Mount Kenya University Institutional Repository
Not a member yet
5772 research outputs found
Sort by
Improving Gonorrhoea Molecular Diagnostics:Genome Mining-Based Identification of Identical Multi-Repeat Sequences (IMRS) in Neisseria gonorrhoeae Genome
No full textPurpose Curable sexually transmitted infections (STIs) such as Neisseria gonorrhoeae (N. gonorrhoeae) is a major cause of poor pregnancy outcome. The infection is often asymptomatic in pregnant women and a syndrome-based approach of testing leads to missed diagnosis. Culture followed by microscopy is inadequate and time-consuming. The gold standard Nucleic Acid Amplification Tests (NAATs) require advanced infrastructure settings whilst point of care tests are limited to immunoassays with sensitivities and specificities insufficient to accurately diagnose asymptomatic cases. This necessitates the development and validation of assays that are fit for purpose.
Materials and methods Here, we have identified new diagnostic target biomarker regions for N. gonorrhoeae using an algorithm for genome mining of identical multi repeat sequences (IMRS). These were then developed as DNA amplification primers to design better diagnostic assays. To test the primer pair, genomic DNA was 10-fold serially diluted (100pg/μL to 1×10-3pg/μL) and used as DNA template for PCR reactions. The gold standard PCR using 16S rRNA primers was also run as a comparative test, and both assay products resolved on 1% agarose gel.
Results Our newly developed N. gonorrhoeae IMRS-PCR assay had an analytical sensitivity of 6 fg/μL representing better sensitivity compared to the 16S rRNA PCR assay with analytical sensitivity of 4.3096 pg/μL. The assay was also successfully validated with clinical urethral swab samples. We further advanced this technique by developing an iso-thermal IMRS, which was both reliable and sensitive for detecting cultured N. gonorrhoeae isolates at a concentration of 38 ng/μL. Combining the iso-thermal IMRS with a low-cost Lateral Flow Assay, we were able to detect N. gonorrhoeae amplicons at a starting concentration of 100 pg/μL.
Conclusion Therefore, there is a potential to implement this concept within miniaturized, isothermal, microfluidic platforms, and laboratory-on-a-chip diagnostic devices for highly reliable point-of-care testing.This research was supported by the Royal Society, Future Leaders African Independent Researchers (FLAIR) Scheme (FLR\R1\201314) to JG
Differential expression of plasma proteins in pregnant women exposed to Plasmodiumfalciparum Malaria
No full textIn sub-Saharan Africa, pregnant women are at greater risk of malaria infection than non-pregnant adult women. The infection may lead to pregnancy-associated malaria (PAM) because of the sequestration of Plasmodium falciparum-infected erythrocytes in the placental intervillous space. Although there are several tools for diagnosing malaria infection during pregnancy, including blood smear microscopic examination, rapid diagnostic tests, and PCR, there are no tools for detecting placental infection and, by extension, any dysfunction associated with PAM. Thus, PAM, specifically placental infection, can only be confirmed via postnatal placental histopathology. Therefore, there is an urgent need for specific serum biomarkers of PAM. Here, we used the high throughput proximity extension assay to screen plasma from malaria-exposed pregnant women for differentially expressed proteins that can predict PAM or adverse malaria outcomes. Such biomarkers may also elucidate the pathophysiology of PAM. We observed that the IgG Fc receptor IIb (Uniprot ID P31994) and HO-1 (P09601) are consistently highly expressed in malaria-positive samples compared to samples from malaria-negative pregnant women. On the contrary, NRTN (Q99748) and IL-20 (Q9NYY1) were differentially expressed in the malaria-negative women. IL-20 exhibited the highest discriminatory power (AUC = 0.815), indicating a strong association with malaria status. These proteins should be considered for further evaluation as biomarkers of malaria-induced placental dysfunction in pregnant women.This work was funded by InDevelops u-landsfond InDevelops u-landsfond grant to MKM and JG, African Academy of Sciences to JG, and the Swedish Research Council under the grant 2020-02258 to MKM. BNK is an EDCTP Fellow under EDCTP2 programme supported by the European Union grant number TMA2020CDF-3203-EndPAMAL. BNK has also received support from Terumo Life Science Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
Autoantibodies inhibit Plasmodium falciparum growth and are associated with protection from clinical malaria
