scholarly journals A scalable method for automatically measuring pharyngeal pumping in C. elegans

2016 ◽  
Author(s):  
Monika Scholz ◽  
Dylan J. Lynch ◽  
Kyung Suk Lee ◽  
Erel Levine ◽  
David Biron
Keyword(s):  
Caenorhabditis Elegans ◽  
Food Availability ◽  
High Throughput ◽  
Visual Inspection ◽  
Automated Analysis ◽  
C Elegans ◽  
Automated Method ◽  
Controlled Environments ◽  
Pharyngeal Pumping ◽  
Feeding Environments

We describe a scalable automated method for measuring the pharyngeal pumping of Caenorhabditis elegans in controlled environments. Our approach enables unbiased measurements for prolonged periods, a high throughput, and measurements in controlled yet dynamically changing feeding environments. The automated analysis compares well with scoring pumping by visual inspection, a common practice in the field. In addition, we observed overall low rates of pharyngeal pumping and long correlation times when food availability was oscillated.

scholarly journals Hi-Cpipe: a pipeline for high-throughput chromosome capture

2015 ◽  
Author(s):  
Giancarlo Castellano ◽  
François Le Dily ◽  
Antonio Hermoso Pulido ◽  
Miguel Beato ◽  
Guglielmo Roma
Keyword(s):  
High Throughput ◽  
Visual Inspection ◽  
Automated Analysis ◽  
Chromatin Conformation ◽  
Interaction Data ◽  
Alignment Quality ◽  
Bioinformatics Pipeline ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Analysis Workflow

Hi-Cpipe is a bioinformatics pipeline for the automated analysis of data generated by high-throughput chromatin conformation capture (HiC). The analysis workflow comprises steps of data formatting, genome alignment, quality control and filtering, identification of genome-wide chromatin interactions, visualization and statistics. An interactive browser enables visual inspection of interaction data and results.

scholarly journals Screening for Presenilin Inhibitors Using the Free-Living Nematode, Caenorhabditis elegans

2004 ◽  
Vol 9 (2) ◽  
pp. 147-152 ◽  
Author(s):  
Brenda R. Ellerbrock ◽  
Eileen M. Coscarelli ◽  
Mark E. Gurney ◽  
Timothy G. Geary
Keyword(s):  
Caenorhabditis Elegans ◽  
High Throughput Screening ◽  
Screening Method ◽  
Genetic System ◽  
Body Cavity ◽  
Egg Laying ◽  
The Body ◽  
Loss Of Function ◽  
C Elegans ◽  
Automated Method

Caenorhabditis elegans contains 3 homologs of presenilin genes that are associated with Alzheimer s disease. Loss-of-function mutations in C. elegans genes cause a defect in egg laying. In humans, loss of presenilin-1 (PS1) function reduces amyloid-beta peptide processing from the amyloid protein precursor. Worms were screened for compounds that block egg laying, phenocopying presenilin loss of function. To accommodate even relatively high throughput screening, a semi-automated method to quantify egg laying was devised by measuring the chitinase released into the culture medium. Chitinase is released by hatching eggs, but little is shed into the medium from the body cavity of a hermaphrodite with an egg laying deficient ( egl) phenotype. Assay validation involved measuring chitinase release from wild-type C. elegans (N2 strain), sel-12 presenilin loss-of-function mutants, and 2 strains of C. elegans with mutations in the egl-36K+ channel gene. Failure to find specific presenilin inhibitors in this collection likely reflects the small number of compounds tested, rather than a flaw in screening strategy. Absent defined biochemical pathways for presenilin, this screening method, which takes advantage of the genetic system available in C. elegans and its historical use for anthelminthic screening, permits an entry into mechanism-based discovery of drugs for Alzheimer s disease. ( Journal of Biomolecular Screening 2004:147-152)

scholarly journals CAENORHABDITIS ELEGANS AS A MODEL OF AIR POLLUTION TOXICITY DURING DEVELOPMENT AND LIFESPAN

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S97-S97
Author(s):  
Amin Haghani ◽  
Hans M Dalton ◽  
Nikoo Safi ◽  
Farimah Shirmohammadi ◽  
Constantinos Sioutas ◽  
...  
Keyword(s):  
Air Pollution ◽  
Caenorhabditis Elegans ◽  
Mouse Models ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Cultured Cells ◽  
Exposure Model ◽  
C Elegans ◽  
Biological Responses ◽  
Short Term Exposure

