计算机视觉在线虫进食行为自动分析中的应用

秀丽隐杆线虫被广泛地用作研究基因与行为关系的绝佳模式生物.线虫的咽部神经元回路控制着复杂的进食行为.为了研究进食行为的分子机制,有必要对线虫进食行为表型分析鉴定.然而,目前为止,几乎所有的线虫进食行为表型鉴定都是通过人眼来判断.因为其泵入食物的肌肉运动频率高,该行为的分析是很困难而且效率低下的.为解决这个问题,我们设计了基于计算机视觉技术的自动化成像系统来高通量分析线虫进食行为表型.此成像系统对进食表型的检测准确率达到98%以上,并使得连续可靠地分析其表型细微变化成为可能.同时,在保证高准确率的前提下单位时间内分析数据的效率比人工分析提高了3倍.     

Chemosensory behavior of semi‐restrained Caenorhabditis elegans

A new behavioral assay is described for studying chemosensation in the nematode Caenorhabditis elegans. This assay presents three main characteristics: (1) the worm is restrained by gluing, preserving correlates of identifiable behaviors; (2) the amplitude and time course of the stimulus are controlled by the experimenter; and (3) the behavior is recorded quantitatively. We show that restrained C. elegans display behaviors comparable to those of freely moving worms. Moreover, the chemosensory response of wild‐type glued animals to changes in salt concentration is similar to that of freely moving animals. This glued‐worm assay was used to reveal new chemosensory deficits of the potassium channel mutant egl‐2. We conclude that the glued worm assay can be used to study the chemosensory regulation of C. elegans behavior and how it is affected by neuronal or genetic manipulations. © 2005 Wiley Periodicals, Inc. J Neurobiol, 2005     

Identifying evolutionarily conserved genes in the dietary restriction response using bioinformatics and subsequent testing in Caenorhabditis elegans

Dietary restriction (DR) increases life span, health span and resistance to stress in a wide range of organisms. Work from a large number of laboratories has revealed evolutionarily conserved mechanisms that mediate the DR response. Here, we analyzed the genome-wide gene expression profiles of Caenorhabditis elegans under DR versus ad libitum conditions. Using the Ortho2ExpressMatrix tool, we searched for C. elegans orthologs of mouse genes that have been shown to be differentially expressed under DR conditions in nearly 600 experiments. Based on our bioinformatic approaches, we obtained 189 DR-responsive genes, and 45 of these are highly conserved from worm to man. Subsequent testing of sixteen genes that are up-regulated under DR identified eight genes that abolish the DR-induced resistance to heat stress in C. elegans. Further analyses revealed that fkb-4, dod-22 and ikb-1 genes also abolish increased life span in response to DR. The identified genes that are necessary for the DR response are sensitive to certain stress signals such as metabolic perturbances (dod-22, fkb-4 and nhr-85), DNA damage (ikb-1), heat shock (hsp-12.6) and cancer-like overgrowth (prk-2 and tsp-15). We propose that most of the DR-responsive genes identified are components of the recently discovered cellular surveillance-activated detoxification and defenses pathway, which is, among others, important for the survival of organisms in times of food deprivation.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-013-0363-5) contains supplementary material, which is available to authorized users.     

Selective Visualization of Fluorescent Sterols in Caenorhabditis elegans by Bleach‐Rate‐Based Image Segmentation

The nematode Caenorhabditis elegans is a genetically tractable model organism to investigate sterol transport. In vivo imaging of the fluorescent sterol, dehydroergosterol (DHE), is challenged by C. elegans’ high autofluorescence in the same spectral region as emission of DHE. We present a method to detect DHE selectively, based on its rapid bleaching kinetics compared to cellular autofluorescence. Worms were repeatedly imaged on an ultraviolet‐sensitive wide field (UV‐WF) microscope, and bleaching kinetics of DHE were fitted on a pixel‐basis to mathematical models describing the intensity decay. Bleach‐rate constants were determined for DHE in vivo and confirmed in model membranes. Using this method, we could detect enrichment of DHE in specific tissues like the nerve ring, the spermateca and oocytes. We confirm these results in C. elegans gut‐granule‐loss (glo) mutants with reduced autofluorescence and compare our method with three‐photon excitation microscopy of sterol in selected tissues. Bleach‐rate‐based UV‐WF imaging is a useful tool for genetic screening experiments on sterol transport, as exemplified by RNA interference against the rme‐2 gene coding for the yolk receptor and for worm homologues of Niemann‐Pick C disease proteins. Our approach is generally useful for identifying fluorescent probes in the presence of high cellular autofluorescence.     

