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1

Antioxidant activity and protective effect of Turnera ulmifolia Linn. var. elegans against carbon tetrachloride-induced oxidative damage in rats.  

PubMed

The present study aimed to determine whether the leaves of Turnera ulmifolia Linn. var. elegans extract exert significant antioxidant activity. The antioxidant activity of its hydroethanolic extract (HEETU) was evaluated by assessing (a) its radical scavenging ability in vitro, and (b) its in vivo effect on lipid peroxidation and antioxidant enzyme activities. The in vitro antioxidant assay (DPPH) clearly supported HEETU free radical scavenging potential. Moreover, glutathione content and antioxidant enzyme activities (glutathione peroxidase, superoxide dismutase and catalase) were significantly enhanced in CCl(4)-treated rats due to oral HEETU-treatment (500 mg/kgb.w.) over 7 and 21 days. In addition, an improvement was observed in lipid peroxidation and serum biochemical parameters (aspartate aminotransferase and alanine aminotransferase), indicating a protective effect against CCl(4)-induced liver injuries, confirmed by histopathological studies. The HEETU effect was comparable to the standard drug Legalon® (50 mg/kgb.w.) under the same experimental condition. Quantitative analysis of the HPLC extract revealed the presence of flavonoids, wich mediate the effects of antioxidant and oxidative stress. In conclusion, extract components exhibit antioxidant and hepatoprotective activities in vitro and in vivo. PMID:22940430

Brito, Naira J N; López, Jorge A; do Nascimento, Maria Aparecida; Macêdo, José B M; Silva, Gabriel Araujo; Oliveira, Cláudia N; de Rezende, Adriana Augusto; Brandão-Neto, José; Schwarz, Aline; Almeida, Maria das Graças

2012-12-01

2

Straightening Caenorhabditis elegans images  

Microsoft Academic Search

Motivation: Caenorhabditis elegans, a roundworm found in soil, is a widely studied model organism with about 1000 cells in the adult. Producing high-resolution fluorescence images of C.elegans to reveal biological insights is becoming routine, motivating the development of advanced computational tools for analyzing the resulting image stacks. For example, worm bodies usually curve significantly in images. Thus one must 'straighten'

Hanchuan Peng; Fuhui Long; Xiao Liu; Stuart K. Kim; Eugene W. Myers

2008-01-01

3

FIONA on C. elegans  

PubMed Central

Despite much work, sub-cellular neurons of Caenorhabditis elegans have not been studied at nanometer resolution with millisecond time resolution. Nor has there been an effective way to immobilize C. elegans. Here we show that, without using anesthetic or paralyzing agents, Fluorescence Imaging with One Nanometer Accuracy (FIONA) can be successfully applied to fluorescently labeled molecules within C. elegans nerves. GFP- and DENDRA2-labeled ELKS punctae can be localized with sub-10 nm accuracy in ~5 milliseconds. Our results show that the protein ELKS is occasionally transferred by microtubule-based motors. This is the first example of FIONA applied to a living organism.

Kural, Comert; Nonet, Michael L.; Selvin, Paul R.

2010-01-01

4

Set-Var  

Microsoft Academic Search

In this paper we describe the rules of the SET-VAR prover, which is an extension of resolution and which handles theorems in a subset of second-order logic. We also give example proofs using the system and show that the rules are sound. We conjecture that the prover, defined by these SET-VAR rules, is complete for a certain extension of first-order

W. W. Bledsoe; Guohui Feng

1993-01-01

5

Inocybe hirsuta var. maxima  

NSDL National Science Digital Library

Inocybe hirsuta var. maxima A. H. Smith (SAT 01-279-08) photographed in the Hoh River Valley in Olympic National Park, Washington, USA. This variety is common in Washington under western hemlock and is also known from eastern North America under eastern hemlock.

Trudell, Steve

2004-03-09

6

Neural Regeneration in Caenorhabditis elegans  

PubMed Central

Axon regeneration is a medically relevant process that can repair damaged neurons. This review describes current progress in understanding axon regeneration in the model organism Caenorhabditis elegans. Factors that regulate axon regeneration in C. elegans have broadly similar roles in vertebrate neurons. This means that using C. elegans as a tool to leverage discovery is a legitimate strategy for identifying conserved mechanisms of axon regeneration.

El Bejjani, Rachid; Hammarlund, Marc

2013-01-01

7

Dielectrophoresis of Caenorhabditis elegans  

PubMed Central

We demonstrate for the first time the dielectrophoretic trapping and manipulation of a whole animal, the nematode Caenorhabditis elegans. We studied the effect of the electric field on the nematode as a function of field intensity and frequency. We identified a range of electric field intensities and frequencies that trap worms without apparent adverse effect on their viability. Worms tethered by dielectrophoresis (DEP) exhibit behavioral responses to blue light, indicating that at least some of the nervous system functions are unimpaired by the electrical field. DEP is useful to dynamically tether nematodes, sort nematodes according to size, and separate dead worms from live ones.

Chuang, Han-Sheng; Raizen, David; Lamb, Annesia; Dabbish, Nooreen; Bau, Haim

2011-01-01

8

Neuropeptide GPCRs in C. elegans  

PubMed Central

Like most organisms, the nematode Caenorhabditis elegans relies heavily on neuropeptidergic signaling. This tiny animal represents a suitable model system to study neuropeptidergic signaling networks with single cell resolution due to the availability of powerful molecular and genetic tools. The availability of the worm’s complete genome sequence allows researchers to browse through it, uncovering putative neuropeptides and their cognate G protein-coupled receptors (GPCRs). Many predictions have been made about the number of C. elegans neuropeptide GPCRs. In this review, we report the state of the art of both verified as well as predicted C. elegans neuropeptide GPCRs. The predicted neuropeptide GPCRs are incorporated into the receptor classification system based on their resemblance to orthologous GPCRs in insects and vertebrates. Appointing the natural ligand(s) to each predicted neuropeptide GPCR (receptor deorphanization) is a crucial step during characterization. The development of deorphanization strategies resulted in a significant increase in the knowledge of neuropeptidergic signaling in C. elegans. Complementary localization and functional studies demonstrate that neuropeptides and their GPCRs represent a rich potential source of behavioral variability in C. elegans. Here, we review all neuropeptidergic signaling pathways that so far have been functionally characterized in C. elegans.

Frooninckx, Lotte; Van Rompay, Liesbeth; Temmerman, Liesbet; Van Sinay, Elien; Beets, Isabel; Janssen, Tom; Husson, Steven J.; Schoofs, Liliane

2012-01-01

9

Meiotic Development in Caenorhabditis elegans  

PubMed Central

Caenorhabditis elegans has become a powerful experimental organism with which to study meiotic processes that promote the accurate segregation of chromosomes during the generation of haploid gametes. Haploid reproductive cells are produced through one round of chromosome replication followed by two successive cell divisions. Characteristic meiotic chromosome structure and dynamics are largely conserved in C. elegans. Chromosomes adopt a meiosis-specific structure by loading cohesin proteins, assembling axial elements, and acquiring chromatin marks. Homologous chromosomes pair and form physical connections though synapsis and recombination. Synaptonemal complex and crossover formation allow for the homologs to stably associate prior to remodeling that facilitates their segregation. This chapter will cover conserved meiotic processes as well as highlight aspects of meiosis that are unique to C. elegans.

Lui, Doris Y.

2013-01-01

10

C. elegans feeding.  

PubMed

C. elegans feeding depends on the action of the pharynx, a neuromuscular pump that joins the mouth to the intestine. The pharyngeal muscle captures food-bacteria-and transports it back to the intestine. It accomplishes this through a combination of two motions, pumping and isthmus peristalsis. Pumping, the most visible and best understood of the two, is a cycle of contraction and relaxation that sucks in liquid from the surrounding environment along with suspended particles, then expels the liquid, trapping the particles. Pharyngeal muscle is capable of pumping without nervous system input, but during normal rapid feeding its timing is controlled by two pharyngeal motor neuron types. Isthmus peristalsis, a posterior moving wave of contraction of the muscle of the posterior isthmus, depends on a third motor neuron type. Feeding motions are regulated by the presence and quality of food in the worm's environment. Some types of bacteria are better at supporting growth than others. Given a choice, worms are capable of identifying and seeking out higher-quality food. Food availability and quality also affect behavior in other ways. For instance, given all the high-quality food they can eat, worms eventually become satiated, stop eating and moving, and become quiescent. PMID:22628186

Avery, Leon; You, Young-Jai

2012-01-01

11

Recovery Plan: 'Chamaecrista glandulosa' var. 'mirabilis'.  

National Technical Information Service (NTIS)

Chamaecrista glandulosa var. mirabilis is listed as endangered. Chamaecrista glandulosa var. mirabilis is a small shrub endemic to the white silica sands of the northern coast of Puerto Rico at elevations near sea level. It is scattered along the southern...

S. Silander

1994-01-01

12

The Caenorhabditis elegans intestine.  

PubMed

The transcriptional regulatory hierarchy that controls development of the Caenorhabditis elegans endoderm begins with the maternally provided SKN-1 transcription factor, which determines the fate of the EMS blastomere of the four-cell embryo. EMS divides to produce the posterior E blastomere (the clonal progenitor of the intestine) and the anterior MS blastomere, a major contributor to mesoderm. This segregation of lineage fates is controlled by an intercellular signal from the neighboring P2 blastomere and centers on the HMG protein POP-1. POP-1 would normally repress the endoderm program in both E and MS but two consequences of the P2-to-EMS signal are that POP-1 is exported from the E-cell nucleus and the remaining POP-1 is converted to an endoderm activator by complexing with SYS-1, a highly diverged ?-catenin. In the single E cell, a pair of genes encoding small redundant GATA-type transcription factors, END-1 and END-3, are transcribed under the combined control of SKN-1, the POP-1/SYS-1 complex, as well as the redundant pair of MED-1/2 GATA factors, themselves direct zygotic targets of SKN-1 in the EMS cell. With the expression of END-1/END-3, the endoderm is specified. END-1 and END-3 then activate transcription of a further set of GATA-type transcription factors that drive intestine differentiation and function. One of these factors, ELT-2, appears predominant; a second factor, ELT-7, is partially redundant with ELT-2. The mature intestine expresses several thousand genes, apparently all controlled, at least in part, by cis-acting GATA-type motifs. PMID:23799580

McGhee, James D

2013-01-01

13

The kinetochores of Caenorhabditis elegans  

Microsoft Academic Search

Light microscopy of the mitotic chromosomes of Caenorhabditis elegans suggests that non-localized kinetochores are present, since the chromosomes appear as stiff rods 1 to 2 µm in length and lack any visible constriction. The holokinetic structure was confirmed by reconstructions of electron micrographs of dividing nuclei in serially sectioned embryos. In prophase the kinetochore appears as an amorphous projection approximately

Donna G. Albertson; J. Nichol Thomson

1982-01-01

14

Bacterial Endosymbionts of Pyrodinium bahamense var. compressum  

Microsoft Academic Search

The study presents evidence in support of the bacterial theory associated with the toxicity of Pyrodinium bahamense var. compressum. Bacterial endosymbionts from Philippine P. bahamense var. compressum strain Pbc MZRVA 042595 were isolated and identified via 16S rDNA sequence analysis. Taxonomic diversity of the identified culturable intracellular microbiota associated with Philippine P. bahamense var. compressum was established to be limited

Ma. Patricia V. Azanza; Rhodora V. Azanza; Vanessa Mercee D. Vargas; Cynthia T. Hedreyda

2006-01-01

15

The Caenorhabditis elegans model of Legionella infection.  

PubMed

Caenorhabditis elegans can serve as a simple genetic host to study interactions between Legionellaceae and their hosts, and to examine the contribution of specific gene products to virulence and immunity. C. elegans nematodes have several appealing attributes as a host organism; they are inexpensive, have robust genetic analysis tools, have a simple anatomy yet display a wide range of complex behaviors, and, as invertebrates, do not require animal ethics protocols. Use of C. elegans as a host model complements cell-based models, providing additional support and consistency of the experimental data obtained from multiple models. The C. elegans innate immune system functions similarly to that of the alveolar macrophage including the apoptosis [e.g. programmed cell death (PCD)] pathway located within the germline. The digestive tract of C. elegans is a primary interface between the innate immune system and bacterial pathogens. Thus, the C. elegans host model provides an alternative approach to investigate Legionella pneumophila immunopathogenesis. PMID:23150413

Brassinga, Ann Karen C; Sifri, Costi D

2013-01-01

16

Meiotic recombination in Caenorhabditis elegans  

Microsoft Academic Search

The faithful segregation of homologous chromosomes during meiosis is dependent on the formation of physical connections (chiasma)\\u000a that form following reciprocal exchange of DNA molecules during meiotic recombination. Here we review the current knowledge\\u000a in the Caenorhabditis elegans meiotic recombination field. We discuss recent developments that have improved our understanding of the crucial steps that\\u000a must precede the initiation and

Tatiana Garcia-Muse; Simon J. Boulton

2007-01-01

17

VAR Models: Estimation, Inferences, and Applications  

Microsoft Academic Search

\\u000a Vector auto-regression (VAR) models have been used extensively in finance and economic analysis. This paper provides a brief\\u000a overview of the basic VAR approach by focusing on model estimation and statistical inferences. Applications of VAR models\\u000a in some finance areas are discussed, including asset pricing, international finance, and market micro-structure. It is shown\\u000a that such approach provides a powerful tool

Yangru Wu; Xing Zhou

18

A new measurement of CP violation parameter. var epsilon. prime /. var epsilon  

SciTech Connect

The E731 experiment at Fermilab has measured the CP violation parameter Re({var epsilon}{prime}/{var epsilon}) in K{sub L,S}{yields}{pi}{pi} decay. Four decay modes were collected simultaneously to reduce systematic errors. The result is Re({var epsilon}{prime}/{var epsilon})={minus}0.0005 {plus minus} 0.0014 (stat.) {plus minus} 0.0006 (syst.), and gives no evidence for direct CP violation. 7 refs., 3 figs., 1 tab.

Yamanaka, Taku.

1990-01-01

19

ACeKit: A Caenorhabditis elegans Survival Kit  

NSDL National Science Digital Library

Developed by elegans_Net, this metasite on _Caenorhabditis elegans provides everything you ever wanted to know about the model organism, including commentary by experts; the value of C. elegans to biology, biotechnology, and medicine; and links to major functional genomics and bioinformatics resources. Also at the site are links to text and images on the dynamics of C. elegans development, C. elegans anatomy, and other miscellany.

