Biology subjects

Herai, R. H.

Publications and source records attributed to Herai, R. H..

3 recordsLinked to original sources

bioRxiv2025

Retinal gene and pathway modulation by benzathine penicillin: A potential link to Extensive Macular Atrophy with Pseudodrusen (EMAP) and neurodegeneration.

Extensive Macular Atrophy with Pseudodrusen (EMAP) is a rare and rapidly progressive retinal disease marked by central vision loss, chorioretinal atrophy, and pseudodrusen, primarily affecting middle-aged individuals. Recent studies have identified a statistically significant association between long-term use of benzathine penicillin (BP) and the onset of EMAP. However, the molecular mechanisms underlying this relationship remain unclear. In this study, we performed an integrative in silico analysis to explore the genes modulated by BP that are expressed in ocular tissues and involved in retinal metabolic pathways. Using public databases (PubChem, GTEx, HPA, EYEDB), we identified 52 BP-responsive genes, with six (CD4, CRP, IL6, IL1R1, TAC1, TNF) directly modulated by BP and expressed in the retina. These genes are implicated in inflammation, immune response, and retinal homeostasis. Expression data show strong presence in eye and brain tissues, and several are associated with age-related macular degeneration (AMD). Network analysis revealed gene-gene and protein-protein interactions, highlighting a shared pathophysiological axis. Notably, IL6 and TNF are involved in oxidative stress, endoplasmic reticulum stress, and chronic inflammation--hallmarks of both EMAP and atrophic AMD. Our findings suggest that BP may induce EMAP by dysregulating retinal genes involved in neurodegeneration, providing new insights into drug safety and retinal disease mechanisms.

genetics↗

bioRxiv2025

A comprehensive identification and annotation of mobile LINE-1 retrotransposons across human reference and personal genomes

LINE-1 (L1) is a type of mobile genetic element (retrotransposon) that can self-copy into distinct parts of its host genome by dynamically shaping its content. In humans, misregulation of these elements have been associated as the potential cause of distinct types of pathologies and neurodevelopmental disorders, including cancer, Rett syndrome and Aicardi Goutierrez disease. However, the precise annotation of these 6 kb long nucleotide sequence is a challenging task due to the high similarity between their internal regions (coding and non-coding) for distinct L1 families. Current L1 reference annotations such as RepeatMasker still lack sequence details and also provide confounding annotated information, that includes thousands of incomplete L1 sequences annotated as representative full-length, and missing information on their regulatory and coding regions (5UTR, ORF1, intron, ORF2 and 3UTR). Additionally, current L1 resources also provide annotations based on consensus reference genomes and does not include individual genome information at allele-level and nucleotide-level resolution. Here, we present L1Farm as a complementary databank and annotation resource that contains a comprehensive analysis and annotation of L1 subfamilies identified in the current human reference genome (build Hg38) and in two individual Asian and Caucasian genomes at allele-level and nucleotide-level resolution. L1 elements sequences were also annotated with genomic loci and ranked according to their full-length content and similarity.

genetics↗

bioRxiv2020

CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages

Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the knowledge base for transcriptome of in vivo citrus interactome, the CitrusKB. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable source of information on citrus and their interaction with the citrus canker bacterium X. citri. The database provides tools for a user-friendly web interface to search and analyze a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease and their interaction, at different stages of infection, with the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue by incorporating annotations and analysis tools. We expect that CitrusKB may substantially contribute to the area of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

genomics↗