An Efficient and Novel Screening Model for Assessing the Bioactivity of Extracts against Multidrug-Resistant Pseudomonas aeruginosa Using Caenorhabditis elegans

As a large number of multidrug-resistant bacteria have emerged, and there is an urgent need for the development of new antibacterial agents. In this study, we developed a liquid-based slow killing assay to be carried out in standard 96-well microtiter plates. This screening method was designed to facilitate high-throughput screening of small molecules and extracts. In antibiotic rescue assays, the Caenorhabditis elegans multidrug-resistant Pseudomonas aeruginosa infection model displayed a high degree of drug resistance in vivo and in vitro. We used the method to screen 1,300 extracts, and found 36 extracts (2.7%) which prolonged the survival of infected nematodes, and four (0.3%) of these extracts showed in vitro and in vivo anti-multidrug resistant P. aeruginosa activity. These results indicate that the whole-animal C. elegans multidrug-resistant bacterial model can be used to screen antibacterial compounds, and can also be useful for bioactive compounds which most likely cannot be identified in vitro.     

Worming Our Way In and Out of the Caenorhabditis elegans Germline and Developing Embryo

The germline and embryo of the nematode Caenorhabditis elegans have emerged as powerful model systems to study membrane dynamics in an intact, developing animal. In large part, this is due to the architecture of the reproductive system, which necessitates de novo membrane and organelle biogenesis within the stem cell niche to drive compartmentalization throughout the gonad syncytium. Additionally, membrane reorganization events during oocyte maturation and fertilization have been demonstrated to be highly stereotypic, facilitating the development of quantitative assays to measure the impact of perturbations on protein transport. This review will focus on regulatory mechanisms that govern protein trafficking, which have been elucidated using a combination of C. elegans genetics, biochemistry and high‐resolution microscopy. Collectively, studies using the simple worm highlight an important niche that the organism holds to define new pathways that regulate vesicle transport, many of which appear to be absent in unicellular systems but remain highly conserved in mammals .     

PAR-3 oligomerization may provide an actin-independent mechanism to maintain distinct par protein domains in the early Caenorhabditis elegans embryo

Par proteins establish discrete intracellular spatial domains to polarize many different cell types. In the single-cell embryo of the nematode worm Caenorhabditis elegans, the segregation of Par proteins is crucial for proper division and cell fate specification. Actomyosin-based cortical flows drive the initial formation of anterior and posterior Par domains, but cortical actin is not required for the maintenance of these domains. Here we develop a model of interactions between the Par proteins that includes both mutual inhibition and PAR-3 oligomerization. We show that this model gives rise to a bistable switch mechanism, allowing the Par proteins to occupy distinct anterior and posterior domains seen in the early C. elegans embryo, independent of dynamics or asymmetries in the actin cortex. The model predicts a sharp loss of cortical Par protein asymmetries during gradual depletion of the Par protein PAR-6, and we confirm this prediction experimentally. Together, these results suggest both mutual inhibition and PAR-3 oligomerization are sufficient to maintain distinct Par protein domains in the early C. elegans embryo.     

Uncover Genetic Interactions in Caenorhabditis elegans by RNA Interference

RNA-mediated interference (RNAi) has emerged recently as one of the most powerful functional genomics tools. RNAi has been particularly effective in the nematode worm C. elegans where RNAi has been used to analyse the loss-of-function phenotypes of almost all predicted genes. In this review, we illustrate how RNAi has been used to analyse gene function in C. elegans as well as pointing to some future directions for using RNAi to examine genetic interactions in a systematic manner.     

Refractory dissolved organic matter can influence the reproduction of Caenorhabditis elegans (Nematoda)

1. We investigated the effect of refractory dissolved organic matter (refractory DOM: fulvic acids (FAs) and ultrafiltrates (UFs)), isolated from five different sources, on the reproduction of the bacterivorous nematode Caenorhabditis elegans. Nematodes were exposed to DOM (0.5–64 mg L?1 dissolved organic carbon) during a whole life cycle (72 h). At the end of the test, the number of offspring per worm was determined.
2. We also studied the effect of refractory DOM on abundance, cell size, and activity of the bacteria (Escherichia coli) that were used as a food source for the nematodes, to assess possible indirect effects of DOM via the food organisms.
3. The effects of DOM on the reproduction of C. elegans varied, depending on the origin and concentration of DOM. FAs isolated from a soil leachate and from the effluent of a waste water plant, as well as UFs from a humic lake and from a marsh, stimulated the reproduction of C. elegans. FAs from ground water had no effect, while FAs from a humic lake inhibited the reproduction of the nematodes. All effects occurred at ecologically relevant DOM concentrations and showed clear dose–response relationships.
4. Neither bacterial abundance nor cell size were influenced by refractory DOM. Bacterial activity was unaffected by four types of DOM. Only FAs from the humic lake caused a significant decrease in bacterial activity over 72 h.
5. The negative effect of FAs from the humic lake on nematode reproduction may be a consequence of a lower bacterial activity in this treatment. The positive effects of refractory DOM, however, could not be related to bacterial parameters. Therefore, we assume that the DOM directly influenced the reproduction of C. elegans. We speculate that refractory DOM can potentially be an additional carbon source or a source of trace nutrients influencing the reproduction of C. elegans. Adsorption of refractory DOM on bacterial cells, serving as food for the nematodes, may have been an important factor for the availability of DOM for C. elegans.     

