The genetic architecture of gene expression in Caenorhabditis elegans

Most organisms are exposed to a continuously changing environment throughout their life. For instance the ambient temperature is usually not constant and many species are exposed to a diverse range of anthropogenic stressors like toxic compounds. Moreover, individuals are prone to genetic changes due to mutation and allelic recombinations. All these factors might affect particular phenotypes, while others remain unchanged. This thesis provides insight into how phenotypic traits are affected by external stress factors and allelic recombinations in the nematode Caenorhabditis elegans (Nematoda; Rhabditidae). Because phenotypes and their variation may be explained by variation in gene expression, this thesis explored the architecture of gene expression and some of the elements that contribute to gene expression. Chapters 2 and 3 focus on environmental stressors with i) a specific target (two organophosphorus pesticides) and ii) a non-target mode of action (temperature) to study their influence on gene expression. A single genotype, the canonical wild type strain Bristol (N2) was used to study the effect of interacting pesticides by exposing nematodes to a toxicant mixture at two different temperatures Analysis revealed common transcriptional responses related to detoxification, stress, innate immunity, and transport of lipids to all treatments. It was found that for both pesticides these similar processes were regulated by different gene transcripts in single and combined treatments. These results also showed that the effect of a mix of low doses of pesticides is not a summed effect of the single components. Moreover, increased temperature elevates the toxic consequences to the pesticides exposures. This toxicity gain is attributed to an elevated uptake and accumulation of the toxicants in the organisms. These results support the idea that the observed higher toxicity of pesticides with temperature might be a consequence of gene-environment interactions affecting detoxification genes. Together, thefirst part of this thesis illustrates the intense crosstalk between gene pathways in response to interacting environmental stressors in C. elegans. The second part of the thesis elaborates on the influence of different genotypes as multiple perturbations on gene expression. How the genotype-phenotype relationship progresses with age was investigated using a quantitative genetics approach (genetical genomics). We performed a genetic mapping strategy of gene transcription variation (expression-QTL, eQTL) to explore the dynamics of regulatory loci affecting genome-wide gene expression at three different ages. We used a recombinant inbred line (RIL) population generated from a cross between the C. elegans strain N2 and the wild type CB4856 in Chapter 4. Also, we investigated the influence of age to reveal a genotype-by-age effect (gxaeQTL) on gene expression. The total number of detected eQTL decreased with age whereas the variation in expression increased. In developing worms, the number of genes with increased expression variation (1282) was similar to the ones with decreased expression variation (1328). In aging worms the number of genes with increased variation (1772) was nearly 5 times higher than the number of genes with a decreased expression variation (373). Furthermore, the number of cis-acting eQTL in juveniles decreased by almost 50% in old worms whereas the number of trans-acting loci decreased by ~27%, indicating that cis-regulation becomes relatively less frequent than trans-regulation in aging worms. Our findings demonstrate that eQTL patterns are strongly affected by age and suggest that gene network integrity declines with age. To better understand the changes in the gene network with age, gene expression profiles of N2 and CB4856 were generated for Chapter 5. We explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in different genotypes. The average broad sense heritability was similar in developing and aging worms; but the gene expression variance that can be attributed to genetic variance in each gene changes with age. It can be proposed that regulation became more polygenic in aging worms. These changes explain the decrease in detected eQTLs. Likewise, it explains the imbalance between highly heritable genes and eQTLs in aging worms. Chapter 6 discusses the main conclusion of this thesis in the context of the robustness theory. Robustness in biological systems provides the potential to survive severe environmental and genetic perturbations in the form of cryptic genetic variation. The variation we observed in gene transcripts due to external and internal perturbations not always translated to physiological phenotypic variation. In some cases however, the mechanisms underlying phenotypic robustness failed and phenotypic variation was observed. Such genetic cryptic variation was revealed as new molecular and physiological phenotypes. </p

Integrated GWAS and Gene Expression Suggest ORM1 as a Potential Regulator of Plasma Levels of Cell-Free DNA and Thrombosis Risk

