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ISSN (Online) 2804-3871
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  • Godinho, Diogo Prino; Fragata, Inês et al. - Spider mites collectively
           avoid plants with cadmium irrespective of their frequency or the presence
           of competitors

    • Abstract: Accumulation of heavy metals by plants can serve as a defence against herbivory. Herbivores, in turn, may avoid feeding on contaminated tissues. Such avoidance, however, may hinge upon the specific conditions faced by herbivores. Here, we tested whether the spider mite Tetranychus urticae avoids tomato plants contaminated with cadmium in presence of conspecifics or heterospecifics and depending on the frequency of contaminated plants. We show that individual spider mite females do not preferentially move to leaf tissues with or without cadmium, despite clear costs on their performance. However, in a set-up where 200 mites were simultaneously given the choice between four plants with or without cadmium, they collectively avoided plants with cadmium, irrespective of the proportion of plants with cadmium. In addition, T. urticae did not discriminate between plants infested with its competitor T. evansi and other uncontaminated plants but they preferred plants with competitors when the other plants contained cadmium. Our results show that aggregation may facilitate avoidance of contaminated plants. They also indicate that cadmium accumulation in plants is a stronger selective pressure than interspecific competition with T. evansi. Therefore, collective avoidance of metal-accumulating plants by herbivores is robust to environmental conditions and may have important consequences for species distribution and interactions in metal contaminated sites.
      PubDate: Thu, 11 Jul 2024 14:40:18 +000
       
  • Billaud, Maud; Theodorou, Ilias et al. - T7 DNA polymerase treatment
           improves quantitative sequencing of both double-stranded and
           single-stranded DNA viruses

    • Abstract: Bulk microbiome, as well as virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes of viruses often consist of a circular single-stranded DNA (ssDNA) molecule. Pre-treatment and amplification of DNA using the multiple displacement amplification (MDA) method enables conversion of ssDNA to dsDNA, but this process can lead to over-representation of these circular ssDNA genomes. A more recent alternative permits to bypass the amplification step, as library adapters are ligated to sheared and denatured DNA, after an end-modification step (xGen kit). However, the sonication step might shear ssDNA more efficiently than dsDNA, therefore introducing another bias in virome sequencing. These limitations prompted us to explore an alternative method of DNA preparation for sequencing mixed ssDNA and dsDNA viromes. Using a synthetic mix of viral particles, we made use of the T7 DNA polymerase (T7pol) to convert viral circular ssDNA molecules to dsDNA, while preventing over-replication of such molecules, as is the case with the Phi29 DNA polymerase. Our findings indicate that using  T7pol  and a mix of degenerated primers to convert ssDNA to dsDNA prior library preparation is a good alternative to the currently used methods. It better represents the original synthetic mixtures compared to MDA or direct application of the xGen kit. Furthermore, when applied to two complex virome samples, the T7pol treatment improved both the richness and abundance in the Microviridae fraction. We conclude that T7pol pretreatment is preferable to MDA for the shotgun sequencing of viromes, which is easy to implement and inexpensive.
      PubDate: Thu, 11 Jul 2024 14:39:57 +000
       
  • Milvus+milvus)&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Sollmann, Rahel; Adenot, Nathalie et al. - Accounting for observation
           biases associated with counts of young when estimating fecundity: case
           study on the arboreal-nesting red kite (Milvus milvus)

