Biology subjects

Ibrahim, A.

Publications and source records attributed to Ibrahim, A..

45 records · Page 3Linked to original sources

bioRxiv2020

A mixed model approach for estimating drivers of microbiota community composition and differential taxonomic abundance

O_LINext-generation sequencing (NGS) and meta-barcoding approaches have revolutionized understanding of within-host communities, such as the gut microbiome, in humans and laboratory animals. The application of such approaches in wild animal populations is growing, but there is a disconnect between the widely-applied generalised linear mixed model (GLMM) approaches commonly used to study phenotypic variation and the statistical toolkit from community ecology which is typically applied to meta-barcoding data. C_LIO_LIHere, we describe and illustrate a novel GLMM-based approach for analysing the taxon-specific sequence read counts derived from standard meta-barcoding data. This approach allows us to decompose the contribution of different drivers of variation in community structure (e.g. year, season, individual host), via interaction terms in the random effects structure of the model. We also show how these models can be used to determine the degree to which specific taxa or taxonomic groups are responsible for variance attributed to different drivers. C_LIO_LITo illustrate this approach, we applied it to two cross-sectional meta-barcoding data sets from the Soay Sheep population of St. Kilda. The GLMM approach yielded results that were in agreement with more classical approaches from community ecology, showing that variation the gut microbiota community in these sheep was better explained by age group than by season. We were able to quantify the contributions of different sources of variation to community structure, and also to drill down into the model predictions to show that the age effects we observed were principally due to increases in taxa of the phyla Bacteroidetes and declines in taxa of the phyla Firmicutes. C_LIO_LIOur proposed models offer a powerful new approach to understanding the drivers of variation in estimates of community structure derived from meta-barcoding data. We discuss how our approach could be readily adapted to allow researchers to estimate that contribution of host genotype, environment, and microbial/parasite phylogeny to observed community structure, and thus provide a powerful means to answer emerging questions surrounding the ecological and evolutionary roles of within-host communities. C_LI

evolutionary biology↗

bioRxiv2020

An evolutionarily diverged mitochondrial protein controls biofilm growth and virulence in Candida albicans

A forward genetic screening approach identified orf19.2500, as a gene controlling Candida albicans biofilm dispersal and biofilm detachment. Three-dimensional (3-D) protein modeling and bioinformatics revealed that orf19.2500 is a conserved mitochondrial protein, structurally similar to, but functionally diverged from, the squalene/phytoene synthases family. The C. albicans orf19.2500 is distinguished by three evolutionarily acquired stretches of amino acid inserts, absent from all other eukaryotes except a small number of ascomycete fungi. Biochemical assays showed that orf19.2500 is required for the assembly and activity of the NADH ubiquinone oxidoreductase Complex I of the respiratory electron transport chain, and was thereby named NDU1. NDU1 is essential for respiration and growth on alternative carbon sources, important for immune evasion, required for virulence in a mouse model of hematogenously disseminated candidiasis, and for potentiating resistance to antifungal drugs. Our study is the first report on a protein that sets the Candida-like fungi phylogenetically apart from all other eukaryotes, based solely on evolutionary "gain" of new amino acid inserts that are also the functional hub of the protein.

microbiology↗

bioRxiv2020

A novel synthetic peptide provides neuroprotection and rescues rat cortical neurons from anesthetic-induced cell death and modulation of growth and synaptic assembly

Anesthetics, although necessary for many modern procedures, exert neurotoxic effects in various experimental models; the underlying mechanisms, however, remain unknown. In the absence of this information, any in vivo mitigation strategy would be challenging. To help address these gaps, we sought to determine whether preserving mitochondrial network integrity with a non-toxic, short-life synthetic peptide, P110, could protect cortical neurons against both inhalational and intravenous anesthetic-induced neurotoxicity. This study provides the first direct comparative account of three key general anesthetics (desflurane, propofol, and ketamine) under identical conditions and demonstrates their impact on cellular viability, neurite outgrowth, and synaptic network assembly on neonatal rat cortical neurons. Further, we discovered that the inhibition of Fis1 receptor-mediated fission reverses anesthetic-induced aberrations in an agent-specific manner. Our data thus underscore the importance of a reductionist approach, offering unique opportunities to explore non-toxic, mitochondria-based therapeutic tools for mitigating anesthetic-induced harm to the developing brain.

neuroscience↗

bioRxiv2020

Baseline epidemiology and associated dog ecology study towards stepwise elimination of rabies in Kwara state, Nigeria

