Biology subjects

Santos, J. L.

Publications and source records attributed to Santos, J. L..

11 recordsLinked to original sources

bioRxiv2026

Divergent transcriptional responses of conserved cellular machinery to warming and phosphorus limitation in freshwater phytoplankton

Lakes are simultaneously warming and becoming phosphorus limited, but whether phytoplankton taxa of the same phylum respond through similar molecular mechanisms remains unclear, challenging a common assumption underlying predictions of ecological responses to environmental change. We cultured four freshwater phytoplankton species, including two diatoms (Fragilaria crotonensis and Nitzschia palea) and two cyanobacteria (Microcystis aeruginosa and Synechococcus sp.), across factorial gradients of temperature (20, 24 and 28 {degrees}C) and phosphorus (P) limitation, and characterized gene expression using RNA-seq, differential expression analysis and signed gene set enrichment. We generated predictions for expected responses for categories of gene functions derived from the growth rate (GRH) and temperature-dependent physiology hypotheses (TDPH). Warming and P limitation engaged largely the predicted functional categories in all species, however the direction of the response was not conserved, even within phyla--the two cyanobacteria regulated photosynthesis, ribosomal and chaperone genes in opposite directions. Ribosome- and translation-related genes gave the strongest warming response and, in N. palea, reversed direction within the species, increasing between 20 and 24 {degrees}C and decreasing between 24 and 28 {degrees}C, below the strain's thermal optimum estimated under moderate P limitation. Ribosomal allocation thus supported each hypothesis in different species and temperature ranges and was not predicted by thermal position alone. Where the interaction effects could be tested, P limitation rarely recruited novel pathways but modified existing warming responses, suppressing them in F. crotonensis and amplifying and redirecting them in M. aeruginosa. Molecular responses to combined drivers therefore diverge among related taxa, cautioning against aggregating species into functional groups when forecasting phytoplankton responses to global change.

molecular biology↗

bioRxiv2026

Genomic evidence for within-species thermal adaptation in collagen genes

Collagen is the most abundant protein in animals. Its thermal stability depends on its specific amino acid composition within the repeated Gly-Xaa-Yaa motifs forming the triple helix structure. Proline increases collagen rigidity, while serine enhances its elasticity--properties that contribute to collagen function and that vary with temperature. Although variation in collagen composition has been linked to temperature adaptation across evolutionary distinct taxa, its role within a species remains unclear. Here, we tested whether collagen genes across populations of the freshwater crustacean, Daphnia magna, show a signature of local adaptation to the ambient temperature. Analysing 39 collagen genes from 215 D. magna populations across three phylogeographic lineages spawning four continents, we found that animals from populations in warmer climates have higher proline and lower serine content in collagen--consistent with enhanced protein stability at higher temperatures. This variation was also associated with experimentally measured upper temperature tolerance. Parallel directional patterns of amino acid change appeared across genetically distinct lineages. Collagen genes also showed strong signatures of positive selection, comparable to that of immune-related genes, supporting a scenario of polygenic molecular role in adaptive responses. Our findings provide evidence of intraspecific molecular evolution in collagen amino acid composition driven by environmental temperature. Additionally, our study bridges macroevolutionary patterns with microevolutionary processes, posing the first intraspecific evidence that collagen genes can contribute to responses to environmental gradients at the molecular level, and thus, advancing our understanding of molecular adaptation of constrained structural proteins in an environmental context.

evolutionary biology↗

bioRxiv2026

Rapid shallow-water saturation and deep-water expansion of an invasive freshwater ecosystem engineer in a deep European lake

