Biology subjects

Chaves, J.

Publications and source records attributed to Chaves, J..

7 recordsLinked to original sources

bioRxiv2024

Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization of Populus roots

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally reproduced one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol into soil isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferred by HGT but is selectively neutral under environmentally-relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting, because the selective benefits are small and negative frequency-dependent.

microbiology↗

bioRxiv2023

Purinergic Preconditioning Induces Epigenomic and Transcriptomic Changes Resembling Epilepsy-associated Microglial States

Microglia, as the main immune effector cells in the central nervous system (CNS), play a crucial role in a diverse range of neuropathological conditions through their exacerbated activation. Microglial inflammatory responses can be influenced by prior exposures to noxious stimuli, such as increased levels of extracellular adenosine and ATP. These conditions are characteristic of brain insults like epileptic seizures and could potentially shape subsequent responses through epigenetic regulation. In this study, we investigated DNA methylation and expression changes in microglia-like cells differentiated from monocytes following ATP-mediated preconditioning. First, during differentiation, we demonstrate that microglia-like cells acquire standard microglial features, including whole transcriptomes and methylomes like in vivo profiles. We show a predominant DNA demethylation in genomic sequences enriched in binding motifs of microglia lineage transcription factors like PU.1, consistent with the relevance of this factor in in vivo microglia. TLR-mediated activation, after a first exposure to ATP, promotes exacerbated pro-inflammatory activation compared to cells not pre-exposed to ATP. These changes are accompanied by DNA methylation and transcriptional reprogramming associated with the acquisition of trained immunity and altered immune-related functions such as with antigen presentation, phagocytosis and cytokine signaling. Finally, the reprogramming associated with ATP-mediated preconditioning leads to profiles found in microglial subsets linked to epilepsy. Purine-driven microglia immune preconditioning drives epigenetic and transcriptional changes that could contribute to altered functions of microglia during seizure development and progression, particularly associated with neuroinflammation.

immunology↗

bioRxiv2022

Energetic costs of bill heat exchange demonstrate contributions to thermoregulation at high temperatures in toco toucans (Ramphastos toco)

Body temperature regulation in the face of changes in ambient temperature and/or in metabolic heat production involves adjustments in heat exchange rates between the animal and the environment. One of those mechanisms include the modulation of the surface temperature of specific areas of the body through vasomotor adjustment and blood flow control, to change the thermal conductance of this region, thereby promoting dissipation or conservation of body heat. In homeotherms, this thermoregulatory adjustment is essential for the maintenance of body temperature over a moderate temperature range, known as the thermal neutral zone (TNZ), without increasing metabolic rate (MR). Thermal windows are poorly insulated body regions and highly vascularized that are particularly efficient for heat dissipation through that mechanism. The bill of the toco toucan (Ramphastos toco) has been described as a highly efficient thermal window and hypothesized to assist in the thermal homeostasis of this bird. Herein, we directly evaluated the contribution of heat exchange through the bill of the toco toucan and role of the bill in the delimitation of the TNZ. To do this, we measured metabolic rate, via oxygen consumption, over a range of ambient temperature from 0 to 35{degrees}C (every 5{degrees}C). MR measurements were made in birds with the bill intact (control group) and with the bill artificially insulated (experimental group). The limits of the TNZ, 10.9-25.0{degrees}C for the control group and 10.8-24.1{degrees}C for the experimental group, did not differ between the treatments. MR differed among treatments only at elevated temperatures (30 and 35{degrees}C), reaching values of 0.97 ml O2{middle dot}g-1{middle dot}h-1{middle dot}{degrees}C-1 ({+/-} 0.06) for the control group and 1.20 ml O2{middle dot}g-1{middle dot}h-1{middle dot}{degrees}C-1 ({+/-} 0.07) for the experimental group at 35{degrees}C. These results indicate that while heat dissipation through the bill does not contribute significantly to widening of the TNZ, it may well be critically important in assisting body temperature regulation at higher temperatures extending above the upper limit of the TNZ. We estimate that the contribution of the bill to total heat exchange approaches 31% of basal metabolic heat production, providing evidence of the substantial role of peripheral heat exchange and linking the role of appendage size as a key factor in the evolution of thermoregulatory responses in endotherms.

zoology↗

bioRxiv2021

Repopulation of a 3D-simulated periapical lesion cavity with triggered osteoblastic-differentiated dental pulp stem cell spheroids.