Plasma cell-free DNA (cfDNA) is a surrogate marker of neutrophil extracellular traps (NETs) that contribute to immunothrombosis. There is growing interest about the mechanisms underlying NET formation and elevated cfDNA, but little is known about the factors involved. We aimed to identify genes involved in the regulation of cfDNA levels using data from the Genetic Analysis of Idiopathic Thrombophilia (GAIT-2) Project. Imputed genotypes, whole blood RNA-Seq data, and plasma cfDNA quantification were available for 935 of the GAIT-2 participants from 35 families with idiopathic thrombophilia. We performed heritability and GWAS analysis for cfDNA. The heritability of cfDNA was 0.26 ( p  = 3.7 × 10 (−6) ), while the GWAS identified a significant association (rs1687391, p  = 3.55 × 10 (−10) ) near the ORM1 gene, on chromosome 9. An eQTL (expression quantitative trait loci) analysis revealed a significant association between the lead GWAS variant and the expression of ORM1 in whole blood ( p  = 6.14 × 10 (−9) ). Additionally, ORM1 expression correlated with levels of cfDNA ( p  = 4.38 × 10 (−4) ). Finally, genetic correlation analysis between cfDNA and thrombosis identified a suggestive association ( ρ (g)  = 0.43, p  = 0.089). All in all, we show evidence of the role of ORM1 in regulating cfDNA levels in plasma, which might contribute to the susceptibility to thrombosis through mechanisms of immunothrombosis

First Results and Status of the LHC Test String 2

After the commissioning of String 2 Phase1 and the powering of the main circuits in autumn 2001, a short yet vigorous experimental program was carried-out to validate the final design choices for the technical systems of LHC. This program included the investigation of thermo-hydraulics of quenches quench propagation, power converter controls and tracking between power converters, as well as the measurement of currents induced in the beam screen after a quench and crossing the interconnects. Parameters significant for the LHC, such as heat loads, were also measured. During the winter shutdown the String was completed to a full cell with the addition of three pre-series dipoles (Phase 2). After a short description of the layout of Phase 1 and Phase 2, the results of the experiments are presented and the future experimental program is outlined

The prevalence of Aphanomyces astaci in invasive signal crayfish from the UK and implications for native crayfish conservation

The crayfish plague agent, Aphanomyces astaci, has spread throughout Europe, causing a significant decline in native European crayfish. The introduction and dissemination of this pathogen is attributed to the spread of invasive North American crayfish, which can act as carriers for A. astaci. As native European crayfish often succumb to infection with A. astaci, determining the prevalence of this pathogen in non-native crayfish is vital to prioritize native crayfish populations for managed translocation. In the current study, 23 populations of invasive signal crayfish (Pacifastacus leniusculus) from the UK were tested for A. astaci presence using quantitative PCR. Altogether, 13 out of 23 (56·5%) populations were found to be infected, and pathogen prevalence within infected sites varied from 3 to 80%. Microsatellite pathogen genotyping revealed that at least one UK signal crayfish population was infected with the A. astaci genotype group B, known to include virulent strains. Based on recent crayfish distribution records and the average rate of signal crayfish population dispersal, we identified one native white-clawed crayfish (Austropotamobius pallipes) population predicted to come into contact with infected signal crayfish within 5 years. This population should be considered as a priority for translocation

Genotype-dependent lifespan effects in peptone deprived Caenorhabditis elegans

Dietary restriction appears to act as a general non-genetic mechanism that can robustly prolong lifespan. There have however been reports in many systems of cases where restricted food intake either shortens, or does not affect, lifespan. Here we analyze lifespan and the effect of food restriction via deprived peptone levels on lifespan in wild isolates and introgression lines (ILs) of the nematode Caenorhabditis elegans. These analyses identify genetic variation in lifespan, in the effect of this variation in diet on lifespan and also in the likelihood of maternal, matricidal, hatching. Importantly, in the wild isolates and the ILs, we identify genotypes in which peptone deprivation mediated dietary restriction reduces lifespan. We also identify, in recombinant inbred lines, a locus that affects maternal hatching, a phenotype closely linked to dietary restriction in C. elegans. These results indicate that peptone deprivation mediated dietary restriction affects lifespan in C. elegans in a genotype-dependent manner, reducing lifespan in some genotypes. This may operate by a mechanism similar to dietary restriction

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020.