    • Abstract: Counting the number of young in a brood from a distance is common practice, for example in tree-nesting birds. These counts can, however, suffer from over and undercounting, which can lead to biased estimates of fecundity (average number of nestlings per brood). Statistical model development to account for observation bias has focused on false negatives (undercounts), yet it has been shown that these models are sensitive to the presence of false positives (overcounts) when they are not accounted for. Here, we develop a model that estimates fecundity while accounting for both false positives and false negatives in brood counts. Its parameters can be estimated using a calibration approach that combines uncertain counts with certain ones, which can be obtained by accessing the brood, for example during ringing. The model uses multinomial distributions to estimate the probabilities of observing  y young conditional on the true state of a brood z (i.e., true number of young) from paired uncertain and certain counts. These classification probabilities are then used to estimate the true state of broods for which only uncertain counts are available. We use a simulation study to investigate bias and precision of the model and parameterize the simulation with empirical data from 26 red kite nests visited with ground and nest-based counts during 2021 and 2022 in central Europe. In these data, bias in counts was at most 1 in either direction, more common in larger broods, and undercounting was more common than overcounting. This led to an overall 5% negative bias in fecundity in uncertain counts. The model produced essentially unbiased estimates (relative bias < 2%) of fecundity across a range of sample sizes. This held true whether or not fecundity was the same  for nests with paired counts and those with uncertain-only counts. But the model could not estimate parameters when true states were missing from the paired data, which happened frequently in small sample sizes (n = 10 or 25). Further, we projected populations 50 years into the future using fecundity estimates corrected for observation biases from the multinomial model, and based on “raw” uncertain observations. We found that ignoring observation bias led to strong negative bias in projected population size for growing populations, but only minor negative bias in declining populations. Accounting for apparently minor biases associated with ground counts is important for ensuring accurate estimates of abundance and population dynamics especially for increasing populations. This could be particularly important for informing conservation decisions in projects aimed at recovering depleted populations.
      PubDate: Tue, 09 Jul 2024 09:27:50 +000
       
  • Gammarus+fossarum&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Bauer, Alexandre; Develay Nguyen, Lucie et al. - Differences in
           specificity, development time and virulence between two acanthocephalan
           parasites, infecting two cryptic species of Gammarus fossarum

    • Abstract: Multi-host parasites can exploit various host species that differ in abundance and susceptibility to infection, which will contribute unequally to their transmission and fitness. Several species of acanthocephalan manipulative parasites (among which Pomphorhynchus laevis and P. tereticollis) use various amphipod species of the genus Gammarus as intermediate hosts. Many Gammarus pulex and G. fossarum cryptic lineages are living in sympatry in European rivers, questioning the spectrum of intermediate hosts that acanthocephalans can use, and their relative contribution to their life cycles. In this work, the respective roles of parasites species (P. laevis and, for the first time, P. tereticollis) and sympatric host cryptic species (the G. fossarum species complex) were studied experimentally on two traits: host susceptibility to infection and parasite virulence. Differences were found, both in terms of infectivity and virulence, between the cryptic hosts and between the two parasite species. We confirm that these acanthocephalans, previously considered as generalists, show specificities among their sympatric hosts. Differences in field prevalence and susceptibility after experimental exposures were more pronounced between cryptic G. fossarum species for P. tereticollis than for P. laevis. The mortality of infected individuals increased significantly after several weeks of development of both parasite species. P. tereticollis was less virulent than P. laevis, perhaps due to differences in host exploitation, since we evidenced that P. tereticollis had a much slower growth rate.
      PubDate: Mon, 08 Jul 2024 06:58:33 +000
       
  • Yacine, Youssef; Loeuille, Nicolas - Attracting pollinators vs escaping
           herbivores: eco-evolutionary dynamics of plants confronted with an
           ecological trade-off

    • Abstract: Many plant traits are subject to an ecological trade-off between attracting pollinators and escaping herbivores. The interplay of both plant-animal interaction types determines their evolution. As most studies focus on either pollination or herbivory, how they jointly affect the eco-evolutionary dynamics of plant-animal communities is often left unknown.  Within a plant-pollinator-herbivore community where interaction strengths depend on trait matching, we consider the evolution of a plant trait involved in both plant-animal interactions. Using adaptive dynamics, we uncover when stabilizing, runaway (i.e. directional) or disruptive selection emerges and its consequences for multispecies coexistence. We find that strong pollination relative to herbivory favors stabilizing selection and coexistence. Strong herbivory relative to pollination fosters runaway selection and threatens coexistence. Importantly, given balanced interactions, joint effects may lead to disruptive selection, allowing the emergence of plant dimorphism. The strength of the ecological trade-off largely explains the occurrence of these contrasting eco-evolutionary dynamics. In particular, plant diversification requires strong trade-offs, with the strongest trade-offs allowing long-term polymorphism. We discuss how our results relate to various empirical cases where the interplay of pollination and herbivory maintains plant polymorphism. Beyond maintenance, our work suggests that it might also have fueled the diversification process itself.
      PubDate: Wed, 03 Jul 2024 13:43:15 +000
       
