Baobab Index

Illegal wildlife trade (IWT) is one of the largest global illegal activities, and it negatively affects biodiversity and sustainable development worldwide. DNA barcoding coupled with high-throughput sequencing (i.e., metabarcoding) is useful in identifying taxa affected by IWT and has been used routinely for decades. However, for countries lacking laboratory infrastructure, sequencing units, and trained staff, the application of DNA barcoding tools in conservation is limited and depends on slow sample transport processes and molecular analyses carried out abroad. Guinea-Bissau, on the West African coast, has one of the lowest human development indices in the world and is a biodiversity hotspot threatened by IWT. We explored the potential use of inexpensive and portable miniaturized laboratory equipment (MLE) and DNA barcoding tools to improve training in conservation genetics and identification of traded species. We tested these technologies in tissue samples collected at different times and contexts in Guinea-Bissau and used 3 primer pairs amplifying mitochondrial DNA fragments. We successfully identified 33 tissue samples to the species level; thus, MLE may accelerate the use of DNA and metabarcoding methods in countries that have low research funding and limited infrastructure. The use of these technologies has the potential to advance the discipline of conservation genetics in Guinea-Bissau and other countries and to train students and employees of government agencies dedicated to investigating environmental crimes. Uso de equipo de laboratorio miniatura y códigos de barras de ADN para mejorar la disciplina de la genética de la conservación e identificar especies comerciadas ilegalmente Resumen El comercio ilegal de vida silvestre (CIVS) es una de las actividades ilegales más importantes a nivel mundial y afecta negativamente a la biodiversidad y al desarrollo sostenible en todo el mundo. El código de barras de ADN, junto con la secuenciación de alto rendimiento (es decir, la meta codificación de barras), es útil para identificar los taxones afectados por el CIVS y se ha utilizado de forma habitual durante décadas. Sin embargo, en los países que carecen de infraestructura de laboratorio, unidades de secuenciación y personal calificado, la aplicación de las herramientas de código de barras de ADN en la conservación es limitada y depende del transporte lento de muestras y análisis moleculares realizados en el extranjero. Guinea‐Bissau, en la costa occidental de África, tiene uno de los índices de desarrollo humano más bajos del mundo y es un punto crítico de biodiversidad amenazado por el CIVS. Exploramos el uso potencial de equipos de laboratorio miniaturizados (ELM) y herramientas de código de barras de ADN, económicos y portátiles, para mejorar la formación en genética de la conservación y la identificación de especies comercializadas. Probamos estas tecnologías en muestras de tejido recogidas en diferentes momentos y contextos en Guinea‐Bissau y utilizamos tres pares de primers que amplifican fragmentos de ADN mitocondrial. Identificamos con éxito 33 muestras de tejido a nivel de especie; por lo tanto, el ELM puede acelerar el uso de métodos de ADN y la meta codificación de barras en países con escasa financiación para la investigación e infraestructuras limitadas. El uso de estas tecnologías tiene el potencial de hacer avanzar la disciplina de la genética de la conservación en Guinea‐Bissau y otros países, y puede utilizarse para formar a estudiantes y empleados de organismos gubernamentales dedicados a la investigación de delitos ambientales. 【摘要】 非法野生动植物贸易(illegal wildlife trade, IWT)是全球最大的非法活动之一, 对全球生物多样性和可持续发展造成了负面影响。DNA条形码与高通量测序相结合(即宏条形码), 有助于识别受IWT影响的类群, 因此几十年来一直得到常规应用。然而, 对于缺乏实验室基础设施、测序设备和训练有素的工作人员的国家来说, DNA条形码工具在保护方面的应用仍很有限, 且依赖于缓慢的样本运输过程和在国外进行的分子分析。几内亚比绍位于西非海岸, 是全球“人类发展指数”最低的国家之一, 也是受IWT威胁的生物多样性热点地区。本研究探讨了平价的便携式微型实验室设备(miniaturized laboratory equipment, MLE)和DNA条形码工具在改善保护遗传学培训和贸易物种鉴定中的潜在应用。我们利用不同时期和条件下在几内亚比绍采集的组织样本, 测试了这些技术的可行性, 并使用了三对引物对线粒体DNA片段进行了扩增。我们成功地对33个组织样本进行了物种鉴定;因此, MLE有利于加快DNA条形码和宏条码方法在研究经费不足、基础设施有限的国家的应用。这些技术的使用有可能推动几内亚比绍和其他国家保护遗传学学科的发展, 并可用于培训专门研究调查环境犯罪的学生和政府机构工作人员。【翻译:胡怡思;审校:聂永刚】.

