Biology subjects

Baur, M.

Publications and source records attributed to Baur, M..

7 recordsLinked to original sources

bioRxiv2026

Workflow for multiplex microsatellite panel development and sample preparation for robust amplicon sequencing of low-template and degraded DNA: validation for non-invasive genotyping in three large carnivore species

High-throughput amplicon sequencing has transformed microsatellite (STR) genotyping by overcoming many of the limitations of fragment-length analysis, enabling more accurate, cost-effective, and standardized genotyping. Yet, protocols specifically designed for high-throughput sequencing (HTS)-based STR genotyping from low-template and degraded DNA remain scarce, despite the prevalence of these challenging sample types in ecological and conservation contexts. We present a methodology for the de novo development of robust STR multiplex panels together with a laboratory protocol for efficient and reliable STR genotyping by sequencing with low quantity and quality DNA samples. The protocol comprises (i) an automated bioinformatic pipeline to design large sets of short tetranucleotide markers optimized for multiplex amplicon sequencing of degraded and low-template DNA; (ii) guidelines for efficient in vitro optimization of multiplex amplification using directly low quantity/quality template DNA; and (iii) a library preparation procedure that improves detection of low-level allele signal while enabling quality assessment of STR amplicon sequencing under limiting DNA conditions. We demonstrate the approach by developing and validating STR panels for non-invasive genotyping of three large carnivore species: a 44-plex for the grey wolf (Canis lupus), a 41-plex for the Eurasian lynx (Lynx lynx), and a 30-plex for the brown bear (Ursus arctos). Multiplex performance was high, with [≥]91% of samples successfully genotyped at [≥]50% of loci (allele size range 28-110 bp across panels) and correctly assigned to known individuals, negligible levels of noise in the controls, and high discriminatory power (PIDsibs [≤]2.4 x 1e-12), also owing to sequence variation among same-length alleles at 15-50% of loci. The approach is broadly applicable to animal and plant species, a wide range of sample types, and large-scale analysis such as genetic monitoring. Our study reinforces the value of STR amplicon sequencing for ecological and conservation applications while highlighting the importance of marker design and laboratory workflows tailored to HTS-based genotyping for accurate and efficient implementation.

ecology↗

bioRxiv2024

Experimental evolution of a pathogen confronted with innate immune memory increases variation in virulence

Understanding the drivers and mechanisms of virulence evolution is still a major goal of evolutionary biologists and epidemiologists. Theory predicts that the way virulence evolves depends on the balance between the benefits and costs it provides to pathogen fitness. Additionally, host responses to infections, such as resistance or tolerance, play a critical role in shaping virulence evolution. But, while the evolution of pathogens has been traditionally studied under the selection pressure of host adaptive immunity, less is known about their evolution when confronted to simpler and less effective forms of immunity such as immune priming. In this study, we used a well-established insect model for immune priming - red flour beetles and their bacterial pathogen Bacillus thuringiensis tenebrionis - to test whether this form of innate immune memory favors the evolution of higher virulence. Through controlled experimental evolution of the pathogen in primed versus non-primed hosts, we found no change in average virulence after eight selection cycles in primed host. However, we found a significant increase in the variation of virulence (i.e., host-killing ability) among independent pathogen lines evolved in primed host, and bacteria were unable to evolve resistance against host priming. Whole genome sequencing revealed increased activity in the bacterial mobilome (prophages and plasmids). Expression of the Cry toxin - a well-known virulence factor - was linked to evolved differences in copy number variation of the cry-carrying plasmid, though this did not correlate directly with virulence. These findings highlight that innate immune memory can drive variability in pathogen traits, which may favor adaptation to variable environments. This underscores the need to consider pathogen evolution in response to innate immune memory when applying these mechanisms in medicine, aquaculture, pest control, and insect mass production.

evolutionary biology↗

bioRxiv2024

Immune priming in the insect gut: a dynamic response revealed by ultrastructural and transcriptomic changes