Abstract Air pollution (AirPoll) is among the leading human mortality risk factors and yet little is known about the molecular mechanisms of this global environmental toxin. Our recent studies using mouse models even showed genetic variation and sex can alter biological responses to air pollution. To expand genetic studies of AirPoll toxicity throughout the lifespan, we introduced Caenorhabditis elegans as a new AirPoll exposure model which has a short lifespan, high throughput capabilities and shared longevity pathways with mammals. Acute exposure of C. elegans to airborne nanosized AirPoll matter (nPM) caused similar gene expression changes to our prior findings in cell culture and mouse models. Initial C. elegans responses to nPM included antioxidant, inflammatory and Alzheimer homolog genes. The magnitude of changes was dependent on the developmental stage of the worms. Even short term exposure of C. elegans to nPM altered developmental and lifespan hormetic effects, with pathways that included skn-1/Nrf family antioxidant responses. We propose C. elegans as a new and complementary model for mouse and cultured cells to study AirPoll across the lifespan. Future chronic nPM exposure and high throughput genetic screening of C. elegans can identify other major regulators of the developmental and lifespan effects of air pollution. This work was supported by grants R01AG051521 (CEF); R21AG05020 (CEF); Cure Alzheimer’s Fund (CEF); R01GM109028 (SPC), F31AG051382 (HMD) and T32AG000037 (HMD), T32AG052374 (AH).

scholarly journals Enhanced Healthspan in Caenorhabditis elegans Treated With Extracts From the Traditional Chinese Medicine Plants Cuscuta chinensis Lam. and Eucommia ulmoides Oliv.

2021 ◽  
Vol 12 ◽  
Author(s):  
Shimaa M. A. Sayed ◽  
Karsten Siems ◽  
Christian Schmitz-Linneweber ◽  
Walter Luyten ◽  
Nadine Saul
Keyword(s):  
Caenorhabditis Elegans ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Eucommia Ulmoides ◽  
Pumping Rate ◽  
C Elegans ◽  
Beneficial Effects ◽  
Physiological Fitness ◽  
Pharyngeal Pumping ◽  
Cuscuta Chinensis

To uncover potential anti-aging capacities of Traditional Chinese Medicine (TCM), the nematode Caenorhabditis elegans was used to investigate the effects of Eucommia ulmoides and Cuscuta chinensis extracts, selected by screening seven TCM extracts, on different healthspan parameters. Nematodes exposed to E. ulmoides and C. chinensis extracts, starting at the young adult stage, exhibited prolonged lifespan and increased survival after heat stress as well as upon exposure to the pathogenic bacterium Photorhabdus luminescens, whereby the survival benefits were monitored after stress initiation at different adult stages. However, only C. chinensis had the ability to enhance physical fitness: the swimming behavior and the pharyngeal pumping rate of C. elegans were improved at day 7 and especially at day 12 of adulthood. Finally, monitoring the red fluorescence of aged worms revealed that only C. chinensis extracts caused suppression of intestinal autofluorescence, a known marker of aging. The results underline the different modes of action of the tested plants extracts. E. ulmoides improved specifically the physiological fitness by increasing the survival probability of C. elegans after stress, while C. chinensis seems to be an overall healthspan enhancer, reflected in the suppressed autofluorescence, with beneficial effects on physical as well as physiological fitness. The C. chinensis effects may be hormetic: this is supported by increased gene expression of hsp-16.1 and by trend, also of hsp-12.6.

scholarly journals Some Phenotypic Characteristics of Nematode Caenorhabditis elegans Strains with Defective Functions of the Sestrin (cSesn) gene

2018 ◽  
Vol 11 (2) ◽  
pp. 759-767 ◽  
Author(s):  
A. O. Zeltukhin ◽  
G. V. Ilyinskaya ◽  
A. V. Budanov ◽  
P. M. Chumakov
Keyword(s):  
Caenorhabditis Elegans ◽  
Redox Homeostasis ◽  
Functional Decline ◽  
Extended Period ◽  
Locomotory Activity ◽  
Pumping Rate ◽  
Phenotypic Differences ◽  
C Elegans ◽  
Age Related ◽  
Pharyngeal Pumping

In mammals a small family of genes called Sestrins play important roles in the maintenance of metabolic and redox homeostasis, suggesting that the genes may positively affect the lifespan and counteract the age-related functional decline. The nematode genome contains a single cSesn gene that makes the Caenorhabditis elegans an excellent model for studying functions of the sestrin family. We describe phenotypic differences of worms that have compromised expression of cSesn gene. By comparing three different cSesn-deficient modes with the wild-type C. elegans strain we show that the abrogation of cSesn expression results in an increased body size, an extended period of body growth, a reduces brood size and number of offspring per a single worm, an accelerated decline in muscular functions revealed as a rapid decrease in the pharyngeal pumping rate and in the overall locomotory activity. The results are consistent with the potential roles of cSesn in counteracting the process of aging in C. elegans.

scholarly journals Reducing Results Variance in Lifespan Machines: An Analysis of the Influence of Vibrotaxis on Wild-Type Caenorhabditis elegans for the Death Criterion

Sensors ◽  
2020 ◽  
Vol 20 (21) ◽  
pp. 5981
Author(s):  
Joan Carles Puchalt ◽  
Pablo E. Layana Castro ◽  
Antonio-José Sánchez-Salmerón
Keyword(s):  
Caenorhabditis Elegans ◽  
Experimental Results ◽  
Artificial Vision ◽  
Wild Type ◽  
Worm Detection ◽  
C Elegans ◽  
Automated Method ◽  
Live Worm ◽  
Lifespan Variability ◽  
Stimulation Of

Nowadays, various artificial vision-based machines automate the lifespan assays of C. elegans. These automated machines present wider variability in results than manual assays because in the latter worms can be poked one by one to determine whether they are alive or not. Lifespan machines normally use a “dead or alive criterion” based on nematode position or pose changes, without poking worms. However, worms barely move on their last days of life, even though they are still alive. Therefore, a long monitoring period is necessary to observe motility in order to guarantee worms are actually dead, or a stimulus to prompt worm movement is required to reduce the lifespan variability measure. Here, a new automated vibrotaxis-based method for lifespan machines is proposed as a solution to prompt a motion response in all worms cultured on standard Petri plates in order to better distinguish between live and dead individuals. This simple automated method allows the stimulation of all animals through the whole plate at the same time and intensity, increasing the experiment throughput. The experimental results exhibited improved live-worm detection using this method, and most live nematodes (>93%) reacted to the vibration stimulus. This method increased machine sensitivity by decreasing results variance by approximately one half (from ±1 individual error per plate to ±0.6) and error in lifespan curve was reduced as well (from 2.6% to 1.2%).

scholarly journals Staphylococcus aureus Virulence Factors Identified by Using a High-Throughput Caenorhabditis elegans-Killing Model

2005 ◽  
Vol 73 (2) ◽  
pp. 872-877 ◽  
Author(s):  
Jakob Begun ◽  
Costi D. Sifri ◽  
Samuel Goldman ◽  
Stephen B. Calderwood ◽  
Frederick M. Ausubel
Keyword(s):  
Staphylococcus Aureus ◽  
Caenorhabditis Elegans ◽  
Dna Replication ◽  
Virulence Factors ◽  
High Throughput ◽  
Human Pathogen ◽  
Renal Abscess ◽  
C Elegans ◽  
Transposon Insertion ◽  
Strain Nctc

ABSTRACT Staphylococcus aureus is an important human pathogen that is also able to kill the model nematode Caenorhabditis elegans. We constructed a 2,950-member Tn917 transposon insertion library in S. aureus strain NCTC 8325. Twenty-one of these insertions exhibited attenuated C. elegans killing, and of these, 12 contained insertions in different genes or chromosomal locations. Ten of these 12 insertions showed attenuated killing phenotypes when transduced into two different S. aureus strains, and 5 of the 10 mutants correspond to genes that have not been previously identified in signature-tagged mutagenesis studies. These latter five mutants were tested in a murine renal abscess model, and one mutant harboring an insertion in nagD exhibited attenuated virulence. Interestingly, Tn917 was shown to have a very strong bias for insertions near the terminus of DNA replication.

scholarly journals Insect-Derived Cecropins Display Activity against Acinetobacter baumannii in a Whole-Animal High-Throughput Caenorhabditis elegans Model

2015 ◽  
Vol 59 (3) ◽  
pp. 1728-1737 ◽  
Author(s):  
Elamparithi Jayamani ◽  
Rajmohan Rajamuthiah ◽  
Jonah Larkins-Ford ◽  
Beth Burgwyn Fuchs ◽  
Annie L. Conery ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Acinetobacter Baumannii ◽  
High Throughput ◽  
Sequence Data ◽  
Treatment Options ◽  
Automated Image Analysis ◽  
Screening Assay ◽  
Content Type ◽  
C Elegans ◽  
Cecropin A

ABSTRACTThe rise of multidrug-resistantAcinetobacter baumanniiand a concomitant decrease in antibiotic treatment options warrants a search for new classes of antibacterial agents. We have found thatA. baumanniiis pathogenic and lethal to the model host organismCaenorhabditis elegansand have exploited this phenomenon to develop an automated, high-throughput, high-content screening assay in liquid culture that can be used to identify novel antibiotics effective againstA. baumannii. The screening assay involves coincubatingC. eleganswithA. baumanniiin 384-well plates containing potential antibacterial compounds. At the end of the incubation period, worms are stained with a dye that stains only dead animals, and images are acquired using automated microscopy and then analyzed using an automated image analysis program. This robust assay yields a Z′ factor consistently greater than 0.7. In a pilot experiment to test the efficacy of the assay, we screened a small custom library of synthetic antimicrobial peptides (AMPs) that were synthesized using publicly available sequence data and/or transcriptomic data from immune-challenged insects. We identified cecropin A and 14 other cecropin or cecropin-like peptides that were able to enhanceC. eleganssurvival in the presence ofA. baumannii. Interestingly, one particular hit, BR003-cecropin A, a cationic peptide synthesized by the mosquitoAedes aegypti, showed antibiotic activity against a panel of Gram-negative bacteria and exhibited a low MIC (5 μg/ml) againstA. baumannii. BR003-cecropin A causes membrane permeability inA. baumannii, which could be the underlying mechanism of its lethality.

scholarly journals Combined flow cytometry and high throughput image analysis for the study of essential genes in Caenorhabditis elegans

2017 ◽  
Author(s):  
Blanca Hernando-Rodríguez ◽  
Annmary Paul Erinjeri ◽  
María Jesús Rodríguez-Palero ◽  
Val Millar ◽  
Sara González-Hernández ◽  
...  
Keyword(s):  
Image Analysis ◽  
Caenorhabditis Elegans ◽  
High Throughput ◽  
Rnai Screen ◽  
Essential Genes ◽  
Genetic Interactions ◽  
Automated Image Analysis ◽  
C Elegans ◽  
Larval Stages ◽  
Lethal Mutations

ABSTRACTBackgroundThe advancement in automated image based microscopy platforms coupled with high throughput liquid workflows has facilitated the design of large scale screens utilizing multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high throughput approaches.ResultsIn C. elegans, non-conditional lethal mutations can be maintained in heterozygosis using chromosome balancers, commonly labelled with GFP in the pharynx. Moreover gene-expression is typically monitored by the use of fluorescent reporters marked with the same fluorophore. Therefore, the separation of the different populations of animals at early larval stages represents a challenge. Here, we develop a sorting strategy capable of selecting homozygous mutants carrying a GFP stress reporter from GFP-balanced animals at early larval stages. Because sorting is not completely error-free, we develop an automated high-throughput image-analysis protocol that identifies and discards animals carrying the chromosome balancer. We demonstrate the experimental usefulness of combining sorting of homozygous lethal mutants and automated image-analysis in a functional genomic RNAi screen for genes that genetically interact with mitochondrial prohibitin (PHB). Lack of PHB results in embryonic lethality, while, homozygous PHB deletion mutants develop into sterile adults due to maternal contribution and strongly induce the mitochondrial unfolded protein response (UPRmt). In a chromosome-wide RNAi screen for C. elegans genes having human orthologues, we uncover both, known and new PHB genetic interactors affecting the UPRmt and growth.ConclusionsA systematic way to analyse genetic interactions of essential genes in multicellular organisms is lacking. The method presented here allows the study of balanced lethal mutations in a high-throughput manner and can be easily adapted depending on the user’s requirements. Therefore, it will serve as a useful resource for the C. elegans community for probing new biological aspects of essential nematode genes as well as the generation of more comprehensive genetic networks.

scholarly journals High-throughput small molecule screen identifies inhibitors of microsporidia invasion and proliferation in C. elegans.

2021 ◽  
Author(s):  
Brandon M. Murareanu ◽  
Jessica Knox ◽  
Peter Roy ◽  
Aaron W. Reinke
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Treatment Options ◽  
Screening Method ◽  
C Elegans ◽  
Automated Method ◽  
Intracellular Parasites ◽  
Chemical Inhibitors ◽  
Animal Phyla ◽  
Small Molecule Screen

Microsporidia are a diverse group of fungal-related obligate intracellular parasites that infect most animal phyla. Despite the emerging threat that microsporidia have become to humans and agricultural animals, few reliable treatment options exist. To identify novel chemical inhibitors of microsporidia infection, we developed a high-throughput screening method using Caenorhabditis elegans and the microsporidia species Nematocida parisii. We screened the Spectrum Collection of 2,560 FDA-approved compounds and natural products to identify compounds that prevent C. elegans progeny inhibition caused by N. parisii infection. We developed a semi-automated method for quantifying C. elegans progeny number in liquid culture, confirming 11 candidate microsporidia inhibitors. We show that five compounds prevent microsporidia infection by inhibiting spore firing, and demonstrate that one compound, dexrazoxane, slows infection progression. Together, our results demonstrate the effectiveness of C. elegans as a model host for drug discovery against intracellular pathogens and provide a scalable high-throughput system for the identification and characterization of additional microsporidia inhibitors.

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