Human breast milk contains RNA in various fractions, including milk cells and milk fat globules (MFG), making it a valuable resource for studying lactation physiology. However, preserving RNA integrity, especially in low-resource or at-home collection settings, is challenging due to rapid RNA degradation.This study aimed to evaluate RNA preservation methods for milk cells and MFG, using RNAlater for stabilization before freezing. Human milk samples (n = 26) were collected from lactating participants and either frozen (standard practice) or mixed with RNAlater (1:1, v/v) before freezing. RNA was extracted from separated cellular and MFG fractions and assessed for concentration, quality (RNA quality number-RQN and 28 S/18S ratio), and gene expression (ACTB, LALBA, PRLR, PTPRC) using RT-qPCR.Samples preserved with RNAlater showed significantly improved RNA integrity, particularly in the MFG fraction, compared to those frozen without RNAlater. Gene expression was largely stable across preservation methods. Delays in mixing with RNAlater led to declining RQN values in milk cell fractions, underscoring the need for prompt stabilization. Lastly, we show that this method can be used in low-resource countries by extracting RNA from samples collected in a randomized clinical trial in Guinea-Bissau and shipped to the US for analysis. This procedure led to improved yield and integrity of these samples.These findings demonstrate that RNAlater pre-freezing stabilization enhances RNA quality and yield, and supports its use for milk gene expression analysis. This approach provides a practical, scalable solution for RNA preservation in clinical and field research, including remote and low-resource settings, as it requires minimal experience and equipment.

Lassa fever remains a major public health threat in West Africa, requiring coordinated scientific, policy, and financing responses. Regional scientific convenings are increasingly used to connect research evidence with policy action, yet their contribution to epidemic preparedness is not well documented. We conducted a qualitative health systems and policy analysis of the 2nd ECOWAS Lassa Fever International Conference (ELFIC 2025) in Abidjan, Côte d'Ivoire. Data sources comprised 302 scientific abstracts, plenary and ministerial session records, and the official Ministerial Joint Communiqué. Using the conference's six thematic pillars as a deductive framework, we conducted a thematic content analysis and synthesized findings into four domains: scientific advances; surveillance and laboratory systems; policy and financing insights; and cross-cutting lessons for regional preparedness. Progress was noted in diagnostics, therapeutics, vaccine development, decentralized laboratory capacity, genomic surveillance, and digital reporting. Persistent gaps remain at sub-national and community levels, in surveillance coverage, workforce capacity, and operational readiness. A major outcome was the Ministerial Joint Communiqué endorsing regional co-financing for Lassa fever vaccine development. ELFIC 2025 demonstrates the role of regional scientific platforms in aligning evidence with policy commitments. Sustained impact will require institutionalized coordination, strengthened accountability, and targeted investments in frontline capacity.

Infectious skin diseases in nonhuman primates are of importance due to their zoonotic transmission potential, especially in biodiversity rich areas where human-wildlife interactions are frequent. Here, we report the presence of a skin disease in unhabituated wild Guinea baboons (Papio papio) inhabiting an agroforest landscape in Cantanhez National Park, Guinea-Bissau, exclusively using non-invasive surveillance methods. We combined 107 georeferenced baboon presence points, camera trap footage obtained during 2224 camera trap days, with molecular analysis of 272 biological samples collected opportunistically. Given the presence of leprosy in western chimpanzees (Pan troglodytes verus) in Cantanhez and yaws in nonhuman primates in Sub-Saharan Africa, we tested the samples using specific PCR protocols for Mycobacterium leprae and Treponema pallidum as possible causative agents. We estimated the minimum ranging area of the baboons, which overlapped with 27.25% of the home range of a chimpanzee community affected by leprosy. We identified at least seven baboons with lesions on the muzzle, eyebrow, ears, tail, hindquarters, joints, hands and/or feet. Clinical signs partially aligned with descriptions of nonhuman primates affected by leprosy and yaws. Molecular analysis failed at conclusively showing the presence of either suspected pathogen. Longitudinal monitoring and additional sampling are needed to identify the causative agent, which may be relevant to conservation and public health, as baboon meat is consumed by humans in Guinea-Bissau.