Quagga mussels (Dreissena rostriformis bugensis) are ecosystem engineers that can alter nutrient cycling, benthic-pelagic coupling, and food-web structure in deep lakes. Although their invasion trajectories are well documented in the Laurentian Great Lakes in North America, depth-specific population dynamics remain poorly resolved in recently invaded European perialpine lakes. We analyzed five annual lake-wide surveys (2021-2025) from 54 stations spanning 2.4-253 m depth in Lake Constance to quantify changes in quagga mussel density, biomass, and shell-length distribution. Contrary to expectations of lake-wide exponential growth, shallow-water populations (< 20 m) showed no significant increase during the study period and appear to have reached carrying capacity before monitoring began. In contrast, densities increased monotonically at intermediate depths (40-125 m), indicating ongoing expansion into deeper strata. Mean shell length declined with depth, and size distributions in shallow waters shifted toward larger individuals, consistent with a transition from active recruitment to somatic growth of established mussels. Compared with the Laurentian Great Lakes, Lake Constance already has substantially higher shallow-water biomass, whereas deeper invasion trajectories are broadly similar. These results show that quagga mussel invasion in deep European lakes can combine rapid littoral saturation with slower profundal expansion, complicating direct transfer of predictions from the Great Lakes. Continued depth-stratified monitoring will be essential for anticipating future ecosystem effects in perialpine lakes.

ecology↗

bioRxiv2024

Genetic dissection of MutL complexes in Arabidopsis meiosis

During meiosis, homologous chromosomes exchange genetic material through crossing-over. The main crossover pathway relies on ZMM proteins, including ZIP4 and HEI10, and is typically resolved by the MLH1/MLH3 heterodimer, MutL{gamma}. Our analysis of plant fertility and bivalent formation revealed that the MUS81 endonuclease can partially compensate for the MutL{gamma} loss. Comparing genome-wide crossover maps of the mlh1 mutant with ZMM-deficient mutants and lines with varying HEI10 levels reveals that while crossover interference persists in mlh1, it is weakened. Additionally, mlh1 show reduced crossover assurance, leading to a higher incidence of aneuploidy in offspring. This is likely due to MUS81 resolving intermediates without the crossover bias seen in MutL{gamma}. Comparing mlh1 mlh3 mus81 and zip4 mus81 mutants suggests that additional crossover pathways emerge in the absence of both MutL{gamma} and MUS81. The loss of MutL{gamma} can also be suppressed by eliminating the FANCM helicase. Elevated expression of MLH1 or MLH3 increases crossover frequency, while their overexpression significantly reduces crossover numbers and plant fertility, highlighting the importance for tight control of MLH1/MLH3 levels. By contrast, PMS1, a component of the MutL endonuclease, appears not to be involved in crossing-over. Together, these findings demonstrate the unique role of MutL{gamma} in ZMM-dependent crossover regulation.

genetics↗

bioRxiv2024

Trehalose mediates salinity-stress tolerance in a crustacean

Salinization poses an increasing problem worldwide, threatening freshwater organisms and raising questions about ability to adapt. We explore the mechanisms enabling a planktonic crustacean to tolerate elevated salinity. By gradually raising water salinity in clonal cultures from 185 Daphnia magna populations, we showed that salt tolerance strongly correlates with native habitat salinity, indicating local adaptation. A GWAS revealed a major effect of the Alpha,alpha-trehalose-phosphate synthase (TPS) gene, suggesting that trehalose production facilitates salinity tolerance. We found a positive correlation between water salinity and trehalose concentrations in tolerant animals, while intolerant animals failed to produce trehalose. Using CRISPR/Cas9, a silenced TPS gene supported the role of trehalose under salt stress. Our study highlights how a keystone freshwater animal adapts to salinity stress using an evolutionarily conserved mechanism known in plants and bacteria, but not in metabolic-active animals. HighlightsO_LISalinity tolerance is a locally adapted trait in Daphnia magna C_LIO_LIThe trehalose TPS gene shows a strong association with salinity tolerance C_LIO_LITrehalose content increases with water salinity allowing survival of tolerant genotypes C_LIO_LINon-functional TPS genes reduce salinity tolerance by preventing trehalose production C_LI

evolutionary biology↗

bioRxiv2022

Beyond inappropriate fire regimes: a synthesis of fire-driven declines of threatened mammals in Australia