We established a proof of concept model system for the biological repair of periapical lesions using stem cell spheroids. A mesenchymal stem cell line isolated from the dental pulp of deciduous teeth (shed cells) was cultured in a 2D monolayer and then in 3D multicellular spheroids. An image of a periapical lesion of an upper lateral incisor tooth was obtained by computed micro tomography, which was used as a model for photopolymer resin 3D printing to generate a negative frame of the lesion. The negative model served to prepare a positive model of the periapical lesion cavity in an agarose gel. Shed cells cultured in monolayers or as spheroids were seeded in the positive lesion mold before or after osteoblastic differentiation. The results showed that compared to cells cultured in monolayers, the spheroids featured uniform cellularity and had a greater viability within the lesion cavity, accompanied by a temporal reduction in the expression of mRNAs typically expressed by stem cells (Cd13, Cd29, Cd44, Cd73, and Cd90). Concomitantly, there was an increase in the expression of protein markers that characterize osteoblastic differentiation (RUNX2, ALP, and BGLAP). These results provide a new perspective for regenerative endodontics with the use of spheroids prepared with shed cells to repair periapical lesions.

bioengineering↗

bioRxiv2021

The genome sequence of the avian vampire fly (Philornis downsi), an invasive nest parasite of Darwins finches in Galpagos

The invasive avian vampire fly (Philornis downsi) is considered one of the greatest threats to the unique and endemic avifauna of the Galapagos Islands, Ecuador. The fly parasitizes nearly every passerine species, including Darwins finches, in the Galapagos. The fly is thought to have been introduced from mainland Ecuador, although the full pathway of invasion is not yet known. The majority of research to date has focused on the effects of the fly on the fitness of avian hosts and explorations of mitigation methods. A lag in research related to the genetics of this invasion demonstrates, in part, a need to develop full-scale genomic resources with which to address further questions within this system. In this study, an adult P. downsi collected from San Cristobal Island within the Galapagos archipelago was sequenced to generate a high-quality genome assembly. We examined various features of the genome (e.g., coding regions, non-coding transposable elements) and carried out comparative genomics analysis against other dipteran genomes. We identified lists of gene families that are significantly expanding/contracting in P. downsi that are related to insecticide resistance, detoxification, and potential feeding ecology and counter defense against host immune responses. The P. downsi genome assembly provides an important foundational resource for studying the molecular basis of its successful invasion in the Galapagos and the dynamics of its population across multiple islands. The findings of significantly changing gene families associated with insecticide resistance and immune responses highlight the need for further investigations into the role of different gene families in aiding the flys successful invasion. Furthermore, this genomic resource will also better help inform future research studies and mitigation strategies aimed at minimizing the flys impact on the birds of the Galapagos.

genomics↗

bioRxiv2020

Gene-tree Species-tree Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

AO_SCPLOWBSTRACTC_SCPLOWThe phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

evolutionary biology↗

bioRxiv2018

Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae)

The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates, Ramphocaenus, a Polioptila guianensis complex, and the remaining members of Polioptila. Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris, which formed a clade sister to all species within Polioptila. Polioptila was composed of two clades, the first of which included the P. guianensis complex; the other contained all remaining species in the genus. Using multispecies coalescent modeling, we inferred a more than 3-fold increase in species diversity, of which 87% represent currently recognized species or subspecies. Much of this diversity corresponded to subspecies that occur in the Neotropics. We identified three polyphyletic species, and delimited 4-6 previously undescribed candidate taxa. Probabilistic modeling of geographic ranges on the species tree indicated that the family likely had an ancestral origin in South America, with all three genera independently colonizing North America. Support for this hypothesis, however, was sensitive to the taxonomic classification scheme used and the number of geographical areas allowed. Our study proposes the first phylogenetic hypothesis for Polioptilidae and provides genealogical support for the reclassification of species limits. Species limits and the resolution of geographical areas that taxa inhabit influence the inferred spatial diversification history.

evolutionary biology↗