Biology subjects

Vasseur, L.

Publications and source records attributed to Vasseur, L..

9 recordsLinked to original sources

bioRxiv2026

Ecosystem disservices are underrepresented in literature on annual crop agroecosystems

Maximising ecosystem service (ES) benefits while minimising ecosystem disservices (EDS) is essential for ecological intensification in annual crop systems. Yet ecosystem disservices are often underreported in the scientific literature, potentially biasing how agroecosystem functioning is understood. To test this, we built a predicted network of plausible links between ecosystem service providers (taxa or functional groups that can deliver ecosystem services or disservices), and the ES or EDS they may provide. We then compared this with a realised network based on systematic Scopus searches of annual crop literature. The predicted network contained 47 nodes and 103 links, whereas the realised network contained 33 nodes and 58 links, representing declines of 29.8% in nodes and 43.7% in links. Overall connectivity declined, especially for highly connected nodes, and four of the nine predicted disservice nodes were absent from the literature. ES links were more likely to be documented than EDS links, and EDS links were three times more likely to be absent. Across all links, ES were reported in 6.6 times more papers than EDS. Projected networks, which map indirect connections by linking ES directly to EDS if they share common providers, showed that these bundled interactions were strongly reduced, obscuring multifunctionality and trade-offs. This systematic underrepresentation of EDS, reflecting a cognitive bias, can inflate perceived benefits, distort the evaluation of key taxa and interactions, and create unrealistic expectations about intervention outcomes in biological crop protection. Addressing EDS alongside ES is therefore essential for more balanced assessments of crop-system management and better-informed decisions.

ecology↗

bioRxiv2026

Adaptive evolution to thermal stress underpins climate resilience in a cosmopolitan arthropod

Adaptive evolution enables species to survive and thrive under changing environmental conditions. In the face of accelerating global climate change, thermal stress represents a major challenge to the persistence of terrestrial arthropods. Understanding the genetic mechanisms underlying thermal adaptation is therefore critical for predicting species evolutionary potential and future success. Here, we combine experimental evolution, phenotypic assays, and multi-omics analyses to investigate the adaptive responses of the diamondback moth (Plutella xylostella), a globally destructive pest of cruciferous crops, to contrasting thermal environments. Populations evolved under hot (32{degrees}C/27{degrees}C) and cold (15{degrees}C/10{degrees}C) regimes exhibited distinct life history and fitness traits relative to those maintained under favorable conditions (26{degrees}C). The hot strain showed accelerated development, higher fecundity, and increased survival under extreme heat, while the cold strain exhibited lower supercooling and freezing points, indicating enhanced cold hardiness. Integrated transcriptomic and metabolomic analyses revealed extensive transcriptional reprogramming and convergent metabolic adjustments, notably a reduction in lipid metabolism to conserve energy under thermal stress. Crucially, non-synonymous mutations in PxSODC enhance superoxide scavenging efficiency, enabling effective oxidative stress management at lower gene expression levels. Furthermore, we identified epigenetic regulation via DNA methylation as a key mediator of this thermal tolerance. Together, these coordinated mutational, epigenetic, and metabolic insights highlight this arthropods capacity for global dispersal and likely persistence under climate change, establishing a framework for understanding equivalent effects in other species.

evolutionary biology↗

bioRxiv2024

Acinetobacter baumannii's Great Escape: How a Membrane Protein Interacts with Fibronectin to Evade Immunity.

Bacterial resistance and nosocomial infections are serious threats compromising public health in numerous countries. Acinetobacter baumannii has been identified as one of the most serious pathogens, due to its potential virulence and the development of multiple resistance. In this contribution by using all-atom molecular dynamics simulation, we analyze the structure and the properties of the OmpA protein, which is present in the bacterial external membrane. We also analyze the structure of possible protein/protein complexes formed between OmpA and the human fibronectin, which may ultimately lead to the immune escaping of the bacteria. For the first time, we provide for the first time plausible structure of the complex also identifying suitable amino acid mediating the interaction, and thus, constituting suitable drug targets to disrupt the complex formation.

biophysics↗

bioRxiv2024

Contribution of GC content to differentiated region formation along a speciation continuum

Genome architecture can interact with evolutionary processes and be involved in the formation of differentiated regions potentially containing adaptation and speciation loci. Regions of low GC content can be linked to low mutation and recombination rates. These effects on the formation of heterozygous differentiation landscapes have not been investigated. Here, we explored mutation accumulation and group divergence along a speciation continuum using 499 genomes of Apis cerana, with a widely distributed Central group diverged with its peripheral groups at both population genetic and phylogenetic timescales. We found that the differentiated regions had generally lower recombination and GC content than the rest of the genome, with lower-than-average divergence (dxy) initially to higher-than-average ones at deeper timescale. Most rare alleles ([~]80%) are AT-biased that derived from GC, resulting in lower AT-biased mutations in low-GC regions. Multiple regression analysis further shows that reduced mutation and recombination rates are associated with decreased diversity, particularly in regions with low GC content. Moreover, in all A. cerana groups, higher mutation load and less efficient selection in low-GC regions compared with high-GC regions suggest that restricted recombination is important in mutation accumulation (e.g., AT-biased) and group divergence. This pattern explains the increased dxy in low-GC regions over evolutionary time. Finally, low-GC regions possess higher proportion of group-specific polymorphisms, which reconciliate discordance between mitochondrial and nuclear phylogenies in A. cerana. Our results highlight the contribution of genome architectures to the formation of differentiation landscapes along divergent groups, emphasizing caution regarding loci identified solely from differentiated regions. Significance StatementThis study shows the low nucleotide diversity in differentiated regions could be simply attributed to genome architectures (e.g., gBGC, local recombination and mutation rates). Further studies should consider the effects of genome architecture on understanding the formation of heterozygous differentiation landscape along diverging groups and identification of adaptive loci.

