Biology subjects

Kery, M.

Publications and source records attributed to Kery, M..

6 recordsLinked to original sources

bioRxiv2023

The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer

Tumor hypoxia has been shown to predict poor patient outcomes in several cancer types, partially because it reduces radiations ability to kill cells. We investigated whether some of the clinical effects of hypoxia could also be due to its impact on the tumor microbiome. We examined the RNA-seq data from the Oncology Research Information Exchange Network (ORIEN) database of colorectal cancer (CRC) patients treated with radiotherapy. For each tumor, we identified microbial RNAs and related them to the hypoxic gene expression scores calculated from host mRNA. Our analysis showed that the hypoxia expression score predicted poor patient outcomes and identified tumors enriched with certain microbes such as Fusobacterium nucleatum. The presence of other microbes, such as Fusobacterium canifelinum, predicted poor patient outcomes, suggesting a potential interaction between hypoxia, the microbiome, and radiation response. To investigate this concept experimentally, we implanted CT26 CRC cells into both immune-competent BALB/c and immune-deficient athymic nude mice. After growth, where tumors passively acquired microbes from the gastrointestinal tract, we harvested tumors, extracted nucleic acids, and sequenced host and microbial RNAs. We stratified tumors based on their hypoxia score and performed metatranscriptomic analysis of microbial gene expression. In addition to hypoxia-trophic and -phobic microbial populations, analysis of microbial gene expression at the strain level showed expression differences based on the hypoxia score. Hypoxia appears to not only associate with different microbial populations but also elicit an adaptive transcriptional response in intratumoral microbes. SIGNIFICANCETumor hypoxia reduces radiations ability to kill cells. We explored whether some of the clinical effects of hypoxia could also be due to interaction with the tumor microbiome. Hypoxic expression scores associated with certain microbes and elicited an adaptive transcriptional response in others.

immunology↗

bioRxiv2022

Fitting individual-based models of species range dynamics to long-term monitoring data

Generating spatial predictions of species distribution is a central task for research and policy. Currently, correlative species distribution models (cSDMs) are among the most widely used tools for this purpose. However, cSDMs fundamental assumption of species distributions in equilibrium with their environment is rarely met in real data and limits their applicability for dynamic projections. Process-based, dynamic SDMs (dSDMs) promise to overcome these limitations as they explicitly represent transient dynamics and enhance spatio-temporal transferability. Software tools for implementing dSDMs become increasingly available, yet their parameter estimation can be complex. Here, we test the feasibility of calibrating and validating a dSDM using long-term monitoring data of Swiss red kites (Milvus milvus). This population has shown strong increases in abundance and a progressive range expansion over the last decades, indicating a non-equilibrium situation. We construct an individual-based model with the RangeShiftR modelling platform and use Bayesian inference for model calibration. This allows the integration of heterogeneous data sources, such as parameter estimates from published literature as well as observational data from monitoring schemes, with coherent assessment of parameter uncertainty. Our monitoring data encompass counts of breeding pairs at 267 sites across Switzerland over 22 years. We validate our model using a spatial-block cross-validation scheme and assess predictive performance with a rank-correlation coefficient. Our model showed very good predictive accuracy of spatial projections and represented well the observed population dynamics over the last two decades. Results suggest that reproductive success was a key factor driving the observed range expansion. According to our model, the Swiss red kite population fills large parts of its current range but has potential for further increases in density. We demonstrate the practicality of data integration and validation for dSDMs using RangeShifteR. This approach can improve predictive performance compared to cSDMs. The workflow presented here can be adopted for any population for which some prior knowledge on demographic and dispersal parameters as well as spatio-temporal observations of abundance or presence/absence are available. The fitted model provides improved quantitative insights into the ecology of a species, which may greatly help conservation and management actions. Open Research statementThis submission uses novel code which is provided in an external repository. All data and code required to replicate the presented analyses are provided as private-for-peer review via a public GitHub repository under the following link: https://github.com/UP-macroecology/Malchow_IBMcalibration_2023 Upon acceptance, this repository will be archived and versioned with Zenodo and its DOI provided. For this study, a tagged development version of the R package RangeShiftR was used that is available at: https://github.com/RangeShifter/RangeShiftR-package/releases/tag/v.1.1-beta.0

ecology↗

bioRxiv2022

Demography-environment relationships improve mechanistic understanding of range dynamics under climate change

Species responses to climate change are widely detected as range and abundance changes. To better explain and predict them, we need a mechanistic understanding of how the underlying demographic processes are shaped by climatic conditions. We built spatially-explicit, process-based models for eight Swiss breeding bird populations. They jointly consider dispersal, population dynamics and the climate-dependence of three demographic processes - juvenile survival, adult survival and fecundity. The models were calibrated to two-decade abundance time-series in a Bayesian framework. We assessed goodness-of-fit and discriminatory power of the models with different metrics, indicating fair to excellent model fit. The most influential climatic predictors for population performance were the mean breeding-season temperature and the total winter precipitation. Maps of overall growth rate highlighted demographically suitable areas. Further, benefits from contemporary climate change were detected for typical mountain birds, whereas lowland birds were adversely affected. Embedding generic process-based models in a solid statistical framework improves our mechanistic understanding of range dynamics and allows disentangling the underlying abiotic and biotic processes. For future research, we advocate a stronger integration of experimental and empirical measurements and more detailed predictors in order to generate precise insights into the processes by which climate affects populations.

