Biology subjects

Valente, G. T.

Publications and source records attributed to Valente, G. T..

5 recordsLinked to original sources

bioRxiv2025

Genome Assembly of Astatotilapia latifasciata Uncovers B Chromosome Linked Chromatin Reorganization

B chromosomes (Bs) are supernumerary genomic elements found in many eukaryotes, yet their full sequence composition, functional potential, and regulatory impact on the host genome remain unclear. Here, we present a chromosome-level genome assembly of the cichlid fish Astatotilapia latifasciata, integrating PacBio long reads, Illumina short reads, and Hi-C chromatin contact maps to resolve both A and B chromosomes. The 0.93 Gb assembly (N50 = 36.2 Mb) includes a 34 Mb B chromosome containing 789 predicted protein-coding genes and a markedly higher density of transposable elements (TEs), especially long terminal repeats (LTR) retrotransposons. Transcriptome profiling revealed that B-linked genes are predominantly transcriptionally repressed relative to their A chromosome paralogs. Hi-C based chromatin modeling uncovered distinct 3D structural configurations associated with the B chromosome, including fewer topologically associating domains (TADs), reduced loop formation, and altered compartmentalization. These changes are linked to long-range chromatin interactions and genomic rearrangements, suggesting that the B chromosome reshapes the nuclear architecture of the host genome. Our study proposes a potential regulatory role of Bs in genome and provides a genomic resource for investigating chromosome evolution in cichlids.

genomics↗

bioRxiv2021

The ethanol tolerance in Saccharomyces cerevisiae under a phenomics perspective

Ethanol (EtOH) is a substantial stressor for Saccharomyces cerevisiae. Data integration from strains with different phenotypes, including EtOH stress-responsive lncRNAs, are still not available. We covered these issues seeking systems modifications that drive the divergences between higher (HT) and lower (LT) EtOH tolerant strains under their highest stress conditions. We showed that these phenotypes are neither related to high viability nor faster population rebound after stress relief. LncRNAs work on many stress-responsive systems in a strain-specific manner promoting the EtOH tolerance. Cells use membraneless RNA/protein storage and degradation systems to endure the stress harming, and lncRNAs jointly promote EtOH tolerance. CTA1 and longevity are primer systems promoting phenotype-specific gene expression. The lower cell viability and growth under stress is a byproduct of sphingolipids and inositol phosphorylceramide dampening, acerbated in HTs by sphinganine, ERG9, and squalene overloads; LTs diminish this harm by accumulating inositol 1-phosphate. The diauxic shift drives an EtOH buffering by promoting an energy burst under stress, mainly in HTs. Analysis of mutants showed genes and lncRNAs in three strains critical for their EtOH tolerance. Finally, longevity, peroxisome, energy and lipid metabolisms, RNA/protein degradation and storage systems are the main pathways driving the EtOH tolerance phenotypes.

systems biology↗

bioRxiv2021

LncRNAs of Saccharomyces cerevisiae dodge the cell cycle arrest imposed by the ethanol stress

Ethanol impairs many subsystems of Saccharomyces cerevisiae, including the cell cycle. Cyclins and damage checkpoints drive the cell cycle. Two ethanol-responsive lncRNAs in yeast interact with cell cycle proteins, and here we investigated the role of these RNAs on the ethanol-stressed cell cycle. Our network dynamic modeling showed that the higher and lower ethanol tolerant strains undergo a cell cycle arrest during the ethanol stress. However, lower tolerant phenotype arrest in a later phase leading to its faster population rebound after the stress relief. Two lncRNAs can skip the arrests mentioned. The in silico overexpression of lnc9136 of SEY6210 (a lower tolerant strain), and CRISPR-Cas9 partial deletions of this lncRNA, evidenced that the one induces a regular cell cycle even under ethanol stress; this lncRNA binds to Gin4 and Hsl1, driving the Swe1p, Clb1/2, and cell cycle. Moreover, the lnc10883 of BY4742 (a higher tolerant strain) interacts to the Mec1p and represses Bub1p, circumventing the DNA and spindle damage checkpoints keeping a normal cell cycle even under DNA damage. Overall, we present the first evidence of the direct roles of lncRNAs on cell cycle proteins, the dynamics of this system in different ethanol tolerant phenotypes, and a new cell cycle model.

systems biology↗

bioRxiv2021

Long non-coding RNAs bind to proteins relevant to the ethanol tolerance in yeast: a systems biology view

The ethanol disturbs the cell cycle, transcription, translation, protein folding, cell wall, membranes, and many Saccharomyces cerevisiae metabolic processes. Long non-coding RNAs (lncRNAs) are regulatory molecules binding onto the genome or proteins. The number of lncRNAs described for yeast is still scarce, and little is known concerning their roles in the system. There is a lack of knowledge concerning how lncRNAs are responsive to the ethanol tolerance in yeast and whether they act in this tolerance. Hence, by using RNA-Seq data from S. cerevisiae strains with different ethanol tolerance phenotypes, we found the severe ethanol responsive lncRNAs. We modeled how they participate in the ethanol tolerance by analyzing lncRNA-protein interactions. The results showed that the EtOH tolerance responsive lncRNAs, in both higher tolerant and lower tolerant phenotypes, work on different pathways: cell wall, cell cycle, growth, longevity, cell surveillance, ribosome biogenesis, intracellular transport, trehalose metabolism, transcription, and nutrient shifts. In summary, lncRNAs seems to interconnect essential systems modules to overcome the ethanol stress. Finally, here we also found the most extensive catalog of lncRNAs in yeast.

microbiology↗

bioRxiv2020

SEEKING CANDIDATE MOLECULES AS PROGNOSTIC HEALING MARKERS IN CHRONIC VENOUS ULCERS

Seeking and identifying biomarker molecules in inflammatory exudate of chronic venous ulcers (CVUs) can aid health professionals in the healing prognosis. The therapeutic failure or cure is related to the quantitative expression of determinate proteins. This work aimed to identify the proteins expressed in inflammatory exudates from CVUs and correlate them with reduction or increase in the wound size. For 90 days, 28 participants that received standard treatment for 37 CVUs were monitored. The inflammatory exudates were collected before treatment initiation (T=0) and analyzed via the Label-free Shotgun. After 90 days the wound area was reduced in 25 (67.6%) of them. Mass spectrometry analysis of all the inflammatory exudates showed four proteins differentially expressed and related to favorable or unfavorable evolution of the healing process. Complement C3 and ceruloplasmin were identified in all the lesions analyzed and were expressed differentially in lesions that presented diminished area in the studied period. Apoliprotein A1 and neutrophil defensin-1 presented differential expression in ulcers that either did not diminish or augmented their wound area through 90 days. These results suggest that Complement C3, Ceruloplasmin, Apoliprotein A1 and Neutrophil-defensin-1 proteins are potential candidate molecules for prognostic healing markers in chronic venous ulcers.

biochemistry↗