<Emphasis Type="Italic">C. elegans</Emphasis> behavior of preference choice on bacterial food

Caenorhabditis elegans is a free living soil nematode and thus in its natural habitat, C. elegans encounters many different species of soil bacteria. Although some soil bacteria may be excellent sources of nutrition for the worm, others may be pathogenic. Thus, we undertook a study to understand how C. elegans can identify their preferred food using a simple behavioral assay. We found that there are various species of soil bacteria that C. elegans prefers in comparison to the standard laboratory E. coli strain OP50. In particular, two bacterial strains, Bacillus mycoides and Bacillus soli, were preferred strains. Interestingly, the sole feeding of these bacteria to wild type animals results in extended lifespan through the activation of the autophagic process. Further studies will be required to understand the precise mechanism controlling the behavior of identification and selection of food in C. elegans.     

Deceptively simple but simply deceptive - Caenorhabditis elegans lifespan studies: Considerations for aging and antioxidant effects

The nematode worm Caenorhabditis elegans (C. elegans) is increasingly popular as a model organism for aging studies as well as for testing antioxidants and other compounds for effects on longevity. However, results in the literature are sometimes confusing and contradictory [1], [2], [3] and [4]. This review introduces C. elegans as a model organism, discusses aspects that make it attractive for aging and antioxidant research, and addresses some problems and potential artifacts.     

Breaking Caenorhabditis elegans the easy way using the Balch homogenizer: An old tool for a new application

The nematode Caenorhabditis elegans is a model organism best known for its powerful genetics. There is an increasing need in the worm community to couple genetics with biochemistry. Isolation of functionally active proteins or nucleic acids without the use of strong oxidizing denaturants or of subcellular compartments from C. elegans has, however, been challenging because of the worms’ thick surrounding cuticle. The Balch homogenizer is a tool that has found much use in mammalian cell culture biology. The interchangeable single ball-bearing design of this instrument permits rapid permeabilization, or homogenization, of cells. Here we demonstrate the utility of the Balch homogenizer for studies with C. elegans. We describe procedures for the efficient breakage and homogenization of every larval stage, including dauers, and show that the Balch homogenizer can be used to extract functionally active proteins. Enzymatic assays for catalase and dihydrolipoamide dehydrogenase show that sample preparation using the Balch homogenizer equals or outperforms conventional methods employing boiling, sonication, or Dounce homogenization. We also describe phenol-free techniques for isolation of genomic DNA and RNA. Finally, we used the tool to isolate coupled mitochondria and polysomes. The reusable Balch homogenizer represents a quick and convenient solution for undertaking biochemical studies on C. elegans.     

Profiling the Anaerobic Response of C. elegans Using GC-MS

The nematode Caenorhabditis elegans is a model organism that has seen extensive use over the last four decades in multiple areas of investigation. In this study we explore the response of the nematode Caenorhabditis elegans to acute anoxia using gas-chromatography mass-spectrometry (GC-MS). We focus on the readily-accessible worm exometabolome to show that C. elegans are mixed acid fermenters that utilize several metabolic pathways in unconventional ways to remove reducing equivalents – including partial reversal of branched-chain amino acid catabolism and a potentially novel use of the glyoxylate pathway. In doing so, we provide detailed methods for the collection and analysis of excreted metabolites that, with minimal adjustment, should be applicable to many other species. We also describe a procedure for collecting highly volatile compounds from C. elegans. We are distributing our mass spectral library in an effort to facilitate wider use of metabolomics.     

