Université de Neuchâtel
  • Neuchâtel, NE, Switzerland
Recent publications
  • Peterson Yuhala
    Peterson Yuhala
  • Pascal Felber
    Pascal Felber
  • Hugo Guiroux
    Hugo Guiroux
  • [...]
  • Gaël Thomas
    Gaël Thomas
The discovery of novel bioactive compounds produced by microorganisms holds significant potential for the development of therapeutics and agrochemicals. In this study, we conducted genome mining to explore the biosynthetic potential of entomopathogenic bacteria belonging to the genera Xenorhabdus and Photorhabdus. By utilizing next-generation sequencing and bioinformatics tools, we identified novel biosynthetic gene clusters (BGCs) in the genomes of the bacteria, specifically plu00736 and plu00747. These clusters were identified as unidentified non-ribosomal peptide synthetase (NRPS) and unidentified type I polyketide synthase (T1PKS) clusters. These BGCs exhibited unique genetic architecture and encoded several putative enzymes and regulatory elements, suggesting its involvement in the synthesis of bioactive secondary metabolites. Furthermore, comparative genome analysis revealed that these BGCs were distinct from previously characterized gene clusters, indicating the potential for the production of novel compounds. Our findings highlighted the importance of genome mining as a powerful approach for the discovery of biosynthetic gene clusters and the identification of novel bioactive compounds. Further investigations involving expression studies and functional characterization of the identified BGCs will provide valuable insights into the biosynthesis and potential applications of these bioactive compounds.
Background In agricultural ecosystems, outbreaks of diseases are frequent and pose a significant threat to food security. A successful pathogen undergoes a complex and well-timed sequence of regulatory changes to avoid detection by the host immune system; hence, well-tuned gene regulation is essential for survival. However, the extent to which the regulatory polymorphisms in a pathogen population provide an adaptive advantage is poorly understood. Results We used Zymoseptoria tritici, one of the most important pathogens of wheat, to generate a genome-wide map of regulatory polymorphism governing gene expression. We investigated genome-wide transcription levels of 146 strains grown under nutrient starvation and performed expression quantitative trait loci (eQTL) mapping. We identified cis-eQTLs for 65.3% of all genes and the majority of all eQTL loci are within 2kb upstream and downstream of the transcription start site (TSS). We also show that polymorphism in different gene elements contributes disproportionally to gene expression variation. Investigating regulatory polymorphism in gene categories, we found an enrichment of regulatory variants for genes predicted to be important for fungal pathogenesis but with comparatively low effect size, suggesting a separate layer of gene regulation involving epigenetics. We also show that previously reported trait-associated SNPs in pathogen populations are frequently cis-regulatory variants of neighboring genes with implications for the trait architecture. Conclusions Overall, our study provides extensive evidence that single populations segregate large-scale regulatory variation and are likely to fuel rapid adaptation to resistant hosts and environmental change.
Seasonal deformation of mountain rock slopes can be driven by groundwater infiltration and depletion. Such processes could explain our field observation in the Aletsch Valley, Switzerland, where GNSS‐derived 3D annual displacement amplitudes reach 3.4 cm. However, the physical mechanisms behind such groundwater‐driven surface displacements are not well understood. Here, we develop a fully coupled hydromechanical model to simulate the relevant processes in a valley slope embedded with numerous fractures of variable sizes. The magnitude and orientation of transient annual slope surface displacement obtained from our model are in overall agreement with the field observations. The key geological factors controlling the type and magnitude of reversible mountain slope deformations are fracture network geometry, fracture aperture, and regional stress field. We show that the heterogeneity and anisotropy of bedrock hydromechanical responses, originating from depth‐dependent variations of fracture properties, play a critical role in groundwater recharge and valley slope deformation. During recharge events, pore pressure perturbations migrate downward from the groundwater table and toward the receiving stream and the deep subsurface. This process driven by pressure diffusion and poroelastic stressing develops in the subsurface with a great reach of up to a few kilometers, called critical hydromechanical response zone, and controls surface deformation patterns. During groundwater recession, this hydromechanical response zone expands downward and ground surface displacement vectors rotate upwards. Our results suggest that slope surface deformation can inform about subsurface permeability structures and pore pressure fluctuations, which have important implications for understanding groundwater flow in fractured bedrock slopes.