  • Galaxea+fascicularis&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Puntin, Giulia; Wong, Jane C. Y. et al. - The bacterial microbiome of
           symbiotic and menthol-bleached polyps of long-term aquarium-reared Galaxea
           fascicularis

    • Abstract: Coral reefs support the livelihood of half a billion people but are at high risk of collapse due to the vulnerability of corals to climate change and local anthropogenic stressors. While understanding coral functioning is essential to guide conservation efforts, research is challenged by the complex nature of corals. They exist as metaorganisms (holobionts), constituted by the association between the (coral) animal host, its obligate endosymbiotic algae (Symbiodiniaceae), and other microorganisms comprising bacteria, viruses, archaea, fungi and other protists. Researchers therefore increasingly turn to model organisms to unravel holobiont complexity, dynamics, and how these determine the health and fitness of corals. The coral Galaxea fascicularis is an emerging model organism for coral symbiosis research with demonstrated suitability to aquarium rearing and reproduction, and to manipulation of the host-Symbiodiniaceae symbiosis. However, little is known about the response of the G. fascicularis microbiome to menthol bleaching—the experimental removal of the Symbiodiniaceae which represents the first step in coral-algal symbiosis manipulation. For this, we characterized the bacterial microbiome of symbiotic and menthol-bleached G. fascicularis originating from the Red Sea and South China Sea (Hong Kong) that were long-term aquarium-reared in separate facilities. We found that the coral-associated microbiomes were composed of relatively few bacterial taxa (10-78 ASVs). Symbiotic polyps (clonal replicates) from the same colony had similar microbiomes, which were distinct from those of other colonies despite co-culturing in shared aquaria. A pattern of seemingly differential response of the bacterial microbiome to menthol bleaching between the two facilities emerged, warranting further investigation into the role of rearing conditions. Nevertheless, the changes in community composition overall appeared to be stochastic suggesting a dysbiotic state. Considering the importance of bleaching treatment of captive corals for symbiosis research, our results—although preliminary—contribute fundamental knowledge for the development of the Galaxea model for coral symbiosis research.
      PubDate: Thu, 27 Jun 2024 07:43:44 +000
       
  • Gaucherel, Cedric; Fayolle, Stolian et al. - Diagnosis of planktonic
           trophic network dynamics with sharp qualitative changes

    • Abstract: Trophic interaction networks are notoriously difficult to understand and to diagnose (i.e., to identify contrasted network functioning regimes). Such ecological networks have many direct and indirect connections between species, and these connections are not static but often vary over time. These topological changes, as opposed to a dynamic on a static (frozen) network, can be triggered by natural forcings (e.g., seasons) and/or by human influences (e.g., nutrient or pollution inputs). Aquatic trophic networks are especially dynamic and versatile, thus suggesting new approaches for identifying network structures and functioning in a comprehensive manner.In this study, a qualitative model was devised for this purpose. Applying discrete-event models from theoretical computer science, a mechanistic and qualitative model was developed that allowed computation of the exhaustive dynamics of a given trophic network and its environment. Once the model definition is assumed, it provides all possible trajectories of the network from a chosen initial state. In a rigorous and analytical approach, for the first time, we validated the model on one theoretical and two observed trajectories recorded at freshwater stations in the La Rochelle region (Western France). The model appears to be easy to build and intuitive, and it provides additional relevant trajectories to the expert community. We hope this formal approach will open a new avenue in identifying and predicting trophic (and non-trophic) ecological networks.
      PubDate: Wed, 26 Jun 2024 07:49:49 +000
       
  • Amin, Bawan; Fishman, Ruth et al. - Sex differences in the relationship
           between maternal and foetal glucocorticoids in a free-ranging large mammal
           