Understanding domestic dog population dynamics and ecology is necessary for any effective rabies control program. This study was conducted as part of the baseline epidemiological studies necessary for the establishment of the Kwara Rabies Rapid Alert System "KRRAS". The aim of this study was to determine the dog population structure of Kwara State by assessing the dog ownership, vaccination status, and prevalence of dog bites. A total of 1,460 questionnaires were administered to respondents in the three senatorial zones of the state using Open Data Kit (ODK) between June 2019 to January 2020. Of the 1460 households surveyed, 293 (20.1%) owned at least one dog with an average of 2.25 dogs per household. The male to female ratio was 2.2:1 and 85% (n=250/293) of the owned dogs were local breeds. A total of 785 dogs was enumerated (659 dogs from 293 households and 126 free-roaming dogs) and 7811 persons which resulted in a dog-human ratio of 1:9.95. The estimated dog population is 376,789 (95% CI: 343,700 - 379,878). The dog anti-rabies vaccination coverage was 31% (n=92/293). The prevalence of dog-bite was 13% (n=193/1460) of which only 27% of the victims (n=61/225) received post-exposure prophylaxis (PEP). The ethnicity of respondents had a significant impact on dog ownership. Yorubas more often (OR: 2.2-5; 95% CI: 1.2 - 12.4; p < 0.001) owned dogs than other tribes. The vaccination status of owned dogs was greatly impacted by the level of education of the respondents (OR: 5.03; 95% CI: 1.5073 - 16.8324; p < 0.001); the breed of the dog with exotic dogs being more vaccinated (OR: 2.8; 95% CI: 0.7150 - 10.857; p < 0.001) and the confinement of the dog (OR: 2.07; 95% CI: 1.1592 - 3.7037; p < 0.001). Always confined dogs were twice more vaccinated than non-confined dogs. The results of the study showed that the vaccination coverage needs to be increased, the number of dog bites needs to be reduced, the number of non-confined dogs needs to be reduced and stray dog control strategies need to be implemented. The findings of this study showed very low vaccination coverage for dogs which is below the 70-80% target recommended for herd immunity by the world health organization.

microbiology↗

bioRxiv2020

Honey bee queen production: Canadian costing case study and profitability analysis

The recent decline in honey bee (Hymenoptera: Apidae) colony health worldwide has had a significant impact on the beekeeping industry as well as on pollination-dependent crop sectors in North America and Europe. The pollinator crisis has been attributed to many environmental and anthropological factors including less nutrient rich agricultural monocultures, pesticide exposure, new parasite and pathogen infestations as well as beekeeper management and weather. Canadian beekeepers have indicated that issues with honey bee queens are the most significant factor affecting their colony health. In Canada, beekeepers manage colony losses by relying on the importation of foreign bees, particularly queens from warmer climates, to lead new replacement colonies. Unfortunately, the risks associated with imported queens include the introduction of new and potentially resistant pests and diseases, undesirable genetics including bees with limited adaptations to Canadas unique climate and bees negatively affected by transportation. Importing a large proportion of our queens each year also creates an unsustainable dependency on foreign bee sources, putting our beekeeping and pollination sectors at an even greater risk in the case of border closures and restrictions. Increasing the domestic supply of queens is one mitigation strategy that could provide Canadian beekeepers, farmers and consumers with a greater level of agricultural stability through locally bred, healthier queens. Our study is the first rigorous analysis of the economic feasibility of Canadian queen production. We present the costs of queen production for three case study operations across Canada over two years as well as the profitability implications. Our results show that for a small to medium sized queen production operation in Canada, producing queen cells and mated queens can be profitable. Using a mated queen market price ranging from $30 to $50, a producer selling mated queens could earn a profit of between $2 and $40 per queen depending on price and the cost structure of his operation. If the producer chose to rear queens for his own operation, the cost savings would also be significant as imported queen prices continue to rise. Our case studies reveal that there is potential for both skilled labour acquisition over time in queen production as well as cost savings from economies of scale. Our queen producers also reduced their production costs by re-using materials year to year. Domestic queen production could be one viable strategy to help address the current pollinator crisis in Canada.

ecology↗

bioRxiv2019

HIV-MALARIA CO-INFECTION AND ITS DETERMINANTS AMONG PATIENTS ATTENDING ANTIRETROVIRAL TREATMENT CLINIC IN ZARIA, NORTH-WESTERN NIGERIA

IntroductionMalaria and HIV are two important global public health problems. Together, they cause more than two million deaths each year. In sub-Saharan Africa alone, more than 29 million people are living with HIV/AIDS and about 70% of population is at risk to malaria infection. Nigeria accounts for about a quarter of the global malaria cases and tenth of the global HIV cases. Recent theories suggested possibilities of high occurrence of HIV-malaria co-infection wherever there is geographical overlap of the two diseases. We therefore conducted this study to determine the prevalence of HIV-malaria co-infection and its determinants in a malaria endemic setting.\n\nMethodsWe conducted a cross-sectional study. Two hundred and sixty-two clients attending antiretroviral treatment (ART) clinic in Zaria, Kaduna State were enrolled between February and April 2018 using systematic sampling technique. Questionnaires were administered to collect information on respondents personal characteristics as well as their knowledge, perception and practices on malaria prevention. Venous blood samples were collected and analyzed for malaria parasite, viral load, CD4, and FBC using Giemsa stained light microscopy, COBAS TaqMan equipment, BD FACS flow cytometer, and Sysmex haematology analyser respectively. Descriptive and inferential statistics were performed, predictors of HIV-malaria co-infection were ascertained at multivariate analysis.\n\nResultsMedian age of the respondents was 33 years, 52% were females, 65% were married, 65% were employed, 57% lived in urban residence, and 34% had tertiary education. The prevalence of malaria co-infection among HIV patients was found to be 22.9%. Significant risk factors for the co-infection were high HIV viral load (aOR= 3.30, C.I = 1.15-9.45), being co-infected with TB (aOR= 5.60, C.I = 1.34-23.33), poor knowledge of malaria infection (aOR= 3.12, C.I = 1.27-7.72) and poor practice of malaria prevention (aOR= 13.30, C.I = 4.88-36.23).\n\nConclusionThe level of occurrence of malaria among HIV infected patients in this setting calls for attention. We recommended that health education on malaria should be a priority in malaria control programme; the programmes for control of HIV, malaria and TB should collaborate to ensure integrated service delivery and that people living with HIV/AIDS should be given special consideration for malaria prevention.