Acacetin promotes healthy aging by altering stress response in Caenorhabditis elegans

The progression in lifespan has been associated with elevated intracellular reactive oxygen species (ROS) and oxidative stress level which contributes to development of age related disorders. The discovery of lifespan modulating phytomolecules may promote development of natural therapies against age related afflictions. Acacetin (5,7-dihydroxy-4-methoxyflavone), is a naturally occurring flavonoid known to possess therapeutic properties. To this end, the present study evaluates effect of acacetin (AC) on lifespan, stress and neurotoxicity for the first time by using well-established free living, multicellular Caenorhabditis elegans model system. The 25?μM dose of AC significantly prolonged the mean lifespan of worms by 27.31% in comparison to untreated control and other tested doses of AC. Additionally, AC enhanced stress resistance against oxidative and thermal stress in worms. Furthermore, AC attenuated age related intracellular ROS level, aggregation of age pigment lipofuscin and increased the mean survival in stress hypersensitive mev-1 mutant by 40.5%. AC supplementation also reduced the alpha synuclein aggregation in transgenic worm model of Parkinson’s disease. The enhanced stress resistance, lifespan and alleviation of age related pathology can be attributed to increment in stress modulatory enzymes like superoxide dismutase (SOD) and catalase (CAT) level. Altogether the results suggest AC exposure maintains stress level, health span and extends mean lifespan of C. elegans. The longevity promoting and neuromodulatory effects of AC are mediated by up regulation of the stress response genes sod-3 and gst-4. The present finding gives new insights of natural remedies and their future prospects in developing therapeutic interventions for managing age related diseases.     

The burrowing behavior of the nematode Caenorhabditis elegans: a new assay for the study of neuromuscular disorders

The nematode Caenorhabditis elegans has been a powerful model system for the study of key muscle genes relevant to human neuromuscular function and disorders. The behavioral robustness of C. elegans, however, has hindered its use in the study of certain neuromuscular disorders because many worm models of human disease show only subtle phenotypes while crawling. By contrast, in their natural habitat, C. elegans likely spends much of the time burrowing through the soil matrix. We developed a burrowing assay to challenge motor output by placing worms in agar‐filled pipettes of increasing densities. We find that burrowing involves distinct kinematics and turning strategies from crawling that vary with the properties of the substrate. We show that mutants mimicking Duchenne muscular dystrophy by lacking a functional ortholog of the dystrophin protein, DYS‐1, crawl normally but are severely impaired in burrowing. Muscular degeneration in the dys‐1 mutant is hastened and exacerbated by burrowing, while wild type shows no such damage. To test whether neuromuscular integrity might be compensated genetically in the dys‐1 mutant, we performed a genetic screen and isolated several suppressor mutants with proficient burrowing in a dys‐1 mutant background. Further study of burrowing in C. elegans will enhance the study of diseases affecting neuromuscular integrity, and will provide insights into the natural behavior of this and other nematodes.     

Using <Emphasis Type="Italic">C. elegans</Emphasis> to screen for targets of ethanol and behavior-altering drugs

Caenorhabditis elegans is an attractive model system for determining the targets of neuroactive compounds. Genetic screens in C. elegans provide a relatively unbiased approach to the identification of genes that are essential for behavioral effects of drugs and neuroactive compounds such as alcohol. Much work in vertebrate systems has identified multiple potential targets of ethanol but which, if any, of those candidates are responsible for the behavioral effects of alcohol is uncertain. Here we provide detailed methodology for a genetic screen for mutants of C. elegans that are resistant to the depressive effects of ethanol on locomotion and for the subsequent behavioral analysis of those mutants. The methods we describe should also be applicable for use in screening for mutants that are resistant or hypersensitive to many neuroactive compounds and for identifying the molecular targets or biochemical pathways mediating drug responses. Published: June 8, 2004.     

On the potential for extinction by Muller's Ratchet in <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>

Background  

The self-fertile hermaphrodite worm C. elegans is an important model organism for biology, yet little is known about the origin and persistence of the self-fertilizing mode of reproduction in this lineage. Recent work has demonstrated an extraordinary degree of selfing combined with a high deleterious mutation rate in contemporary populations. These observations raise the question as to whether the mutation load might rise to such a degree as to eventually threaten the species with extinction. The potential for such a process to occur would inform our understanding of the time since the origin of self-fertilization in C. elegans history.     

Dopamine Signaling Architecture in Caenorhabditis elegans

1. Aims: In this review, we highlight the identification and analysis of molecules orchestrating dopamine (DA) signaling in the nematode Caenorhabditis elegans, focusing on recent characterizations of DA transporters and receptors.2. Methods: We illustrate the isolation and characterization of molecules important for C. elegans DA synthesis, packaging, reuptake and signaling and examine how mutations in these proteins are being exploited through in vitro and in vivo paradigms to yield novel insights of protein structure, DA signaling pathways and DA-supported behaviors.3. Results: DA signaling in the worm, as in man, arises by synaptic and nonsynaptic release from a small number of cells that exert modulatory control over a larger network underlying C. elegans behavior.4. Conclusions: The C. elegans model system offers unique opportunities to elucidate ill-defined pathways that support DA release, inactivation, and signaling in addition to clarifying mechanisms of DA-mediated behavioral plasticity. Further use of the model offers prospects for the identification of novel genes and proteins whose study may yield benefits for DA-supported neural disorders in man.