    • Abstract: Maternal phenotypes can have long-term effects on offspring phenotypes. These maternal effects may begin during gestation, when maternal glucocorticoid (GC) levels may affect foetal GC levels, thereby having an organizational effect on the offspring phenotype. Recent studies have showed that maternal effects may be different between the sexes. However, how maternal GC levels relate to foetal levels is still not completely understood. Here we related, for the first time in a free-ranging large mammal, the fallow deer (Dama dama), maternal GC levels with foetal in utero GC levels. We did this in a non-invasive way by quantifying cortisol metabolites from faecal samples collected from pregnant does during late gestation, as proxy for maternal GC level. These were then related to GC levels from hair of their neonate offspring (n = 40). We have shown that maternal GC levels were positively associated with foetal GC levels, but only in female offspring. These findings highlight sex differences, which may have evolved to optimize male growth at the cost of survival.
      PubDate: Thu, 20 Jun 2024 13:53:29 +000
       
  • Kra, Arsène Kouassi; Fotso, Arlette Simo et al. - HIV self-testing
           positivity rate and linkage to confirmatory testing and care: a telephone
           survey in Côte d’Ivoire, Mali, and Senegal

    • Abstract: HIV self-testing (HIVST) empowers individuals to decide when and where to test and with whom to share their results. From 2019 to 2022, the ATLAS program distributed ∼ 400 000 HIVST kits in Côte d’Ivoire, Mali, and Senegal. It prioritised key populations, including female sex workers and men who have sex with men, and encouraged secondary distribution of HIVST to their partners, peers and clients.To preserve the confidential nature of HIVST, use of kits and their results were not systematically tracked. Instead, an anonymous phone survey was carried out in two phases during 2021 to estimate HIVST positivity rates (phase 1) and linkage to confirmatory testing (phase 2). Initially, participants were recruited via leaflets from March to June and completed a sociobehavioural questionnaire. In the second phase (September-October), participants who had reported two lines or who reported a reactive result were recontacted to complete another questionnaire. Of the 2 615 initial participants, 89.7% reported a consistent response between the number of lines on the HIVST and their interpretation of the result (i.e., ‘non-reactive’ for 1 line, ‘reactive’ for 2 lines).Overall positivity rate based on self-interpreted HIVST results was 2.5% considering complete responses, and could have ranged from 2.4% to 9.1% depending on the interpretation of incomplete responses. Using the reported number of lines, this rate was estimated at 4.5% (ranging from 4.4% to 7.2%). Positivity rates were significantly lower only among respondents with higher education. No significant difference was observed by age, key population profile, country or history of HIV testing.The second phase saw 78 out of 126 eligible participants complete the questionnaire. Of the 27 who reported a consistent reactive response in the first phase, 15 (56%, 95%CI: 36 to 74%) underwent confirmatory HIV testing, with 12 (80%) confirmed as HIV-positive, all of whom began antiretroviral treatment.The confirmation rate of HIVST results was fast, with 53% doing so within a week and 91% within three months of self-testing. Two-thirds (65%) went to a general public facility, and one-third to a facility dedicated to key populations.The ATLAS HIVST distribution strategy reached people living with HIV in West Africa. Linkage to confirmatory testing following a reactive HIVST remained relatively low in these first years of HIVST implementation. However, if confirmed HIV-positive, almost all initiated treatment. HIVST constitutes a relevant complementary tool to existing screening services.
      PubDate: Thu, 13 Jun 2024 13:54:56 +000
       
  • Blackwell, Samantha E M; Pasquier, Laura et al. - Relationship between
           weapon size and six key behavioural and physiological traits in males of
           the European earwig

    • Abstract: In many animals, male weapons are large and extravagant morphological structures that typically enhance fighting ability and reproductive success. It is generally assumed that growing and carrying large weapons is costly, thus only males in the best condition can afford it. In the European earwig, males carry weapons in the form of forceps-like cerci, which can vary widely in size within populations. While long forceps appear to increase male’s access to females, it is unknown whether it also correlates with other important male life-history traits. This information is important, however, in determining the potential reliability of forceps length as an indicator of male quality and the stability of this signalling system. Here, we tested whether forceps length is associated with six important behavioural and physiological traits in males of the European earwig. We sampled hundreds of males from two populations, selected 60 males with the longest and shortest forceps from each population, and then measured locomotor performance, boldness, aggregation behaviour, survival under harsh conditions, sperm storage, and survival after pathogen exposure. Contrary to our predictions, we detected no main association between forceps length and the traits measured. This lack of association was consistent between the two populations, although there were population-specific levels of boldness, aggregation and survival in harsh conditions (for long-forceps males only). Overall, these results challenge our current understanding of the function and quality signal of forceps length in this species and raise questions about the evolutionary drivers that could explain the maintenance of weapon size diversity within and between populations.
      PubDate: Thu, 13 Jun 2024 13:54:07 +000
       