20

Prion protein in Caenorhabditis elegans  

PubMed Central

The infectious agent of prion diseases is believed to be nucleic acid-free particles composed of misfolded conformational isomers of a host protein known as prion protein (PrP). Although this “protein-only” concept is generally accepted, decades of extensive research have not been able to elucidate the mechanisms by which PrP misfolding leads to neurodegeneration and infectivity. The challenges in studying prion diseases relate in part to the limitations of mammalian prion models, which include the long incubation period post-infection until symptoms develop, the high expense of maintaining mammals for extended periods, as well as safety issues. In order to develop prion models incorporating a genetically tractable simple system with a well-defined neuronal system, we generated transgenic C. elegans expressing the mouse PrP behind the pan-neuronal ric-19 promoter (Pric-19). We show here that high expression of Pric-19::PrP in C. elegans can result in altered morphology, defective mobility and shortened lifespan. Low expression of Pric-19::PrP, however, does not cause any detectable harm. Using the dopamine neuron specific promoter Pdat-1, we also show that expression of the murine BAX, a pro-apoptotic member of the Bcl-2 family, causes dopamine neuron destruction in the nematode. However, co-expression of PrP inhibits BAX-mediated dopamine neuron degeneration, demonstrating for the first time that PrP has anti-BAX activity in living animals. Thus, these distinct PrP-transgenic C. elegans lines recapitulate a number of functional and neuropathological features of mammalian prion models and provide an opportunity for facile identification of genetic and environmental contributors to prion-associated pathology.

Park, Kyung-Won

2011-01-01

21

Using C. elegans for antimicrobial drug discovery  

PubMed Central

Introduction The number of microorganism strains with resistance to known antimicrobials is increasing. Therefore, there is a high demand for new, non-toxic and efficient antimicrobial agents. Research with the microscopic nematode Caenorhabditis elegans can address this high demand for the discovery of new antimicrobial compounds. In particular, C. elegans can be used as a model host for in vivo drug discovery through high-throughput screens of chemical libraries. Areas covered This review introduces the use of substitute model hosts and especially C. elegans in the study of microbial pathogenesis. The authors also highlight recently published literature on the role of C. elegans in drug discovery and outline its use as a promising host with unique advantages in the discovery of new antimicrobial drugs. Expert opinion C. elegans can be used, as a model host, to research many diseases, including fungal infections and Alzheimer’s disease. In addition, high-throughput techniques, for screening chemical libraries, can also be facilitated. Nevertheless, C. elegans and mammals have significant differences that both limit the use of the nematode in research and the degree by which results can be interpreted. That being said, the use of C. elegans in drug discovery still holds promise and the field continues to grow, with attempts to improve the methodology already underway.

Desalermos, Athanasios; Muhammed, Maged; Glavis-Bloom, Justin; Mylonakis, Eleftherios

2011-01-01

22

Analyses of C. elegans fat metabolic pathways.  

PubMed

In Caenorhabdatis elegans as in other animals, fat regulation reflects the outcome of behavioral, physiological, and metabolic processes. The amenability of C. elegans to experimentation has led to utilization of this organism for elucidating the complex homeostatic mechanisms that underlie energy balance in intact organisms. The optical advantages of C. elegans further offer the possibility of studying cell biological mechanisms of fat uptake, transport, storage, and utilization, perhaps in real time. Here, we discuss the rationale as well as advantages and potential pitfalls of methods used thus far to study metabolism and fat regulation, specifically triglyceride metabolism, in C. elegans. We provide detailed methods for visualization of fat depots in fixed animals using histochemical stains and in live animals by vital dyes. Protocols are provided and discussed for chloroform-based extraction of total lipids from C. elegans homogenates used to assess total triglyceride or phospholipid content by methods such as thin-layer chromatography or used to obtain fatty acid profiles by methods such as gas chromatography/mass spectrometry. Additionally, protocols are provided for the determination of rates of intestinal fatty acid uptake and fatty acid breakdown by ?-oxidation. Finally, we discuss methods for determining rates of de novo fat synthesis and Raman scattering approaches that have recently been employed to investigate C. elegans lipids without reliance on invasive techniques. As the C. elegans fat field is relatively new, we anticipate that the indicated methods will likely be improved upon and expanded as additional researchers enter this field. PMID:22226531

Barros, Alexandre Guimarães de Almeida; Liu, Jason; Lemieux, George A; Mullaney, Brendan C; Ashrafi, Kaveh

2012-01-01

23

Axon regeneration mechanisms: insights from C. elegans  

PubMed Central

Understanding the mechanisms of axon regeneration is of great importance to develop therapeutic treatments for spinal cord injury or stroke. Axon regeneration has long been studied in various vertebrate and invertebrate models, but until recently had not been analyzed in the genetically tractable model organism Caenorhabditis elegans. The small size, simple neuroanatomy, and transparency of C. elegans allows single fluorescently labeled axons to be severed in live animals using laser microsurgery. Many neurons in C. elegans are capable of regenerative regrowth, and can in some cases re-establish functional connections. Large-scale genetic screens have begun to elucidate the genetic basis of axon regrowth.

Chen, Lizhen; Chisholm, Andrew D.

2011-01-01

24

VAR forecasting using Bayesian variable selection  

Microsoft Academic Search

This paper develops methods for automatic selection of variables in forecasting Bayesian vector autoregressions (VARs) using the Gibbs sampler. In particular, I provide computationally efficient algorithms for stochastic variable selection in generic (linear and nonlinear) VARs. The performance of the proposed variable selection method is assessed in a small Monte Carlo experiment, and in forecasting 4 macroeconomic series of the

Dimitris Korobilis

2009-01-01

25

Gait synchronization in Caenorhabditis elegans.  

PubMed

Collective motion is observed in swarms of swimmers of various sizes, ranging from self-propelled nanoparticles to fish. The mechanisms that govern interactions among individuals are debated, and vary from one species to another. Although the interactions among relatively large animals, such as fish, are controlled by their nervous systems, the interactions among microorganisms, which lack nervous systems, are controlled through physical and chemical pathways. Little is known, however, regarding the mechanism of collective movements in microscopic organisms with nervous systems. To attempt to remedy this, we studied collective swimming behavior in the nematode Caenorhabditis elegans, a microorganism with a compact nervous system. We evaluated the contributions of hydrodynamic forces, contact forces, and mechanosensory input to the interactions among individuals. We devised an experiment to examine pair interactions as a function of the distance between the animals and observed that gait synchronization occurred only when the animals were in close proximity, independent of genes required for mechanosensation. Our measurements and simulations indicate that steric hindrance is the dominant factor responsible for motion synchronization in C. elegans, and that hydrodynamic interactions and genotype do not play a significant role. We infer that a similar mechanism may apply to other microscopic swimming organisms and self-propelled particles. PMID:24778261

Yuan, Jinzhou; Raizen, David M; Bau, Haim H

2014-05-13

26

Axon pruning: C. elegans makes the cut.  

PubMed

Axon pruning has recently been described in the simple nervous system of the nematode Caenorhabditis elegans. Generating excess processes and pruning may be a phylogenetically conserved feature reflecting a flexibility to modify neural circuits. PMID:16213809

Wadsworth, William G

2005-10-11

27

Biomechanical Profiling of Caenorhabditis elegans Motility  

PubMed Central

Caenorhabditis elegans locomotion is a stereotyped behavior that is ideal for genetic analysis. We integrated video microscopy, image analysis algorithms, and fluid mechanics principles to describe the C. elegans swim gait. Quantification of body shapes and external hydrodynamics and model-based estimates of biomechanics reveal that mutants affecting similar biological processes exhibit related patterns of biomechanical differences. Therefore, biomechanical profiling could be useful for predicting the function of previously unstudied motility genes.

Krajacic, Predrag; Shen, Xiaoning; Purohit, Prashant K.; Arratia, Paulo; Lamitina, Todd

2012-01-01

28

Biomechanical profiling of Caenorhabditis elegans motility.  

PubMed

Caenorhabditis elegans locomotion is a stereotyped behavior that is ideal for genetic analysis. We integrated video microscopy, image analysis algorithms, and fluid mechanics principles to describe the C. elegans swim gait. Quantification of body shapes and external hydrodynamics and model-based estimates of biomechanics reveal that mutants affecting similar biological processes exhibit related patterns of biomechanical differences. Therefore, biomechanical profiling could be useful for predicting the function of previously unstudied motility genes. PMID:22554893

Krajacic, Predrag; Shen, Xiaoning; Purohit, Prashant K; Arratia, Paulo; Lamitina, Todd

2012-07-01

29

Cancer models in C. elegans  

PubMed Central

Although now dogma, the idea that non-vertebrate organisms such as yeast, worms, and flies could inform, and in some cases even revolutionize, our understanding of oncogenesis in humans was not immediately obvious. Aided by the conservative nature of evolution and the persistence of a cohort of devoted researchers, the role of model organisms as a key tool in solving the cancer problem has, however, become widely accepted. In this review, we focus on the nematode Caenorhabditis elegans and its diverse and sometimes surprising contributions to our understanding of the tumorigenic process. Specifically, we discuss findings in the worm that address a well-defined set of processes known to be deregulated in cancer cells including cell cycle progression, growth factor signaling, terminal differentiation, apoptosis, the maintenance of genome stability, and developmental mechanisms relevant to invasion and metastasis.

Kirienko, Natalia V.; Mani, Kumaran; Fay, David S.

2013-01-01

30

The C. elegans Lifespan Machine  

PubMed Central

The measurement of lifespan pervades aging research. Because lifespan results from complex interactions between genetic, environmental and stochastic factors, it varies widely even among isogenic individuals. The action of molecular mechanisms on lifespan is therefore visible only through their statistical effects on populations. Survival assays in C. elegans provided critical insights into evolutionarily conserved determinants of aging. To enable the rapid acquisition of survival curves at arbitrary statistical resolution, we developed a scalable imaging and analysis platform to observe nematodes over multiple weeks across square meters of agar surface at 8 ?m resolution. The method generates a permanent visual record of individual deaths from which survival curves are constructed and validated, producing data consistent with the manual method for several mutants in both standard and stressful environments. Our approach allows rapid, detailed reverse-genetic and chemical screens for effects on survival and enables quantitative investigations into the statistical structure of aging.

Stroustrup, Nicholas; Ulmschneider, Bryne E.; Nash, Zachary M.; Lopez Moyado, Isaac F.; Apfeld, Javier; Fontana, Walter

2013-01-01

31

Chemically Defined Medium and Caenorhabditis elegans: A Powerful Approach.  

National Technical Information Service (NTIS)

C. elegans has been established as a powerful genetic system. Growth in a chemically defined medium (C. elegans Maintenance Medium (CeMM)) now allows standardization and systematic manipulation of the nutrients that animals receive. Liquid cultivation all...

N. J. Szewczyk E. Kozak C. A. Conley

2003-01-01

32

Microsporidia Are Natural Intracellular Parasites of the Nematode Caenorhabditis elegans  

Microsoft Academic Search

For decades the soil nematode Caenorhabditis elegans has been an important model system for biology, but little is known about its natural ecology. Recently, C. elegans has become the focus of studies of innate immunity and several pathogens have been shown to cause lethal intestinal infections in C. elegans. However none of these pathogens has been shown to invade nematode

Emily R Troemel; Marie-Anne Félix; Noah K Whiteman; Antoine Barrière; Frederick M Ausubel

2008-01-01

33

NYMPHAEA ELEGANS (NYMPHAEACEAE) NUEVA CITA PARA LA FLORA ARGENTINA  

Microsoft Academic Search

Tur, N. M. 2003. Nymphaea elegans (Nymphaeaceae), a new record for the flora of Argentina. Hickenia 3(42): 167-169. Nymphaea elegans is recorded for the first time for Argentina, from Misiones province. The species is described and illustrated. Up to the present N. elegans was recorded for United States (Texas), Mexico and Guatemala.

NUNCIA MARÍA TUR

34

Chemically defined medium and Caenorhabditis elegans  

NASA Technical Reports Server (NTRS)

BACKGROUND: C. elegans has been established as a powerful genetic system. Use of a chemically defined medium (C. elegans Maintenance Medium (CeMM)) now allows standardization and systematic manipulation of the nutrients that animals receive. Liquid cultivation allows automated culturing and experimentation and should be of use in large-scale growth and screening of animals. RESULTS: We find that CeMM is versatile and culturing is simple. CeMM can be used in a solid or liquid state, it can be stored unused for at least a year, unattended actively growing cultures may be maintained longer than with standard techniques, and standard C. elegans protocols work well with animals grown in defined medium. We also find that there are caveats to using defined medium. Animals in defined medium grow more slowly than on standard medium, appear to display adaptation to the defined medium, and display altered growth rates as they change the composition of the defined medium. CONCLUSIONS: As was suggested with the introduction of C. elegans as a potential genetic system, use of defined medium with C. elegans should prove a powerful tool.

Szewczyk, Nathaniel J.; Kozak, Elena; Conley, Catharine A.

2003-01-01

35

The ecology and biodemography of Caenorhabditis elegans.  

PubMed

The nematode Caenorhabditis elegans is a well-known model organism for research on aging and life span, but very little is known about its ecology and natural history. The strain N2 is the standard wild-type C. elegans and arose from the progeny of a single hermaphrodite. Since N2 has passed through laboratory culture, the influence of inadvertent selection and genetic drift on C. elegans strains kept in culture is unclear. Because it seems that other wild-type strains have also been subject to lengthy laboratory culture, the life span and biodemography of wild-caught C. elegans is of interest. We recovered C. elegans from snails (Helix aspersa) in ca. 50% of the California locations where we made collections. In experiments with one of the wild-caught isolates, it differed in important demographic properties, mortality, fertility, fitness, and activity patterns, from the standard N2 strain, when both strains were evaluated in a common laboratory environment. The differences were not only statistically significant; they were also large enough to be biologically important. The differences are consistent with the hypothesis that N2 has adapted to laboratory conditions. PMID:16963216

Chen, J; Lewis, E E; Carey, J R; Caswell, Hal; Caswell-Chen, E P

2006-10-01

36

Host-Microbe Interactions in Caenorhabditis elegans.  

PubMed

A good understanding of how microbes interact with hosts has a direct bearing on our capability of fighting infectious microbial pathogens and making good use of beneficial ones. Among the model organisms used to study reciprocal actions among microbes and hosts, C. elegans may be the most advantageous in the context of its unique attributes such as the short life cycle, easiness of laboratory maintenance, and the availability of different genetic mutants. This review summarizes the recent advances in understanding host-microbe interactions in C. elegans. Although these investigations have greatly enhanced our understanding of C. elegans-microbe relationships, all but one of them involve only one or few microbial species. We argue here that more research is needed for exploring the evolution and establishment of a complex microbial community in the worm's intestine and its interaction with the host. PMID:23984180

Zhang, Rui; Hou, Aixin

2013-01-01

37

Analysis of Apoptosis in Caenorhabditis elegans.  

PubMed

The nematode worm Caenorhabditis elegans has provided researchers with a wealth of information on the molecular mechanisms controlling programmed cell death (apoptosis). Its genetic tractability, optical clarity, and relatively short lifespan are key advantages for rapid assessment of apoptosis in vivo. The use of forward and reverse genetics methodology, coupled with in vivo imaging, has provided deep insights into how a multicellular organism orchestrates the self-destruction of specific cells during development and in response to exogenous stresses. Strains of C. elegans carrying mutations in the core elements of the apoptotic pathway, or in tissue-specific regulators of apoptosis, can be used for genetic analyses to reveal conserved mechanisms by which apoptosis is regulated in the somatic and reproductive (germline) tissue. Here we present an introduction to the study of apoptosis in C. elegans, including current techniques for visualization, analysis, and screening. PMID:24786497

Lant, Benjamin; Derry, W Brent

2014-01-01

38

Complete mitochondrial genome sequence of Nectogale elegans.  