Following its emergence in late 2019, the spread of SARS-CoV-21,2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail3–5. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel within Europe resumed in the summer of 2020. Here we report on a SARS-CoV-2 variant, 20E (EU1), that was identified in Spain in early summer 2020 and subsequently spread across Europe. We find no evidence that this variant has increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant’s success. Despite travel restrictions, we estimate that 20E (EU1) was introduced hundreds of times to European countries by summertime travellers, which is likely to have undermined local efforts to minimize infection with SARS-CoV-2. Our results illustrate how a variant can rapidly become dominant even in the absence of a substantial transmission advantage in favourable epidemiological settings. Genomic surveillance is critical for understanding how travel can affect transmission of SARS-CoV-2, and thus for informing future containment strategies as travel resumes. © 2021, The Author(s), under exclusive licence to Springer Nature Limited

Base de datos de abejas ibéricas

Las abejas son un grupo extremadamente diverso con más de 1000 especies descritas en la península ibérica. Además, son excelentes polinizadores y aportan numerosos servicios ecosistémicos fundamentales para la mayoría de ecosistemas terrestres. Debido a los diversos cambios ambientales inducidos por el ser humano, existen evidencias del declive de algunas de sus poblaciones para ciertas especies. Sin embargo, conocemos muy poco del estado de conservación de la mayoría de especies y de muchas de ellas ignoramos cuál es su distribución en la península ibérica. En este trabajo presentamos un esfuerzo colaborativo para crear una base de datos de ocurrencias de abejas que abarca la península ibérica e islas Baleares que permitirá resolver cuestiones como la distribución de las diferentes especies, preferencia de hábitat, fenología o tendencias históricas. En su versión actual, esta base de datos contiene un total de 87 684 registros de 923 especies recolectados entre 1830 y 2022, de los cuales un 87% presentan información georreferenciada. Para cada registro se incluye información relativa a la localidad de muestreo (89%), identificador y colector de la especie (64%), fecha de captura (54%) y planta donde se recolectó (20%). Creemos que esta base de datos es el punto de partida para conocer y conservar mejor la biodiversidad de abejas en la península ibérica e Islas Baleares. Se puede acceder a estos datos a través del siguiente enlace permanente: https://doi.org/10.5281/zenodo.6354502ABSTRACT: Bees are a diverse group with more than 1000 species known from the Iberian Peninsula. They have increasingly received special attention due to their important role as pollinators and providers of ecosystem services. In addition, various rapid human-induced environmental changes are leading to the decline of some of its populations. However, we know very little about the conservation status of most species and for many species, we hardly know their true distributions across the Iberian Peninsula. Here, we present a collaborative effort to collate and curate a database of Iberian bee occurrences to answer questions about their distribution, habitat preference, phenology, or historical trends. In total we have accumulated 87 684 records from the Iberian Peninsula and the Balearic Islands of 923 different species with 87% of georeferenced records collected between 1830 and 2022. In addition, each record has associated information such as the sampling location (89%), collector and person who identified the species (64%), date of the capture (54%) and plant species where the bees were captured (20%). We believe that this database is the starting point to better understand and conserve bee biodiversity in the Iberian Peninsula. It can be accessed at: https://doi.org/10.5281/zenodo.6354502Esta base de datos se ha realizado con la ayuda de los proyectos EUCLIPO (Fundação para a Ciência e a Tecnologia, LISBOA-01-0145-FEDER-028360/EUCLIPO) y SAFEGUARD (ref. 101003476 H2020 -SFS-2019-2).info:eu-repo/semantics/publishedVersio

