bioRxiv Science⌕ Search

Biology subjects

Kaag, M.

Publications and source records attributed to Kaag, M..

4 recordsLinked to original sources

New perspectives in assessing environmental risks for birds: a simple TKTD framework to link growth and reproduction energy budget to chemical stress

Assessing the risk of pesticides to birds requires models that can extrapolate laboratory data to realistic exposure scenarios. In this work, we propose a new modeling framework BIRDkiss (Bird - Impact on Reproduction via Diet, keep it simple and suitable). This framework integrates a simplified Dynamic Energy Budget (DEBkiss) of organisms and the toxicokinetic-toxicodynamic (TKTD) of chemical substances according to a trait-based approach, thereby reducing the number of parameters to identify and strengthening the statistical robustness of the critical endpoints. The BIRDkiss model describes how food intake and toxicant exposure affect growth and egg production in birds over time. The model is fully embedded within an R package, including routines for calibration, validation and prediction under single-compound scenarios performed via Bayesian inference using standard data from the OECD avian reproduction tests. The BIRDkiss model also allows the simulations of scenarios under both varying food availability and multi-compound exposures based on the two classical mixture-toxicity paradigms: Concentration Addition (CA) and Independent Action (IA). The results of calibration for single compounds show good results matching with observed weights and egg counts. From these calibrations, predictions for new exposure scenarios can be readily generated. For mixtures, the IA algorithm is simpler and does not require to scale variables as in CA. Simulations indicate that high food levels do not further increase egg production (saturation), whereas substantial food reductions markedly decrease reproduction because energy is reallocated to maintenance. Exposure to chemicals combined to low food availability amplify the decline in reproductive output. The ready-to-use mechanistic, open-source BIRDkiss tool enables predicting the impact of pesticides on avian reproduction under realistic dietary exposure profiles. The implementation of CA and IA models is a first step toward mechanistic assessment of chemical mixtures, although validation still requires empirical mixture data. The model highlights the importance of food availability and shows that chemical stress can exacerbate the negative effects of nutritional stress. Integrating such models into regulatory frameworks could improve the ecological relevance of risk assessments.

systems biology↗

A cryogenic, coincident fluorescence, electron and ion beam microscope

Cryogenic electron tomography (cryo-ET) combined with sub-tomogram averaging, allows in-situ visualisation and structure determination of macromolecular complexes at sub-nanometre resolution. Cryogenic focused ion beam (cryo-FIB) micromachining is used to prepare a thin lamella-shaped sample out of a frozen-hydrated cell for cryo-ET imaging, but standard cryo-FIB fabrication is blind to the precise location of the structure or proteins of interest. Fluorescence-guided focused ion beam (FIB) milling at target locations requires multiple sample transfers prone to contamination, and relocation and registration accuracy is often insufficient for 3D targeting. Here, we present in-situ fluoresence microscopy-guided FIB fabrication of a frozen-hydrated lamella to solve this problem: we built a coincident 3-beam cryogenic correlative microscope by retrofitting a compact cryogenic microcooler, custom positioning stage, and an inverted widefield fluorescence microscope (FM) on an existing focused ion-beam scanning electron microscope (FIB-SEM). We show FM controlled targeting at every milling step in the lamella fabrication process, validated with transmission electron microscope (TEM) tomogram reconstructions of the target regions. The ability to check the lamella during and after the milling process results in a higher success rate in the fabrication process and will increase the throughput of fabrication for lamellae suitable for high-resolution imaging.

molecular biology↗

rbioacc: an R-package to analyse toxicokinetic data

O_LI rbioacc is an R-package dedicated to the analysis of experimental data collected from bioaccumulation tests during which organisms are exposed to a chemical (exposure phase) and then put into a clean media (depuration phase). Internal concentrations are regularly measured over time all along the experiment. C_LIO_LI rbioacc provides ready-to-use functions to visualize and fully analyze such data. Under a Bayesian framework, this package fits a generic one-compartment toxicokinetic (TK) model automatically built from the data. It provides TK parameter estimates (appropriate uptake and elimination rates) and bioaccumulation metrics (e.g., BCF, BSAF, BMF). All parameter estimates, bioaccumulation metrics as well as predictions of internal concentrations into organisms are delivered with their uncertainty. C_LIO_LIBioaccumulation metrics are primarily provided in support of environmental risk assessment, in full compliance with regulatory requirements required to approve marketing applications of chemical substances. C_LIO_LIThis paper gives brief worked examples of the use of rbioacc from data collected through standard bioaccumulation tests, and publicly available within the scientific literature. These examples constitute step-by-step user-guides to analyze any new data set, uploaded in the right format. C_LI

ecology↗

Repression of Transcription Factor AP-2 Alpha by Peroxisome Proliferator Activated Receptor Gamma Reveals a Novel Transcriptional Circuit in basal-squamous Bladder Cancer

The discovery of bladder cancer transcriptional subtypes provides an opportunity to identify high risk patients, and tailor disease management. Recent studies suggest tumor heterogeneity contributes to \"plasticity\" of molecular subtype during progression and following treatment. Nonetheless, the transcriptional drivers of the aggressive basal-squamous subtype remain unidentified. As PPAR{gamma} has been repeatedly implicated in the luminal subtype of bladder cancer, we hypothesized inactivation of this transcriptional master regulator during progression results in increased expression of basal-squamous specific transcription factors (TFs) which act to drive aggressive behavior. We initiated a pharmacologic and RNA-seq-based screen to identify PPAR{gamma}-repressed, basal-squamous specific TFs. Hierarchical clustering of RNA-seq data following treatment of a panel of human bladder cancer cell lines with a PPAR{gamma} agonist identified a number of TFs regulated by PPAR{gamma} activation, several of which are implicated in urothelial and squamous differentiation. One PPAR{gamma}-repressed TF implicated in squamous differentiation identified is Transcription Factor Activating Protein 2 alpha (TFAP2A). We show TFAP2A and its paralog TFAP2C are overexpressed in basal-squamous bladder cancer and in squamous areas of cystectomy samples, and that overexpression is associated with increased lymph node metastasis and distant recurrence, respectively. Biochemical analysis confirmed the ability of PPAR{gamma} activation to repress TFAP2A, while PPAR{gamma} antagonist studies indicate the requirement of a functional receptor. In vivo tissue recombination studies show TFAP2A and TFAP2C promote tumor growth in line with the aggressive nature of basal-squamous bladder cancer. Our findings suggest PPAR{gamma} inactivation, as well as TFAP2A and TFAP2C overexpression cooperate with other TFs to promote the basal-squamous transition.

cancer biology↗