PubMed

Abstract The elegant water shrew (Nectogale elegans) belongs to the family Soricidae, and distributes in northern South Asia, central and southern China and northern Southeast Asia. In this study, the complete mitochondrial genome of N. elegans was sequenced. It was determined to be 17,460 bases, and included 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and one non-coding region, which is similar to other mammalian mitochondrial genomes. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand concatenated PCGs. Phylogenetic analyses further confirmed that Crocidurinae diverged prior to Soricinae, and Sorex unguiculatus differentiated earlier than N. elegans. PMID:23795853

Huang, Ting; Yan, Chaochao; Tan, Zheng; Tu, Feiyun; Yue, Bisong; Zhang, Xiuyue

2014-08-01

39

Eph receptor signaling in C. elegans  

PubMed Central

Eph receptor protein-tyrosine kinases are among the oldest known animal receptors and have greatly expanded in number during vertebrate evolution. Their complex transduction mechanisms are capable of bidirectional and bimodal (multi-response) signaling. Eph receptors are expressed in almost every cell type in the human body, yet their roles in development, physiology, and disease are incompletely understood. Studies in C. elegans have helped identify biological functions of these receptors, as well as transduction mechanisms. Here we review advances in our understanding of Eph receptor signaling made using the C. elegans model system.

Miller, Michael A.; Chin-Sang, Ian D.

2014-01-01

40

Ascaroside signaling in C. elegans*  

PubMed Central

Over the past 10 years, the relevance of small-molecule signaling for many aspects of C. elegans development and behavior has become apparent. One prominent group of small-molecule signals are the ascarosides, which control dauer entry and exit as well as a variety of sex-specific and social behaviors, including male attraction, hermaphrodite repulsion, olfactory plasticity, and aggregation. This wide range of biological functions is facilitated by a great diversity of ascaroside chemical structures. These are based on the sugar ascarylose, which is linked to fatty acid-like side chains of varying lengths and often decorated further with building blocks derived from amino acids, folate, and other primary metabolites. Different ascarosides or combinations of ascarosides mediate different phenotypes, and even small differences in chemical structures are often associated with strongly altered activity profiles. Additional complexity arises from concentration-dependent effects and synergism between different ascarosides. The ascarosides are sensed by several types of chemosensory head neurons, including the ASK, ASI, and ADL neurons as well as the male-specific CEM neurons. Ascaroside perception is mediated by diverse families of G-protein coupled membrane receptors that act upstream of conserved signal transduction pathways, including insulin/IGF-1 signaling and transforming growth factor beta (TGF-?) signaling. Biosynthesis of the ascarosides appears to integrate input from several primary metabolic pathways, including peroxisomal ?-oxidation of long-chain fatty acids and amino acid catabolism. Life stage, sex, as well as food availability and other environmental factors affect ascaroside biosynthesis, suggesting that ascaroside signaling communicates detailed information about life history and metabolic state.

Ludewig, Andreas H.; Schroeder, Frank C.

2013-01-01

41

Volatiles of Chrysanthemum zawadskii var. latilobum K  

PubMed Central

The volatile aroma constituents of Chrysanthemum zawadskii var. latilobum K. were separated by hydro distillation extraction (HDE) method using a Clevenger-type apparatus, and analyzed by gas chromatography-mass spectrometry (GC/MS). The yield of C. zawadskii var. latilobum K. flower essential oil (FEO) was 0.12% (w/w) and the color was light green. Fifty-five volatile chemical components, which make up 88.38% of the total aroma composition, were tentatively characterized. C. zawadskii var. latilobum K. FEOs contained 27 hydrocarbons, 12 alcohols, 7 ketones, 4 esters, 1 aldehyde, 1 amine, and 3 miscellaneous components. The major functional groups were terpene alcohol and ketone. Borneol (12.96), (±)-7-epi-amiteol (12.60), and camphor (10.54%) were the predominant volatiles. These compounds can be used in food and pharmaceutical industries due to their active bio-functional properties.

Chang, Kyung-Mi; Kim, Gun-Hee

2012-01-01

42

Organogenesis of the Caenorhabditis elegans Intestine  

Microsoft Academic Search

The intestine of Caenorhabditis elegans is an epithelial tube consisting of only 20 cells and is derived clonally from a single embryonic blastomere called E. We describe the cellular events that shape the intestine. These events include cytoplasmic polarization of cells in the intestinal primordium, the intercalation of specific sets of cells, the generation of an extracellular cavity within the

Ben Leung; Greg J Hermann; James R Priess

1999-01-01

43

Neurogenetics of vesicular transporters in C. elegans  

Microsoft Academic Search

The nematode Caenorhabditis elegans has a number of advantages for the analysis of synaptic molecules. These include a simple nervous system in which all cells are identified and synaptic connectivity is known and reproducible, a large collection of mutants and powerful methods of genetic analysis, simple methods for the generation and analysis of transgenic animals, and a number of relatively

JAMES B. RAND; JANET S. DUERR; DENNIS L. FRISBY

2000-01-01

44

Comparative Toxicology of Mercurials in Caenorhabditis elegans  

PubMed Central

Mercury is a toxic metal that can exist in multiple chemical species. Humans are commonly exposed to methylmercury and mercury vapor, which is converted to mercuric mercury in the body. Despite years of research, there is a paucity of information on the similarity and differences in the mechanisms of mercury toxicity. The relative toxicity of mercuric chloride (HgCl2) and methylmercury chloride (MeHgCl) in C. elegans was determined using assays that measured growth, feeding, reproduction, and locomotion. The effect of HgCl2 and MeHgCl on the expression of several archetypal stress-response genes was also determined. There was no significant difference between the EC50s of the two mercurials on C. elegans growth. However, MeHgCl was more toxic to C. elegans than HgCl2 when assessing feeding, movement and reproduction, all of which require proper neuromuscular activity. Methylmercury chloride exposure resulted in increased steady-state levels of the stress response genes at lower concentrations than HgCl2. In general, MeHgCl was more toxic to C. elegans than HgCl2, particularly when assaying behaviors that require neuromuscular function.

McElwee, Matthew K.; Freedman, Jonathan H.

2011-01-01

45

Dietary Restriction in the Nematode Caenorhabditis elegans  

Microsoft Academic Search

The first observation of the positive effect of reduced food intake on mammalian life span was made 70 years ago (1). In the decades that followed, researchers successfully applied this method to increase the life span of a very wide range of animals. The nematode Caenorhabditis elegans is an excellent model organism for studying the aging process. However, relatively little

Koen Houthoofd; Thomas E. Johnson; Jacques R. Vanfleteren

2005-01-01

46

CAENORHABDITIS ELEGANS AS AN ALTERNATIVE ANIMAL SPECIES  

Microsoft Academic Search

Caenorhabditis elegans has proven useful in toxicity testing of known toxicants, but its potential for assessing the toxicity of new pharmaceuticals is relatively unexplored. In this study the procedures used in aquatic testing of toxicants were modified to permit testing of small amounts (<40 mg) of gadolinium-based magnetic resonance imaging (MRI) compounds. Five blinded compounds were tested. The toxicity of

Phillip L. Williams; Gary L. Anderson; John L. Johnstone; Adrian D. Nunn; Michael F. Tweedle; Paul Wedeking

2000-01-01

47

Basic Caenorhabditis elegans Methods: Synchronization and Observation  

PubMed Central

Research into the molecular and developmental biology of the nematode Caenorhabditis elegans was begun in the early seventies by Sydney Brenner and it has since been used extensively as a model organism 1. C. elegans possesses key attributes such as simplicity, transparency and short life cycle that have made it a suitable experimental system for fundamental biological studies for many years 2. Discoveries in this nematode have broad implications because many cellular and molecular processes that control animal development are evolutionary conserved 3. C. elegans life cycle goes through an embryonic stage and four larval stages before animals reach adulthood. Development can take 2 to 4 days depending on the temperature. In each of the stages several characteristic traits can be observed. The knowledge of its complete cell lineage 4,5 together with the deep annotation of its genome turn this nematode into a great model in fields as diverse as the neurobiology 6, aging 7,8, stem cell biology 9 and germ line biology 10. An additional feature that makes C. elegans an attractive model to work with is the possibility of obtaining populations of worms synchronized at a specific stage through a relatively easy protocol. The ease of maintaining and propagating this nematode added to the possibility of synchronization provide a powerful tool to obtain large amounts of worms, which can be used for a wide variety of small or high-throughput experiments such as RNAi screens, microarrays, massive sequencing, immunoblot or in situ hybridization, among others. Because of its transparency, C. elegans structures can be distinguished under the microscope using Differential Interference Contrast microscopy, also known as Nomarski microscopy. The use of a fluorescent DNA binder, DAPI (4',6-diamidino-2-phenylindole), for instance, can lead to the specific identification and localization of individual cells, as well as subcellular structures/defects associated to them.

Porta-de-la-Riva, Montserrat; Fontrodona, Laura; Villanueva, Alberto; Ceron, Julian

2012-01-01

48

Power electronics in electric utilities: Static var compensators  

Microsoft Academic Search

This paper deals with dynamic var compensation of electric power systems, applying power electronics for reactive power generation and control. After an overview of the emergence and status of modern, solid-state var compensators in utility and industrial applications, the first part of the paper explains how dynamic var compensation increases transmittable power by providing voltage support, transient stability improvement, and

L. Gyugyi

1988-01-01

49

Lignans from Syringa pinnatifolia Hemsl. Var. alashanensis.  

PubMed

Two new lignans, syripinnalignans A and B (1 and 2), together with two known lignans, were isolated from the stem of Syringa pinnatifolia Hemsl. Var. alashanensis. The structures of 1 and 2 were elucidated by spectroscopic methods, including extensive 1D and 2D NMR techniques. PMID:22375878

Ao, Wu-Li-Ji; Bao, Xiao-Hua; Wu, Xiao-Lan; Wang, Qing-Hu

2012-01-01

50

Bacterial endosymbionts of Pyrodinium bahamense var. compressum.  

PubMed

The study presents evidence in support of the bacterial theory associated with the toxicity of Pyrodinium bahamense var. compressum. Bacterial endosymbionts from Philippine P. bahamense var. compressum strain Pbc MZRVA 042595 were isolated and identified via 16S rDNA sequence analysis. Taxonomic diversity of the identified culturable intracellular microbiota associated with Philippine P. bahamense var. compressum was established to be limited to the Phyla Proteobacteria, Actinobacteria, and Firmicutes. Major endosymbionts identified included Moraxella spp., Erythrobacter spp., and Bacillus spp., whereas Pseudomonas putida, Micrococcus spp., and Dietzia maris were identified as minor isolates. All identified strains except D. maris, P. putida, and Micrococcus spp. were shown to contain either saxitoxin or neo saxitoxin or both at levels < or =73 ng/10(7) bacterial cells based on high-performance liquid chromatography analysis. Paralytic shellfish poisoning-like physiologic reactions in test animals used in the mouse assay were recorded for the endosymbionts except for P. putida. The study is the first to elucidate the possible contribution of bacterial endosymbionts in the toxicity of P. bahamense var. compressum isolated in the Philippines. PMID:16944340

Azanza, Ma Patricia V; Azanza, Rhodora V; Vargas, Vanessa Mercee D; Hedreyda, Cynthia T

2006-11-01

51

Averaging Forecasts from VARs with Uncertain Instabilities.  

National Technical Information Service (NTIS)

A body of recent work suggests commonly used VAR models of output, inflation, and interest rates may be prone to instabilities. In the face of such instabilities, a variety of estimation or forecasting methods might be used to improve the accuracy of fore...

T. E. Clark M. W. McCracken

2006-01-01

52

[New antibiotic, parvulomycin, produced by a culture of Actinomyces parvullus var. chromogenes var. nov].  

PubMed

Actinomycete LIA-O784 was isolated from a soil sample. By its morphological and cultural properties the isolate was close to Act. parvullus but differed from it in synthesis of melanoid pygment, thyrosinase, hydrogen sulphide and pronounced antifungal activity. The actinomycete was classified as a new variant and designated as Actinomyces parvullus var. chromogenes var. nov. The culture produced a new polyglycoside antibiotic named parvulomycin. The physico-chemical characteristics of the antibiotic is presented. PMID:1275453

Iakovleva, E P; Omel'chenko, V N; Tsyganov, V A; Shenin, Iu D

1976-01-01

53

Large scale voltage stability constrained optimal VAr planning and voltage stability applications using existing OPF\\/optimal VAr planning tools  

Microsoft Academic Search

Traditionally in optimal VAr planning, the feasible operation has been translated as observing voltage profile criteria ensuring that the system voltage profile is acceptable for system normal and post contingency conditions. This feasibility definition is not sufficient when considering the VAr planning practice of the utilities concerned with voltage stability problems. Presently, these utilities use two reinforcement criteria for VAr

Ebrahim Vaahedi; J. Tamby; Y. Mansour; Wenyuan Li; D. Sun

1999-01-01

54

Chemical detoxification of small molecules by C. elegans  

PubMed Central

Caenorhabditis elegans lives in compost and decaying fruit, eats bacteria and is exposed to pathogenic microbes. We show that C. elegans is able to modify diverse microbial small-molecule toxins via both O-and N-glucosylation as well as unusual 3?-O-phosphorylation of the resulting glucosides. The resulting glucosylated derivatives have significantly reduced toxicity to C. elegans, suggesting that these chemical modifications represent a general mechanism for worms to detoxify their environments.

Stupp, Gregory S.; von Reuss, Stephan H.; Izrayelit, Yevgeniy; Ajredini, Ramadan; Schroeder, Frank C.; Edison, Arthur S.

2012-01-01

55

Transcriptional responses to pathogens in Caenorhabditis elegans  

PubMed Central

Summary Evolutionarily conserved signaling pathways, such as the p38 and ERK MAPK pathways, the TGF-? pathway, and the insulin signaling pathway are required for resistance to pathogens in C. elegans. Recent microarray expression profiling studies have identified both candidate immune effector genes which may recognize and eliminate microbial pathogens as well as uncharacterized gene classes that are broadly induced in response to pathogen. Comparative analysis of these microarray studies is suggestive of basal versus induced components of the ancient innate immune response in C. elegans. In particular, whereas the PMK-1 p38 MAPK pathway regulates genes that are induced by pathogen, the Forkhead family transcription factor DAF-16 confers pathogen resistance through the regulation of genes that are non-overlapping with pathogen-induced genes.

Shivers, Robert P.; Youngman, Matthew J.; Kim, Dennis H.

2008-01-01

56

Mechanisms of iron metabolism in Caenorhabditis elegans  

PubMed Central

Iron is involved in many biological processes essential for sustaining life. In excess, iron is toxic due to its ability to catalyze the formation of free radicals that damage macromolecules. Organisms have developed specialized mechanisms to tightly regulate iron uptake, storage and efflux. Over the past decades, vertebrate model organisms have led to the identification of key genes and pathways that regulate systemic and cellular iron metabolism. This review provides an overview of iron metabolism in the roundworm Caenorhabditis elegans and highlights recent studies on the role of hypoxia and insulin signaling in the regulation of iron metabolism. Given that iron, hypoxia and insulin signaling pathways are evolutionarily conserved, C. elegans provides a genetic model organism that promises to provide new insights into mechanisms regulating mammalian iron metabolism.

