Biology subjects

Feriani, L.

Publications and source records attributed to Feriani, L..

7 recordsLinked to original sources

bioRxiv2025

Cilia dynamics creates a dynamic barrier to penetration of the periciliary layer in human airway epithelia

The ciliated epithelium of the human respiratory tract is covered by the airway surface liquid (ASL), a protective fluid consisting of two layers: the periciliary layer (PCL), where motile cilia reside and generate fluid flow, and an overlying mucus layer. The complex structure and stratified nature of the PCL complicate both the prediction and quantification of fluid flow at the scale of individual or small groups of cilia, making it difficult to connect microscopic flows to macroscopic clearance. To tackle this challenge, we developed a novel methodology that involves un-caging a fluorescent compound to trace the flow field within the PCL. Fluorescence is activated at micrometric spots within the cilia layer, and displacement vectors and diffusion are recorded using high-speed video. Our experiments reveal a complex fluid transport pattern, with displacement velocity along the epithelial surface varying due to a non-uniform vertical flow field. Additionally, we observed that cilia expel fluid at their tips, a mechanism likely aimed at preventing pathogen access to the epithelium. Simulations, where cilia are modeled as arrays of rigid rods with length asymmetry, support these findings and offer new insights into the dynamics of fluid transport in the respiratory tract and the critical role of cilia coordination. Significance StatementThis study introduces an experimental pipeline to investigate fluid velocity and diffusion within the PCL of the human respiratory tract. By integrating experimental data with simulations of ciliary motion, we offer a robust framework to understand how cilia, depending on their collective beating properties, propel periciliary fluid in this structurally and dynamically complex environment. Our findings significantly expand the understanding of ciliary function, revealing that when cilia are beating coherently near cilia tips fluid is actively driven away from the epithelial surface. This suggests that coordinated cilia movement not only plays a key role in maintaining respiratory health by clearing mucus, but may also provide a dynamic barrier against pathogen entry.

biophysics↗

bioRxiv2024

An improved neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens

High-resolution posture tracking of C. elegans has applications in genetics, neuroscience, and drug screening. While classic methods can reliably track isolated worms on uniform backgrounds, they fail when worms overlap, coil, or move in complex environments. Model-based tracking and deep learning approaches have addressed these issues to an extent, but there is still significant room for improvement in tracking crawling worms. Here we train a version of the DeepTangle algorithm developed for swimming worms using a combination of data derived from Tierpsy tracker and hand-annotated data for more difficult cases. DeepTangleCrawl (DTC) outperforms existing methods, reducing failure rates and producing more continuous, gap-free worm trajectories that are less likely to be interrupted by collisions between worms or self-intersecting postures (coils). We show that DTC enables the analysis of previously inaccessible behaviours and increases the signal-to-noise ratio in phenotypic screens, even for data that was specifically collected to be compatible with legacy trackers including low worm density and thin bacterial lawns. DTC broadens the applicability of high-throughput worm imaging to more complex behaviours that involve worm-worm interactions and more naturalistic environments including thicker bacterial lawns.

animal behavior and cognition↗

bioRxiv2023

Systematic creation and phenotyping of Mendelian disease models in C. elegens: towards large-scale drug repurposing

There are thousands of Mendelian diseases with more being discovered weekly and the majority have no approved treatments. To address this need, we require scalable approaches that are relatively inexpensive compared to traditional drug development. In the absence of a validated drug target, phenotypic screening in model organisms provides a route for identifying candidate treatments. Success requires a screenable phenotype, however the right phenotype and assay may not be obvious for pleiotropic neuromuscular disorders. Here we show that high-throughput imaging and quantitative phenotyping can be conducted systematically on a panel of C. elegans disease model strains. We used CRISPR genome-editing to create 25 worm models of human Mendelian diseases and phenotyped them using a single standardised assay. All but two strains were significantly different from wild-type controls in at least one feature. The observed phenotypes were diverse, but mutations of genes predicted to have related functions in their human orthologs led to similar behavioural differences in worms. As a proof-of-concept, we performed a drug repurposing screen of an FDA approved compound library, and identified two compounds that rescued the behavioural phenotype of a model of UNC80 deficiency. Our results show that a single assay to measure multiple phenotypes can be applied systematically to diverse Mendelian disease models. The relatively short time and low cost associated with creating and phenotyping multiple strains suggests that high-throughput worm tracking could provide a scalable approach to drug repurposing commensurate with the number of Mendelian diseases.