Background Within the Hymenoptera, bees are notable for their relationship with flowering plants, being almost entirely dependent on plant pollen and nectar. Though functionally herbivorous, as a result of their role as pollinators, bees have received comparatively little attention as models for insect herbivory. Bees often display dietary specialization, but quantitative comparison against other herbivorous insects has not previously been conducted. Results In the most comprehensive analysis to date for 860 bee species, dietary specialization amounted to 50.1% of studied species collecting pollen from between 1 and 2 botanical families with a relatively long tail of dietary generalists, with 11.1% of species collecting from more than 10 botanical families. This distribution deviated from the truncated Pareto distribution of dietary breadth seen in other herbivorous insect lineages. However, this deviation was predominantly due to eusocial bee lineages, which show a range of dietary breadths that conformed to a normal distribution, while solitary bees show a typical truncated distribution not strongly different from other herbivorous insects. We hypothesize that the relatively low level of dietary specialization in bees as a whole reflects the relaxation of the constraints typically observed in herbivorous insects with a comparatively reduced importance of plant chemistry and comparatively increased importance of phenology and foraging efficiency. The long flight periods of eusocial bees that are necessary to allow overlapping generations both allows and necessitates the use of multiple flowering resources, whereas solitary bees with short flight periods have more limited access to varied resources within a constrained activity period. Conclusions Collectively, solitary bees show slightly lower specialization compared to other herbivorous insects, possibly due to their balanced relationship with plants, rather than direct antagonism such as seen in the direct consumption of plant tissues. An additional factor may be the mediocre diversity of bees at low latitudes combined with low levels of dietary specialization, whereas these areas typically display a high rate of specialization by herbivorous insects in general. Though the most important factors structuring dietary specialization in bees appear to differ from many other herbivorous insects, solitary bees show a surprisingly similar overall pattern of dietary specialization.
1. Ticks and tick-borne diseases (TBDs) form a significant and growing threat to human health and well-being in Europe, with increasing numbers of tick-borne encephalitis (TBE) and Lyme borreliosis cases being reported during the past few decades. Increasing knowledge of tick risk areas and seasonal activity remains the primary method for preventing TBDs. Crowdsourcing provides the best alternative for rapidly obtaining data on tick occurrence on a national level. 2. In order to produce and share up-to-date data of tick risk areas in Finland, an on-line platform, Punkkilive (www. punkk ilive. fi/ en), was launched April 2021. On the website, users can submit and browse tick observations, report tick numbers and hosts, and upload pictures of ticks. 3. Here, we looked at trends in the crowdsourced data from 2021, assessed the effect of local tick species on seasonality of observations and examined sampling bias in the data. 4. The high number of tick observations (n = 78,837) highlights that there was demand for such a service. Approximately 97% of 5573 uploaded pictures represented ticks. Seasonal patterns of tick observations varied across Finland, highlighting variability in the risk associated with the two human-biting tick species Ixodes ricinus and I. persulcatus, the latter having a shorter, unimodal activity peak in late spring-early summer. Tick numbers were low and the proportion of new sightings high in northern Finland, as may be expected near the latitudinal distribution limits of both species. While the number of inhabitants generally explained the number of tick observations well, geographically weighted regression models also identified areas that deviated from this general pattern. 5. This study offers a prime example of how crowdsourcing can be applied to track vectors of zoonotic diseases, to the benefit of both researchers and the public. Areas with more or less observations than predicted based on number of inhabitants were revealed, wherein more specific analyses may reveal factors contributing to lower or higher risk levels that may be used in increasing awareness. We hope that the success of Punkkilive serves to highlight the usefulness of citizen science in the prevention of vector-borne diseases.