Anderson, Cole P.; Leibold, Elizabeth A.

2014-01-01

57

Isolation of C. elegans and related nematodes.  

PubMed

Isolating Caenorhabditis and other nematodes from the wild first requires field sampling (reviewed in Section 1). The easiest and most efficient way to recover the animals from any substrate is to place the sample onto a standard C. elegans culture plate (Section 2.1). Alternative methods used by nematologists to recover soil nematodes (Sections 2.2, 2.3, and 2.4) are in our hands more difficult to implement and only yield a fraction of the individuals in the sample. A tricky step is to recognize your species of interest out of the zoo of nematode species that comes with a typical sample (Section 3). Culture (Section 4) and freezing (Section 5) conditions are then reviewed. Finally, we briefly summarize the organization and timing of an isolation experiment (Section 6), as well as the available collections (Section 7). Bear in mind that this chapter is strongly focused towards the isolation of Caenorhabditis elegans and close relatives. PMID:24803426

Barrière, Antoine; Félix, Marie-Anne

2014-01-01

58

Biogenic magnetite in the nematode caenorhabditis elegans.  

PubMed Central

The nematode Caenorhabditis elegans is widely used as a model system in biological research. Recently, examination of the production of heat-shock proteins in this organism in response to mobile phone-type electromagnetic field exposure produced the most robust demonstration to date of a non-thermal, deleterious biological effect. Though these results appear to be a sound demonstration of non-thermal bioeffects, to our knowledge, no mechanism has been proposed to explain them. We show, apparently for the first time, that biogenic magnetite, a ferrimagnetic iron oxide, is present in C. elegans. Its presence may have confounding effects on experiments involving electromagnetic fields as well as implications for the use of this nematode as a model system for iron biomineralization in multi-cellular organisms.

Cranfield, Charles G; Dawe, Adam; Karloukovski, Vassil; Dunin-Borkowski, Rafal E; de Pomerai, David; Dobson, Jon

2004-01-01

59

Metal-induced neurodegeneration in C. elegans  

PubMed Central

The model species, Caenorhabditis elegans, has been used as a tool to probe for mechanisms underlying numerous neurodegenerative diseases. This use has been exploited to study neurodegeneration induced by metals. The allure of the nematode comes from the ease of genetic manipulation, the ability to fluorescently label neuronal subtypes, and the relative simplicity of the nervous system. Notably, C. elegans have approximately 60–80% of human genes and contain genes involved in metal homeostasis and transport, allowing for the study of metal-induced degeneration in the nematode. This review discusses methods to assess degeneration as well as outlines techniques for genetic manipulation and presents a comprehensive survey of the existing literature on metal-induced degeneration studies in the worm.

Chen, Pan; Martinez-Finley, Ebany J.; Bornhorst, Julia; Chakraborty, Sudipta; Aschner, Michael

2013-01-01

60

Caenorhabditis elegans Pheromones Regulate Multiple Complex Behaviors  

PubMed Central

Summary of recent advances A family of small molecules called ascarosides act as pheromones to control multiple behaviors in the nematode Caenorhabditis elegans. At picomolar concentrations, a synergistic mixture of at least three ascarosides produced by hermaphrodites causes male-specific attraction. At higher concentrations, the same ascarosides, perhaps in a different mixture, induce the developmentally arrested stage known as dauer. The production of ascarosides is strongly dependent on environmental conditions, although relatively little is known about the major variables and mechanisms of their regulation. Thus, male mating and dauer formation are linked through a common set of small molecules whose expression is sensitive to a given microenvironment, suggesting a model by which ascarosides regulate the overall life cycle of C. elegans.

Edison, Arthur S.

2009-01-01

61

Dietary choice behavior in Caenorhabditis elegans  

PubMed Central

Animals have evolved diverse behaviors that serve the purpose of finding food in the environment. We investigated the food seeking strategy of the soil bacteria-eating nematode Caenorhabditis elegans. C. elegans bacterial food varies in quality: some species are easy to eat and support worm growth well, while others do not. We show that worms exhibit dietary choice: they hunt for high quality food and leave hard-to-eat bacteria. This food seeking behavior is enhanced in animals that have already experienced good food. When hunting for good food, worms alternate between two modes of locomotion, known as dwelling: movement with frequent stops and reversals; and roaming: straight rapid movement. On good food, roaming is very rare, while on bad food it is common. Using laser ablations and mutant analysis, we show that the AIY neurons serve to extend roaming periods, and are essential for efficient food seeking.

Shtonda, Boris Borisovich; Avery, Leon

2005-01-01

62

Fungal biotransformation of mosapride by Cunninghamella elegans  

Microsoft Academic Search

The filamentous fungus, Cunninghamella elegans AS 3.156, was used as a microbial model of mammalian metabolism to transform mosapride, a selective 5-HT4-receptor agonist. The fungal metabolites of mosapride were separated and detected by ultra performance liquid chromatography–tandem mass spectrometric method. After incubation for 120h, the parent drug was metabolized to thirteen metabolites, one of which was known major mammalian metabolite,

Xiao-Hong Sun; Feng Man; Li-Yan Pang; Gui-Hua Gao; Xiao-Qin Li; Xiu-Lan Qi; Fa-Mei Li

2009-01-01

63

Acute carbon dioxide avoidance in Caenorhabditis elegans.  

PubMed

Carbon dioxide is produced as a by-product of cellular respiration by all aerobic organisms and thus serves for many animals as an important indicator of food, mates, and predators. However, whether free-living terrestrial nematodes such as Caenorhabditis elegans respond to CO2 was unclear. We have demonstrated that adult C. elegans display an acute avoidance response upon exposure to CO2 that is characterized by the cessation of forward movement and the rapid initiation of backward movement. This response is mediated by a cGMP signaling pathway that includes the cGMP-gated heteromeric channel TAX-2/TAX-4. CO2 avoidance is modulated by multiple signaling molecules, including the neuropeptide Y receptor NPR-1 and the calcineurin subunits TAX-6 and CNB-1. Nutritional status also modulates CO2 responsiveness via the insulin and TGFbeta signaling pathways. CO2 response is mediated by a neural circuit that includes the BAG neurons, a pair of sensory neurons of previously unknown function. TAX-2/TAX-4 function in the BAG neurons to mediate acute CO2 avoidance. Our results demonstrate that C. elegans senses and responds to CO2 using multiple signaling pathways and a neural network that includes the BAG neurons and that this response is modulated by the physiological state of the worm. PMID:18524955

Hallem, Elissa A; Sternberg, Paul W

2008-06-10

64

Dissection of Genetic Pathways in C. elegans  

PubMed Central

With unique genetic and cell biological strengths, C. elegans has emerged as a powerful model system for studying many biological processes. These processes are regulated by complex genetic networks consisting of arrays of genes. Identifying those genes and organizing them into genetic pathways are two major steps towards understanding the mechanisms that regulate biological events. Forward genetic screens with various designs are a traditional approach for identifying candidate genes. The completion of the genome sequencing in C. elegans and the advent of high-throughput experimental techniques have led to the development of two additional powerful approaches: functional genomics and systems biology. Genes that are identified by all these approaches can be ordered into interacting pathways through a variety of strategies, involving genetics, cell biology, biochemistry and functional genomics, to gain a complete understanding of how gene regulatory networks control a particular biological process. The aim of this review is to provide an overview of the approaches available to identify and construct the genetic pathways using C. elegans.

Wang, Zheng; Sherwood, David R.

2014-01-01

65

Proteins interacting with Caenorhabditis elegans Galpha subunits.  

PubMed

To identify novel components in heterotrimeric G-protein signalling, we performed an extensive screen for proteins interacting with Caenorhabditis elegans Galpha subunits. The genome of C. elegans contains homologues of each of the four mammalian classes of Galpha subunits (Gs, Gi/o, Gq and G12), and 17 other Galpha subunits. We tested 19 of the GGalpha subunits and four constitutively activated Galpha subunits in a largescale yeast two-hybrid experiment. This resulted in the identification of 24 clones, representing 11 different proteins that interact with four different Galpha subunits. This set includes C. elegans orthologues of known interactors of Galpha subunits, such as AGS3 (LGN/PINS), CalNuc and Rap1Gap, but also novel proteins, including two members of the nuclear receptor super family and a homologue of human haspin (germ cell-specific kinase). All interactions were found to be unique for a specific Galpha subunit but variable for the activation status of the Galpha subunit. We used expression pattern and RNA interference analysis of the G-protein interactors in an attempt to substantiate the biological relevance of the observed interactions. Furthermore, by means of a membrane recruitment assay, we found evidence that GPA-7 and the nuclear receptor NHR-22 can interact in the animal. PMID:18629017

Cuppen, Edwin; van der Linden, Alexander M; Jansen, Gert; Plasterk, Ronald H A

2003-01-01

66

In vivo imaging of C. elegans endocytosis.  

PubMed

Over the past decade, the early Caenorhabditis elegans embryo has proven to be a useful animal model to study a variety of membrane trafficking events, at least in part due to its large size, optical transparency, and ease of manipulation. Importantly, the stereotypic nature of membrane remodeling that occurs during early embryogenesis has enabled quantitative measurement of endocytic flux. In the absence of exogenous stimulation, resumption of the cell cycle triggered by fertilization is coupled to a dramatic redistribution of plasma membrane content. Numerous proteins are rapidly internalized via clathrin-mediated endocytosis, and the fate of these cargoes can be followed precisely using live imaging in utero. Key to these studies is the maintenance of animal health and their immobilization, which can become technically challenging during extended imaging sessions. Here we highlight recent advances in live imaging techniques that have facilitated the interrogation of endocytic transport in live animals. We focus on the use of transgenic C. elegans strains that stably express fluorescently-tagged proteins, including components of the endosomal system and cargo molecules that traverse this network of membranes. Our findings demonstrate the utility of the C. elegans embryo in defining regulatory mechanisms that control the numerous steps of endocytic trafficking. PMID:24704355

Wang, Lei; Audhya, Anjon

2014-08-01

67

Constituents of Juniperus recurva var. squamata Oil.  

PubMed

The essential oil of leaves and twigs of JUNIPERUS RECURVA VAR. SQUAMATA (Cupressaceae) was investigated by GLC, MS, and NMR spectroscopy. Main constituents were monoterpene hydrocarbons (68%); in addition, about 12% of sesquiterpene hydrocarbons, 9% of oxygenated sesquiterpenes, and 5% of oxygenated monoterpenes were identified. 4beta-Hydroxygermacra-1(10),5-diene ( 28), beta-oplopenone ( 29A), oplopanone ( 34), 8-acetoxy elemol ( 35), and manool ( 36) were found as trace components. PMID:17265267

Weyerstahl, P; Marschall-Weyerstahl, H; Manteuffel, E; Kaul, V K

1988-06-01

68

Phragmalin limonoids from Chukrasia tabularis var. velutina.  

PubMed

Two new C-15-acyl phragmalin limonoids, velutinalides A and B, featuring a C-16/C-30 ?-lactone ring, and a new structurally related natural product, R310B8, were isolated from the leaves of Chukrasia tabularis var. velutina. Their structures were elucidated on the basis of extensive spectroscopic data analyses and by comparison of their NMR data with those of related known compounds. PMID:22134848

Chen, Xue-Lian; Liu, Hai-Li; Guo, Yue-Wei

2012-02-01

69

Karyotype analysis of Ascaris lumbricoides var. suum  

Microsoft Academic Search

Twelve synaptonemal complexes are present in both oocyte and spermatocyte pachytene nuclei ofAscaris lumbricoides var.suum, as determined by 3-D reconstruction of the nuclear contents from electron microscopy of serial sections and therefore, n=12 in the strain ofAscaris described here. In the female the heterochromatic end of each synaptonemal complex is attached to the nuclear envelope and the other end is

Paul Goldstein; Peter B. Moens

1976-01-01

70

Cell tracking in live Caenorhabditis elegans embryos via third harmonic generation imaging microscopy measurements  

Microsoft Academic Search

In this study, we demonstrate the potential of employing third harmonic generation (THG) imaging microscopy measurements for cell tracking studies in live Caenorhabditis elegans (C. elegans) embryos. A 1028-nm femtosecond laser was used for the excitation of unstained C. elegans samples. Different C. elegans embryonic stages (from two-cell to threefold) were imaged. Live biological specimens were irradiated for prolonged periods

George J. Tserevelakis; George Filippidis; Evgenia V. Megalou; Costas Fotakis; Nektarios Tavernarakis

2011-01-01

71

Specificity and Complexity of the Caenorhabditis elegans Innate Immune Response  

Microsoft Academic Search

In response to infection, Caenorhabditis elegans produces an array of antimicrobial proteins. To understand the C. elegans immune response, we have investigated the regulation of a large, representative sample of candidate antimicrobial genes. We found that all these putative antimicrobial genes are expressed in tissues exposed to the environment, a position from which they can ward off infection. Using RNA

Scott Alper; Sandra J. McBride; Brad Lackford; Jonathan H. Freedman; David A. Schwartz

2007-01-01

72

Antifungal Chemical Compounds Identified Using a C. elegans Pathogenicity Assay  

Microsoft Academic Search

There is an urgent need for the development of new antifungal agents. A facile in vivo model that evaluates libraries of chemical compounds could solve some of the main obstacles in current antifungal discovery. We show that Candida albicans, as well as other Candida species, are ingested by Caenorhabditis elegans and establish a persistent lethal infection in the C. elegans

Julia Breger; Beth Burgwyn Fuchs; George Aperis; Terence I Moy; Frederick M Ausubel; Eleftherios Mylonakis

2007-01-01

73

A novel mode of ecdysozoan growth in Caenorhabditis elegans  

Microsoft Academic Search

SUMMARY Whereas growth in many ecdysozoa is associ- ated with only molting, larval growth in nematodes, specifical- ly Caenorhabditis elegans , is thought to be continuous and exponential. However, this has never been closely investigat- ed. Here we report several detailed studies of growth in wild- type and dwarf C. elegans strains. We find that apparent ex- ponential growth between

Christopher G. Knight; Mavji N. Patel; Ricardo B. R. Azevedo; Armand M. Leroi

2002-01-01

74

Polymorphic segmental duplication in the nematode Caenorhabditis elegans  

Microsoft Academic Search

BACKGROUND: The nematode Caenorhabditis elegans was the first multicellular organism to have its genome fully sequenced. Over the last 10 years since the original publication in 1998, the C. elegans genome has been scrutinized and the last gaps were filled in November 2002, which present a unique opportunity for examining genome-wide segmental duplications. RESULTS: Here, we performed analysis of the

Ismael A Vergara; Allan K Mah; Jim C Huang; Maja Tarailo-Graovac; Robert C Johnsen; David L Baillie; Nansheng Chen

2009-01-01

75

Evaluation of the pathogenicity of Listeria spp. in Caenorhabditis elegans.  