  • van Iersel, Leo; Jones, Mark et al. - When Three Trees Go to War

    • Abstract: How many reticulations are needed for a phylogenetic network to display a given set of k phylogenetic trees on n leaves' For k = 2, Baroni et al. [Ann. Comb. 8, 391-408 (2005)] showed that the answer is n − 2. Here, we show that, for k ≥ 3 the answer is at least (3 /2 − ε)n. Concretely, we prove that, for each ε > 0, there is some n ∈ N such that three n-leaf caterpillar trees can be constructed in such a way that any network displaying these caterpillars contains at least (3 /2 − ε)n reticulations. The case of three trees is interesting since it is the easiest case that cannot be equivalently formulated in terms of agreement forests. Instead, we base the result on a surprising lower bound for multilabelled trees (MUL-trees) displaying the caterpillars. Indeed, we show that one cannot do (more than an ε) better than the trivial MUL-tree resulting from a simple concatenation of the given caterpillars. The results are relevant for the development of methods for the Hybridization Number problem on more than two trees. This fundamental problem asks to construct a binary phylogenetic network with a minimum number of reticulations displaying a given set of phylogenetic trees.
      PubDate: Tue, 04 Jun 2024 07:22:46 +000
       
  • Sidous, Mellina; Cubaynes, Sarah et al. - Insights on the effect of
           mega-carcass abundance on the population dynamics of a facultative
           scavenger predator and its prey

    • Abstract: The interplay between facultative scavenging and predation has gained interest in the last decade. The prevalence of scavenging induced by the availability of large carcasses may modify predator density or behaviour, potentially affecting prey. In contrast to behavioural mechanisms through which scavenging affects predation, the demographic effects of facultative scavenging on predator and prey populations remain poorly studied. We used the semi-natural experimental opportunity in Hwange National Park, Zimbabwe, where contrasted management measures (culling and artificial supply of water) have led to fluctuations in elephant carrion abundance, to identify the consequences of facultative scavenging on the population dynamics of a large mammalian carnivore, the spotted hyaena (Crocuta crocuta), and its prey. Using a 50-year dataset and Multivariate Autoregressive State Space models, we estimated hyaena and prey densities over four periods contrasted in elephant carrion availability due to management practices. Models that allow hyaena and their prey populations’ growth rate to vary depending on these four periods contributed significantly to explain variations in their density, which is consistent with an effect of management measures on the population dynamics of hyaena and its prey.  Although our results support a predominant role of bottom-up mechanisms, whereby hyaena density is driven by herbivore density, itself driven by resources availability, some subtle patterns of densities could be interpreted as consequences of changes in predation pressure following changes in scavenging opportunities. We discuss why signals of prey and predator population dynamics decoupling are less likely to be observed in systems with a high diversity of prey, such as African savannas, and why inputs of mega-carcasses as pulsed resources hardly impacted top-down relationships in the long run. This study represents a first investigation of the long-term effects of carrion pulses, whose frequency may increase with climate changes, on the classical predator-prey coupling for large mammals.
      PubDate: Thu, 30 May 2024 05:50:48 +000
       
  • Sicard, Vianney; Picault, Sébastien et al. - Pig herd management and
           infection transmission dynamics: a challenge for modellers