Research on forms of memory in innate immune systems has recently gained momentum with the study of trained immunity in vertebrates and immune priming in invertebrates. Immune priming provides protection against previously encountered pathogens. However, causes and mechanisms of immune priming are still not well understood in most organisms. In this work, we combine RNA sequencing with transmission electron microscopy to investigate the dynamic processes during priming in the gut of a well-established model for oral immune priming, consisting of the host Tribolium castaneum and its entomopathogen Bacillus thuringiensis tenebrionis (Btt). We show that priming with specific, pathogen-derived virulence-relevant factors causes damage in the gut of T. castaneum larvae, which leads to an early physiological stress response as well as the upregulation of a specific set of immune genes. This response diminishes over time yet enables the gut to upregulate genes known to interfere with Btt virulence when T. castaneum larvae are later exposed to infectious Btt spores. The identification of these processes increases our understanding of immune priming as a dynamic process where cellular responses in concert with specific gene regulation prepare the gut tissue and thereby enable more efficient protection against infection. Such work can further help us understand the origin and mechanism of innate immune memory. Author summaryInvertebrate animals do not possess a classical adaptive immune system. And yet, many of these animals show forms of immune memory, collectively called immune priming. In this work, we investigate the causes of oral immune priming in the red flour beetle Tribolium castaneum in response to its bacterial entomopathogen Bacillus thuringiensis tenebrionis. Primary exposure to Btt spent culture media supernatants enables the larvae of T. castaneum to better withstand a subsequent infection with infectious Btt spores. We show that exposing T. castaneum larvae to those supernatants leads to damage in the gut resulting in a strong stress and immune response early after priming and a targeted up-regulation of beneficial genes upon the secondary re-encounter with Btt. These results suggest fundamental stress responses can be involved in innate immune memory phenomena, which has implications in translational research across species.

evolutionary biology↗

bioRxiv2024

Impact of vertebrate host parasitaemia on Plasmodium development within mosquitoes

BackgroundIn vector-borne diseases, invertebrate hosts are exposed to highly variable quantities of parasites during their blood meal. This heterogeneity may partly explain the overdispersed distribution of parasites within the vector population, as well as the variability in the extrinsic incubation period (EIP) of the parasite. Indeed, the quantity of parasites ingested is often considered as a good predictor of the quantity of parasites that will develop within the vectors, as well as the speed at which they will develop (EIP). However, density-dependent processes can strongly influence the relationship between parasite burden in the vertebrate host and in vectors, making this relationship not always clear. MethodsHere, we used the avian malaria system to investigate whether the proportion of red blood cells infected by sexual and/or asexual stages of malaria parasite influences the intensity of malaria infection and the EIP of Plasmodium within the invertebrate vectors. For this purpose, we have experimentally infected twelve vertebrate hosts in order to generate a range of intensity of infection. More than a thousand mosquitoes took a blood meal on these hosts and the development of Plasmodium within the vectors was followed for more than 20 days. ResultsThe main finding presented in this study reveals a negative relationship between the intensity of infection in the vertebrate host and the EIP. Four days were sufficient for 10% of infected mosquitoes fed on the most infected hosts to become infectious. However, the number of transmissible stages did not significantly vary according to the vertebrate host intensity of infection. ConclusionWhile the quantity of ingested parasites had no impact on the density of transmissible stages in infectious mosquitoes, the EIP was affected. Studies have demonstrated that small changes in the EIP can have a significant effect on the number of mosquitoes living long enough to transmit parasites. Here, we observed a difference of 4-6 days in the detection of the first transmissible stages, depending on the intensity of infection of the bitten vertebrate host. Considering that a gonotrophic cycle lasts 3-4 days, the shortened EIP observed here may have significant effects on Plasmodium transmission.

pathology↗

bioRxiv2024

Oomycete communities in lowland tropical forest soils vary in abundance and are composed of saprophytes and pathogens of seeds and seedlings of multiple plant species.