PubMed

Caenorhabditis has proven to be a useful model for studying host-pathogen interactions as well as the ability of nematodes to serve as vectors for the dispersal of foodborne pathogens. In this study, we evaluated whether C. elegans can serve as a host for Listeria spp. While there was an effect of growth media on C. elegans killing, C. elegans exposed to L. monocytogenes and L. innocua pregrown in Luria-Bertani medium showed reduced survival when compared to nonpathogenic E. coli OP50, while L. seeligeri showed survival similar to E. coli OP50. In a preference assay, C. elegans preferred E. coli over L. monocytogenes and L. innocua, but showed no preference between L. monocytogenes and L. innocua. A gentamicin assay indicated that L. monocytogenes did not persist within the C. elegans intestinal tract. Our findings that L. monocytogenes and L. innocua strains tested have equally deleterious effects on C. elegans and that L. monocytogenes did not establish intestinal infection conflict with other recently published results, which found intestinal infection and killing of C. elegans by L. monocytogenes. Further studies are thus needed to clarify the interactions between L. monocytogenes and C. elegans, including effects of environmental conditions and strain differences on killing and intestinal infection. PMID:17378710

Forrester, Stacyann; Milillo, Sara Rose; Hoose, Wendy A; Wiedmann, Martin; Schwab, Ute

2007-01-01

76

Caenorhabditis elegans swimming in a saturated particulate system  

NASA Astrophysics Data System (ADS)

Caenorhabditis elegans (C. elegans) is a nematode that often swims in saturated soil in nature. We investigated the locomotive behavior of C. elegans swimming in a fluid with particles of various sizes and found that the nematode swims a greater distance per undulation than it does in a fluid without particles. The Strouhal number (a ratio of lateral to forward velocity) of C. elegans significantly decreases in a saturated particulate medium (0.50+/-0.13) in comparison to a fluid without particles (1.6+/-0.27). This result was unexpected due to the generally low performance of a body moving in a high drag medium. In our model, a saturated granular system is approximated as a porous medium where only the hydrodynamic forces on the body are considered. Combining these assumptions with resistive force theory, we find that a porous medium provides more asymmetric drag on a slender body, and consequently that C. elegans locomotes with a greater distance per undulation.

Jung, Sunghwan

2010-03-01

77

Caenorhabditis elegans as a model in developmental toxicology  

PubMed Central

A number of practical advantages have made the nematode Caenorhabditis elegans a useful model for genetic and developmental biological research. These same advantages, along with conservation of disease and stress response pathways, availability of mutant and transgenic strains, and wealth of biological information, have led to the increased use of C. elegans in toxicological studies. Although the potential to study the mechanisms of developmental toxicology in C. elegans is promising, embryonic and larval growth tests to identify compounds that affect the nematode have remained the primary use of C. elegans in developmental toxicology. Here, we describe a C. elegans larval growth and development assay for medium and high throughput screening using the COPAS Biosort flow cytometer and provide descriptions of the data and subsequent analysis.

Boyd, Windy A.; Smith, Marjolein V.; Freedman, Jonathan H.

2012-01-01

78

Neurodegenerative disorders: insights from the nematode Caenorhabditis elegans  

PubMed Central

Neurodegenerative diseases impose a burden on society, yet for the most part, the mechanisms underlying neuronal dysfunction and death in these disorders remain unclear despite the identification of relevant disease genes. Given the molecular conservation in neuronal signaling pathways across vertebrate and invertebrate species, many researchers have turned to the nematode Caenorhabditis elegans to identify the mechanisms underlying neurodegenerative disease pathology. C. elegans can be engineered to express human proteins associated with neurodegeneration; additionally, the function of C. elegans orthologs of human neurodegenerative disease genes can be dissected. Herein, we examine major C. elegans neurodegeneration models that recapitulate many aspects of human neurodegenerative disease and we survey the screens that have identified modifier genes. This review highlights how the C. elegans community has used this versatile organism to model several aspects of human neurodegeneration and how these studies have contributed to our understanding of human disease.

Dimitriadi, Maria; Hart, Anne C.

2010-01-01

79

Detoxification of Benzoxazolinone Allelochemicals from Wheat by Gaeumannomyces graminis var. tritici, G. graminis var. graminis, G. graminis var. avenae, and Fusarium culmorum  

PubMed Central

The ability of phytopathogenic fungi to overcome the chemical defense barriers of their host plants is of great importance for fungal pathogenicity. We studied the role of cyclic hydroxamic acids and their related benzoxazolinones in plant interactions with pathogenic fungi. We identified species-dependent differences in the abilities of Gaeumannomyces graminis var. tritici, Gaeumannomyces graminis var. graminis, Gaeumannomyces graminis var. avenae, and Fusarium culmorum to detoxify these allelochemicals of gramineous plants. The G. graminis var. graminis isolate degraded benzoxazolin-2(3H)-one (BOA) and 6-methoxy-benzoxazolin-2(3H)-one (MBOA) more efficiently than did G. graminis var. tritici and G. graminis var. avenae. F. culmorum degraded BOA but not MBOA. N-(2-Hydroxyphenyl)-malonamic acid and N-(2-hydroxy-4-methoxyphenyl)-malonamic acid were the primary G. graminis var. graminis and G. graminis var. tritici metabolites of BOA and MBOA, respectively, as well as of the related cyclic hydroxamic acids. 2-Amino-3H-phenoxazin-3-one was identified as an additional G. graminis var. tritici metabolite of BOA. No metabolite accumulation was detected for G. graminis var. avenae and F. culmorum by high-pressure liquid chromatography. The mycelial growth of the pathogenic fungi was inhibited more by BOA and MBOA than by their related fungal metabolites. The tolerance of Gaeumannomyces spp. for benzoxazolinone compounds is correlated with their detoxification ability. The ability of Gaeumannomyces isolates to cause root rot symptoms in wheat (cultivars Rektor and Astron) parallels their potential to degrade wheat allelochemicals to nontoxic compounds.

Friebe, A.; Vilich, V.; Hennig, L.; Kluge, M.; Sicker, D.

1998-01-01

80

Pharmacognostical studiies on aglaia roxburghiana miq. Var. Beddomei.  

PubMed

Morphological, anatomical, quantitative microscopy powder microscopy, physical constant preliminary phytochemical analysis and fluorescence analysis of the leaves of Aglaia roxburghiana Var. Beddome were carried out. PMID:22556922

Sasikala, E; Janaki, S; Rao, B; Vijayasekaran, V

1999-07-01

81

Dietary restriction in C. elegans: recent advances.  

PubMed

The nematode Caenorhabditis elegans continues to serve as a useful model of life extension caused by dietary restriction. Using this model, downstream effectors of dietary restriction-induced longevity have been elucidated, including neuropeptides and cell-surface receptors. Although it remains possible that different forms of dietary restriction may utilize both specific and overlapping mechanisms to promote longevity, the nematode model has revealed roles for autophagy, metabolic energy-sensing and the hypoxic response. The nematode has also been used to identify specific tissues required for life extension via DR, including coelomocytes, intestine, and neurons. PMID:23462461

Cypser, James R; Kitzenberg, David; Park, Sang-Kyu

2013-10-01

82

Longevity and stress in Caenorhabditis elegans  

PubMed Central

It has long been understood that many of the same manipulations that increase longevity in Caenorhabditis elegans also increase resistance to various acute stressors, and vice-versa; moreover these findings hold in more complex organisms as well. Nevertheless, the mechanistic relationship between these phenotypes remains unclear, and in many cases the overlap between stress resistance and longevity is inexact. Here we review the known connections between stress resistance and longevity, discuss instances in which these connections are absent, and summarize the theoretical explanations that have been posited for these phenomena.

Zhou, Katherine I.; Pincus, Zachary; Slack, Frank J.

2011-01-01

83

Regulation of hemagglutinin/protease expression by the VarS/VarA-CsrA/B/C/D system in Vibrio cholerae.  

PubMed

In this study, through the analysis of Vibrio cholerae 2740-80 mutant strains produced by the cholera toxin subunit B gene containing Mariner-based transposon, we found that disruption of the varS gene, a member of the recently reported sensory system VarS/VarA-CsrA/B/C/D, resulted in altered expression of hemagglutinin/protease A. To further investigate the connection between VarS and HapA, we generated an additional varS mutant, V. cholerae 2740-80-VS, and examined the effect of this mutation on expression of HapA and of genes in the VarS/VarA-CsrA/B/C/D system. 2740-80-VS showed decreased expression of varS, csrB/C, hapR, and hapA along with increased biofilm production. Interestingly, expression of the alternative sigma factor sigma(s), which is important for adaptation to environmental stress, was also decreased in this mutant. These results indicate that the VarS/VarA-CsrA/B/C/D system is involved in the control of HapA expression and biofilm production in V. cholerae 2740-80 through HapR regulation, and also that VarS/VarA controls expression of sigma(s) for HapA regulation. PMID:20307644

Jang, Jeyoun; Jung, Kyung-Tae; Yoo, Cheon-Kwon; Rhie, Gi-Eun

2010-06-01

84

Cryptococcus neoformans var. neoformans (Serotype D) Strains Are More Susceptible to Heat than C. neoformans var. grubii (Serotype A) Strains  

PubMed Central

Cryptococcus neoformans var. neoformans (serotype D) and C. neoformans var. grubii (serotype A) differ in geographic prevalence and dermatotropism, with C. neoformans var. neoformans strains being more prevalent among isolates from temperate countries as well as from skin infections. Analysis of 19 strains from each serotype revealed wide variation in thermal susceptibility, with C. neoformans var. neoformans strains being more susceptible, on average, to heat killing. The results suggest a consistent explanation for the geographic differences between serotype A and D strains and for the dermatotropism of serotype D strains.

Martinez, Luis. R; Garcia-Rivera, Javier; Casadevall, Arturo

2001-01-01

85

Cryptococcus neoformans var. neoformans (serotype D) strains are more susceptible to heat than C. neoformans var. grubii (serotype A) strains.  

PubMed

Cryptococcus neoformans var. neoformans (serotype D) and C. neoformans var. grubii (serotype A) differ in geographic prevalence and dermatotropism, with C. neoformans var. neoformans strains being more prevalent among isolates from temperate countries as well as from skin infections. Analysis of 19 strains from each serotype revealed wide variation in thermal susceptibility, with C. neoformans var. neoformans strains being more susceptible, on average, to heat killing. The results suggest a consistent explanation for the geographic differences between serotype A and D strains and for the dermatotropism of serotype D strains. PMID:11526180

Martinez, L R; Garcia-Rivera, J; Casadevall, A

2001-09-01

86

Caenorhabditis elegans as a model for intracellular pathogen infection.  

PubMed

The genetically tractable nematode Caenorhabditis elegans is a convenient host for studies of pathogen infection. With the recent identification of two types of natural intracellular pathogens of C. elegans, this host now provides the opportunity to examine interactions and defence against intracellular pathogens in a whole-animal model for infection. C. elegans is the natural host for a genus of microsporidia, which comprise a phylum of fungal-related pathogens of widespread importance for agriculture and medicine. More recently, C. elegans has been shown to be a natural host for viruses related to the Nodaviridae family. Both microsporidian and viral pathogens infect the C. elegans intestine, which is composed of cells that share striking similarities to human intestinal epithelial cells. Because C. elegans nematodes are transparent, these infections provide a unique opportunity to visualize differentiated intestinal cells in vivo during the course of intracellular infection. Together, these two natural pathogens of C. elegans provide powerful systems in which to study microbial pathogenesis and host responses to intracellular infection. PMID:23617769

Balla, Keir M; Troemel, Emily R

2013-08-01

87

Caenorhabditis elegans as a model for intracellular pathogen infection  

PubMed Central

Summary The genetically tractable nematode Caenorhabditis elegans is a convenient host for studies of pathogen infection. With the recent identification of two types of natural intracellular pathogens of C. elegans, this host now provides the opportunity to examine interactions and defence against intracellular pathogens in a whole-animal model for infection. C. elegans is the natural host for a genus of microsporidia, which comprise a phylum of fungal-related pathogens of widespread importance for agriculture and medicine. More recently, C. elegans has been shown to be a natural host for viruses related to the Nodaviridae family. Both microsporidian and viral pathogens infect the C. elegans intestine, which is composed of cells that share striking similarities to human intestinal epithelial cells. Because C. elegans nematodes are transparent, these infections provide a unique opportunity to visualize differentiated intestinal cells in vivo during the course of intracellular infection. Together, these two natural pathogens of C. elegans provide powerful systems in which to study microbial pathogenesis and host responses to intracellular infection.

Balla, Keir M.; Troemel, Emily R.

2014-01-01

88

Characterization of the effects of methylmercury on Caenorhabditis elegans  

SciTech Connect

The rising prevalence of methylmercury (MeHg) in seafood and in the global environment provides an impetus for delineating the mechanism of the toxicity of MeHg. Deleterious effects of MeHg have been widely observed in humans and in other mammals, the most striking of which occur in the nervous system. Here we test the model organism, Caenorhabditis elegans (C. elegans), for MeHg toxicity. The simple, well-defined anatomy of the C. elegans nervous system and its ready visualization with green fluorescent protein (GFP) markers facilitated our study of the effects of methylmercuric chloride (MeHgCl) on neural development. Although MeHgCl was lethal to C. elegans, induced a developmental delay, and decreased pharyngeal pumping, other traits including lifespan, brood size, swimming rate, and nervous system morphology were not obviously perturbed in animals that survived MeHgCl exposure. Despite the limited effects of MeHgCl on C. elegans development and behavior, intracellular mercury (Hg) concentrations ({<=} 3 ng Hg/mg protein) in MeHgCl-treated nematodes approached levels that are highly toxic to mammals. If MeHgCl reaches these concentrations throughout the animal, this finding indicates that C. elegans cells, particularly neurons, may be less sensitive to MeHgCl toxicity than mammalian cells. We propose, therefore, that C. elegans should be a useful model for discovering intrinsic mechanisms that confer resistance to MeHgCl exposure.

Helmcke, Kirsten J. [Pharmacology Department, Vanderbilt University Medical Center, Nashville, TN (United States); Syversen, Tore [Department of Neuromedicine, Norwegian University of Science and Technology, Trondheim (Norway); Miller, David M. [Department of Cell and Developmental Biology and Program in Neuroscience, Vanderbilt University Medical Center, Nashville, TN (United States); Aschner, Michael [Pharmacology Department, Vanderbilt University Medical Center, Nashville, TN (United States); Pediatrics Department, Vanderbilt University Medical Center, Nashville, TN (United States)], E-mail: Michael.Aschner@vanderbilt.edu

2009-10-15

89

Caenorhabditis elegans as a model for obesity research.  

