Biology subjects

Fahmi, M.

Publications and source records attributed to Fahmi, M..

3 recordsLinked to original sources

bioRxiv2023

Genetic and Geographic Patterns of Woody Plant Biosynthesis

BackgroundNatural products (NPs) are vital for promoting human health. Given the increasing threats of biodiversity loss and ecosystem degradation, understanding the geographical hotspots of NPs is essential to strategically prioritize areas for conservation, ensuring the sustained availability of these invaluable medicinal resources. MethodsWe constructed a global diversity map for 1,434 woody angiosperm species, each represented by existing genomic or transcriptomic data. We curated a list of 166 enzymes essential for the biosynthesis and structural diversity of NPs, and identified geographical hotspots of NPs by averaging enzyme presence across the grids. We also examined the distribution pattern of each enzyme. To gain deeper insights into NP distribution patterns, we performed a comparative analysis of enzyme groups responsible for the biosynthesis of two pharmacologically significant compounds with distinct biosynthetic pathways, shikonin derivatives and benzylisoquinoline alkaloids. FindingsOur study reveals a correlation between NP hotspots and biodiversity hotspots, with a subset of markers displaying unique, region-specific patterns. Comparative analysis of enzymes for shikonin derivatives and benzylisoquinoline alkaloids biosynthetic pathways shows similar pattern, with the former demonstrating a unique and region-specific distribution. InterpretationOur findings emphasize the importance of preserving biodiversity hotspots for sustaining NP-based medicinal resources. Additionally, the specific distribution of certain enzyme markers, such as those related to shikonin derivatives, suggests that some NPs may necessitate targeted conservation strategies. This study provides a foundational roadmap for identifying the geographical hotspots of NPs and developing targeted conservation strategies. FundingJapan Society for the Promotion of Science through the Grant-in-Aid for Scientific Research (A) 20H00651.

ecology↗

bioRxiv2020

Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors, LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development

Histone deacetylases (HDACs) are divided into four classes. Class-I HDAC, HDAC-1 forms three types of complexes, namely the Nucleosome Remodeling Deacetylase complex, the Sin3 complex, and the CoREST complex, with specific corepressor component Mi2/CHD-3, Sin3, and RCOR1 in human, respectively. The functions of these HDAC-1 complexes are regulated by their corepressors, however, their exact mechanistic roles in several biological processes remain unexplored, such as in embryonic development. Here, we report that each of the corepressors, LET-418, SIN-3, and SPR-1, the homologous of Mi2, Sin3, and RCOR1, respectively, were expressed throughout Caenorhabditis elegans embryonic development and served essential roles in the process. Moreover, genetic analysis suggested that three pathways (i.e., LET-418- SIN-3-SPR-1, SIN-3-SPR-1, and LET-418) participated in embryonic development. Our terminal-phenotype observations of single mutants of each corepressor implied that LET-418, SIN-3, and SPR-1 played similar roles in promoting advancement to the middle and late embryonic stages. Genome-wide comparative-transcriptome analysis indicated that 47.5% and 42.3% of genes were commonly increased and decreased in sin-3 and spr-1 mutants, respectively. These results suggest that among the three pathways studied, the SIN-3-SPR-1 pathway mainly serves to regulate embryonic development. Comparative-Gene Ontology analysis indicated that these three pathways played overlapping and distinct roles in regulating C. elegans embryonic development.

developmental biology↗

bioRxiv2019

Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans

Obtaining a comprehensive understanding of the gene regulatory networks, or gene cascades, involved in cell fate determination and cell lineage segregation in Caenorhabditis elegans is a long-standing challenge. Although RNA-sequencing (RNA-Seq) is a promising technique to resolve these questions, the bioinformatics tools to identify associated gene cascades from RNA-Seq data remain inadequate. To overcome these limitations, we developed Gene Cascade Finder (GCF) as a novel tool for building gene cascades by comparison of mutant and wild-type RNA-Seq data along with integrated information of protein-protein interactions, expression timing, and domains. Application of GCF to RNA-Seq data confirmed that SPN-4 and MEX-3 regulate the canonical Wnt pathway during embryonic development. Moreover, lin-35, hsp-3, and gpa-12 were found to be involved in MEX-1-dependent neurogenesis, and MEX-3 was found to control the gene cascade promoting neurogenesis through lin-35 and apl-1. Thus, GCF could be a useful tool for building gene cascades from RNA-Seq data.

genomics↗