    • Abstract: The control of epidemics requires a thorough understanding of the complex interactions between pathogen transmission, disease impact, and population dynamics and management. Mechanistic epidemiological modelling is an effective way to address this issue, but handling highly structured and dynamic systems, remains challenging. We therefore developed a novel approach that combines Multi-Level Agent-Based Systems (MLABS) with spatial and temporal organization, allowing for a tuned representation of the transmission processes amongst the host population. We applied this method to model the spread of a PRRSv-like virus in pig farms, integrating the clinical consequences (conception and reproduction failures), in terms of animal husbandry practices. Results highlighted the importance to account for spatial and temporal structuring and herd management policies in epidemiological models. Indeed, disease-related abortions, inducing reassignments of sows in different batches, was shown to enhance the transmission process, favouring the persistence of the virus at the herd level. Supported by a declarative Domain-Specific Language (DSL), our approach provides flexible and powerful solutions to address the issues of on-farm epidemics and broader public health concerns. The present application, based on a simple Susceptible-Exposed-Infected-Recovered (SEIR) model, opens the way to the representation of more complex epidemiological systems, including more specific features such as maternally derived antibodies, vaccination, or dual infections, along with their respective clinical consequences on the management practices.
      PubDate: Wed, 29 May 2024 12:56:51 +000
       
  • Gammarus fossarum&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Gestin, Ophélia; Lopes, Christelle et al. - Assimilation efficiencies and
           elimination rates of silver, cadmium and zinc accumulated by trophic
           pathway in Gammarus fossarum

    • Abstract: To improve the assessment of metal toxicity in aquatic organisms, it is important to consider the different uptake pathways (i.e. trophic or aqueous). The bioaccumulation of dissolved metals such as Cd and Zn in gammarids is beginning to be well described. However, there are very few data on the contribution of the dietary pathway, and its associated toxicokinetic parameters. Among these, the assimilation efficiency (AE) is an essential parameter for the implementation of models that take the trophic pathway into account. This study aims to estimate the assimilation efficiencies and elimination rates of two types of food, i.e. alder leaves and chironomid larvae, contaminated with three metals (Ag, Cd and Zn) of major concern for the Water Framework Directive (WFD). The pulse-chase-feeding method was used. Gammarids were fed with alder leaves or chironomid larvae previously contaminated with 110mAg, 109Cd or 65Zn, for a short period of time (1 to 5 hours), followed by an elimination phase of 14 days. At different time points, the gammarids were placed alive on the gamma detector to individually quantify whole body concentrations of 110mAg, 109Cd or 65Zn. Our results indicate that: i) Cd has the highest assimilation efficiency (39% for leaves and 19% for larvae), followed by Zn (15% for leaves and 9% for larvae) and Ag (5% for leaves); ii) for Cd and Zn, the AE were higher when gammarids were fed with leaves than with larvae; iii) the elimination rates of metals seem to depend more on the food matrix than on the metal assimilated; and thus iv) the biological half-life calculated from the kes is 5.1 days for Ag, between 4.9 and 13 days for Cd and between 3.8 and 13 days for Zn.
      PubDate: Tue, 28 May 2024 14:58:23 +000
       
  • Torun, Funda; Hostins, Barbara et al. - Molybdate delays sulphide
           formation in the sediment and transfer to the bulk liquid in a model
           shrimp pond

    • Abstract: Shrimp are commonly cultured in earthen aquaculture ponds where organic-rich uneaten feed and faeces accumulate on and in the sediment to form anaerobic zones. Since the pond water is rich in sulphate, these anaerobic conditions eventually lead to the production of sulphide. Sulphides are toxic and even lethal to the shrimp that live on the pond sediment, but physicochemical and microbial reactions that occur during the accumulation of organic waste and the subsequent formation of sulphide in shrimp pond sediments remain unclear. Molybdate treatment is a promising strategy to inhibit sulphate reduction, thus, preventing sulphide accumulation. We used an experimental shrimp pond model to simulate the organic waste accumulation and sulphide formation during the final 61 days of a full shrimp growth cycle. Sodium molybdate (5 and 25 mg/L Na2MoO4.2H2O) was applied as a preventive strategy to control sulphide production before oxygen depletion. Molybdate addition partially mitigated H2S production in the sediment, and delayed its transfer to the bulk liquid by pushing the higher sulphide concentration zone towards deeper sediment layers. Molybdate treatment at 25 mg/L significantly impacted the overall microbial community composition and treated samples (5 and 25 mg/L molybdate) had about 50% higher relative abundance of sulphate reducing bacteria than the control (no molybdate) treatment. In conclusion, molybdate has the potential to work as mitigation strategy against sulphide accumulation in the sediment during shrimp growth by directly steering the microbial community in a shrimp pond system.
      PubDate: Tue, 28 May 2024 14:44:23 +000
       