PubMed

Caenorhabditis elegans (C. elegans) is a small nematode that conserves 65% of the genes associated with human disease, has a 21-day lifespan, reproductive cycles of 3 days, large brood sizes, lives in an agar dish and does not require committee approvals for experimentation. Research using C. elegans is encouraged and a Caenorhabditis Genetics Center (CGC, Minnesota) is funded by the National Institutes of Health-National Center for Research Resources. Many genetically manipulated strains of C. elegans are available at nominal cost from the CGC. Studies using the C. elegans model have explored insulin signaling, response to dietary glucose, the influence of serotonin on obesity, satiety, feeding and hypoxia-associated illnesses. C. elegans has also been used as a model to evaluate potential obesity therapeutics, explore the mechanisms behind single gene mutations related to obesity and to define the mechanistic details of fat metabolism. Obesity now affects a third of the US population and is becoming a progressively more expensive public health problem. Faster and less expensive methods to reach more effective treatments are clearly needed. We present this review hoping to stimulate interest in using the C. elegans model as a vehicle to advance the understanding and future treatment of obesity. PMID:21556043

Zheng, J; Greenway, F L

2012-02-01

90

Characterization of the effects of methylmercury on Caenorhabditis elegans  

PubMed Central

The rising prevalence of methylmercury (MeHg) in seafood and in the global environment provides an impetus for delineating the mechanism of the toxicity of MeHg. Deleterious effects of MeHg have been widely observed in humans and in other mammals, the most striking of which occur in the nervous system. Here we test the model organism, Caenorhabditis elegans (C. elegans), for MeHg toxicity. The simple, well-defined anatomy of the C. elegans nervous system and its ready visualization with green fluorescent protein (GFP) markers facilitated our study of the effects of methylmercuric chloride (MeHgCl) on neural development. Although MeHgCl was lethal to C. elegans, induced a developmental delay, and decreased pharyngeal pumping, other traits including lifespan, brood size, swimming rate, and nervous system morphology were not obviously perturbed in animals that survived MeHgCl exposure. Despite the limited effects of MeHgCl on C. elegans development and behavior, intracellular mercury (Hg) concentrations (? 3 ng Hg/mg protein) in MeHgCl-treated nematodes approached levels that are highly toxic to mammals. If MeHgCl reaches these concentrations throughout the animal, this finding indicates that C. elegans cells, particularly neurons, may be less sensitive to MeHgCl toxicity than mammalian cells. We propose, therefore, that C. elegans should be a useful model for discovering intrinsic mechanisms that confer resistance to MeHgCl exposure.

Helmcke, Kirsten J.; Syversen, Tore; Miller, David M.; Aschner, Michael

2009-01-01

91

Glucose kinases from Streptomyces peucetius var. caesius.  

PubMed

Glucose kinases (Glks) are enzymes of the glycolytic pathway involved in glucose phosphorylation. These enzymes can use various phosphoryl donors such as ATP, ADP, and polyphosphate. In several streptomycetes, ATP-glucose kinase (ATP-Glk) has been widely studied and regarded as the main glucose phosphorylating enzyme and is likely a regulatory protein in carbon catabolite repression. In cell extracts from the doxorubicin overproducing strain Streptomyces peucetius var. caesius, grown in glucose, a polyphosphate-dependent Glk (Pp-Glk) was detected by zymogram. Maximum activity was observed during the stationary growth phase (48 h) of cells grown in 100 mM glucose. No activity was detected when 20 mM glutamate was used as the only carbon source, supporting a role for glucose in inducing this enzyme. Contrary to wild-type strains of Streptomyces coelicolor, Streptomyces lividans, and Streptomyces thermocarboxydus K-155, S. peucetius var. caesius produced 1.8 times more Pp-Glk than ATP-Glk. In addition, this microorganism produced five and four times more Pp-Glk and anthracyclines, respectively, than its wild-type S. peucetius parent strain, supporting a role for this enzyme in antibiotic production in the overproducer strain. A cloned 726-bp DNA fragment from S. peucetius var. caesius encoded a putative Pp-Glk, with amino acid identities between 83 and 87 % to orthologous sequences from the above-cited streptomycetes. The cloned fragment showed the polyphosphate-binding sequences GXDIGGXXIK, TXGTGIGSA, and KEX(4)SWXXWA. Sequences for the Zn-binding motif were not detected in this fragment, suggesting that Pp-Glk is not related to the Glk ROK family of proteins. PMID:24687748

Ruiz-Villafán, Beatriz; Rodríguez-Sanoja, Romina; Aguilar-Osorio, Guillermo; Gosset, Guillermo; Sanchez, Sergio

2014-07-01

92

Microsporidia Are Natural Intracellular Parasites of the Nematode Caenorhabditis elegans  

PubMed Central

For decades the soil nematode Caenorhabditis elegans has been an important model system for biology, but little is known about its natural ecology. Recently, C. elegans has become the focus of studies of innate immunity and several pathogens have been shown to cause lethal intestinal infections in C. elegans. However none of these pathogens has been shown to invade nematode intestinal cells, and no pathogen has been isolated from wild-caught C. elegans. Here we describe an intracellular pathogen isolated from wild-caught C. elegans that we show is a new species of microsporidia. Microsporidia comprise a large class of eukaryotic intracellular parasites that are medically and agriculturally important, but poorly understood. We show that microsporidian infection of the C. elegans intestine proceeds through distinct stages and is transmitted horizontally. Disruption of a conserved cytoskeletal structure in the intestine called the terminal web correlates with the release of microsporidian spores from infected cells, and appears to be part of a novel mechanism by which intracellular pathogens exit from infected cells. Unlike in bacterial intestinal infections, the p38 MAPK and insulin/insulin-like growth factor (IGF) signaling pathways do not appear to play substantial roles in resistance to microsporidian infection in C. elegans. We found microsporidia in multiple wild-caught isolates of Caenorhabditis nematodes from diverse geographic locations. These results indicate that microsporidia are common parasites of C. elegans in the wild. In addition, the interaction between C. elegans and its natural microsporidian parasites provides a system in which to dissect intracellular intestinal infection in vivo and insight into the diversity of pathogenic mechanisms used by intracellular microbes.

Troemel, Emily R; Felix, Marie-Anne; Whiteman, Noah K; Barriere, Antoine; Ausubel, Frederick M

2008-01-01

93

Morphogenesis of the C. elegans vulva  

PubMed Central

Understanding how cells move, change shape, and alter cellular behaviors to form organs, a process termed morphogenesis, is one of the great challenges of developmental biology. Formation of the C. elegans vulva is a powerful, simple, and experimentally accessible model for elucidating how morphogenetic processes produce an organ. In the first step of vulval development, three epithelial precursor cells divide and differentiate to generate 22 cells of seven different vulval subtypes. The 22 vulval cells then rearrange from a linear array into a tube, with each of the seven cell types undergoing characteristic morphogenetic behaviours that construct the vulva. Vulval morphogenesis entails many of the same cellular activities that underlie organogenesis and tissue formation across species, including invagination, lumen formation, oriented cell divisions, cell-cell adhesion, cell migration, cell fusion, extracellular matrix remodelling and cell invasion. Studies of vulval development have led to pioneering discoveries in a number of these processes and are beginning to bridge the gap between the pathways that specify cells and their connections to morphogenetic behaviors. The simplicity of the vulva and the experimental tools available in C. elegans will continue to make vulval morphogenesis a powerful paradigm to further our understanding of the largely mysterious mechanisms that build tissues and organs.

Schindler, Adam J

2012-01-01

94

Macrorestriction Analysis of Caenorhabditis Elegans Genomic DNA  

PubMed Central

The usefulness of genomic physical maps is greatly enhanced by linkage of the physical map with the genetic map. We describe a ``macrorestriction mapping'' procedure for Caenorhabditis elegans that we have applied to this endeavor. High molecular weight, genomic DNA is digested with infrequently cutting restriction enzymes and size-fractionated by pulsed field gel electrophoresis. Southern blots of the gels are probed with clones from the C. elegans physical map. This procedure allows the construction of restriction maps covering several hundred kilobases and the detection of polymorphic restriction fragments using probes that map several hundred kilobases away. We describe several applications of this technique. (1) We determined that the amount of DNA in a previously uncloned region is <220 kb. (2) We mapped the mes-1 gene to a cosmid, by detecting polymorphic restriction fragments associated with a deletion allele of the gene. The 25-kb deletion was initially detected using as a probe sequences located ~400 kb away from the gene. (3) We mapped the molecular endpoint of the deficiency hDf6, and determined that three spontaneously derived duplications in the unc-38-dpy-5 region have very complex molecular structures, containing internal rearrangements and deletions.

Browning, H.; Berkowitz, L.; Madej, C.; Paulsen, J. E.; Zolan, M. E.; Strome, S.

1996-01-01

95

Visualizing neuroblast cytokinesis during C. elegans embryogenesis.  

PubMed

This protocol describes the use of fluorescence microscopy to image dividing cells within developing Caenorhabditis elegans embryos. In particular, this protocol focuses on how to image dividing neuroblasts, which are found underneath the epidermal cells and may be important for epidermal morphogenesis. Tissue formation is crucial for metazoan development and relies on external cues from neighboring tissues. C. elegans is an excellent model organism to study tissue morphogenesis in vivo due to its transparency and simple organization, making its tissues easy to study via microscopy. Ventral enclosure is the process where the ventral surface of the embryo is covered by a single layer of epithelial cells. This event is thought to be facilitated by the underlying neuroblasts, which provide chemical guidance cues to mediate migration of the overlying epithelial cells. However, the neuroblasts are highly proliferative and also may act as a mechanical substrate for the ventral epidermal cells. Studies using this experimental protocol could uncover the importance of intercellular communication during tissue formation, and could be used to reveal the roles of genes involved in cell division within developing tissues. PMID:24686748

Wernike, Denise; van Oostende, Chloe; Piekny, Alisa

2014-01-01

96

Alcohol Disinhibition of Behaviors in C. elegans  

PubMed Central

Alcohol has a wide variety of effects on physiology and behavior. One of the most well-recognized behavioral effects is disinhibition, where behaviors that are normally suppressed are displayed following intoxication. A large body of evidence has shown that alcohol-induced disinhibition in humans affects attention, verbal, sexual, and locomotor behaviors. Similar behavioral disinhibition is also seen in many animal models of ethanol response, from invertebrates to mammals and primates. Here we describe several examples of disinhibition in the nematode C. elegans. The nematode displays distinct behavioral states associated with locomotion (crawling on land and swimming in water) that are mediated by dopamine. On land, animals crawl and feed freely, but these behaviors are inhibited in water. We found that additional behaviors, including a variety of escape responses are also inhibited in water. Whereas alcohol non-specifically impaired locomotion, feeding, and escape responses in worms on land, alcohol specifically disinhibited these behaviors in worms immersed in water. Loss of dopamine signaling relieved disinhibition of feeding behavior, while loss of the D1-like dopamine receptor DOP-4 impaired the ethanol-induced disinhibition of crawling. The powerful genetics and simple nervous system of C. elegans may help uncover conserved molecular mechanisms that underlie alcohol-induced disinhibition of behaviors in higher animals.

Topper, Stephen M.; Aguilar, Sara C.; Topper, Viktoria Y.; Elbel, Erin; Pierce-Shimomura, Jonathan T.

2014-01-01

97

The twisted pharynx phenotype in C. elegans  

PubMed Central

Background The pharynx of C. elegans is an epithelial tube whose development has been compared to that of the embryonic heart and the kidney and hence serves as an interesting model for organ development. Several C. elegans mutants have been reported to exhibit a twisted pharynx phenotype but no careful studies have been made to directly address this phenomenon. In this study, the twisting mutants dig-1, mig-4, mnm-4 and unc-61 are examined in detail and the nature of the twist is investigated. Results We find that the twisting phenotype worsens throughout larval development, that in most mutants the pharynx retains its twist when dissected away from the worm body, and that double mutants between mnm-4 and mutants with thickened pharyngeal domains (pha-2 and sma-1) have less twisting in these regions. We also describe the ultrastructure of pharyngeal tendinous organs that connect the pharyngeal basal lamina to that of the body wall, and show that these are pulled into a spiral orientation by twisted pharynges. Within twisted pharynges, actin filaments also show twisting and are longer than in controls. In a mini screen of adhesionmolecule mutants, we also identified one more twisting pharynx mutant, sax-7. Conclusion Defects in pharyngeal cytoskeleton length or its anchor points to the extracellular matrix are proposed as the actual source of the twisting force. The twisted pharynx is a useful and easy-to-score phenotype for genes required in extracellular adhesion or organ attachment, and perhaps forgenes required for cytoskeleton regulation.

Axang, Claes; Rauthan, Manish; Hall, David H; Pilon, Marc

2007-01-01

98

Origin of Cryptococcus neoformans var. neoformans Diploid Strains  

Microsoft Academic Search

The basidiomycetous yeast Cryptococcus neoformans is an important human fungal pathogen. Two varieties, C. neoformans var. neoformans and C. neoformans var. gattii, have been identified. Both are heterothallic with two mating types, MATa and MAT. Some rare isolates are self-fertile and are considered occasional diploid or aneuploid strains. In the present study, 133 isolates, mostly from Italian patients, were investigated

MASSIMO COGLIATI; MARIA C. ESPOSTO; DAVID L. CLARKE; BRIAN L. WICKES; MARIA A. VIVIANI

2001-01-01

99

Microfluidics as a tool for C. elegans research.  

PubMed

Microfluidics has emerged as a set of powerful tools that have greatly advanced some areas of biological research, including research using C. elegans. The use of microfluidics has enabled many experiments that are otherwise impossible with conventional methods. Today there are many examples that demonstrate the main advantages of using microfluidics for C. elegans research, achieving precise environmental conditions and facilitating worm handling. Examples range from behavioral analysis under precise chemical or odor stimulation, locomotion studies in well-defined structural surroundings, and even long-term culture on chip. Moreover, microfluidics has enabled coupling worm handling and imaging thus facilitating genetic screens, optogenetic studies, and laser ablation experiments. In this article, we review some of the applications of microfluidics for C. elegans research and provide guides for the design, fabrication, and use of microfluidic devices for C. elegans research studies. PMID:24065448

San-Miguel, Adriana; Lu, Hang

2013-01-01

100

Caenorhabditis elegans: An Emerging Model in Biomedical and Environmental Toxicology  

PubMed Central

The nematode Caenorhabditis elegans has emerged as an important animal model in various fields including neurobiology, developmental biology, and genetics. Characteristics of this animal model that have contributed to its success include its genetic manipulability, invariant and fully described developmental program, well-characterized genome, ease of maintenance, short and prolific life cycle, and small body size. These same features have led to an increasing use of C. elegans in toxicology, both for mechanistic studies and high-throughput screening approaches. We describe some of the research that has been carried out in the areas of neurotoxicology, genetic toxicology, and environmental toxicology, as well as high-throughput experiments with C. elegans including genome-wide screening for molecular targets of toxicity and rapid toxicity assessment for new chemicals. We argue for an increased role for C. elegans in complementing other model systems in toxicological research.

Leung, Maxwell C. K.; Williams, Phillip L.; Benedetto, Alexandre; Au, Catherine; Helmcke, Kirsten J.; Aschner, Michael; Meyer, Joel N.

2008-01-01

101

Immunostaining for Markers of Apoptosis in the Caenorhabditis elegans Germline.  