animal behavior and cognition↗

bioRxiv2021

Megapixel camera arrays for high-resolution animal tracking in multiwell plates

Tracking small laboratory animals such as flies, fish, and worms is used for phenotyping in neuroscience, genetics, disease modelling, and drug discovery. Current imaging systems are limited either in spatial resolution or throughput. A system capable of imaging a large number of animals with sufficient resolution to estimate their pose would enable a new class of experiments where detailed behavioural differences are quantified but at a scale where hundreds of treatments can be tested simultaneously. Here we report a new imaging system consisting of an array of six 12-megapixel cameras that can simultaneously record from all the wells of a 96-well plate with a resolution of 80 pixels/mm at 25 frames per second. We show that this resolution is sufficient to estimate the pose of nematode worms including head identification and to extract high-dimensional phenotypic fingerprints. We use the system to study behavioural variability across wild isolates, the sensitisation of worms to repeated blue light stimulation, the phenotypes of worm disease models, and worms behavioural responses to drug treatment. Because the system is compatible with standard multiwell plates, it makes computational ethological approaches accessible in existing high-throughput pipelines and greatly increases the scale of possible phenotypic screening experiments in C. elegans.

animal behavior and cognition↗

bioRxiv2021

Behavioral fingerprints predict insecticide and anthelmintic mode of action

Novel invertebrate-killing compounds are required in agriculture and medicine to overcome resistance to existing treatments. Because insecticides and anthelmintics are discovered in phenotypic screens, a crucial step in the discovery process is determining the mode of action of hits. Visible whole-organism symptoms are combined with molecular and physiological data to determine mode of action. However, manual symptomology is laborious and requires symptoms that are strong enough to see by eye. Here we use high-throughput imaging and quantitative phenotyping to measure C. elegans behavioral responses to compounds and train a classifier that predicts mode of action with an accuracy of 88% for a set of ten common modes of action. We also classify compounds within each mode of action to discover pharmacological relationships that are not captured in broad mode of action labels. High-throughput imaging and automated phenotyping could therefore accelerate mode of action discovery in invertebrate-targeting compound development and help to refine mode of action categories.

systems biology↗

bioRxiv2019

A How-To guide to: Quantitative high-speed video profiling to discriminate between variants of primary ciliary dyskinesia

This document presents detailed steps to analysing the waveforms of beating cilia, measured in high speed video microscopy. We show that in the case of PCD caused by mutations in DNAH11 and HYDIN the classification by a handful of parameters describing ciliary dynamics allows to distinguish the genotype, as well as (much more easily) distinguishing healthy from PCD samples. This document is intended to complement the brief highlight (1) and presents the details of the datasets used in that letter.

cell biology↗

bioRxiv2017

Phenotyping ciliary dynamics and coordination in response to CFTR-modulators in Cystic Fibrosis respiratory epithelial cells

The diagnosis and treatment of respiratory disorders are challenging and would benefit from new approaches to systematically assess ciliary beating dynamics and to test new drugs. A novel approach based on multiscale differential dynamic microscopy (multi-DDM) is shown to quantitatively assess collective beating of cilia in a non-biased automated manner, in human airway epithelial cells (HAECs) derived from subjects with cystic fibrosis (CF) and grown in 2D air-liquid interface culture. Multi-DDM can readily detect changes in both ciliary beat frequency (CBF) and cilia coordination that result from perturbations to the mucosal layer. The efficacy of three CFTR-modulating treatments is investigated: ivacaftor (VX-770) with lumacaftor (VX-809), VX-809 alone and Thymosin alpha 1 (T1) alone. All three treatments restore coordination of cilia beating in the CF cells, albeit to varying degrees. We argue cilia are affected by these treatments through the physical properties of the mucus. Phenotyping cilia dynamics through multi-DDM provides novel insight into the response of ciliary beating following treatment with drugs, and has application in the broader context of respiratory disease and for drug screening.\n\nOne sentence summaryA semi-automated and unbiased assay based on multiscale differential dynamic microscopy (multi-DDM) detects changes in the coordination and frequency of ciliary beating in F508del/F508del primary human airway cells under different conditions and in response to CFTR-modulating compounds.

physiology↗