Africa provides a distinctive context for twin research, with high rates of dizygotic twinning and remarkable population diversity. Yet, the region remains underrepresented in global twin and genetic association studies. Likewise, more data is also needed on overall twin health in the region, particularly in early life when neonatal and infant twin mortality has historically been very high. The African Twins and Multiple Births Research Foundation (ATMBRF), established in 2025 by Malcolm Odion Eremionkhale, addresses this gap through research coordination, advocacy, and infrastructure development. Central to its mission is the African Twin Registry (AfTR), a continent-wide initiative designed to identify and follow twins and higher order multiples via standardized protocols and record linkage methodologies. By integrating registry data with civil and health records, the AfTR will enable comprehensive cohort construction and longitudinal analyses across diverse settings. Its approach aims to combine community engagement, prospective and retrospective recruitment, and anticipated incorporation of genomic data. The AfTR's data will inform clinical guidelines, health system planning, and culturally grounded interventions addressing multiple births in Africa. This initiative will advance global twin and genetics research by incorporating genetically diverse populations and enhancing the evidence base for precision medicine.

Clustering algorithms are widely used for phenotypic characterization and germplasm management, particularly in data-scarce crops such as neglected and underutilized species (NUS) that lack genomic resources. However, their performance under biologically realistic conditions remains poorly understood. Standard clustering methods commonly applied in crop research often assume distinct, isotropic, and homogeneous clusters, assumptions rarely satisfied in real-world phenotypic datasets. We developed a flexible and empirically calibrated simulation framework, using phenotypic data from West African fonio (Digitaria exilis), to benchmark the performance of eleven clustering algorithms under both idealized and realistic scenarios. Our simulations integrated heterogeneous trait distributions (normal, gamma), strong inter-trait correlations (up to r = -0.84), heteroscedasticity, and moderate population structure (mean Pst = 0.16 ± 0.001, achieved through iterative calibration). Each scenario was replicated 100 times, with clustering accuracy evaluated using external (ARI, NMI) and internal (Silhouette, Davies-Bouldin) validation metrics under standardized conditions. The results revealed consistently poor algorithm performance under realistic conditions (e.g., ARI < 0.07), including for widely used methods in Neglected and Underutilized Species (NUS) research such as K-means, GMM, and PAM. Notably, conventional validation metrics failed to detect biologically meaningful structure revealed by geometric diagnostics, highlighting a critical methodological limitation. Performance markedly improved under idealized conditions, validating our simulation framework. These findings highlight the risk of overinterpreting clustering outputs from weakly structured phenotypic datasets and expose key limitations in current biodiversity analysis practices, particularly those guiding plant genetic resource conservation programs. We provide an open-source R-based diagnostic tool, with parameter specifications to assist practitioners in selecting reproducible and interpretable clustering approaches for germplasm management and biodiversity assessment in data-scarce crops.

