Biology subjects

Dalmolin, R. J. S.

Publications and source records attributed to Dalmolin, R. J. S..

4 recordsLinked to original sources

bioRxiv2024

Integrative systems neuroimmunology reveals leukocyte-expressing PAX6 as a critical predictor of major depressive disorder

Major depressive disorder (MDD) is a complex psychiatric condition with a significant global impact. This study applied a genomic-driven integrative systems neuroimmunology approach to analyze transcriptomic data from 3,114 individuals (1,877 MDD patients and 1,237 controls). The analysis revealed neuroimmunological transcriptomic alterations, indicating cross-talk between the immune and nervous systems in peripheral blood mononuclear cells (PBMCs) and specific brain regions. Among 31 shared genes, NEGR1, PPP6C, SORCS3, and PAX6 emerged as significant predictors of MDD in patients PBMCs. Notably, PAX6 was also identified as a differentially expressed gene (DEG) in the amygdala, while NEGR1, PPP6C, and SORCS3 showed no significant differential expression in other central nervous system (CNS) regions. Validation by immunophenotyping in a mouse model of chronic stress demonstrated increased PAX6 expression in PBMCs, a gene previously associated with MDD in GWAS studies. Collectively, our findings suggest the existence of shared transcriptomic modules across the brain and immune system, highlighting PAX6 as a potential therapeutic target in MDD.

systems biology↗

bioRxiv2022

A survey of transcriptomic datasets identifies ABA-responsive factors as regulators of photomorphogenesis in Arabidopsis

Following germination, seedlings grown in light show a photomorphogenic development with open and green cotyledons and a robust root system. The light perception by the photoreceptors activate autotrophic photosynthetic metabolism to sustain growth of the whole plant. Several studies have evaluated transcriptional responses to light signals. Nevertheless, evaluating a single source experiment might bias the identificationof general, reproducible light responses. In order to identify widespread light-dependent signaling events that control early seedling photomorphogenesis we performed a survey comparing commonly regulated genes in transcriptomic public datasets derived from etiolated seedlings exposed to short light treatments. By compiling commonly regulated genes from different datasets, we obtained broadly representative regulated processes concerning general light transcriptional response. Our analysis shows that light primarly affects shoot gene expression promoting the assembly of photosynthetic machinery, signaling and redox responses. We observed that Transcriptograms allowed a better comparison among different experiments than DEseq analysis. We also identified that, transcriptional regulation of early light response is centered in the transcription factor ABA-Insensitive5 (ABI5) along with other bZIP transcription factors suggesting a mechanism by which dark expressed transcription factors guide the activation of early photomorphogenic genes. Key MessageComparative analisys of seedling deetiolation transcriptomic datasets identified ABA-responsive bZIP transcription factors as central regulators of early photomorphogenesis

plant biology↗

bioRxiv2020

Characterization and analysis of the transcriptome in Arapaima gigas using multi-tissue RNA-sequencing

Arapaima gigas is a giant bony tongue air-breathing fish, and a promising species for aquaculture due to its particular features. However, there is still a lack of information on its biology and few transcriptome studies are available. Our aim was to characterize the transcriptome of arapaima in order to shed light on molecular networks contributing to its unique traits. Through RNA-sequencing, we generated a transcriptome from eight tissues (brain, pituitary, heart, muscle, kidney, lung, ovary, and testis) collected from arapaima adults specimens. Using a genome-guided strategy associated with homologous protein evidence, 57,706 transcripts were assembled, which aligned to 23,353 high confidence protein-coding genes. The analysis revealed a global view of expression patterns, as well as it allowed us to identify tissue-specific gene clusters, transcription factors within the clusters, and to compare expression patterns between male and female. These analyses has generated tissue-specific and sex-biased transcriptome profiles, which will be helpful to understand its molecular biology, evolution, and also guide future functional studies of the arapaima.

genomics↗

bioRxiv2020

CoRINs: A tool to compare residue interaction networks from homologous proteins and conformers

MotivationA useful approach to evaluate protein structure and quickly visualize crucial physicochemical interactions related to protein function is to construct Residue Interactions Networks (RINs). By using this application of graphs theory, the amino acid residues constitute the nodes, and the edges represent their interactions with other structural elements. Although several tools that construct RINs are available, many of them do not compare RINs from distinct protein structures. This comparison can give valuable insights into the understanding of conformational changes and the effects of amino acid substitutions in protein structure and function. With that in mind, we present CoRINs (Comparator of Residue Interaction Networks), a software tool that extensively compares RINs. The program has an accessible and user-friendly web interface, which summarizes the differences in several network parameters using interactive plots and tables. As a usage example of CoRINs, we compared RINs from conformers of two cancer-associated proteins. AvailabilityThe program is available at https://github.com/LasisUFRN/CoRINs.

bioinformatics↗