No full textMany infections, including malaria, are associated with an increase in autoantibodies (AAbs). Prior studies have reported an association between genetic markers of susceptibility to autoimmune disease and resistance to malaria, but the underlying mechanisms are unclear. Here, we performed a longitudinal study of children and adults (n = 602) in Mali and found that high levels of plasma AAbs before the malaria season independently predicted a reduced risk of clinical malaria in children during the ensuing malaria season. Baseline AAb seroprevalence increased with age and asymptomatic Plasmodium falciparum infection. We found that AAbs purified from the plasma of protected individuals inhibit the growth of blood-stage parasites and bind P. falciparum proteins that mediate parasite invasion. Protected individuals had higher plasma immunoglobulin G (IgG) reactivity against 33 of the 123 antigens assessed in an autoantigen microarray. This study provides evidence in support of the hypothesis that a propensity toward autoimmunity offers a survival advantage against malaria
Highly Sensitive Molecular Assay for the Detection of Treponema pallidum infection
No full textIntroduction: According to the World Health Organization (WHO) more than 7 million new Treponema pallidum (T. pallidum) infections were reported among people aged 15–49 years in 2020 globally, the majority of them in developing countries. Syphilis, which is caused by T. pallidum is transmitted through contact with active lesions of a sexual partner or from an infected pregnant woman to her foetus. Gold standard T. pallidum laboratory diagnosis methods include dark-field microscopy, silver staining, direct fluorescence immunoassays and the rabbit infectivity test. However, these tests are associated with false positive or negative results. The gold standard 16S ribosomal (rRNA) gene polymerase chain reaction (PCR) is used for routine amplification of T. pallidum conserved genes. Here we report on an ultrasensitive syphilis diagnostic method, based on de novo genome mining of the T. pallidum DNA to identify identical multi repeat sequences (IMRS) as amplification primers.
Methods: We used genome-mining approaches to find IMRS distributed throughout the T. pallidum genome to design a primer pair that target four repeat sequences. Genomic T. pallidum DNA was diluted from 8.14×104 to 8.14×10− 2 genome copies/l and used as template in the IMRS-based amplification assay. For performance comparison, 16S rRNA PCR assay was employed. Probit analysis was used to calculate the lower limit of detection of the T. pallidum-IMRS PCR and the conventional 16S rRNA PCR assays.
Results: Probit analysis confirmed that the T. pallidum-IMRS primers offered higher test sensitivity of 0.03 fg/L compared to the 16S rRNA PCR (0.714 pg/L). Using the T. pallidum-IMRS primers, we were able to observe considerable isothermal amplification of genomic DNA at a starting concentration of 0.01 pg/µL.
Conclusion: De novo genome mining of T. pallidum IMRS as amplification primers can serve as a platform for developing ultrasensitive diagnostics for Syphilis and potentially a wide range of infectious pathogens
Unraveling the “indirect effects” of interventions against malaria endemicity: A systematic scoping review
No full textThere is an urgent need to maximize the effectiveness of existing malaria interventions and optimize the deployment of novel countermeasures. When assessing the effects of interventions against malaria, it is imperative to consider the interdependence of people and the resulting indirect effects, without which the impact on health outcomes and their cost-effectiveness may be miscalculated. Here, we conducted a scoping review of existing literature on the indirect effects of malaria interventions. We observed a recent increase in both the number of reports and the variety of terms used to denote indirect effects. We further classified eight categories of comparative analysis to identify the indirect effects, proposed common terms for the indirect effects, and highlighted the potential benefits of mathematical models in estimating indirect effects. Improving the study design and reporting the indirect effects of malaria interventions will lead to better informed decisions by policymakers
Sentence Level Analysis Model for Phishing Detection Using KNN
Full text linkPhishing emails have experienced a rapid surge in cyber threats globally, especially following the emergence of the COVID-19 pandemic. This form of attack has led to substantial financial losses for numerous organizations. Although various models have been constructed to differentiate legitimate emails from phishing attempts, attackers continuously employ novel strategies to manipulate their targets into falling victim to their schemes. This form of attack has led to substantial financial losses for numerous organizations. While efforts are ongoing to create phishing detection models, their current level of accuracy and speed in identifying phishing emails is less than satisfactory. Additionally, there has been a concerning rise in the frequency of phished emails recently. Consequently, there is a pressing need for more efficient and high-performing phishing detection models to mitigate the adverse impact of such fraudulent messages. In the context of this research, a comprehensive analysis is conducted on both components of an email message—namely, the email header and body. Sentence-level characteristics are extracted and leveraged in the construction of a new phishing detection model. This model utilizes K Nearest Neighbor (KNN) introducing the novel dimension of sentence-level analysis. Established datasets from Kaggle were employed to train and validate the model. The evaluation of this model’s effectiveness relies on key performance metrics including accuracy of 0.97, precision, recall, and F1-measure