Fire can promote biodiversity but changing patterns of fire threaten species worldwide. While scientific literature often describes inappropriate fire regimes as a significant threat to biodiversity, less attention has been paid to the characteristics that make a fire regime inappropriate. We go beyond this generic description and synthesize how inappropriate fire regimes contribute to declines of animal populations, using threatened mammals as a case study. We developed a demographic framework for classifying mechanisms by which fire regimes cause population decline, and applied the framework in a systematic review to identify fire characteristics and interacting threats associated with population declines in Australian threatened land mammals (n=99). Inappropriate fire regimes threaten 88% of Australian threatened land mammals. Our review indicates that intense, large, and frequent fires are the primary cause of fire-related population declines, particularly through their influence on survival rates. However, several species are threatened by a lack of fire and there is considerable uncertainty in the evidence base for fire-related declines. Climate change and predation are documented or predicted to interact with fire to exacerbate mammalian declines. This demographic framework will help target conservation actions globally and would be enhanced by empirical studies of animal survival, dispersal, and reproduction.

ecology↗

bioRxiv2019

The independent and combined influence of schizophrenia polygenic risk score and heavy cannabis use on risk for psychotic disorder: A case-control analysis from the EUGEI study.

Background: Some recent studies have challenged the direction of causality for the association between cannabis use and psychotic disorder, suggesting that cannabis use initiation is explained by common genetic variants associated with risk of schizophrenia. We used data from the European Union Gene-Environment Interaction consortium (EUGEI) case-control study to test for the independent and combined effect of heavy cannabis use, and of Schizophrenia Polygenic risk score (SZ PRS), on risk for psychotic disorder. Methods: Genome-wide data were obtained from 492 first episode psychosis patients (FEPp) and from 787 controls of European Ancestry, and used to generate SZ PRS from the summary results of an independent meta-analysis. Information on pattern of cannabis use was used to build a 7-level frequency-type composite cannabis use measure that we previously found was a strong predictor of psychotic disorder. Results: SZ PRS did not predict cannabis initiation (b=0.027; p=0.51) or how frequently controls (b=0.027; p=0.06) or FEPp (b=0.006; p=0.91) used it, or the type of cannabis they used (Controls: b = 0.032; p=0.31); FEPp: b= 0.005; p=0.89). The frequency-type composite cannabis use measure (OR=1.32; 95% CI 1.22-1.44) and SZ PRS (OR=2.29; 95%CI 1.71-3.05) showed independent effects from each other on the OR for psychotic disorder. Conclusion: SZ PRS does not predict an individual s propensity to try cannabis, frequency of use, or the potency of the cannabis used. Our findings provide the first evidence that SZ PRS and heavy cannabis use exert effects independent from each other on the risk for psychotic disorder.

genetics↗

bioRxiv2019

Jumping To Conclusions, General Intelligence, And Psychosis Liability: Findings From The Multicentric EU-GEI Case-Control Study

BackgroundThe \"jumping to conclusions\" (JTC) bias is associated with both psychosis and general cognition but their relationship is unclear. In this study, we set out to clarify the relationship between the JTC bias, IQ, psychosis and polygenic liability to schizophrenia and IQ.\n\nMethods817 FEP patients and 1294 population-based controls completed assessments of general intelligence (IQ), and JTC (assessed by the number of beads drawn on the probabilistic reasoning \"beads\" task) and provided blood or saliva samples from which we extracted DNA and computed polygenic risk scores for IQ and schizophrenia.\n\nResultsThe estimated proportion of the total effect of case/control differences on JTC mediated by IQ was 79%. Schizophrenia Polygenic Risk Score (SZ PRS) was non-significantly associated with a higher number of beads drawn (B= 0.47, 95% CI -0.21 to 1.16, p=0.17); whereas IQ PRS (B=0.51, 95% CI 0.25 to 0.76, p<0.001) significantly predicted the number of beads drawn, and was thus associated with reduced JTC bias. The JTC was more strongly associated with higher level of psychotic-like experiences (PLE) in controls, including after controlling for IQ (B= -1.7, 95% CI -2.8 to -0.5, p=0.006), but did not relate to delusions in patients.\n\nConclusionsthe JTC reasoning bias in psychosis is not a specific cognitive deficit but is rather a manifestation or consequence, of general cognitive impairment. Whereas, in the general population, the JTC bias is related to psychotic-like experiences, independent of IQ. The work has potential to inform interventions targeting cognitive biases in early psychosis.