Objectives High-quality species-specific transposable element (TE) libraries are required for studies to elucidate the evolutionary dynamics of TEs and gain an understanding of their impacts on host genomes. Such high-quality TE resources are severely lacking for species in the fungal kingdom. To facilitate future studies on the putative role of TEs in rapid adaptation observed in the fungal wheat pathogen Zymoseptoria tritici , we produced a manually curated TE library. This was generated by detecting TEs in 19 reference genome assemblies representing the global diversity of the species supplemented by multiple sister species genomes. Improvements over previous TE libraries have been made on TE boundary resolution, detection of ORFs, TE domains, terminal inverted repeats, and class-specific motifs. Data description A TE consensus library for Z. tritici formatted for use with RepeatMasker. This data is relevant to other researchers investigating TE-host evolutionary dynamics in Z. tritici or who are interested in comparative studies of the fungal kingdom . Further, this TE library can be used to improve gene annotation. Finally, this TE library increases the number of manually curated TE datasets, providing resources to further our understanding of TE diversity.
We studied the transformation of ⁵⁷ Fe-labelled ferrihydrite and lepidocrocite mixed with a flooded paddy soil by using ⁵⁷ Fe-Mössbauer spectroscopy.
Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici . We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.
While immune responses can be energetically costly, quantifying these costs is challenging. We tested the metabolic costs of immune activation in damselfish (Pomacentrus amboinensis Bleeker, 1868) following a mass-adjusted injection of lipopolysaccharide (LPS) endotoxin. Fish were divided into eight treatments: two controls (handling and saline injection) and six LPS groups with concentrations ranging from 3 to 100mg kg-1. We used intermittent flow respirometry to measure differences in oxygen uptake (deltaṀO2) 20h before versus 20h after LPS injection and changes in metabolic traits (lowest, routine and peak metabolic rates) as proxies of the aerobic costs of metabolism. Spleen somatic index (SSI) and gene expression in spleens were measured to assess immune activation. We found no difference in metabolic traits or SSI but observed different non-linear patterns of deltaṀO2 in fish exposed to 50 and 100mg kg-1 LPS compared to lower doses and controls. Fish exposed to high doses of LPS also had lower residual aerobic scope compared to controls and lower LPS doses. Fish exposed to doses of 3, 50, and 100mg kg-1 showed altered gene expression compared to the handling control. Overall, our results suggest that immune activation has measurable effects on metabolic traits that are both dose and time-dependent.
The lockdowns imposed upon cities, regions, and countries as a response to the COVID-19 pandemic are extraordinary state-sanctioned spatial interventions, both in terms of scale and scope. However, rather than a time-delimited event nor an exceptional circumstance of a temporary crisis, the pandemic lockdown was entangled with long-standing and on-going intimate and embodied histories of political violence, upheaval, militarization, displacement and dispossession. Be it as a result of war, terrorism, natural disaster, or pandemic – lockdown is more than an intervention in physical space and infrastructure alone. It is also an intervention that mobilizes, and often relies on, the sphere of the intimate along different and often unequal geographies of vulnerability. In this Theme Issue, we build on feminist geopolitics and feminist political geography to examine the intimacies of lockdown, seen through the experiences of refugees, migrants, low-income residents, as well as within the contexts of war and terrorism. Here, the politics of embodiment, domesticity and affectivity is central for understanding how lockdowns actively shape and are shaped by intimate geographies, thus advancing the theorization of the lockdown more broadly. The contributions to this Theme Issue gather around the following questions: how does the spatial politics of lockdown mobilize the sphere of the intimate? More broadly, how does the intimate help forge possibilities and places of counter-narratives of solidarity, shared vulnerabilities and care in contrast to renewed militarization, rising authoritarianism, violence, and the expanding spatialities of confinement in everyday life?