Identification of conserved cross-species B-cell linear epitopes in human malaria: a subtractive proteomics and immuno-informatics approach targeting merozoite stage proteins
No full textHuman malaria, caused byfive Plasmodium species (P. falciparum, P. vivax, P.malariae, P. ovale,andP. knowlesi), remains a significant global health burden.While most interventions targetP. falciparum, the species associated with highmortality rates and severe clinical symptoms, non-falciparum species exhibitdifferent transmission dynamics, remain hugely neglected, and pose a significantchallenge to malaria elimination efforts. Recent studies have reported the presenceof antigens associated with cross-protective immunity, which can potentiallydisrupt the transmission of various Plasmodium species. With the sequencing ofthe Plasmodium genome and the development of immunoinformatic tools, in thisstudy, we sought to exploit the evolutionary history of Plasmodium species toidentify conserved cross-species B-cell linear epitopes in merozoite proteins. Weretrieved Plasmodium proteomes associated with human malaria and applied asubtractive proteomics approach focusing on merozoite stage proteins. Bepipred2.0 and Epidope were used to predict B-cell linear epitopes usingP. falciparumasthe reference species. The predictions were further compared against human andnon-falciparum databases and their antigenicity, toxicity, and allergenicityassessed. Subsequently, epitope conservation was carried out using locallysequencedP. falciparumisolates from a malaria-endemic region in westernKenya (n=27) and Kenyan isolates from MalariaGEN version 6 (n=131). Finally,physiochemical characteristics and tertiary structure of the B-cell linear epitopeswere determined. The analysis revealed eight epitopes that showed high similarity(70-100%) between falciparum and non-falciparum species. These epitopes werehighly conserved when assessed across local isolates and those from theMalariaGEN database and showed desirable physiochemical properties. Ourresults show the presence of conserved cross-species B-cell linear epitopes thatcould aid in targeting multiple Plasmodium species. Nevertheless, validating theirefficacyin-vitroandin-vivoexperimentally is essentialThe author(s) declarefinancial support was received for theresearch, authorship, and/or publication of this article. BK is anEDCTP fellow under the EDCTP2 program supported by theEuropean Union grant number TMA2020CDF-3203-EndPAMAL.JG is supported by the African Academy of Sciences and RoyalSociety FLAIR grant number FLR\R1\201314
Evaluation of the protective efficacy of OlysetPlus ceiling nets for reduction of malaria incidence in children in Homa Bay County, Kenya: a cluster-randomized controlled study protocol
No full textIntroduction Malaria is still a major health problem in sub-Saharan Africa, where 98% of global malaria mortality occurs. In addition, the spread of Plasmodium falciparum with partial artemisinin resistance in East Africa and beyond is a great concern. The establishment of more effective vector control, in addition to the current long-lasting insecticide-treated net (LLIN) distribution program, is an urgent task in these areas. One novel vector control candidate is the Olyset®Plus ceiling nets which can overcome the problems of variations in net use behaviors and metabolic resistance to insecticide in vectors. Our preliminary study suggests the protective efficacy and high acceptability of this tool. With this proposed second trial, we aim to evaluate the impact of this tool in a different eco-epidemiological setting in the lake endemic region of Kenya.
Methods A cluster randomized controlled trial is designed to evaluate the impact of Olyset®Plus ceiling nets in Ndhiwa Sub-County, Homa Bay County, Kenya. A total of 44 clusters will be randomly assigned in a 1:1 ratio to the intervention group (Olyset®Plus ceiling nets) and the control group. The assignment will be accomplished through covariate-constrained randomization of clusters. For the primary outcome of clinical malaria incidence, 38 children from each cluster will be enrolled in a cohort and followed for 18 months. We will also evaluate the effects of the intervention on entomological indicators as well as its acceptance by communities and cost-effectiveness.