PubMed

The transparency of Caenorhabditis elegans makes it an ideal organism for visualizing proteins by immunofluorescence microscopy; however, the tough cuticle of worms and the egg shell surrounding embryos pose challenges in achieving effective fixation so that antibodies can diffuse into cells. In this protocol, we describe immunostaining of apoptosis-related proteins in the C. elegans adult germline using fluorescent reagents. Protein localization and abundance can be determined in various mutant backgrounds and under a variety of conditions, such as exposure to genotoxic stress. The number of antibodies specific to C. elegans proteins is quite limited compared with other organisms, but there is a growing list of immunological reagents directed against proteins in other organisms that cross-react with the homologous C. elegans proteins. PMID:24786502

Lant, Benjamin; Derry, W Brent

2014-01-01

102

A uniform genetic nomenclature for the nematode Caenorhabditis elegans  

Microsoft Academic Search

A uniform system of genetic nomenclature for the nematode Caenorhabditis elegans is described. Convenient ways are specified to designate genes, mutations and strains, and to attempt to avoid name duplications.

H. Robert Horvitz; Sydney Brenner; Jonathan Hodgkin; Robert K. Herman

1979-01-01

103

Lipid droplets as fat storage organelles in Caenorhabditis elegans  

PubMed Central

Lipid droplets are evolutionarily conserved organelles where cellular fat storage and mobilization are exquisitely regulated. Recent studies have defined lipid droplets in C. elegans and explored how they are regulated by genetic and dietary factors. C. elegans offers unique opportunities to visualize lipid droplets at single-cell resolution in live animals. The development of novel microscopy techniques and protein markers for lipid droplets will accelerate studies on how nutritional states and subcellular organization are linked in vivo. Together with powerful tools for genetic and biochemical analysis of metabolic pathways, alteration in lipid droplet abundance, size, and distribution in C. elegans can be readily connected to whole-animal energy homeostasis, behavior, and life span. Therefore, further studies on lipid droplets in C. elegans promise to yield valuable insights that complement our knowledge gained from yeast, Drosophila, and mammalian systems on cellular and organismal fat storage.

Mak, Ho Yi

2012-01-01

104

Genetic maps for Pinus elliottii var. elliottii and P. caribaea var. hondurensis using AFLP and microsatellite markers.  

PubMed

Genetic maps for individual Pinus elliottii var. elliottii and P. caribaea var. hondurensis trees were generated using a pseudo-testcross mapping strategy. A total of 329 amplified fragment length polymorphic (AFLP) and 12 microsatellite markers were found to segregate in a sample of 93 interspecfic F(1) progeny. The male P. caribaea var. hondurensis parent was more heterozygous than the female P. elliottii var. elliottii parent with 19% more markers segregating on the male side. Framework maps were constructed using a LOD 5 threshold for grouping and interval support threshold of LOD 2. The framework map length for the P. elliottii var. elliottii megagametophyte parent (1,170 cM Kosambi; 23 linkage groups) was notably smaller than the P. caribaea var. hondurensis pollen parent (1,658 cM Kosambi; 27 linkage groups). The difference in map lengths was assumed to be due to sex-related recombination variation, which has been previously reported for pines, as the difference in map lengths not be accounted for by the larger number of markers mapping to the P. caribaea var. hondurensis parent - 109 compared with 78 in P. elliottii var. elliottii parent. Based on estimated genome sizes for these species, the framework maps for P. elliottii var. elliottii and P. caribaea var. hondurensis covered 82% and 88% of their respective genomes. The pseudo-testcross strategy was extended to include AFLP and microsatellite markers in an intercross configuration. These comprehensive maps provided further genome coverage, 1,548 and 1,828 cM Kosambi for P. elliottii var. elliottii and P. caribaea var. hondurensis, respectively, and enabled homologous linkage groups to be identified in the two parental maps. Homologous linkage groups were identified for 11 out of 24 P. elliottii var. elliottii and 10 out of 25 P. caribaea var. hondurensis groups. A higher than expected level of segregation distortion was found for both AFLP and microsatellite markers. An explanation for this segregation distortion was not clear, but it may be at least in part due to genetic mechanisms for species isolation in this wide cross. PMID:12750783

Shepherd, M; Cross, M; Dieters, M J; Henry, R

2003-05-01

105

Tat-mediated protein delivery in living Caenorhabditis elegans  

Microsoft Academic Search

The Tat protein from HIV-1 fused with heterologous proteins traverses biological membranes in a transcellular process called: protein transduction. This has already been successfully exploited in various biological models, but never in the nematode worm Caenorhabditis elegans. TAT-eGFP or GST-eGFP proteins were fed to C. elegans worms, which resulted in the specific localization of Tat-eGFP to epithelial intestinal cells. This

Frédéric Delom; Delphine Fessart; Marie-Elaine Caruso; Eric. Chevet

2007-01-01

106

Proteins interacting withCaenorhabditis elegans G? subunits  

Microsoft Academic Search

To identify novel components in heterotrimeric G-protein signalling, we performed an extensive screen for proteins interacting with Caenorhabditis elegans G? subunits. The genome of C. elegans contains homologues of each of the four mammalian classes of G? subunits (Gs, Gi\\/o, Gq and G12), and 17 other G? subunits. We tested 19 of the G? subunits and four constitutively activated G?

Edwin Cuppen; Alexander M. van der Linden; Gert Jansen; Ronald H. A. Plasterk

2003-01-01

107

BROAD OXYGEN TOLERANCE IN THE NEMATODE CAENORHABDITIS ELEGANS  

Microsoft Academic Search

This study examined the effects of oxygen tensions ranging from 0 to 90 kPa on the metabolic rate (rate of carbon dioxide production), movement and survivorship of the free-living soil nematode Caenorhabditis elegans. C. elegans requires oxygen to develop and survive. However, it can maintain a normal metabolic rate at oxygen levels of 3.6 kPa and has near-normal metabolic rates

WAYNE A. VAN VOORHIES; SAMUEL WARD

108

Sensing of Heavy Metals Using Caenorhabditis elegans DNA Microarray  

Microsoft Academic Search

Abstract—Previously we reported that the possibility of sensing of chemical substances using gene expression patterns analyzed,by DNA microarray using Caenorhabditis elegans( C. elegans) as a sensor (Matsuno et al., 2002, 2006). In this study, we evaluated sensitivity and selectivity of above system using a customized,DNA microarray ,for heavy ,metal responded ,genes. The results showed,that this system ,showed ,high sensitivity and

Nobuaki TOMINAGA; Tetsuya MATSUNO; Shinya KOHRA; Koji ARIZONO

109

BACTERIAL ATTRACTION AND QUORUM SENSING INHIBITION IN CAENORHABDITIS ELEGANS EXUDATES  

PubMed Central

Caenorhabditis elegans, a bacterivorous nematode, lives in complex rotting fruit, soil, and compost environments, and chemical interactions are required for mating, monitoring population density, recognition of food, avoidance of pathogenic microbes, and other essential ecological functions. Despite being one of the best-studied model organisms in biology, relatively little is known about the signals that C. elegans uses to chemically interact with its environment or as defense. C. elegans exudates were analyzed using several analytical methods and found to contain 36 common metabolites including organic acids, amino acids and sugars, all in relatively high abundance. Furthermore, the concentrations of amino acids in the exudates were dependent on developmental stage. The C. elegans exudates were tested for bacterial chemotaxis using Pseudomonas putida (KT2440), a plant growth promoting rhizobacterium, Pseudomonas aeruginosa (PAO1), a soil bacterium pathogenic to C. elegans, and E. coli (OP50), a non-motile bacterium tested as a control. The C. elegans exudates attracted the two Psuedomonas species, but had no detectable antibacterial activity against P. aeruginosa. To our surprise, the exudates of young adult and adult life stages of C. elegans exudates inhibited quorum sensing in the reporter system based on the LuxR bacterial quorum sensing (QS) system, which regulates bacterial virulence and other factors in Vibrio fischeri. We were able to fractionate the QS inhibition and bacterial chemotaxis activities, demonstrating that these activities are chemically distinct. Our results demonstrate that C. elegans can attract its bacterial food and has the potential of partially regulating the virulence of bacterial pathogens by inhibiting specific QS systems.

KAPLAN, FATMA; BADRI, DAYAKAR V.; ZACHARIAH, CHERIAN; AJREDINI, RAMADAN; SANDOVAL, FRANCISCO J; ROJE, SANJA; LEVINE, LANFANG H.; ZHANG, FENGLI; ROBINETTE, STEVEN L.; ALBORN, HANS T.; ZHAO, WEI; STADLER, MICHAEL; NIMALENDRAN, RATHIKA; DOSSEY, AARON T.; BRUSCHWEILER, RAFAEL; VIVANCO, JORGE M.; EDISON, ARTHUR S.

2014-01-01

110

Japanese studies on neural circuits and behavior of Caenorhabditis elegans.  

PubMed

The nematode Caenorhabditis elegans is an ideal organism for studying neural plasticity and animal behaviors. A total of 302 neurons of a C. elegans hermaphrodite have been classified into 118 neuronal groups. This simple neural circuit provides a solid basis for understanding the mechanisms of the brains of higher animals, including humans. Recent studies that employ modern imaging and manipulation techniques enable researchers to study the dynamic properties of nervous systems with great precision. Behavioral and molecular genetic analyses of this tiny animal have contributed greatly to the advancement of neural circuit research. Here, we will review the recent studies on the neural circuits of C. elegans that have been conducted in Japan. Several laboratories have established unique and clever methods to study the underlying neuronal substrates of behavioral regulation in C. elegans. The technological advances applied to studies of C. elegans have allowed new approaches for the studies of complex neural systems. Through reviewing the studies on the neuronal circuits of C. elegans in Japan, we will analyze and discuss the directions of neural circuit studies. PMID:24348340

Sasakura, Hiroyuki; Tsukada, Yuki; Takagi, Shin; Mori, Ikue

2013-01-01

111

Polymorphic segmental duplication in the nematode Caenorhabditis elegans  

PubMed Central

Background The nematode Caenorhabditis elegans was the first multicellular organism to have its genome fully sequenced. Over the last 10 years since the original publication in 1998, the C. elegans genome has been scrutinized and the last gaps were filled in November 2002, which present a unique opportunity for examining genome-wide segmental duplications. Results Here, we performed analysis of the C. elegans genome in search for segmental duplications using a new tool–OrthoCluster–we have recently developed. We detected 3,484 duplicated segments–duplicons–ranging in size from 234 bp to 108 Kb. The largest pair of duplicons, 108 kb in length located on the left arm of Chromosome V, was further characterized. They are nearly identical at the DNA level (99.7% identity) and each duplicon contains 26 putative protein coding genes. Genotyping of 76 wild-type strains obtained from different labs in the C. elegans community revealed that not all strains contain this duplication. In fact, only 29 strains carry this large segmental duplication, suggesting a very recent duplication event in the C. elegans genome. Conclusion This report represents the first demonstration that the C. elegans laboratory wild-type N2 strains has acquired large-scale differences.

2009-01-01

112

Key players in chromosome segregation in Caenorhabditis elegans.  

PubMed

In contrast to many eukaryotic organisms in which kinetochores are assembled on localized centromeres of monocentric chromosomes, Caenorhabditis elegans has diffuse kinetochores, termed holo-kinetochores, which are assembled along the entire length of the mitotic chromosome. Despite this cytologically distinct chromosomal architecture, holo-kinetochores of C. elegans and kinetochores of other eukaryotes share structurally and functionally conserved properties. The amphitelic attachment of sister kinetochores to microtubules can be achieved by proper chromosomal organization, which relies on spatiotemporally orchestrated functions of conserved protein complexes such as the cohesin, condensin, and chromosomal passenger complexes during mitosis and meiosis in C. elegans. Moreover, the structure of spindle assembly checkpoint components and their safeguard function are also well conserved in C. elegans. Extensive efforts in the last few years to elucidate the molecular mechanisms of the C. elegans spindle assembly checkpoint have revealed its unique features. In this review, I will focus on the conservation and diversity of proteins that are required to maintain chromosome transmission fidelity during mitosis and meiosis in C. elegans. PMID:19273145

Kitagawa, Risa

2009-01-01

113

Incremental VaR and VaR with background risk: traps and misinterpretations  

Microsoft Academic Search

In recent …nancial literature the Incremental Value-at-Risk (IVaR), i.e., the incremental eect on VaR of adding a new instrument to the existing portfolio, has become a standard tool for making portfolio-hedging decisions. Since, calculating the exact IVaR value could be computationally very costly, approximate formulas have been developed. According to the most commonly used formula, IVaR is approximately equal to

Luisa Tibiletti

2000-01-01

114

Agrobacterium tumefaciens -mediated transformation of broccoli ( Brassica oleracea var. italica ) and cabbage ( B. oleracea var. capitata )  

Microsoft Academic Search

Transgenic broccoli (Brassica oleracea var. italica) was produced by two Agrobacterium tumefaciens-mediated transformation methods. One used flowering stalk explants from mature plants; the other used hypocotyl and petiole explants from in vitro-grown seedlings. Several hundred transformants containing a Bacillus thuringiensis ?-endotoxin gene (CryIA(c)-type) and the neomycin phosphotransferase gene were recovered. Rooted transformants were obtained in as little as 3 months

Timothy D. Metz; Ram Dixit; Elizabeth D. Earle

1995-01-01

115

Developmental biomarkers of aging in C. elegans  

PubMed Central

The developmental process of the nematode Caenorhabditis elegans is famously invariant; however these animals have surprisingly variable lifespans, even in extremely homogenous environments. Inter-individual differences in muscle-function decline, accumulation of lipofuscin in the gut, internal growth of food bacteria, and ability to mobilize heat-shock responses all appear to be predictive of a nematode's remaining lifespan; whether these are causal, or mere correlates of individual decline and death, has yet to be determined. Moreover, few “upstream” causes of inter-individual variability have been identified. It may be the case that variability in lifespan is entirely due to stochastic damage accumulation; alternately, perhaps such variability has a developmental origin and/or genes involved in developmental canalization also act to buffer phenotypic heterogeneity later in life. We review these two hypotheses with an eye toward whether they can be experimentally differentiated.

Pincus, Zachary; Slack, Frank J.

2011-01-01

116

Ultrafast endocytosis at Caenorhabditis elegans neuromuscular junctions  

PubMed Central

Synaptic vesicles can be released at extremely high rates, which places an extraordinary demand on the recycling machinery. Previous ultrastructural studies of vesicle recycling were conducted in dissected preparations using an intense stimulation to maximize the probability of release. Here, a single light stimulus was applied to motor neurons in intact Caenorhabditis elegans nematodes expressing channelrhodopsin, and the animals rapidly frozen. We found that docked vesicles fuse along a broad active zone in response to a single stimulus, and are replenished with a time constant of about 2 s. Endocytosis occurs within 50 ms adjacent to the dense projection and after 1 s adjacent to adherens junctions. These studies suggest that synaptic vesicle endocytosis may occur on a millisecond time scale following a single physiological stimulus in the intact nervous system and is unlikely to conform to current models of endocytosis. DOI: http://dx.doi.org/10.7554/eLife.00723.001

Watanabe, Shigeki; Liu, Qiang; Davis, M Wayne; Hollopeter, Gunther; Thomas, Nikita; Jorgensen, Nels B; Jorgensen, Erik M

2013-01-01

117

Common Cyclical Features Analysis in VAR Models with Cointegration  

Microsoft Academic Search

The paper considers n-dimensional VAR models for variables exhibiting cointegration and common cyclical features. Two specific reduced rank vector error correction models are discussed. In one, named the \\

Alain Hecq; Franz C. Palm; Jean-Pierre Urbain

2003-01-01

118

All About Value at Risk (VaR)  

NSDL National Science Digital Library

All about Value at Risk (VaR) is a wonderful resource for those interested in this form of risk management assessment. Created by Barry Schacter, the head of Enterprise Risk Management for Caxton Corporation, this site is a clearinghouse for VaR resources including information on various forms of RiskMatrics, a vast collection of published and working papers on VaR, and links to regulatory materials from international organizations such as the Basel Committee on Banking Supervision and the International Organization of Securities Commissions, as well as from the US, Austria, Canada, Australia, the UK, and Hong Kong. Interested users may also register for a free VaR weekly electronic newsletter.