  • Barny, Marie-Anne; Thieffry, Sylvia et al. - Bacterial pathogens dynamic
           during multi-species infections

    • Abstract: Soft rot Pectobacteriacea (SRP) gathers more than 30 bacterial species that collectively rot a wide range of plants by producing and secreting a large set of plant cell wall degrading enzymes (PCWDEs). Worldwide potato field surveys identified 15 different SRP species on symptomatic plants and tubers. The abundance of each species observed during outbreaks varies over space and time and the mechanisms driving species shift during outbreak are unknown. Furthermore, multi-species infections are frequently observed and the dynamics of these coinfections are not well understood.To understand the dynamics of coinfections, we set up 16 different synthetic communities of 6 SRP strains to mimic coinfections. The bacteria present in each tested community were representative of 2 different species, with 3 strains per species. These communities were inoculated in potato tubers or on synthetic media and their outcome was followed by amplification and Illumina sequencing of the discriminatory housekeeping gene gapA. We also compared disease incidence and bacterial multiplication in potato tubers during mixed-species infection and single-species infection. A species that was unable to induce disease in potato was efficiently maintained and eventually became dominant in some of the communities tested, indicating that cheating can shape dominant species. Modeling indicates that the cost of PCWDEs production and secretion, the rate of potato degradation and the diffusion rate of degraded substrate could favor the cheater species. Interaction outcomes differed between potato tuber and synthetic medium, highlighting the driving effect of environmental conditions, with higher antagonistic interactions observed in potato tubers. Antagonistic interactions were strain specific and not species specific. Toxicity interference was also observed within some communities, allowing the maintenance of strains otherwise sensitive to toxic compounds. Overall, the results indicate that intraspecific competition, cooperation through trophic interaction and toxicity interference contribute to the maintenance of SRP diversity. The implications of these processes for epidemiological surveillance are discussed.
      PubDate: Wed, 22 May 2024 11:28:28 +000
       
  • Hartmann, Clara; Mahajan, Ambika et al. - The Switchmaze: an open-design
           device for measuring motivation and drive switching in mice

    • Abstract: Animals need to switch between motivated behaviours, like drinking, feeding or social interaction, to meet environmental availability, internal needs and more complex ethological needs such as hiding future actions from competitors. Inflexible, repetitive behaviours are a hallmark of many neuropsychiatric disorders. However, how the brain orchestrates switching between the neural mechanisms controlling motivated behaviours, or drives, is unknown. This is partly due to a lack of appropriate measurement systems. We designed an automated extended home-cage, the Switchmaze, using open-source hardware and software. In this study, we use it to establish a behavioural assay of motivational switching in mice. Individual animals access the Switchmaze from the home-cage and choose between entering one of two chambers containing different goal objects or returning to the home-cage. Motivational switching is measured as a ratio of switching between chambers and continuous exploitation of one chamber. Behavioural transition analysis is used to further dissect altered motivational switching. As proof-of-concept, we show environmental manipulation, and targeted brain manipulation experiments which altered motivational switching without effect on traditional behavioural parameters. Chemogenetic inhibition of the prefrontal-hypothalamic axis increased the rate of motivation switching, highlighting the involvement of this pathway in drive switching. This work demonstrates the utility of open-design in understanding animal behaviour and its neural correlates.
      PubDate: Wed, 24 Apr 2024 06:55:49 +000
       
  • k-mers&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2024&rft.volume=">Parmigiani, Luca; Wittler, Roland et al. - Revisiting pangenome openness
           with k-mers