evolutionary biology↗

bioRxiv2024

Interaction Between Yersinia pestis Ail Outer Membrane Protein and the C-Terminal Domain of Human Vitronectin

Yersinia pestis, the causative agent of plague, is capable to evade human immune system response by recruiting the plasma circulating vitronectin proteins, which acts as a shield and avoids its lysis. Vitronectin recruitment is mediated by its interaction with the bacterial transmembrane protein Ail, protruding from Y. pestis outer membrane. By using all atom long-scale molecular dynamic simulations of Ail embedded in a realistic model of the bacterial membrane, we have shown that vitronectin forms a stable complex, mediated by interactions between the disordered moieties of the two proteins. The main amino acids driving the complexation have also been evidenced, thus favoring the possible rational design of specific peptides which, by inhibiting vitronectin recruitment, could act as original antibacterial agents. TOC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/574511v1_ufig1.gif" ALT="Figure 1"> View larger version (140K): org.highwire.dtl.DTLVardef@1f43519org.highwire.dtl.DTLVardef@1ca1b0forg.highwire.dtl.DTLVardef@1b68510org.highwire.dtl.DTLVardef@1d9fe1d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

Genomic variation in the tea leafhopper reveals the basis of adaptive evolution

The tea green leafhopper (TGL), Empoasca onukii, is of biological and economic interest. Despite numerous studies, the mechanisms underlying its adaptation and evolution remain enigmatic. Here, we used previously untapped genome and population genetics approaches to examine how this pest so rapidly has adapted to different environmental variables and thus has expanded geographically. We complete a chromosome-level assembly and annotation of the E. onukii genome, showing notable expansions of gene families associated with adaptation to chemoreception and detoxification. Genomic signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse regions. Patterns of genetic variation among 54 E. onukii samples unveil the population structure and evolutionary history across different tea-growing regions in China. Our results demonstrate that the genomic change in key pathways, including those linked to metabolism, circadian rhythms and immune system function, may underlie the successful spread and adaptation of E. onukii. This work highlights the genetic and molecular bases underlying the evolutionary success of a species with broad economic impact, and provides insight into insect adaptation to host plants, which will ultimately facilitate more sustainable pest management.

genomics↗

bioRxiv2020

A comparative analysis reveals irreproducibility in searches of scientific literature

Repeatability is the cornerstone of science and it is particularly important for systematic reviews. However, little is known on how database and search engine choices influence replicability. Here, we present a comparative analysis of time-synchronized searches at different locations in the world, revealing a large variation among the hits obtained within each of the several search terms using different search engines. We found that PubMed and Scopus returned geographically consistent results to identical search strings, Google Scholar and Web of Science varied substantially both in the number of returned hits and in the list of individual articles depending on the search location and computing environment. To maintain scientific integrity and consistency, especially in systematic reviews, action is needed from both the scientific community and scientific search platforms to increase search consistency. Researchers are encouraged to report the search location, and database providers should make search algorithms transparent and revise access rules to titles behind paywalls.View Full Text

scientific communication and education↗

bioRxiv2019

Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data

MotivationHigh-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximises analytic power while minimising noise from unspecified environmental factors.\n\nResultsHere we introduce \"soft windowing\", a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant p-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft windowed and non-windowed approaches, respectively, from a set of 2,082 mutant mouse lines. Our method is generalisable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources.\n\nAvailability and ImplementationThe method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin.

bioinformatics↗

bioRxiv2018

Biological control protects tropical forests

Biological control of invasive species can restore crop yields, and thus ease land pressure and contribute to forest conservation. In this study, we show how biological control against the mealybug Phenacoccus manihoti (Hemiptera) slowed deforestation across Southeast Asia. In Thailand, the newly-arrived mealybug caused an 18% decline in cassava yields over 2009-2010, a shortfall in national production and an escalation in the price of cassava products. This spurred an expansion of cassava cropping in neighboring countries from 713,000 ha in 2009 to >1 million ha by 2011: satellite imagery reveal 388%, 330%, 185% and 608% increases in peak deforestation rates in Cambodia, Lao PDR, Myanmar and Viet Nam focused in cassava crop expansion areas. Following release of the host-specific natural enemy Anagyrus lopezi (Hymenoptera) in 2010, mealybug outbreaks were reduced, cropping area contracted and associated deforestation slowed by 31-94% in individual countries. When used with due caution and according to current guidelines, biological control offers broad benefits for people and the environment.

ecology↗