Biology subjects

Macharia, R. W.

Publications and source records attributed to Macharia, R. W..

3 recordsLinked to original sources

bioRxiv2024

Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons

BackgroundAnimals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While the composition of bacterial and viral components of animal microbiota are increasingly well understood, eukaryotic composition remains neglected. Here we characterized eukaryotic diversity in the microbiomes in wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, and season of sample collection. ResultsWe analyzed a total of 75 fecal samples collected between 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of samples, respectively. Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effect of season, host age, and host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples). ConclusionsProtista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is essential for primate health monitoring and management strategies.

microbiology↗

bioRxiv2021

Inference of Rift Valley Fever pathogenesis in Bos taurus using a gene co-expression network

BackgroundRift Valley Fever (RVF) is a viral disease caused by the Rift Valley Fever virus and spread mainly by the Aedes and Culex mosquito species. The disease primarily infects domestic animals such as sheep, goats, and cattle, resulting in a spectrum of clinical outcomes including morbidity, massive storm abortions, and neonatal fatalities. RVF outbreaks are closely linked to above-average rainfall and flooding, which create an ideal environment for mosquitos to breed, multiply, and transmit the virus to animals. The outcomes of human RVF infection range from self-limiting febrile illness to potentially fatal hemorrhagic diatheses and miscarriage in pregnant women. Collectively, the economic losses due to the zoonotic RVF disease is immense. MethodsUsing the Weighted Gene Co-expression Network Analysis (WGCNA) package, RNA-Seq data generated from five healthy Bos taurus steer calves aged 4-6 months was obtained from the Gene Expression Omnibus (GEO) database (Accession number GSE71417). The data was utilized to construct a gene co-expression network. Enriched modules containing genes potentially involved in RVF infection progression were identified. Moreover, using the Multiple Expectation Maximizations for Motif Elicitation (MEME) suite, consensus regulatory motifs of enriched gene clusters were deciphered and the most abundant putative regulatory motif in each enriched module unveiled by comparative analysis with publicly available motifs using the TOMTOM motif comparison tool. The potential roles of the identified regulatory motifs were inferred by literature mining. ResultsThe constructed gene co-expression network revealed thirty-three (33) modules, nine of which were enriched for Gene Ontology terms linked to RVF pathogenesis. Functional enrichment in two (red and turquoise) of the nine modules was significant. ASH1-like histone lysine methyltransferase and Astrotactin were the hub genes for the red and turquoise modules respectively. ASH1-like histone lysine methyltransferase gene is involved in chromatin epigenetic modification while Astrotactin is a vertebrate-specific gene that plays an important role in neurodevelopment. Additionally, consensus regulatory motifs located on the 3' end of genes in each enriched module was identified. ConclusionsIn this study, we have developed a gene co-expression network that has aided in the unveiling of functionally related genes, intramodular hub genes, and immunity genes potentially involved in RVF pathogenesis. The discovery of functional genes with putative critical roles in the establishment of RVF infection establishment will contribute to the understanding of the molecular mechanism of RVF pathogenesis. Importantly, the putative regulatory motifs identified are plausible targets for RVF drug and vaccine development.

systems biology↗

bioRxiv2019

The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes

BackgroundTsetse flies (Glossina sp.) are the sole vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood specific diet by both sexes and obligate bacterial symbiosis. This work describes comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans (G.m. morsitans), G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes) and Fusca (G. brevipalpis) which represent different habitats, host preferences and vectorial capacity. ResultsGenomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex linked scaffolds show increased rates of female specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse specific genes are enriched in protease, odorant binding and helicase activities. Lactation associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other characterized insects. Vision associated Rhodopsin genes show conservation of motion detection/tracking functions and significant variance in the Rhodopsin detecting colors in the blue wavelength ranges. ConclusionsExpanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.

genomics↗