Biology subjects

Moraes, A.

Publications and source records attributed to Moraes, A..

3 recordsLinked to original sources

bioRxiv2026

GLESKit: an MCP-based system for gene-level biomedical investigation and evidence synthesis

Biomedical investigation at the gene level requires researchers to combine expression data, functional annotations, pathways, interaction networks, genetic associations, drug evidence and literature. Accessing these resources involves databases, analysis tools and scripts that require bioinformatics expertise, complicating the production of clear, reviewable reports. We present GLESKit, a gene centred system that connects these steps through the Model Context Protocol and retains data, analyses, sources and reports within a study workspace. We evaluated report production with 15 author curated GeneReportBench tasks and question answering with a gene level subset of BixBench, a reference biology benchmark for agentic systems. GLESKit completed all 15 reports with a mean committee score of 0.904, although evidence quality varied, and earned positive credit on 35 of 39 scored human BixBench questions with a mean of 0.438. In paired tests, configurations with skills scored 0.145 higher across 20 questions and 0.085 higher across five reports.

bioinformatics↗

bioRxiv2024

Cigarette smoking drives accelerated aging across human tissues

Tobacco smoke is the main cause of preventable mortality worldwide. Smoking increases the risk of developing many diseases and has been proposed as an aging accelerator. Yet, the molecular mechanisms driving smoking-related health decline and aging acceleration in most tissues remain unexplored. Here, we characterize gene expression, alternative splicing, DNA methylation and histological alterations induced by cigarette smoking across human tissues. We show that smoking impacts tissue architecture and triggers systemic inflammation. We find that in many tissues, the effects of smoking significantly overlap those of aging in the same direction. Specifically, both age and smoking upregulate inflammatory genes and drive hypomethylation at enhancers. In addition, we observe widespread smoking-driven hypermethylation at target regions of the Polycomb repressive complex, which is a well-known aging effect. Smoking-induced epigenetic changes overlap causal aging CpGs, suggesting that these methylation changes may directly mediate aging acceleration observed in smokers. Finally, we find that smoking effects that are shared with aging are more persistent over time. Overall, our multi-tissue and multi-omic analysis of the effects of cigarette smoking provides an extensive characterization of the impact of tobacco smoke across tissues and unravels the molecular mechanisms driving smoking-induced tissue homeostasis decline and aging acceleration.

bioinformatics↗

bioRxiv2020

Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

genetics↗