Ethics and dissemination Ethics approval was provided by the Mount Kenya University Institutional Scientific Ethics Review Committee. Study results will be shared with study participants and communities, the Homa Bay County Government and the Kenya National Malaria Control Programme. Results will also be disseminated through publications, conferences and workshops to help the development of novel malaria control strategies in other malaria-endemic countries.YKK and MK were financially supported by the Japan Society for the Promotion of Science. AK and JG received support from JICA/AMED joint research project (SATREPS) (Grant no. 20JM0110020H0002), Hitachi Fund Support for Research Related to Infectious Diseases, and Sumitomo Chemical Corporation. The funding bodies play no role in the study design, data collection, analysis, interpretation, and publication
The Lived Experiences of Individuals and Coping Strategies in the Context of Internet Gaming Disorder: A Qualitative Study Within Higher Education Setting in Uganda
No full textBackground: Internet Gaming Disorder (IGD), recognized as a mental disorder in both the Diagnostic and Statistical Manual (DSM-5) and International Classification of Diseases (ICD-11), poses significant threats to physical, social, and mental well-being. This study aims to delve into the experiences of individuals grappling with IGD.
Methods and Materials: The study employed an interpretive phenomenology, conducting interviews with 10 graduate students at Makerere University. Participants were purposefully sampled until data saturation was achieved during interviews, which took place between May and July 2023. An interview guide facilitated data collection (Supplementary File 1), and thematic analysis was manually applied for data interpretation, utilizing intuition and imaginative approaches.
Results: The findings revealed that the majority of participants started gaming during childhood, starting with offline games. Exposure to gadgets and games, idle time, and stress emerged as key triggers for IGD. Participants reported experiencing sleep deficits, deteriorating interpersonal relationships, declining job performance, unhealthy eating habits, academic challenges, and wastage of money and time. The study also identified strategies employed by participants to mitigate their gaming behaviors, such as refraining from purchasing data, seeking support from friends, and uninstalling the game app, although relapses were common.
Conclusion: The study highlights a global pattern of early initiation into gaming, emphasizing the need for early intervention and preventive measures. Factors such as easy accessibility and affordability of gaming platforms, idleness, and stress play significant roles in motivating internet gaming, contributing to a higher prevalence among the studied population. The research underscores the adverse effects of IGD on students, affecting academic performance, interpersonal relationships, and job performance. Notably, participants demonstrate agency in addressing IGD through practical coping strategies, including controlling data access, seeking social support, and uninstalling games. These coping mechanisms provide valuable insights into the complex nature of addressing IGD and form a basis for developing targeted interventions and support systems within the higher education setting in Uganda
Factors Contributing to the Prevalence of Prenatal Depression among Adolescent Mothers Seeking Ante- Natal Care at Wajir County Referral Hospital
No full textThis thesis discusses the significance of prenatal depression among adolescent mothers, focusing on its prevalence and associated factors. Prenatal depression, a type of clinical depression occurring during pregnancy, affects both mothers and children. The study highlights negative outcomes such as decreased maternal confidence and increased likelihood of subsequent pregnancies. Global prevalence rates, particularly higher in Low- and Middle-Income Countries (LMICs), are noted. In the African context, cultural and social factors exacerbate mental health challenges among pregnant and postpartum adolescents. The research aims to address prenatal depression in Wajir County, Kenya, citing the lack of studies in Africa and the need for tailored interventions. Objectives include determining prevalence and identifying associated factors. Factors contributing to prenatal depression include economic status, socio-demographics, cultural aspects, adverse life events, and healthcare-related issues. The study utilizes a hospital-based case-control design, recruiting adolescent mothers from Wajir County Referral Hospital. Data collection involves questionnaire administration and EPDS scale assessment. Findings reveal a prevalence of 33.3%, with socio-cultural, maternal, and healthcare factors influencing depression rates. Recommendations include routine screening, community-based awareness campaigns, targeted interventions, enhanced healthcare training, and advocacy for mental health integration in antenatal care