Biology subjects

Almeida, R. N.

Publications and source records attributed to Almeida, R. N..

3 recordsLinked to original sources

bioRxiv2018

Molecular Evolution of Pseudomonas syringae Type III Secreted Effector Proteins

Diverse Gram-negative pathogens like Pseudomonas syringae employ type III secreted effector (T3SE) proteins as primary virulence factors that combat host immunity and promote disease. T3SEs can also be recognized by plant hosts and activate an effector triggered immune (ETI) response that shifts the interaction back towards plant immunity. Consequently, T3SEs are pivotal in determining the virulence potential of individual P. syringae strains, and ultimately restrict P. syringae pathogens to a subset of potential hosts that are unable to recognize their repertoires of T3SEs. While a number of effector families are known to be present in the P. syringae species complex, one of the most persistent challenges has been documenting the complex variation in T3SE contents across a diverse collection of strains. Using the entire pan-genome of 494 P. syringae strains isolated from more than 100 hosts, we conducted a global analysis of all known and putative T3SEs. We identified a total of 14,613 T3SEs, 4,636 of which were unique at the amino acid level, and show that T3SE repertoires of different P. syringae strains vary dramatically, even among strains isolated from the same hosts. We also find that dramatic diversification has occurred within many T3SE families, and in many cases find strong signatures of positive selection. Furthermore, we identify multiple gene gain and loss events for several families, demonstrating an important role of horizontal gene transfer (HGT) in the evolution of P. syringae T3SEs. These analyses provide insight into the evolutionary history of P. syringae T3SEs as they co-evolve with the host immune system, and dramatically expand the database of P. syringae T3SEs alleles.

evolutionary biology↗

bioRxiv2018

A Single Dose Of Ayahuasca Modulates Salivary Cortisol In Treatment-Resistant Depression

Major depression is a highly prevalent mood disorder, affecting about 350 million people, and around 30% of the patients are resistant to currently available antidepressant medications. Recent evidence from a randomized placebo-controlled trial supports the rapid antidepressant effects of the psychedelic ayahuasca in treatment-resistant depression. The aim of this study was to explore the effect of ayahuasca on plasma cortisol and awakening salivary cortisol response, in the same group of treatment-resistant patients and in healthy volunteers. Subjects received a single dose of ayahuasca or placebo, and both plasma and awakening salivary cortisol response were measured at baseline (before dosing) and 48h after the dosing session. Baseline assessment (D0) showed blunted awakening salivary cortisol response and hypocortisolemia in patients (DM), both with respect to healthy controls group (C). Salivary cortisol also was measured during dosing session and we observed a large increased for both C and DM that ingested ayahuasca, than placebo groups. After 48h of the dosing session (D2) with ayahuasca, awakening salivary cortisol response (for both sexes) of treated patients became similar to levels detected in controls. This was not observed in patients that ingested placebo. No changes in plasma cortisol were observed after 48 hours of ayahuasca or placebo ingestion for both groups and sexes. Therefore, these findings point to new evidence of modulation of ayahuasca on salivary cortisol levels, as cortisol acts in regulation of distinct physiological pathways, emotional and cognitive processes related to etiology of depression, this modulation could be an important part of the antidepressant effects observed with ayahuasca. Moreover, this study highlights the importance of psychedelics in the treatment of human mental disorders.

physiology↗

bioRxiv2017

Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex

Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crop species. Here, we examine the evolutionary relationships of 391 agricultural and environmental strains from the P. syringae species complex using whole-genome sequencing and evolutionary genomic analyses. Our collection includes strains from 11 of the 13 previously described phylogroups isolated off of over 90 hosts. We describe the phylogenetic distribution of all orthologous gene families in the P. syringae pan-genome, reconstruct the phylogeny of P. syringae using a core genome alignment and a hierarchical clustering analysis of pan-genome content, predict ecologically and evolutionary relevant loci, and establish the forces of molecular evolution operating on each gene family. We find that the common ancestor of the species complex likely carried a Rhizobium-like type III secretion system (TTSS) and later acquired the canonical TTSS. The phylogenetic analysis also showed that the species complex is subdivided into primary and secondary phylogroups based on genetic diversity and rates of genetic exchange. The primary phylogroups, which largely consist of agricultural isolates, are no more divergent than a number of other bacterial species, while the secondary phylogroups, which largely consists of environmental isolates, have levels of diversity more in line with multiple distinct species within a genus. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also found that \"ecologically significant\" virulence-associated loci and \"evolutionary significant\" loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange. These results indicate that while inter-phylogroup recombination occurs relatively rarely in the species complex, it is an important force of genetic cohesion, particularly among the strains in the primary phylogroups. This level of genetic cohesion and the shared plant-associated niche argues for considering the primary phylogroups as a true biological species.

genomics↗