile individuals in Ondo, Benue, Plateau, and Osun States from June 2023 to July 2024. Plasma samples were analyzed for antibodies targeting MPXV A35R and A29L antigens. A manual-based 3-standard-deviation threshold method and an R-based SeroNIST analytical framework were used. Statistical analyses assessed assay reliability and identified potential risk factors associated with MPXV exposure. Both antigens showed comparable exposure patterns (

Soil salinity is an issue in agriculture. It also has a vast effect on decreasing agrarian productivity, as it limits the availability of nutrients and results in physiological stress on plants. Traditional methods of managing and treating soil cannot be used in saline and mineral-deficient conditions. As a solution to these problems, fungi are important biological agents for sustainable solutions. This review concentrates on fungal diversity and its aptitude to alleviate salinity stress and enhance nutrient availability through mineral solubilization and mobilization and, in selected plant-fungus associations, facilitate subsequent nutrient acquisition by the plant. The adverse effects of salinity on plant growth, nutrient uptake, and overall physiological performance are discussed, and the mechanisms of stress mitigation and enhancement of mineral availability mediated by fungi are described, such as organic acid synthesis and ion homeostasis. Plant-fungal interactions enhance salinity stress resistance, as discussed in this review. Moreover, developments in the field of molecular and omics-based studies cannot be overestimated in terms of acquiring an understanding of the genetic and molecular pathways of plant-fungal interactions in saline and mineral-deficient environments.

Stroke and dementia are leading causes of death and disability worldwide, requiring enhanced preventive strategies. Glucagon-like peptide-1 receptor agonists (GLP-1RA), widely used for type 2 diabetes (T2D) and obesity, have demonstrated pleiotropic effects, including cardiovascular benefits, with mounting evidence also suggesting potential beneficial effects on brain health. The objective of this study was to investigate the genetically proxied effect of GLP-1RA on stroke, Alzheimer disease (AD), and related endophenotypes, in a cross-ancestry setting. We conducted a 2-sample Mendelian randomization (MR) study using both a locus-based and a protein quantitative trait loci (pQTL)-based approach. The study leveraged summary statistics from large-scale genome-wide association studies (GWAS). These GWAS comprised participants of European, East-Asian, and African ancestry with and without T2D, stroke, and AD, and with measurements of fasting glucose, glycated hemoglobin, stroke, and AD endophenotypes. Sample size ranged from 3,026 to 1,812,017 individuals. Genetically proxied GLP-1RA exposure was instrumented using independent T2D-associated variants ( In Europeans, locus-based MR indicated significant protective associations of GLP-1RA with any stroke and ischemic stroke ( GLP-1RAs may confer protective effects against stroke (especially ischemic and cardioembolic) and AD risk, across ancestries. These findings warrant further investigation in experimental models and clinical trials to confirm benefits on brain health and understand underlying mechanisms.