Biology subjects

Moura, A.

Publications and source records attributed to Moura, A..

7 recordsLinked to original sources

bioRxiv2023

The firing dynamics of replication origins affect their genome distribution

DNA replication in yeast and in many other organisms starts from well-defined locations on the DNA known as replication origins. The spatial distribution of these origins in the genome is particularly important in ensuring that replication is completed quickly. Cells are more vulnerable to DNA damage and other forms of stress while they are replicating their genome. This raises the possibility that the spatial distribution of origins is under selection pressure. In this work we investigate the hypothesis that natural selection favours origin distributions leading to shorter replication times. Using a simple mathematical model, we show that this hypothesis leads to two main predictions about the origin distributions: that neighbouring origins that are inefficient (less likely to fire) are more likely to be close to each other than efficient origins; and that neighbouring origins with larger differences in firing times are more likely to be close to each other than origins with similar firing times. We test these predictions using next-generation sequencing data, and show that they are both supported by the data.

systems biology↗

bioRxiv2023

First genome-based characterization of Listeria monocytogenes in Costa Rica

Genomic data on the foodborne pathogen Listeria monocytogenes from Central America are scarse. We analysed 92 isolates collected in Costa Rica over a decade from different regions, compared them to publicly available genomes and identified unnoticed outbreaks. This study calls for mandatory reporting of listeriosis to improve pathogen surveillance.

genomics↗

bioRxiv2021

Listeria monocytogenes faecal carriage is common and driven by microbiota

Listeria genus comprises two opportunistic pathogenic species, L. monocytogenes (Lm) and L. ivanovii, and several non-pathogenic species. All can thrive as saprophytes, whereas only pathogenic species cause systemic infections in human and cattle. Identifying Listeria species respective biotopes is critical to understand the ecological contribution of Listeria pathogenic potential. Here, we aimed at detecting Listeria in samples of diverse origins, to highlight ecological differences between pathogenic and non-pathogenic species. We retrieved 16S rDNA datasets from the metagenomics MG-RAST database and determined the prevalence and abundance of Listeria species in various sources. Overall, Listeria was detected in 14% of datasets. Lm was the most prevalent species, most abundant both in soil and host-associated environments, including in 5% of human stools. Lm was also detected in 10% of human stool samples from an independent cohort of 900 healthy asymptomatic donors. A specific microbiota signature was associated with Lm faecal carriage in human, as well as in experimentally inoculated mice, in which it preceded Lm long-term gut colonization, indicating that gut microbiota composition influences Lm faecal carriage. These results suggest that asymptomatic faecal carriage, rather than disease, exerts purifying selection on Lm "virulence genes".

microbiology↗

bioRxiv2020

Emergence and global spread of Listeria monocytogenes main clinical clonal complex

Retracing microbial emergence and spread is essential to understanding the evolution and dynamics of pathogens. The bacterial foodborne pathogen Listeria monocytogenes clonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with listeriosis, and is strongly associated with cattle and dairy products. Here we analysed 2,021 Lm-CC1 isolates collected from 40 countries, since the first Lm isolation to the present day, to define its evolutionary history and population dynamics. Our results suggest that Lm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming in the 20th century. Lm-CC1 then firmly established at a local level, with limited inter-country spread. This study provides an unprecedented insight into Lm-CC1 phylogeography and dynamics and can contribute to effective disease surveillance to reduce the burden of listeriosis.

genomics↗

bioRxiv2020

Road to ruin: Herbivory in a common tropical weed (Turnera subulata) along a rural-urban gradient

Urbanization is associated with numerous changes to the biotic and abiotic environment, many of which degrade the environment and lead to a loss of biodiversity. Cities often have elevated pollution levels that harm wildlife; however, the increased concentration of some pollutants can fertilize urban plants, leading to corresponding positive effects on herbivore populations. Increases in herbivory rates may lead to natural selection for greater defence phenotypes in plants. However, evidence supporting increased herbivory leading to the evolution of plant defence in urban environments is contradictory, and entirely absent from tropical regions of the world. To address these research gaps, we evaluated herbivory on Turnera subulata, a common urban wildflower, along an urbanization gradient in Joao Pessoa, Brazil. We predicted that higher rates of herbivory in urban areas would lead these populations to evolve cyanogenesis, a chemical defence found in a closely related Turnera species. We assessed herbivory and screened for cyanogenesis in 32 populations along the urbanization gradient, quantified by the Human Footprint Index. Our results show that urbanization is significantly associated with increased herbivory rates in T. subulata populations. Despite elevated herbivory, we found no evidence for the evolution of cyanongenesis in any of the populations, suggesting that the fitness effects of leaf herbivory are not extreme enough to select for the evolution of plant defence in these populations. Habitat loss, predator release, and nutrient enrichment likely act together to increase the abundance of herbivorous arthropods, influencing the herbivory patterns observed in our study.

ecology↗

bioRxiv2019

Seminal quality and global proteomic analysis of spermatozoa from captive Amazon squirrel monkeys (Saimiri collinsi Osgood, 1916) during the dry and rainy seasons

The squirrel monkey (Saimiri collinsi), a Neotropical primate endemic to the Amazon in Brazil, is used as a biological model for reproductive research on the genus Saimiri. Although this animal is known to exhibit reproductive seasonality, nothing is known about the differences in its seminal quality, sperm protein composition, or sperm protein profile between the breeding (dry) and non-breeding (rainy) seasons. Thus, the aims of this study were to evaluate the quality of S. collinsi semen during the dry and rainy seasons and to describe the global sperm proteomics and expression variations in the sperm proteins during the two seasons. Aside from the pH, there was no difference in the seminal quality between the dry and rainy seasons. The study approach based on bottom-up proteomics allowed the identification of 2343 proteins present in the sperm samples throughout these two seasons. Of the 79 proteins that were differentially expressed between the two seasons, 39 proteins that were related to spermatogenesis, sperm motility, capacitation, fecundation, and defense systems against oxidative stress were upregulated in the dry season. Knowledge on the sperm proteins provides crucial information for elucidating the underlying mechanisms associated with sperm functionality. Thus, our results help to advance our understanding of the reproductive physiology of S. collinsi, providing valuable information for the improvement of protocols used in assisted reproduction techniques for the conservation of endangered Saimiri species.

cell biology↗

bioRxiv2019

Specific targeting of intestinal Prevotella copri by a Listeria monocytogenes bacteriocin

Deciphering the specific function of every microorganism in microbial gut communities is a key issue to interrogate their role during infection. Here, we report the discovery of a Listeria bacteriocin, Lmo2776, that specifically targets the abundant gut commensal Prevotella copri and affects Listeria infection. Oral infection of conventional mice with a {Delta}lmo2776 mutant leads to a thinner intestinal mucus layer and higher Listeria loads both in the intestinal content and deeper tissues compared to WT Listeria, while no difference is observed in germ-free mice. This microbiota-dependent effect is phenocopied by precolonization of germ-free mice before Listeria infection, with P. copri, but not with other commensals. Together, these data unveil a role for Prevotella in controlling intestinal infection, highlighting that pathogens may selectively deplete microbiota to avoid excessive inflammation.

microbiology↗