This study reports the draft genome of an

From August to October 2022, a therapeutic efficacy study of Niger's first-line antimalarial, artemether-lumefantrine (AL), was conducted in four sites (Aderbissinat, Boboye, Aguié, and Baban Tabki) to evaluate its therapeutic efficacy and investigate for molecular markers of antimalarial drug resistance. Children aged 5 to 15 years old with uncomplicated malaria were assessed in a 28 day in vivo efficacy study. Genotyping using three markers (msp1, msp2 and the PolyA microsatellite) and match counting using the WHO three-out-of-three algorithm, were used to distinguish recrudescences from new infections. A two-out-of-three algorithm was also utilized as a sensitivity analysis. PCR uncorrected and corrected efficacy results at day 28 were calculated. Resistance markers were analysed by next-generation sequencing. Uncorrected treatment efficacies were 62.0% (95% CI 54-74) in Aderbissinat, 95.4% (95% CI 91-100) in Aguié, 98.7% (95% CI 96-100) in Boboye, and 50.6% (95% CI 42-62) in Baban Tabki. After PCR correction, AL efficacy was 100%, 97.5%, 100%, and 93.5%, respectively. Marker analysis revealed a high prevalence of S108N, C59R, and N51I mutations in the pfdhfr gene, and S436A and A437G mutations in the pfdhps gene. No validated or candidate pfkelch13 mutations were observed. In all four sites evaluated, AL retains therapeutic efficacies above the 90% WHO-recommended threshold using the primary three-out-of-three match criteria. In Aguié and Baban Tabki, efficacy remained above the threshold with certain match criteria and statistical approaches but fell below the cutoff using two-out-of-three matching and per-protocol methods, suggesting emerging efficacy concerns in southern parts of the country.

Nigeria ranks second in Africa for the highest number of mpox cases. This study aimed to evaluate the knowledge and awareness of mpox among Nigerians living in endemic regions and their willingness to accept the mpox vaccine when available. we conducted a cross-sectional study using a multi-stage sampling technique. Data was collected from eligible individuals in Bayelsa, Delta, Lagos, and Rivers, Nigeria, between September 1 and November 30, 2023, using a standardized structured questionnaire. Descriptive analysis was conducted, and inferential analyses were performed using binary logistic regression (p < 0.05). five hundred and twenty-four (524) persons with a mean age of 33.9 ± 10.4 years participated in this study. Fifty-eight percent (58%) were aware of mpox, and 15.5% of participants had heard about the mpox vaccine. Participants from Delta State were 70 percent less likely, while those from Lagos and Rivers States were 2.5 times and 1.04 times, respectively (OR= 2.48, p=0.012; OR= 1.04, p=0.89) more likely to receive the mpox vaccine when compared with participants from Bayelsa State. Eighty-four (84.5%) of respondents were unwilling to take the vaccine if they had to pay for it. although many people were aware of the mpox infection, only a few people were aware of the vaccine. Health intervention programs to improve knowledge of mpox and increase the uptake of mpox vaccines should be co-designed with community stakeholders, while mpox vaccines, when available, should be made accessible at subsidized or at no cost to Nigerians to improve uptake.

African trypanosomes exhibit significant genetic diversity but share similar morphological characteristics, making effective surveillance and diagnosis challenging with conventional microscopy and other detection methods. While polymerase chain reaction (PCR) offers enhanced specificity and sensitivity, it requires DNA extraction, making it time-consuming and costly, especially for resource-limited regions such as ours (Africa). Additionally, amplification using DNA from the host's whole blood often fails due to the presence of polymerase inhibitors or low parasite DNA, particularly during chronic infections. This study introduces a novel PCR method that overcomes these challenges by using purified trypanosome cells as templates, bypassing the need for DNA extraction. Trypanosoma brucei brucei cells were isolated from mice blood using DEAE-cellulose anion-exchange chromatography and directly used in PCR amplification of the ITS-1 ribosomal RNA gene. Successful amplification was achieved with as few as 1.25 × 10⁵ isolated trypanosome cells, while gDNA extracted from parasitized blood failed to amplify. This cost-effective and highly sensitive method improves species differentiation and enhances diagnostic capabilities, especially in cases of low parasitemia. The approach represents a significant advancement in trypanosome diagnosis, offering a faster, affordable, and reliable alternative to traditional methods. These findings support improved epidemiological surveillance and may contribute to the World Health Organization's goal of eliminating African trypanosomiasis, a disease that continues to present major economic and public health challenges in Africa. A graphical abstract of this study is presented in Figure 1. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Isolation of Trypanosoma brucei brucei from parasitized blood Basic Protocol 2: PCR characterization of isolated T. brucei brucei.