epidemiology↗

bioRxiv2017

Game theoretic consideration of transgenic bacteria in the human gut microbiota as a pro-biotic prophylactic for metabolic syndrome

A game theoretic treatment is introduced to explore the role of nutrition of the gut bacterial microflora as a potential pro-biotic therapy. Rational design of functional foods and nutraceuticals has far reaching public health and therapeutic benefits. Understanding ecological dynamics and how phenotypic manipulations of microbe-microbe interactions of the gut microbiota can provide direct health benefit is currently a fundamental question in bioengineering and more widely in the food, diet and health industries. This work considers a hypothetical adjustment of the microbiome by introducing a transgenic bacterial species that contributes to increased exposure of omega 3 fats in the gut by converting them from the omega 6 fats, dominant in the Western diet. The ratio of the two fats circulating in blood are risk markers, indicators of metabolic syndrome and related conditions. In this work, we consider nutritional exposure to a pro-biotic, a live culture of transgenic bacteria contributing omega 3 fats from omega 6 in the diet. Maintaining a long-term co-existence between native (indigenous) and transgenic bacteria is a challenge. Game theory is the appropriate tool for handling this conflict. The long-term co-existence is guaranteed if the two strains engage in the Snowdrift game. Our game theoretic treatment provides the basis of a model mechanism for prophylactic nutritional therapy for metabolic syndrome by the transgenic bacteria, providing support of indigenous gut microbiota and additional supplementation of a pro-biotic.

bioengineering↗

bioRxiv2017

Comparison of algorithms for the detection of enteroviruses in stool specimens from children diagnosed with Acute Flaccid Paralysis

With poliovirus eradication within reach, the WHO has included in its recommendations a cell-culture independent algorithm for enterovirus surveillance. This study was designed to compare both the cell culture dependent and independent algorithms and assess how either might impact our perception of the diversity of enterovirus types present in a sample.\n\nSixteen paired samples (16 isolates from RD cell culture and their corresponding stool suspension. i.e. 32 samples) from AFP cases in Nigeria were analyzed in this study. One of these 16 sample pairs (the control) was previously identified and confirmed as poliovirus 2 (PV-2). All the samples were subjected to RNA extraction, cDNA synthesis, RT-snPCR (the WHO recommended cell-culture independent algorithm) and its modifications for co-infection detection and resolution. Amplicons were sequenced and strains identified using the enterovirus genotyping tool and phylogenetic analysis.\n\nThe enterovirus diversity was shown to be the same between RD cell culture isolates and fecal suspension for the control and five (7, 10, 11, 12 & 14) of the samples analyzed. It was however, different for the remaining 10 (62.5%) samples analyzed. Fourteen different enterovirus types were identified in this study. To be precise, 9 (CV-B4, E6, E7, E13, E14, E19, E29, EV-B75 and EV-B77) and 5 (CV-A1, CV-A11, CV-A13, EV-C99 and PV2) EV-B and EV-C types, respectively where detected in this study. It is crucial to mention that E19 and EV-B75were only recovered from RD cell culture isolates while E14, EV-B77, CV-A11 and CV-A13 were only recovered from fecal suspension.\n\nThe results of this study show that both the cell culture dependent and independent protocols recommended by the WHO for enterovirus detection unavoidably bias our perception of the diversity of enterovirus types present in a sample. Hence, rather than jettison one for the other, effort should be directed at harmonizing both for increased sensitivity.

microbiology↗

bioRxiv2017

Reversal of cardiac and skeletal manifestations of Duchenne muscular dystrophy by cardiosphere-derived cells and their exosomes in mdx dystrophic mice and in human Duchenne cardiomyocytes

Genetic deficiency of dystrophin leads to disability and premature death in Duchenne muscular dystrophy, affecting the heart as well as skeletal muscle. Here we report that cardiosphere-derived cells (CDCs), which are being tested clinically for the treatment of Duchenne cardiomyopathy, improve cardiac and skeletal myopathy in the mdx mouse model of DMD and in human Duchenne cardiomyocytes. Injection of CDCs into the hearts of mdx mice augments cardiac function, ambulatory capacity and survival. Exosomes secreted by human CDCs reproduce the benefits of CDCs in mdx mice and in human Duchenne cardiomyocytes. The findings further motivate the testing of CDCs in Duchenne patients, while identifying exosomes as next-generation therapeutic candidates.

physiology↗