In the late eighteenth century, the practice of measuring the pulse with a mechanical watch became the symbol of the search for accuracy and objectivity in medicine, embraced by several physicians who looked up to the hard sciences, and rejected by others in the name of anti-reductionism. In the late seventeenth and early eighteenth century, however, this polarization was not yet fully established, and the two opposite approaches—the “mechanist” and the “holistic”—could be combined in original ways. In this chapter, I analyze an emblematic instance of a hybrid system, namely that proposed the English physician John Floyer (1649–1734), who combined a mechanist approach with a qualitative study of the pulse. The study of Floyer’s views will provide new insights to assess the relationship between the early modern practitioner’s body and the technological apparatus, which is rarely discussed in reference to medical work. Moreover, the analysis of Floyer’s eclectic natural philosophy will make it possible to reflect upon the frailty of doctrinal boundaries when one’s main concern was of a practical nature, such as patient care: Floyer hybridized different if not incompatible theories, insofar as it was functional to make sense of the phenomena encountered in the practice.
Background Ticks are major vectors of diseases affecting humans such as Lyme disease or domestic animals such as anaplasmosis. Cross-alteration of the vertebrate host skin microbiome and the tick microbiome may be essential during the process of tick feeding and for the mechanism of pathogen transmission. However, it has been poorly investigated. Methods We used mice bitten by field-collected ticks (nymphs and adult ticks) in different experimental conditions to investigate, by 16S rRNA gene metabarcoding, the impact of blood feeding on both the mouse skin microbiome and the tick microbiome. We also investigated by PCR and 16S rRNA gene metabarcoding, the diversity of microorganisms transmitted to the host during the process of tick bite at the skin interface and the dissemination of the pathogen in host tissues (blood, heart, and spleen). Results Most of the commensal bacteria present in the skin of control mice were replaced during the blood-feeding process by bacteria originating from the ticks. The microbiome of the ticks was also impacted by the blood feeding. Several pathogens including tick-borne pathogens (Borrelia/Borreliella, Anaplasma, Neoehrlichia, Rickettsia) and opportunistic bacteria (Williamsia) were transmitted to the skin microbiome and some of them disseminated to the blood or spleen of the mice. In the different experiments of this study, skin microbiome alteration and Borrelia/Borreliella transmission were different depending on the tick stages (nymphs or adult female ticks). Conclusions Host skin microbiome at the bite site was deeply impacted by the tick bite, to an extent which suggests a role in the tick feeding, in the pathogen transmission, and a potentially important impact on the skin physiopathology. The diversified taxonomic profiles of the tick microbiome were also modified by the blood feeding. FNmPmXVvH5C8zJYmhgJpvuVideo Abstract
Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.
Categorical parameter distributions consisting of geologic facies with distinct properties, e.g., high‐permeability channels embedded in a low‐permeability matrix, are common at contaminated sites. At these sites, low‐permeability facies store solute mass, acting as secondary sources to higher‐permeability facies, sustaining concentrations for decades while increasing risk and cleanup costs. Parameter estimation is difficult in such systems because the discontinuities in the parameter space hinder the inverse problem. This paper presents a novel approach based on Traveling Pilot points (TRIPS) and an iterative ensemble smoother (IES) to solve the categorical inverse problem. Groundwater flow and solute transport in a hypothetical aquifer with a categorical parameter distribution are simulated using MODFLOW 6. Heads and concentrations are recorded at multiple monitoring locations. IES is used to generate posterior ensembles assuming a TRIPS prior and an approximate multiGaussian prior. The ensembles are used to predict solute concentrations and mass into the future. The evaluation also includes an assessment of how the number of measurements and the choice of the geological prior determine the characteristics of the posterior ensemble and the resulting predictions. The results indicate that IES was able to efficiently sample the posterior distribution and showed that even with an approximate geological prior, a high degree of parameterization and history matching could lead to parameter ensembles that can be useful for making certain types of predictions (heads, concentrations). However, the approximate geological prior was insufficient for predicting mass. The analysis demonstrates how decision‐makers can quantify uncertainty and make informed decisions with an ensemble‐based approach. This article is protected by copyright. All rights reserved.