PremiseThe soils in lowland tropics are teeming with microbial life which can impact plant community structure and diversity through plant-soil feedbacks. While bacteria and fungi have been the focus of most studies in the tropics, the oomycetes may have an outsized effect on seed and seedling health and survival, given their affinity for environments with increased precipitation and temperature. MethodsWe assessed the diversity and pathogenicity of oomycete species present in a lowland tropical forest in Panama. We used both a culture dependent leaf-baiting assay and culture independent soil DNA metabarcoding methods to quantify zoospore abundance and species diversity. A subset of the isolates from the baiting assay were used to evaluate pathogenicity and aggressiveness on seedlings of three tree species. Key resultsOomycetes are ubiquitous and common members of the soil microbial community in lowland tropical forests and zoospore abundance was far greater compared to similar studies from temperate and mediterranean forests. We also observed variation in oomycete species ability to infect host plants. Species of Pythium were more aggressive, while species of Phytopythium caused less disease but were more diverse and commonly isolated from the soil. Finally, we found that individual hosts accumulate a distinct oomycete community and was the only factor that had an effect community structure. ConclusionsCollectively, these finding demonstrate that oomycetes are ubiquitous, host-generalist pathogens and saprophytes, that have the potential to impact seed and seedling survival in lowland tropical forests

ecology↗

bioRxiv2021

Determinants of haemosporidian single and co-infections risks in western paleartic birds

Co-infections with multiple pathogens are common in the wild and may act as a strong selective pressure on both host and parasite evolution. Yet, contrary to single infection, the factors that shape co-infection risk are largely under-investigated. Here, we explored the extent to which bird ecology and phylogeny impact single and co-infection probabilities by haemosporidian parasites using large datasets from museum collections and a Bayesian phylogenetic modelling framework. While both phylogeny and species attributes (e.g. size of the geographic range, life-history strategy, migration) were relevant predictors of co-infection risk, these factors were less pertinent in predicting the probability of being single infected. Our study suggests that co-infection risk is under a stronger deterministic control than single-infection risk. These results underscore the combined influence of host evolutionary history and species attributes in determining single and co-infection pattern providing new avenues regarding our ability to predict infection risk in the wild.

ecology↗

bioRxiv2021

Animal-appropriate housing of ball pythons (Python regius)-- Behavior-based evaluation of two types of housing systems

Considering animal welfare, animals should be kept in animal-appropriate and stress-free housing conditions in all circumstances. To assure such conditions, not only basic needs must be met, but also possibilities must be provided that allow animals in captive care to express all species-typical behaviors. Rack housing systems for snakes have become increasingly popular and are widely used; however, from an animal welfare perspective, they are no alternative to furnished terrariums. In this study, we therefore evaluated two types of housing systems for ball pythons (Python regius) by considering the welfare aspect animal behavior. In Part 1 of the study, ball pythons (n = 35) were housed individually in a conventional rack system. The pythons were provided with a hiding place and a water bowl, temperature control was automatic, and the lighting in the room served as indirect illumination. In Part 2 of the study, the same ball pythons, after at least 8 weeks, were housed individually in furnished terrariums. The size of each terrarium was correlated with the body length of each python. The terrariums contained substrate, a hiding place, possibilities for climbing, a water basin for bathing, an elevated basking spot, and living plants. The temperature was controlled automatically, and illumination was provided by a fluorescent tube and a UV lamp. The shown behavior spectrum differed significantly between the two housing systems (p < 0.05). The four behaviors basking, climbing, burrowing, and bathing could only be expressed in the terrarium. Abnormal behaviors that could indicate stereotypies were almost exclusively seen in the rack system. The results show that the housing of ball pythons in a rack system leads to a considerable restriction in species-typical behaviors; thus, the rack system does not meet the requirements for animal-appropriate housing.

animal behavior and cognition↗