Biology subjects

Santana, R.

Publications and source records attributed to Santana, R..

5 recordsLinked to original sources

bioRxiv2024

A super-pangenome for cultivated citrus reveals evolutive features during the allopatric phase of their reticulate evolution

Most of the rich genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa, C. medica, C. reticulata, C. maxima and C. micrantha, whose radiation occurred in allopatry. In such an evolutive context, genome diversity studies, GWAS analysis and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super-pangenome for cultivated citrus, established with de novo assemblies in pseudochromosomes of C. medica (346 Mb), C. reticulata (332 Mb) and C. micrantha (333 Mb), released for the first time alongside a previously published chromosome-scale assembly of C. maxima. Gene annotation of these four genome assemblies revealed 28,090, 29,477, 29,258 and 30,101 genes, respectively, with a focus on pattern recognition receptors. Repetitive element annotation revealed that nearly half of each genome consisted of transposable elements or DNA-satellites. The 3 new genome assemblies display strong synteny and collinearity, while significant discrepancies are observed with the C. maxima assembly. Resequencing information (single nucleotide polymorphisms [SNPs], small indels and gene presence-absence variation [PAV]) from 55 accessions were used to explore the intra- and interspecific diversity of the four ancestral taxa and their relationships with the main horticultural groups resulting from reticulate evolution. Diagnostic SNPs of the ancestral taxa, all over the four genomes assemblies, revealed interspecific introgressions in several accessions representative of C. reticulata, C. maxima and C. medica as well as insights into the origin and phylogenomic structures of modern horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa (dPAV). Interestingly, diagnostic PAV (dPAV) analysis uncovered a large chloroplastic introgression in chromosome 4 of C. medica, inherited in horticultural groups and recent hybrids having this species as the male parent. Implementing the super-pangenome combined the identification of orthologous genes across the four genome assemblies and the PAV information from the resequencing data. Significant inter- and intraspecific variations were highlighted, including 25,291 core, 2,431 soft-core and 5,171 dispensable genes. The analysis of the functional enrichment and species-specific adaptations in the citrus super-pangenome revealed distinct functional specializations. This highlights the evolutionary paths that have shaped each species, contributing to the diversity in the citrus super-pangenome while maintaining a shared foundation of essential biological processes. The development of this super-pangenome is a significant milestone in citrus genomics, providing a comprehensive resource that captures the extensive genetic diversity of modern cultivated citrus. Additionally, we established a dedicated Genome Hub, offering a platform for continuous genomic research and allowing for ongoing updates and future inclusion of additional ancestral species.

genomics↗

bioRxiv2022

Assessing the brain representation of conscious and unconscious visual contents using encoding based representational similarity analysis

The development of novel frameworks to understand the properties of unconscious representations and how they differ from the conscious counterparts may be critical to make progress in the neuroscience of vision consciousness. Here we re-analysed data from a within-subject, high-precision, highly-sampled fMRI study (N=7) coupled with model-based representational similarity analysis (RSA) in order to provide an information-based approach to study the representation of conscious and unconscious visual contents The standard whole-brain searchlight RSA revealed that the hidden representations of convolutional neural network models explained brain activity patterns in response to unconscious contents in the ventral visual pathway in the majority of the observers, particularly for models that ranked high in explaining the variance of the visual cortex (i.e., VGGNet and ResNet50). Also five of seven subjects showed brain activity patterns that correlated with the model in frontoparietal areas in the unconscious trials. However, the results of an encoding-based RSA analyses in the unconscious condition were mixed and somehow difficult to interpret, including negative correlations between the representations of the computer vision models and the brain activity in frontal areas in a substantial amount of the observers.

neuroscience↗

bioRxiv2021

Informative neural representations of unseen objects during higher-order processing in human brains and deep artificial networks

A framework to pinpoint the scope of unconscious processing is critical to improve our models of visual consciousness. Previous research observed brain signatures of unconscious processing in visual cortex but these were not reliably identified. Further, whether unconscious content is represented in high-level stages of the ventral visual stream and linked parieto-frontal areas remains unknown. Using a within-subject, high-precision fMRI approach, we show that unconscious contents can be decoded from multivoxel patterns that are highly distributed alongside the ventral visual pathway and also involving parieto-frontal substrates. Classifiers trained with multivoxel patterns of conscious items generalised to predict the unconscious counterparts, indicating that their neural representations overlap. These findings suggest revisions to models of consciousness such as the neuronal global workspace. We then provide a computational simulation of visual processing/representation without perceptual sensitivity by using deep neural networks performing a similar visual task. The work provides a framework for pinpointing the representation of unconscious knowledge across different task domains.

neuroscience↗

bioRxiv2019

Decoding and encoding models reveal how the depth of processing shapes the brain representation of meaning

How the brain representation of conceptual knowledge vary as a function of processing goals, strategies and task-factors remains a key unresolved question in cognitive neuroscience. Here we asked how the brain representation of semantic categories is shaped by the depth of processing during mental simulation. Participants were presented with visual words during functional magnetic resonance imaging (fMRI). During shallow processing, participants had to read the items. During deep processing, they had to mentally simulate the features associated with the words. Multivariate classification, informational connectivity and encoding models were used to reveal how the depth of processing determines the brain representation of word meaning. Decoding accuracy in putative substrates of the semantic network was enhanced when the depth processing was high, and the brain representations were more generalizable in semantic space relative to shallow processing contexts. This pattern was observed even in association areas in inferior frontal and parietal cortex. Deep information processing during mental simulation also increased the informational connectivity within key substrates of the semantic network. To further examine the properties of the words encoded in brain activity, we compared computer vision models - associated with the image referents of the words - and word embedding. Computer vision models explained more variance of the brain responses across multiple areas of the semantic network. These results indicate that the brain representation of word meaning is highly malleable by the depth of processing imposed by the task, relies on access to visual representations and is highly distributed, including prefrontal areas previously implicated in semantic control.

neuroscience↗

bioRxiv2018

Reactivation of latent HIV-1 in vitro using an alcoholic extract from Euphorbia umbellata (Euphorbiaceae) latex.

Euphorbia umbellata (E. umbellata) belongs to Euphorbiaceae family, popularly known as Janauba, and contains in its latex a combination of phorbol esters with biological activities described to different cellular protein kinase C (PKC) isoforms. Here, we identified deoxi-phorbol esters present in E. umbellata latex alcoholic extract able to increase HIV transcription and reactivate HIV from latency models. This activity was mediated by NF-kB activation followed by nuclear translocation and binding to HIV LTR promoter. In addition, E. umbellate latex extract induced the production of pro inflammatory cytokines together with IL21 in in vitro human PBMC cultures. Our latex extract activates latent HIV in human PBMCs isolated from HIV positive patients as well as latent SIV in non-human primate primary CD4+ T lymphocytes. These results strongly indicate that the phorbol esters present in E. umbellata latex are promising candidate compounds for future clinical trials for shock and kill therapy to promote HIV cure and eradication.

microbiology↗