The genetic architecture of gene expression in Caenorhabditis elegans

Most organisms are exposed to a continuously changing environment throughout their life. For instance the ambient temperature is usually not constant and many species are exposed to a diverse range of anthropogenic stressors like toxic compounds. Moreover, individuals are prone to genetic changes due to mutation and allelic recombinations. All these factors might affect particular phenotypes, while others remain unchanged. This thesis provides insight into how phenotypic traits are affected by external stress factors and allelic recombinations in the nematode Caenorhabditis elegans (Nematoda; Rhabditidae). Because phenotypes and their variation may be explained by variation in gene expression, this thesis explored the architecture of gene expression and some of the elements that contribute to gene expression. Chapters 2 and 3 focus on environmental stressors with i) a specific target (two organophosphorus pesticides) and ii) a non-target mode of action (temperature) to study their influence on gene expression. A single genotype, the canonical wild type strain Bristol (N2) was used to study the effect of interacting pesticides by exposing nematodes to a toxicant mixture at two different temperatures Analysis revealed common transcriptional responses related to detoxification, stress, innate immunity, and transport of lipids to all treatments. It was found that for both pesticides these similar processes were regulated by different gene transcripts in single and combined treatments. These results also showed that the effect of a mix of low doses of pesticides is not a summed effect of the single components. Moreover, increased temperature elevates the toxic consequences to the pesticides exposures. This toxicity gain is attributed to an elevated uptake and accumulation of the toxicants in the organisms. These results support the idea that the observed higher toxicity of pesticides with temperature might be a consequence of gene-environment interactions affecting detoxification genes. Together, thefirst part of this thesis illustrates the intense crosstalk between gene pathways in response to interacting environmental stressors in C. elegans. The second part of the thesis elaborates on the influence of different genotypes as multiple perturbations on gene expression. How the genotype-phenotype relationship progresses with age was investigated using a quantitative genetics approach (genetical genomics). We performed a genetic mapping strategy of gene transcription variation (expression-QTL, eQTL) to explore the dynamics of regulatory loci affecting genome-wide gene expression at three different ages. We used a recombinant inbred line (RIL) population generated from a cross between the C. elegans strain N2 and the wild type CB4856 in Chapter 4. Also, we investigated the influence of age to reveal a genotype-by-age effect (gxaeQTL) on gene expression. The total number of detected eQTL decreased with age whereas the variation in expression increased. In developing worms, the number of genes with increased expression variation (1282) was similar to the ones with decreased expression variation (1328). In aging worms the number of genes with increased variation (1772) was nearly 5 times higher than the number of genes with a decreased expression variation (373). Furthermore, the number of cis-acting eQTL in juveniles decreased by almost 50% in old worms whereas the number of trans-acting loci decreased by ~27%, indicating that cis-regulation becomes relatively less frequent than trans-regulation in aging worms. Our findings demonstrate that eQTL patterns are strongly affected by age and suggest that gene network integrity declines with age. To better understand the changes in the gene network with age, gene expression profiles of N2 and CB4856 were generated for Chapter 5. We explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in different genotypes. The average broad sense heritability was similar in developing and aging worms; but the gene expression variance that can be attributed to genetic variance in each gene changes with age. It can be proposed that regulation became more polygenic in aging worms. These changes explain the decrease in detected eQTLs. Likewise, it explains the imbalance between highly heritable genes and eQTLs in aging worms. Chapter 6 discusses the main conclusion of this thesis in the context of the robustness theory. Robustness in biological systems provides the potential to survive severe environmental and genetic perturbations in the form of cryptic genetic variation. The variation we observed in gene transcripts due to external and internal perturbations not always translated to physiological phenotypic variation. In some cases however, the mechanisms underlying phenotypic robustness failed and phenotypic variation was observed. Such genetic cryptic variation was revealed as new molecular and physiological phenotypes