neuroscience↗

bioRxiv2018

MOMO - Multi-Objective Metabolic mixed integer Optimization: application to yeast strain engineering

In this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering.\n\nProduction of ethanol by the widely used cell factory Saccharomyces cerevisiae was adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did an in vivo validation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain. The multi-objective programming framework we developed, called Momo, is open-source and uses PolySCIP{ddagger} as underlying multi-objective solver. Momo is available at http://momo-sysbio.gforge.inria.fr

systems biology↗

bioRxiv2018

Wolbachia both aids and hampers the performance of spider mites on different host plants

In the last decades, many studies had revealed the potential role of arthropod bacterial endosymbionts in shaping the host range of generalist herbivores and their performance on different host plants, which, in turn, might affect endosymbiont distribution in herbivores populations. We tested this by measuring the prevalence of endosymbionts in natural populations of the generalist spider mite Tetranychus urticae on different host plants. Focusing on Wolbachia, we then analysed how symbionts affected mite life-history traits on the same host-plants in the laboratory. Overall, the prevalences of Cardinium and Rickettsia were low, whereas that of Wolbachia was high, with the highest values on bean and eggplant and the lowest on purple, tomato and zuchini. Although most mite life-history traits were affected by the plant species only, Wolbachia infection was detrimental for egg hatching rate on purple and zucchini, and led to a more female-biased sex ratio on purple and eggplant. These results suggest that endosymbionts may affect the host range of polyphagous herbivores, both by aiding and hampering their performance, depending on the host plant and on the life-history trait that affects performance the most. Conversely, endosymbiont spread may be facilitated or hindered by the plants on which infected herbivores occur.

ecology↗

bioRxiv2018

Common variants in ABCG8 and TRAF3 genes confer risk for gallstone disease and gallbladder cancer in admixed Latinos with Mapuche Native American ancestry

BackgroundLatin Americans and Chilean Amerindians have the highest prevalence of cholesterol gallstone disease (GSD) and gallbladder cancer (GBC) in the world. A handful of loci have been associated with GSD in populations of predominantly European ancestry, however they only explain a small portion of the population-attributable risk of the disease.\n\nMethodsWe performed a genome-wide association study (GWAS) for GSD in 1,095 admixed Latinos with Mapuche Native American Ancestry, followed by a replication analysis of 10 candidate single nucleotide polymorphisms (SNPs) with suggestive genome-wide significance (P<1x10-5) in 1,643 individuals. Disease status was assessed by cholecystectomy or abdominal ultrasonography. Logistic regression analyses were adjusted for age, sex, BMI, Type 2 Diabetes and Amerindian ancestry. Associated variants were further examined in two large GSD European populations and in a Chilean gallbladder cancer (GBC) cohort. We determined the expression levels of a novel GSD-candidate gene in normal and GSD-tissue samples.\n\nResultsWe consistently replicated the ABCG8 gene (rs11887534; P=3.24x10-8, OR=1.74) associated with GSD in admixed Latinos and identified a novel candidate signal within the TRAF3 gene on chromosome 14 (rs12882491; P=1.11x10-7, OR=1.40). ABCG8 and TRAF3 variants also conferred risk to GBC. Gene expression analyses indicated that TRAF3 levels were significantly decreased in the gallbladder (P=0.015) and the duodenal mucosa (P=0.001) of affected GSD individuals compared to healthy controls.\n\nConclusionsWe confirmed ABCG8 and identified TRAF3 both associated with GSD and GBC in admixed Latinos. Decreased TRAF3 expression levels could enhance gallbladder inflammation as is observed in GSD and GSD-associated GBC.

genetics↗