Dataset Information

Automated scoring of nematode nictation on a textured background.

ABSTRACT: Entomopathogenic nematodes including Steinernema spp. play an increasingly important role as biological alternatives to chemical pesticides. The infective juveniles of these worms use nictation - a behavior in which animals stand on their tails - as a host-seeking strategy. The developmentally-equivalent dauer larvae of the free-living nematode Caenorhabditis elegans also nictate, but as a means of phoresy or "hitching a ride" to a new food source. Advanced genetic and experimental tools have been developed for C. elegans , but time-consuming manual scoring of nictation slows efforts to understand this behavior, and the textured substrates required for nictation can frustrate traditional machine vision segmentation algorithms. Here we present a Mask R-CNN-based tracker capable of segmenting C. elegans dauers and S. carpocapsae infective juveniles on a textured background suitable for nictation, and a machine learning pipeline that scores nictation behavior. We use our system to show that the nictation propensity of C. elegans from high-density liquid cultures largely mirrors their development into dauers, and to quantify nictation in S. carpocapsae infective juveniles in the presence of a potential host. This system is an improvement upon existing intensity-based tracking algorithms and human scoring which can facilitate large-scale studies of nictation and potentially other nematode behaviors.

SUBMITTER: McClanahan PD

PROVIDER: S-EPMC10055289 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Automated scoring of nematode nictation on a textured background.

McClanahan Patrick D PD Golinelli Luca L Le Tuan Anh TA Temmerman Liesbet L

bioRxiv : the preprint server for biology 20230715

Entomopathogenic nematodes including <i>Steinernema</i> spp. play an increasingly important role as biological alternatives to chemical pesticides. The infective juveniles of these worms use nictation - a behavior in which animals stand on their tails - as a host-seeking strategy. The developmentally-equivalent dauer larvae of the free-living nematode <i>Caenorhabditis elegans</i> also nictate, but as a means of phoresy or "hitching a ride" to a new food source. Advanced genetic and experimental ...[more]

PMID: 36993316

Similar Datasets

Project description:PurposeMany neonates undergo electroencephalogram (EEG) monitoring to identify and manage acute symptomatic seizures. Information about brain function contained in the EEG background data may also help predict neurobehavioral outcomes. For EEG background features to be useful as prognostic indicators, the interpretation of these features must be standardized across electroencephalographers. We aimed at determining the interrater and intrarater agreement among electroencephalographers interpreting neonatal EEG background patterns.MethodsFive neonatal electroencephalographers reviewed 5-to-7.5-minute epochs of EEG from full-term neonates who underwent continuous conventional EEG monitoring. The EEG assessment tool used to classify background patterns was based on the American Clinical Neurophysiology Society's guideline for neonatal EEG terminology. Interrater and intrarater agreement were measured using Kappa coefficients.ResultsInterrater agreement was consistently highest for voltage (binary: substantial, kappa = 0.783; categorical: moderate, kappa = 0.562), seizure presence (fair-substantial; kappa = 0.375-0.697), continuity (moderate; kappa = 0.481), burst voltage (moderate; kappa = 0.574), suppressed background presence (moderate-substantial; kappa = 0.493-0.643), delta activity presence (fair-moderate; kappa = 0.369-0.432), theta activity presence (fair-moderate; kappa = 0.347-0.600), presence of graphoelements (fair; kappa = 0.381), and overall impression (binary: moderate, kappa = 0.495; categorical: fair-moderate, kappa = 0.347, 0.465). Agreement was poor or inconsistent for all other patterns. Intrarater agreement was variable, with highest average agreement for voltage (binary: substantial, kappa = 0.75; categorical: substantial, kappa = 0.714) and highest consistent agreement for continuity (moderate-substantial; kappa = 0.43-0.67) and overall impression (moderate-substantial; kappa = 0.42-0.68).ConclusionsThis study demonstrates substantial variability in neonatal EEG background interpretation across electroencephalographers, indicating a need for educational and technological strategies aimed at improving performance.

Project description:Studies of the biological effects of low-level and below-background radiation are important in understanding the potential effects of radiation exposure in humans. To study this issue we exposed the nematode Caenorhabditis elegans to average background and below-background radiation levels. Two experiments were carried-out in the underground radiation biology laboratory at the Waste Isolation Pilot Plant (WIPP) in New Mexico USA. The first experiment used naïve nematodes with data collected within 1 week of being placed underground. The second experiment used worms that were incubated for 8 months underground at below background radiation levels. Nematode eggs were placed in two incubators, one at low radiation (ca.15.6 nGy/hr) and one supplemented with 2 kg of natural KCl (ca. 67.4 nGy/hr). Phenotypic variables measured were: (1) egg hatching success (2) body size from larval development to adulthood, (3) developmental time from egg to egg laying adult, and (4) egg laying rate of young adult worms. Transcriptome analysis was performed on the first experiment on 72 h old adult worms. Within 72 h of being underground, there was a trend of increased egg-laying rate in the below-background radiation treatment. This trend became statistically significant in the group of worms exposed to below-background radiation for 8 months. Worms raised for 8 months in these shielded conditions also had significantly faster growth rates during larval development. Transcriptome analyses of 72-h old naïve nematode RNA showed significant differential expression of genes coding for sperm-related proteins and collagen production. In the below-background radiation group, the genes for major sperm protein (msp, 42% of total genes) and sperm-related proteins (7.5%) represented 49.5% of the total genes significantly up-regulated, while the majority of down-regulated genes were collagen (col, 37%) or cuticle-related (28%) genes. RT-qPCR analysis of target genes confirmed transcriptomic data. These results demonstrate that exposure to below-background radiation rapidly induces phenotypic and transcriptomic changes in C. elegans within 72 h of being brought underground.

Dataset Information

Automated scoring of nematode nictation on a textured background.

Publications

Automated scoring of nematode nictation on a textured background.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets