scholarly journals Comparative Transcriptomics of heads and tails between Steinernema carpocapsae and Caenorhabditis elegans

2020 ◽  
Author(s):  
Isaryhia Maya Rodriguez ◽  
Lorrayne Serra Clague ◽  
Cassandra Joan McGill ◽  
Bryan Rodriguez ◽  
Ali Mortazavi
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Neuronal Development ◽  
Model Organism ◽  
The Body ◽  
Steinernema Carpocapsae ◽  
Specific Gene ◽  
Body Parts ◽  
C Elegans

AbstractSteinernema nematodes have been widely studied for insect infection and mutualism, but little is known about the patterns of gene expression along the body of these worms or how these compare to the model organism Caenorhabditis elegans. Here we perform the first comparative analysis between the heads and tail regions of Steinernema carpocapsae and C. elegans Infective Juveniles (IJs)/dauers and young adults using single-worm RNA-seq. While we find overall agreement in gene expression there were several sets of genes with substantial differences between the two species. Gene expression in the S. carpocapsae female compared to the C. elegans hermaphrodite heads and tails revealed differences in metabolism, aging, and determination of lifespan. Young adult male heads and tails showed major differences in developmental related processes such as morphogenesis as well as neuronal development and signaling. We also found head- and tail-specific gene expression differences between S. carpocapsae IJs and C. elegans dauers for genes related to growth and development as well as neuronal signaling and activity. This study is one of the first comparative transcriptomic analyses of body parts between distantly related species of nematodes and provides insight into both the highly conserved and genetically distinctive characteristics of both species.

scholarly journals Caenorhabditis elegans as a Model Organism to Evaluate the Antioxidant Effects of Phytochemicals

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3194
Author(s):  
Begoña Ayuda-Durán ◽  
Susana González-Manzano ◽  
Ana M. González-Paramás ◽  
Celestino Santos-Buelga
Keyword(s):  
Oxidative Stress ◽  
Caenorhabditis Elegans ◽  
Model Organism ◽  
Lipid Peroxides ◽  
Biological Research ◽  
Loss Of Function ◽  
Fluorescent Reporters ◽  
C Elegans ◽  
High Degree

The nematode Caenorhabditis elegans was introduced as a model organism in biological research by Sydney Brenner in the 1970s. Since then, it has been increasingly used for investigating processes such as ageing, oxidative stress, neurodegeneration, or inflammation, for which there is a high degree of homology between C. elegans and human pathways, so that the worm offers promising possibilities to study mechanisms of action and effects of phytochemicals of foods and plants. In this paper, the genes and pathways regulating oxidative stress in C. elegans are discussed, as well as the methodological approaches used for their evaluation in the worm. In particular, the following aspects are reviewed: the use of stress assays, determination of chemical and biochemical markers (e.g., ROS, carbonylated proteins, lipid peroxides or altered DNA), influence on gene expression and the employment of mutant worm strains, either carrying loss-of-function mutations or fluorescent reporters, such as the GFP.

scholarly journals Maternal and zygotic gene regulatory effects of endogenous RNAi pathways

2018 ◽  
Author(s):  
Miguel Vasconcelos Almeida ◽  
António Miguel de Jesus Domingues ◽  
René F. Ketting
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Gene Silencing ◽  
Small Rnas ◽  
Self Regulation ◽  
Fine Tuning ◽  
Specific Gene ◽  
Next Generation ◽  
C Elegans ◽  
Argonaute Proteins

AbstractEndogenous small RNAs (sRNAs) and Argonaute proteins are ubiquitous regulators of gene expression in germline and somatic tissues. sRNA-Argonaute complexes are often expressed in gametes and are consequently inherited by the next generation upon fertilization. In Caenorhabditis elegans, 26G-RNAs are primary endogenous sRNAs that trigger the expression of downstream secondary sRNAs. Two subpopulations of 26G-RNAs exist, each of which displaying strongly compartmentalized expression: one is expressed in the spermatogenic gonad and associates with the Argonautes ALG-3/4; plus another expressed in oocytes and in embryos, which associates with the Argonaute ERGO-1. The determinants and dynamics of gene silencing elicited by 26G-RNAs are largely unknown. Here, we provide diverse new insights into these endogenous sRNA pathways of C. elegans. Using genetics and deep sequencing, we dissect a maternal effect of the ERGO-1 branch sRNA pathway. We find that maternal primary sRNAs can trigger the production of zygotic secondary sRNAs that are able to silence targets, even in the absence of zygotic primary triggers. Thus, the interaction of maternal and zygotic sRNA populations, assures target gene silencing throughout animal development. Furthermore, we find that sRNA abundance, the pattern of origin of sRNA and 3’ UTR length are predictors of the regulatory outcome by the Argonautes ALG-3/4. Lastly, we discovered that ALG-3- and ALG-4-bound 26G-RNAs are dampening the expression of their own mRNAs, revealing a negative feedback loop. Altogether, we provide several new regulatory insights on the dynamics, target regulation and self-regulation of the endogenous RNAi pathways of C. elegans.Author SummarySmall RNAs (sRNAs) and their partner Argonaute proteins regulate the expression of target RNAs. When sperm and egg meet upon fertilization, a diverse set of proteins and RNA, including sRNA-Argonaute complexes, is passed on to the developing progeny. Thus, these two players are important to initiate specific gene expression programs in the next generation. The nematode Caenorhabditis elegans expresses several classes of sRNAs. 26G-RNAs are a particular class of sRNAs that are divided into two subpopulations: one expressed in the spermatogenic gonad and another expressed in oocytes and in embryos. In this work, we describe the dynamics whereby oogenic 26G-RNAs setup gene silencing in the next generation. We also show several ways that spermatogenic 26G-RNAs and their partner Argonautes, ALG-3 and ALG-4, use to regulate their targets. Finally, we show that ALG-3 and ALG-4 are fine-tuning their own expression, a rare role of Argonaute proteins. Overall, we provide new insights into how sRNAs and Argonautes are regulating gene expression.

Assessment of lead toxicity on locomotion and growth in a nematode Caenorhabditis elegans

2020 ◽  
Vol 12 (1) ◽  
pp. 36-41
Author(s):  
Shashank Shekhar Tiwari ◽  
Francis Tambo ◽  
Rakhi Agarwal
Keyword(s):  
Caenorhabditis Elegans ◽  
Lead Exposure ◽  
Anthropogenic Activities ◽  
Model Organism ◽  
Lead Toxicity ◽  
Future Generation ◽  
Exposure Dose ◽  
The Body ◽  
Young Generation ◽  
C Elegans

Due to anthropogenic activities and natural abundance, lead exposure is a common phenomenon. Neurotoxic and genotoxic effects of lead are widely known. Recent studies have suggested that lead exposure can affect young generation and transfer to the progeny thus posing a great threat for future generation. The present study was focused on lead toxicity in terms of locomotion and growth of Caenorhabditis elegans (N2 wild type) at three sub-lethal doses (3µM, 15 µM and 30 µM) of Pb (NO3)2 for 24 hours (sub-chronic exposure). Caenorhabditis elegans is a nematode with an established eco- toxicity marker model organism, due to its short life cycle and ease to monitor. After lead  exposure, significant toxic manifestations were observed in locomotion of the nematode in terms of omega bends (+350% for 30 µM exposure dose, p<0.001), reversals (-26.98%, -49% and -66.35% for 3 µM, 15 µM and 30 µM exposure doses respectively, p<0.001), turn counts (-38.66%, -62.61% and -81.93% for 3 µM, 15 µM and 30 µM exposure doses respectively, p<0.001 ) and peristaltic speed alterations (+97.83%, +225.92% and +454.63% for 3 µM, 15 µM and 30 µM exposure doses respectively, p<0.001). Successive reduction in the body length at lower doses shows remarkable toxic alterations in nematodes. The obtained data may be useful to extrapolate the effects of lead exposure on humans, as many of the similar pathways and cellular processes affected by Pb in humans are also present in C. elegans.

scholarly journals Roll maneuvers are essential for active reorientation of Caenorhabditis elegans in 3D media

2018 ◽  
Vol 115 (16) ◽  
pp. E3616-E3625 ◽  
Author(s):  
Alejandro Bilbao ◽  
Amar K. Patel ◽  
Mizanur Rahman ◽  
Siva A. Vanapalli ◽  
Jerzy Blawzdziewicz
Keyword(s):  
Caenorhabditis Elegans ◽  
Symmetry Axis ◽  
Model Organism ◽  
The Body ◽  
Forward Motion ◽  
C Elegans ◽  
Viscous Forces ◽  
3D Space ◽  
Undulatory Locomotion ◽  
Nonzero Torsion

Locomotion of the nematode Caenorhabditis elegans is a key observable used in investigations ranging from behavior to neuroscience to aging. However, while the natural environment of this model organism is 3D, quantitative investigations of its locomotion have been mostly limited to 2D motion. Here, we present a quantitative analysis of how the nematode reorients itself in 3D media. We identify a unique behavioral state of C. elegans—a roll maneuver—which is an essential component of 3D locomotion in burrowing and swimming. The rolls, associated with nonzero torsion of the nematode body, result in rotation of the plane of dorsoventral body undulations about the symmetry axis of the trajectory. When combined with planar turns in a new undulation plane, the rolls allow the nematode to reorient its body in any direction, thus enabling complete exploration of 3D space. The rolls observed in swimming are much faster than the ones in burrowing; we show that this difference stems from a purely hydrodynamic enhancement mechanism and not from a gait change or an increase in the body torsion. This result demonstrates that hydrodynamic viscous forces can enhance 3D reorientation in undulatory locomotion, in contrast to known hydrodynamic hindrance of both forward motion and planar turns.

scholarly journals Multigenerational Regulation of the Caenorhabditis elegans Chromatin Landscape by Germline Small RNAs

2019 ◽  
Vol 53 (1) ◽  
pp. 289-311 ◽  
Author(s):  
Natasha E. Weiser ◽  
John K. Kim
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Small Rnas ◽  
Model Organism ◽  
Epigenetic Inheritance ◽  
Small Interfering Rnas ◽  
Transgenerational Epigenetic Inheritance ◽  
C Elegans ◽  
Small Noncoding Rnas ◽  
Rna Pathways

In animals, small noncoding RNAs that are expressed in the germline and transmitted to progeny control gene expression to promote fertility. Germline-expressed small RNAs, including endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), drive the repression of deleterious transcripts such as transposons, repetitive elements, and pseudogenes. Recent studies have highlighted an important role for small RNAs in transgenerational epigenetic inheritance via regulation of heritable chromatin marks; therefore, small RNAs are thought to convey an epigenetic memory of genomic self and nonself elements. Small RNA pathways are highly conserved in metazoans and have been best described for the model organism Caenorhabditis elegans. In this review, we describe the biogenesis, regulation, and function of C. elegans endo-siRNAs and piRNAs, along with recent insights into how these distinct pathways are integrated to collectively regulate germline gene expression, transgenerational epigenetic inheritance, and ultimately, animal fertility.

scholarly journals An efficient FLP-based toolkit for spatiotemporal control of gene expression in Caenorhabditis elegans

2017 ◽  
Author(s):  
Celia María Muñoz-Jiménez ◽  
Cristina Ayuso ◽  
Agnieszka Dobrzynska ◽  
Antonio Torres ◽  
Patricia de la Cruz Ruiz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Developmental Stages ◽  
Model Organism ◽  
Cell Types ◽  
Single Copy ◽  
Conditional Knockout ◽  
Control Of Gene Expression ◽  
C Elegans ◽  
Cell Ablation

AbstractSite-specific recombinases are potent tools to regulate gene expression. In particular, the Cre and FLP enzymes are widely used to either activate or inactivate genes in a precise spatiotemporal manner. Both recombinases work efficiently in the popular model organism Caenorhabditis elegans but their use in this nematode is still only sporadic. To increase the utility of the FLP system in C. elegans we have generated a series of single-copy transgenic strains that stably express an optimized version of FLP in specific tissues or by heat induction. We show that recombination efficiencies reach 100 percent in several cell types, such as muscles, intestine and serotonin producing neurons. Moreover, we demonstrate that most promoters drive recombination exclusively in the expected tissues. As examples of the potentials of the FLP lines we describe novel tools for induced cell ablation by expression of the PEEL-1 toxin and a versatile FLP-out cassette for generation of GFP-tagged conditional knockout alleles. Together with other recombinase-based reagents created by the C. elegans community this toolkit increases the possibilities for detailed analyses of specific biological processes at developmental stages inside intact animals.

scholarly journals Experimental investigation using micro-PIV of the effect of microRNA-1 deficiency on motility in Caenorhabditis elegans

2020 ◽  
Author(s):  
S. Ravikumar ◽  
M. Fedrizzi ◽  
R. Prabhakar ◽  
R. Pocock ◽  
M. K. O’Bryan ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Swimming Speed ◽  
Model Organism ◽  
The Body ◽  
Wild Type ◽  
Mean Power ◽  
C Elegans ◽  
Micro Piv ◽  
Image Velocimetry ◽  
Beating Frequency

AbstractCaenorhabditis elegans is a microscopic nematode used extensively as a model organism in studies of neuromuscular function and neurodegenerative disorders. A mutation in mir-1 affects signalling at the neuromuscular junction. We investigate the effect of this mutation on the propulsive power exerted by nematodes as they grow in size with age. We compare the motility of wild-type and mir-1(gk276) mutant nematodes in a Newtonian fluid using a two-component, two dimensional (2C-2D) Digital Microscopic Particle Image Velocimetry (µ-PIV) technique. Beating amplitudes of the head and tail, the wavelength of undulatory waves and the swimming speed scale linearly with size in both the wild-type and mutant strains. The beating frequency is independent of size or position along the body. Differences in the magnitudes of these kinematic parameters between the two strains, however, grow systematically with age. The swimming speed scales linearly with the wave speed of the neuromuscular undulation in both nematode strains with a conserved ratio. The magnitude of mean power and mean local fluid circulation in the mutant is significantly lower compared to those of the wild-type animals of the same age. This indicates that a mutation in mir-1 adversely affects motility in C. elegans.

A Cuticle Collagen Encoded by the lon-3 Gene May Be a Target of TGF-β Signaling in Determining Caenorhabditis elegans Body Shape

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1631-1639
Author(s):  
Yo Suzuki ◽  
Gail A Morris ◽  
Min Han ◽  
William B Wood
Keyword(s):  
Caenorhabditis Elegans ◽  
Body Shape ◽  
Small Body ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Cellular Mechanisms ◽  
C Elegans ◽  
Gene Expression Analyses ◽  
Dose Dependent

Abstract The signaling pathway initiated by the TGF-β family member DBL-1 in Caenorhabditis elegans controls body shape in a dose-dependent manner. Loss-of-function (lf) mutations in the dbl-1 gene cause a short, small body (Sma phenotype), whereas overexpression of dbl-1 causes a long body (Lon phenotype). To understand the cellular mechanisms underlying these phenotypes, we have isolated suppressors of the Sma phenotype resulting from a dbl-1(lf) mutation. Two of these suppressors are mutations in the lon-3 gene, of which four additional alleles are known. We show that lon-3 encodes a collagen that is a component of the C. elegans cuticle. Genetic and reporter-gene expression analyses suggest that lon-3 is involved in determination of body shape and is post-transcriptionally regulated by the dbl-1 pathway. These results support the possibility that TGF-β signaling controls C. elegans body shape by regulating cuticle composition.

scholarly journals Mutations Affecting Nerve Attachment of Caenorhabditis elegans

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1611-1622 ◽  
Author(s):  
Go Shioi ◽  
Michinari Shoji ◽  
Masashi Nakamura ◽  
Takeshi Ishihara ◽  
Isao Katsura ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Nerve Cord ◽  
Ventral Nerve Cord ◽  
Body Wall ◽  
The Body ◽  
Genetic Loci ◽  
Muscle Attachment ◽  
C Elegans ◽  
Ventral Cord ◽  
Excretory Canal

Abstract Using a pan-neuronal GFP marker, a morphological screen was performed to detect Caenorhabditis elegans larval lethal mutants with severely disorganized major nerve cords. We recovered and characterized 21 mutants that displayed displacement or detachment of the ventral nerve cord from the body wall (Ven: ventral cord abnormal). Six mutations defined three novel genetic loci: ven-1, ven-2, and ven-3. Fifteen mutations proved to be alleles of previously identified muscle attachment/positioning genes, mup-4, mua-1, mua-5, and mua-6. All the mutants also displayed muscle attachment/positioning defects characteristic of mua/mup mutants. The pan-neuronal GFP marker also revealed that mutants of other mua/mup loci, such as mup-1, mup-2, and mua-2, exhibited the Ven defect. The hypodermis, the excretory canal, and the gonad were morphologically abnormal in some of the mutants. The pleiotropic nature of the defects indicates that ven and mua/mup genes are required generally for the maintenance of attachment of tissues to the body wall in C. elegans.

Behavioral Effects of Volatile Anesthetics in Caenorhabditis elegans

1996 ◽  
Vol 85 (4) ◽  
pp. 901-912 ◽  
Author(s):  
Michael C. Crowder ◽  
Laynie D. Shebester ◽  
Tim Schedl
Keyword(s):  
Nervous System ◽  
Caenorhabditis Elegans ◽  
Time Course ◽  
Model Organism ◽  
Volatile Anesthetic ◽  
Volatile Anesthetics ◽  
Effective Concentration ◽  
Forward Genetics ◽  
C Elegans ◽  
Median Effective Concentration

Background The nematode Caenorhabditis elegans offers many advantages as a model organism for studying volatile anesthetic actions. It has a simple, well-understood nervous system; it allows the researcher to do forward genetics; and its genome will soon be completely sequenced. C. elegans is immobilized by volatile anesthetics only at high concentrations and with an unusually slow time course. Here other behavioral dysfunctions are considered as anesthetic endpoints in C. elegans. Methods The potency of halothane for disrupting eight different behaviors was determined by logistic regression of concentration and response data. Other volatile anesthetics were also tested for some behaviors. Established protocols were used for behavioral endpoints that, except for pharyngeal pumping, were set as complete disruption of the behavior. Time courses were measured for rapid behaviors. Recovery from exposure to 1 or 4 vol% halothane was determined for mating, chemotaxis, and gross movement. All experiments were performed at 20 to 22 degrees C. Results The median effective concentration values for halothane inhibition of mating (0.30 vol%-0.21 mM), chemotaxis (0.34 vol%-0.24 mM), and coordinated movement (0.32 vol% - 0.23 mM) were similar to the human minimum alveolar concentration (MAC; 0.21 mM). In contrast, halothane produced immobility with a median effective concentration of 3.65 vol% (2.6 mM). Other behaviors had intermediate sensitivities. Halothane's effects reached steady-state in 10 min for all behaviors tested except immobility, which required 2 h. Recovery was complete after exposure to 1 vol% halothane but was significantly reduced after exposure to immobilizing concentrations. Conclusions Volatile anesthetics selectively disrupt C. elegans behavior. The potency, time course, and recovery characteristics of halothane's effects on three behaviors are similar to its anesthetic properties in vertebrates. The affected nervous system molecules may express structural motifs similar to those on vertebrate anesthetic targets.

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