ecology↗

bioRxiv2020

Illegal hunting threatens the establishment of a lynx population and highlights the need of a centralized judiciary approach

O_LIIllegal hunting (poaching) represents a major threat to the conservation of large predators. Yet, its impact remains difficult to quantify as there are strong incentives to conceal this criminal activity. Attributing changes in the population status of large carnivores in part to poaching is therefore an important conservation challenge. C_LIO_LIWe present a case study of lynx (Lynx lynx) in southwestern Switzerland (canton of Valais) where the current distribution range is much smaller than it was in the recent past and population density is now >80% lower than in other lynx populations in the Swiss Alps, particularly in the adjacent Pre-Alps. We tested four hypotheses to explain this far lower density: 1) a too low density of trail camera-traps deployed for lynx surveys in Valais compared to the Pre-Alps (i.e. a methodological artefact); 2) less favourable environmental conditions around the camera-trap sites; 3) lower densities of the main prey; and 4) poaching. C_LIO_LIWe estimated lynx and ungulate densities and environmental conditions at trail camera sites, and were able to clearly reject the first three hypotheses: 1) the monitoring protocol was similarly effective; 2) environmental conditions around the trapping sites in Valais were even more favourable to lynx detection than in the Pre-Alps; and 3) prey supply was even larger. Concerning hypothesis 4, we discovered a local, but dense network of 17 illegal lynx traps in the narrow main immigration corridor into Valais from the thriving adjacent lynx population in the Pre-Alps, suggesting intense local poaching. C_LIO_LIOur findings substantiate the suspicions of long-lasting lynx poaching as a threat to the establishment and survival of the Valais population. The fact that instances of poaching were publicly known since 1995 but remained unabated for at least two decades, until a first conviction occurred, questions the commitment of local authorities to address this case of wildlife crime. Our study shows that inquiries about wildlife crime such as top predator poaching may need to be carried out at the highest levels of jurisdiction to avoid any risk of collusion between law enforcement agents and poachers. C_LI

ecology↗

bioRxiv2019

Full-annual demography and seasonal cycles in a resident vertebrate

Demography is usually studied at a single point in time within a year when species, mostly long-distance migrants, are more active and easier to find. However, this provides only a low-resolution glimpse into demographic temporal patterns, compromising a complete understanding of species population dynamics over full annual cycles. The full annual cycle is often influenced by environmental seasonality, which induces a cyclic behavior in many species. However, cycles have rarely been explicitly included in models for demographic parameters, and most information on full annual cycle demography is restricted to migratory species. Here we used a high-resolution capture-recapture study of a resident tropical lizard to assess the full intra-annual demography and within-year periodicity in survival, temporary emigration and recapture probabilities. We found important variation over the annual cycle and up to 92% of the total monthly variation explained by cycles. Fine-scale demographic studies and assessments on the importance of cycles within parameters are fundamental to understand population persistence over time.

ecology↗

bioRxiv2019

Sex-specific population dynamics and demography of capercaillie (Tetrao urogallus L.) in a patchy environment

O_LIModeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Open population spatial capture-recapture (SCR) models are ideally suited to quantify population trends, but have seen only limited use since their introduction.\nC_LIO_LITo investigate population trend and sex-specific population dynamics, we applied an open SCR model to a capercaillie (Tetrao urogallus) population in Switzerland living in eight distinct forest patches totalling 22 km2 within a region of 908 km2. The population was surveyed using genetic sampling of scat in 2009, 2012 and 2015. We fit an open SCR model with sex-specific detection and population dynamics parameters while accounting for the patchy distribution of habitat and the uncertainty introduced by observing the population in three years only.\nC_LIO_LIBetween 2009 and 2015, a total of 143 males, 112 females and 4 individuals of uncertain sex were detected. The annual per capita recruitment rate was estimated at 0.115 (SE 0.0144) for males and 0.127 (0.0168) for females. The estimated annual survival probability for males was 0.758 (0.0241) and 0.707 (0.0356) for females. The population trajectory implied by these survival and recruitment estimates was a decline of 2% per year; however, the sex specificity of the model revealed a decline in the male population only, with no evidence of decline in the female population. Further, the population decline observed in males was explained by the demography of just two of the eight patches.\nC_LIO_LIUsing a customized open population SCR model, we determined that the endangered capercaillie in our Swiss study area had a stable female population and a declining male population, with the male decline due to population dynamics in a subset of the study area. Our study highlights the flexibility of open population SCR models for assessing population trajectories through time and across space and emphasizes the desirability of estimating sex-stratified population trends especially in species of conservation concern.\nC_LI

ecology↗