This dialogue, taking place between Prof. Whether and Prof. What, focuses on the nature of the relationship between ontology, conceived as the branch of philosophy concerned with the question of what entities exist, and metaphysics, conceived as the complementary part of philosophy that seeks to explain, of those entities, what they are. Most philosophers claim that it is not possible to address the first question without at the same time addressing the second, since knowing whether an entity exists requires knowing what that entity is. Prof. Whether argues against this popular position and offers a detailed analysis of the idea according to which it is possible to do ontology without engaging in metaphysics. Prof. Whether and Prof. What agree that, rather than being merely possible, in some cases it is, for methodological reasons, even preferable to start with a metaphysics-free ontology, postponing any inquiry concerning the nature of the entities included in the ontological inventory to a later stage. However, Prof. What notes that it is not always possible to do ontology without metaphysics, because there are certain kinds of entities, such as universals and possible worlds, that necessarily need a prior metaphysical characterization.
Main conclusion Our results indicate caterpillars and aphids cause similar levels of induced defences and resistance against caterpillars in wild cotton plants. These symmetrical effects are not consistent with patterns predicted by plant defensive signaling crosstalk and call for further work addressing the biochemical mechanisms underpinning these results. Abstract Plant-induced responses to attack often mediate interactions between different species of insect herbivores. These effects are predicted to be contingent on the herbivore’s feeding guild, whereby prior feeding by insects should negatively impact subsequent feeding by insects of the same guild (induced resistance) but may positively influence insects of a different guild (induced susceptibility) due to interfering crosstalk between plant biochemical pathways specific to each feeding guild. We compared the effects of prior feeding by leaf-chewing caterpillars (Spodoptera frugiperda) vs. sap-sucking aphids (Aphis gossypii) on induced defences in wild cotton (Gossypium hirsutum) and the consequences of these attacks on subsequently feeding caterpillars (S. frugiperda). To this end, we conducted a greenhouse experiment where cotton plants were either left undamaged or first exposed to caterpillar or aphid feeding, and we subsequently placed caterpillars on the plants to assess their performance. We also collected leaves to assess the induction of chemical defences in response to herbivory. We found that prior feeding by both aphids and caterpillars resulted in reductions in consumed leaf area, caterpillar mass gain, and caterpillar survival compared with control plants. Concomitantly, prior aphid and caterpillar herbivory caused similar increases in phenolic compounds (flavonoids and hydroxycinnamic acids) and defensive terpenoids (hemigossypolone) compared with control plants. Overall, these findings indicate that these insects confer a similar mode and level of induced resistance in wild cotton plants, calling for further work addressing the biochemical mechanisms underpinning these effects.
The effect of COVID-19 lockdowns on the shift from in-person (offline) social interactions to online interactions and its consequences on social support and stress attracted scholarly attention. However, much less is known about how individuals’ prior mobility experiences have influenced coping with this shift. In the present research, we hypothesized that people with mobility experiences should already be more familiar with, and could profit more from, online social interactions before the pandemic, which might buffer against the negative impact of the pandemic on the emotional social support they obtained and the stress they felt during these interactions. In order to investigate this issue, we collected data ( N = 875) in Germany during the lockdown between April and May 2021. We measured mobility by introducing a novel approach that encompasses the act of moving houses (both within a country and internationally), commuting patterns, and nationality (migration background). Participants also reported the frequency of their online and offline interactions (before and during the lockdown), as well as the emotional support they obtained from online and offline interactions and the stress felt during lockdown interactions (as compared to before the lockdown). Results provide quantitative evidence in support of the main hypothesis especially regarding migration background. We discuss the relevance of these findings for research on migration and mobility.
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2,793 members
Mihaela Nedelcu
  • Institut de sociologie (ISOCIO)
Alexander Kolpakov
  • Institut de mathématiques (IMA)
Nathalie Vuillemin
  • Chaire de littérature et savoirs
Jean-Marc Neuhaus
  • Institut de biologie (IBIOL)
Fabrice Clément
  • Cognitive Science Centre
Faubourg de l’Hôpital 41, 2000, Neuchâtel, NE, Switzerland
Head of institution
Prof. Dr. Kilian Stoffel, Rector of the University of Neuchâtel
+41 32 718 10 20 (Rectorat)