    • Abstract: Pangenomics is the study of related genomes collectively, usually from the same species or closely related taxa. Originally, pangenomes were defined for bacterial species. After the concept was extended to eukaryotic genomes, two definitions of pangenome evolved in parallel: the gene-based approach, which defines the pangenome as the union of all genes, and the sequence-based approach, which defines the pangenome as the set of all nonredundant genomic sequences. Estimating the total size of the pangenome for a given species has been subject of study since the very first mention of pangenomes. Traditionally, this is performed by predicting the ratio at which new genes are discovered, referred to as the openness of the species. Here, we abstract each genome as a set of items, which is entirely agnostic of the two approaches (gene-based, sequence-based). Genes are a viable option for items, but also other possibilities are feasible, e.g., genome sequence substrings of fixed length k (k-mers). In the present study, we investigate the use of k-mers to estimate the openness as an alternative to genes, and compare the results. An efficient implementation is also provided.
      PubDate: Tue, 23 Apr 2024 12:54:22 +000
       
  • Bartholdy, Bjørn Peare; Hasselstrøm, Jørgen B. et al. - Multiproxy
           analysis exploring patterns of diet and disease in dental calculus and
           skeletal remains from a 19th century Dutch population

    • Abstract: Dental calculus is an excellent source of information on the dietary patterns of past populations, including consumption of plant-based items. The detection of plant-derived residues such as alkaloids and their metabolites in dental calculus provides direct evidence of consumption by individuals within a population. We conducted a study on 41 individuals from Middenbeemster, a 19th century rural  Dutch archaeological site. Skeletal and dental analysis was performed to explore potential relationships between pathological lesions and presence of alkaloids. Dental calculus was analysed using ultra-high-performance liquid chromatography-tandem  mass spectrometry (UHPLC-ESI-MS/MS). We were able to detect nicotine, cotinine, caffeine, theophylline, and salicylic acid, suggesting the consumption of tea and coffee and smoking of tobacco on an individual scale, which is also confirmed by historic documentation and identification of pipe notches in the dentition. Nicotine and/or cotinine was present in 56% of individuals with at least one visible pipe notch. There is some influence of skeletal preservation on the detection of alkaloids, with higher quantities of compounds extracted from well-preserved individuals, and we observe a positive relationship between weight of the calculus sample and quantity of detected compounds, as well as between chronic maxillary sinusitis and the presence of multiple alkaloids. There are many limitations that will need to be addressed going forward with this type of analysis; we stress the need for more systematic research on the consumption of alkaloid-containing items and their subsequent concentration and preservation in dental calculus, in addition to how mode of consumption may affect concentrations in the dentition. Despite the limitations, this preliminary study illustrates many benefits of using calculus to target a variety of compounds that could have been consumed as medicine or diet. This method allows us to directly address specific individuals, which can be especially useful in individuals that are not always well-documented in historic documentation, such as rural populations, and especially children and women.
      PubDate: Tue, 23 Apr 2024 12:53:49 +000
       
  • Niskanen, Alina K.; Kujala, Sonja T. et al. - Does the seed fall far from
           the tree' Weak fine-scale genetic structure in a continuous Scots pine
           population

    • Abstract: Knowledge of fine-scale spatial genetic structure, i.e., the distribution of genetic diversity at short distances, is important in evolutionary research and in practical applications such as conservation and breeding programs. In trees, related individuals often grow close to each other due to limited seed and/or pollen dispersal. The extent of seed dispersal also limits the speed at which a tree species can spread to new areas. We studied the fine-scale spatial genetic structure of Scots pine (Pinus sylvestris) in two naturally regenerated sites located 20 km from each other in continuous south-eastern Finnish forest. We genotyped almost 500 adult trees for 150k SNPs using a custom made Affymetrix array. We detected some pairwise relatedness at short distances, but the average relatedness was low and decreased with increasing distance, as expected. Despite the clustering of related individuals, the sampling sites were not differentiated (FST = 0.0005). According to our results, Scots pine has a large neighborhood size (Nb = 1680–3210), but a relatively short gene dispersal distance (σg = 36.5–71.3 m). Knowledge of Scots pine fine-scale spatial genetic structure can be used to define suitable sampling distances for evolutionary studies and practical applications. Detailed empirical estimates of dispersal are necessary both in studying post-glacial recolonization and predicting the response of forest trees to climate change.
      PubDate: Mon, 15 Apr 2024 09:15:48 +000
       
 
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