2007-05-13

119

Michigan Monkey-Flower ('Mimulus glabratus var. michiganensis') Recovery Plan.  

National Technical Information Service (NTIS)

Mirnulus glabratus var. michiganensis (Pennell) Fassett, (Michigan monkey-flower), a member of the Scrophulariaceae (snapdragon family), is an endemic variety of a widespread and diverse complex of yellow monkey-flowers. The taxon is known from only 15 ex...

M. R. Penskar

1997-01-01

120

Epidemiological aspects of Trichophyton rubrum var. raubitschekii in Japan.  

PubMed

Trichophyton rubrum var. raubitschekii is a rare anthropophilic dermatophyte isolated around the world from tinea corporis, tinea cruris, tinea pedis and tinea unguium. In this study, the isolation rate of T. rubrum var. raubitschekii was studied in 200 cases of tinea pedis and tinea unguium in Japan. The 200 clinical isolates were shown to be of downy type as their colonies on Sabouraud's dextrose agar were white to cream, suede-like to downy, with a yellow-brown to wine-red reverse, and they produced few macroconidia. The type strain of T. rubrum var. raubitschekii (CBS 100084) and one clinical isolate (KMU 8337; isolated at Kanazawa) of downy type tested positive for urease, but the reference strain of T. rubrum (CBS 392.58) and the remaining 199 clinical isolates tested negative. Further epidemiological investigations are required to study human cases of infection with the granular type of T. rubrum and T. rubrum var. raubitschekii in Japan. PMID:22900925

Hiruma, Midori; Kano, Rui; Sugita, Takashi; Mochizuki, Takashi; Hasegawa, Atsuhiko; Hiruma, Masataro

2012-12-01

121

3-hydroxycoumarin glycosides from Alyxia reinwardti var. Lucida.  

PubMed

Investigation of the inner bark of Alyxia reinwardti var. lucida led to the isolation of two new coumarin glycosides, 1 and 2, whose structures were determined by interpretation of their spectroscopic data, particularly NMR spectroscopy. PMID:7764154

Lin, L J; Lin, L Z; Ruangrungsi, N; Cordell, G A

1993-10-01

122

Steamboat Buckwheat ('Eriogonum ovalifolium' var. 'williamsiae') Recovery Plan.  

National Technical Information Service (NTIS)

Steamboat buckwheat (Eriogonum ovailfolium Nutt. var. wihiamsiae Reveal) is a small, densely matted herbaceous plant endemic to substrates derived from hot springs deposits in the Steamboat Hills, located approximately 15 kilometers (kin), (10 miles) sout...

1995-01-01

123

Thoughts on VaR and CVaR  

Microsoft Academic Search

Value at Risk (VaR) is an important issue for banks since its adoption as a primary risk metric in the Basel Accords and the requirement that it is calculated on a daily basis. VaR calculates maximum expected losses over a given time period at a given tolerance level. Conditional Value at Risk (CVaR) measures extreme risk. It calculates the risk

David E Allen; Robert J Powell

2007-01-01

124

Dimorphism and hydrocarbon metabolism in Yarrowia lipolytica var. indica.  

PubMed

Yarrowia lipolytica is able to metabolize high Mr hydrophobic natural compounds such as fatty acids and hydrocarbons. Characteristically, strains of Y. lipolytica can grow as populations with variable proportions of yeast and filamentous forms. In the present study, we describe the dimorphic characteristics of a variant designated as Y. lipolytica var. indica isolated from petroleum contaminated sea water and the effect of cell morphology on hydrocarbon metabolism. The variant behaved as a yeast monomorphic strain, under conditions at which terrestrial Y. lipolytica strain W29 and its derived strains, grow as almost uniform populations of mycelial cells. Using organic nitrogen sources and N-acetylglucosamine as carbon source, var. indica was able to form mycelial cells, the proportion of which increased when incubated under semi-anaerobic conditions. The cell surface characteristics of var. indica and W29 were found to be different with respect to contact angle and percent hydrophobicity. For instance, percent hydrophobicity of var. indica was 89.93 ± 1.95 while that of W29 was 70.78 ± 1.1. Furthermore, while all tested strains metabolize hydrocarbons, only var. indica was able to use it as a carbon source. Yeast cells of var. indica metabolized hexadecane with higher efficiency than the mycelial form, whereas the mycelial form of the terrestrial strain metabolized the hydrocarbon more efficiently, as occurred with the mycelial monomorphic mutant AC11, compared to the yeast monomorphic mutant AC1. PMID:24842274

Palande, A S; Kulkarni, S V; León-Ramirez, C; Campos-Góngora, E; Ruiz-Herrera, J; Deshpande, M V

2014-08-01

125

Chemically Defined Medium and Caenorhabditis elegans: A Powerful Approach  

NASA Technical Reports Server (NTRS)

C. elegans has been established as a powerful genetic system. Growth in a chemically defined medium (C. elegans Maintenance Medium (CeMM)) now allows standardization and systematic manipulation of the nutrients that animals receive. Liquid cultivation allows automated culturing and experimentation and should be of me in large-scale growth and screening of animals. Here we present our initial results from developing culture systems with CeMM. We find that CeMM is versatile and culturing is simple. CeMM can be used in a solid or liquid state, it can be stored unused for at least a year, unattended actively growing cultures may be maintained longer than with standard techniques, and standard C. elegans protocols work well with animals grown in defined medium. We also find that there are caveats of using defined medium. Animals in defined medium grow more slowly than on standard medium, appear to display adaptation to the defined medium, and display altered growth rates as they change defined medium composition. As was suggested with the introduction of C. elegans as a potential genetic system, use of defined medium with C. elegans should prove a powerful tool.

Szewczyk, N. J.; Kozak, E.; Conley, C. A.

2003-01-01

126

Genetic Dissection of Late-Life Fertility in Caenorhabditis elegans  

PubMed Central

The large post-reproductive life span reported for the free-living hermaphroditic nematode, Caenorhabditis elegans, which lives for about 10 days after its 5-day period of self-reproduction, seems at odds with evolutionary theory. Species with long post-reproductive life spans such as mammals are sometimes explained by a need for parental care or transfer of information. This does not seem a suitable explanation for C elegans. Previous reports have shown that C elegans can regain fertility when mated after the self-fertile period but did not report the functional limits. Here, we report the functional life span of the C elegans germ line when mating with males. We show that C elegans can regain fertility late in life (significantly later than in previous reports) and that the end of this period corresponds quite well to its 3-week total life span. Genetic analysis reveals that late-life fertility is controlled by conserved pathways involved with aging and dietary restriction.

Wu, Deqing; Park, Sang-Kyu; Cypser, James R.; Tedesco, Patricia M.; Phillips, Patrick C.; Johnson, Thomas E.

2011-01-01

127

Two novel ergtoxins, blockers of K+-channels, purified from the Mexican scorpion Centruroides elegans elegans.  

PubMed

Voltage-gated potassium channels of the ether-a-go-go related gene (ERG) family are implicated in many important cellular processes. Three such genes have been cloned (erg1, erg2 and erg3) and shown to be expressed in the central nervous system (CNS) of mammalians. This communication describes the isolation and characterization of two isoforms of scorpion toxin (CeErg4 and CeErg5, systematic nomenclature gamma-KTx1.7 and gamma-KTx1.8, respectively) that can discriminate the various subtypes of ERG channels of human and rat. These peptides were purified from the venom of the Mexican scorpion Centruroides elegans elegans. They contain 42 amino acid residues, tightly folded by four disulfide bridges. Both peptides block in a reversible manner human and rat ERG1 channels, but have no effect on human ERG2. They also block completely and irreversibly the rat ERG2 and the human ERG3 channels hence are excellent tools for the discrimination of the various sub-types of ion-channels studied. PMID:18338253

Restano-Cassulini, Rita; Olamendi-Portugal, Timoteo; Zamudio, Fernando; Becerril, Baltazar; Possani, Lourival Domingos

2008-08-01

128

Bacteria and the aging and longevity of Caenorhabditis elegans.  

PubMed

The molecular genetic analysis of longevity of Caenorhabditis elegans has yielded fundamental insights into evolutionarily conserved pathways and processes governing the physiology of aging. Recent studies suggest that interactions between C. elegans and its microbial environment may influence the aging and longevity of this simple host organism. Experimental evidence supports a role for bacteria in affecting longevity through distinct mechanisms--as a nutrient source, as a potential pathogen that induces double-edged innate immune and stress responses, and as a coevolved sensory stimulus that modulates neuronal signaling pathways regulating longevity. Motivating this review is the anticipation that the molecular genetic dissection of the integrated host immune, stress, and neuroendocrine responses to microbes in C. elegans will uncover basic insights into the cellular and organismal physiology that governs aging and longevity. PMID:24274752

Kim, Dennis H

2013-01-01

129

Proprioceptive coupling within motor neurons drives C. elegans forward locomotion  

PubMed Central

Summary Locomotion requires coordinated motor activity throughout an animal’s body. In both vertebrates and invertebrates, chains of coupled Central Pattern Generators (CPGs) are commonly evoked to explain local rhythmic behaviors. In C. elegans, we report that proprioception within the motor circuit is responsible for propagating and coordinating rhythmic undulatory waves from head to tail during forward movement. Proprioceptive coupling between adjacent body regions transduces rhythmic movement initiated near the head into bending waves driven along the body by a chain of reflexes. Using optogenetics and calcium imaging to manipulate and monitor motor circuit activity of moving C. elegans held in microfluidic devices, we found that the B-type cholinergic motor neurons transduce the proprioceptive signal. In C. elegans, a sensorimotor feedback loop operating within a specific type of motor neuron both drives and organizes body movement.

Wen, Quan; Po, Michelle; Hulme, Elizabeth; Chen, Sway; Liu, Xinyu; Kwok, Sen Wai; Gershow, Marc; Leifer, Andrew M; Butler, Victoria; Fang-Yen, Christopher; Kawano, Taizo; Schafer, William R; Whitesides, George

2012-01-01

130

Solid Plate-based Dietary Restriction in Caenorhabditis elegans  

PubMed Central

Reduction of food intake without malnutrition or starvation is known to increase lifespan and delay the onset of various age-related diseases in a wide range of species, including mammals. It also causes a decrease in body weight and fertility, as well as lower levels of plasma glucose, insulin, and IGF-1 in these animals. This treatment is often referred to as dietary restriction (DR) or caloric restriction (CR). The nematode Caenorhabditis elegans has emerged as an important model organism for studying the biology of aging. Both environmental and genetic manipulations have been used to model DR and have shown to extend lifespan in C. elegans. However, many of the reported DR studies in C. elegans were done by propagating animals in liquid media, while most of the genetic studies in the aging field were done on the standard solid agar in petri plates. Here we present a DR protocol using standard solid NGM agar-based plate with killed bacteria.

Ching, Tsui-Ting; Hsu, Ao-Lin

2011-01-01

131

Femtosecond laser dissection in C. elegans neural circuits  

NASA Astrophysics Data System (ADS)

The nematode C. elegans, a millimeter-long roundworm, is a well-established model organism for studies of neural development and behavior, however physiological methods to manipulate and monitor the activity of its neural network have lagged behind the development of powerful methods in genetics and molecular biology. The small size and transparency of C. elegans make the worm an ideal test-bed for the development of physiological methods derived from optics and microscopy. We present the development and application of a new physiological tool: femtosecond laser dissection, which allows us to selectively ablate segments of individual neural fibers within live C. elegans. Femtosecond laser dissection provides a scalpel with submicrometer resolution, and we discuss its application in studies of neural growth, regenerative growth, and the neural basis of behavior.

Samuel, Aravinthan D. T.; Chung, Samuel H.; Clark, Damon A.; Gabel, Christopher V.; Chang, Chieh; Murthy, Venkatesh; Mazur, Eric

2006-03-01

132

Formation and Regulation of Adaptive Response in Nematode Caenorhabditis elegans  

PubMed Central

All organisms respond to environmental stresses (e.g., heavy metal, heat, UV irradiation, hyperoxia, food limitation, etc.) with coordinated adjustments in order to deal with the consequences and/or injuries caused by the severe stress. The nematode Caenorhabditis elegans often exerts adaptive responses if preconditioned with low concentrations of agents or stressor. In C. elegans, three types of adaptive responses can be formed: hormesis, cross-adaptation, and dietary restriction. Several factors influence the formation of adaptive responses in nematodes, and some mechanisms can explain their response formation. In particular, antioxidation system, heat-shock proteins, metallothioneins, glutathione, signaling transduction, and metabolic signals may play important roles in regulating the formation of adaptive responses. In this paper, we summarize the published evidence demonstrating that several types of adaptive responses have converged in C. elegans and discussed some possible alternative theories explaining the adaptive response control.

Zhao, Y.-L.; Wang, D.-Y.

2012-01-01

133

Lessons from C. elegans: Signaling pathways for longevity  

PubMed Central

Recent research using model organisms such as the nematode Caenorhabditis elegans has highlighted a critical role for several conserved signaling pathways in longevity determination. Here, we review three major endocrine- and nutrient-sensing signaling pathways with influence on lifespan, the insulin/insulin-like growth factor (IGF), target of rapamycin (TOR), and germline signaling pathways. Although these pathways engage distinct sets of transcription factors, the three pathways appear to modulate aging in C. elegans through partially overlapping effector mechanisms, including lipid metabolism and autophagy. This review highlights the latest advances in our understanding of how the insulin/IGF-1, TOR, and germline signaling pathways utilize different transcription factors to modulate aging in C. elegans with special emphasis on the role of lipid metabolism and autophagy.

Lapierre, Louis R.; Hansen, Malene

2012-01-01

134

Locomotion Control of Caenorhabditis elegans through Confinement  

PubMed Central

The model organism Caenorhabditis elegans shows two distinct locomotion patterns in laboratory situations: it swims in low viscosity liquids and it crawls on the surface of an agar gel. This provides a unique opportunity to discern the respective roles of mechanosensation (perception and proprioception) and mechanics in the regulation of locomotion and in the gait selection. Using an original device, we present what to our knowledge are new experiments where the confinement of a worm between a glass plate and a soft agar gel is controlled while recording the worm's motion. We observed that the worm continuously varied its locomotion characteristics from free swimming to slow crawling with increasing confinement so that it was not possible to discriminate between two distinct intrinsic gaits. This unicity of the gait is also proved by the fact that wild-type worms immediately adapted their motion when the imposed confinement was changed with time. We then studied locomotory deficient mutants that also exhibited one single gait and showed that the light touch response was needed for the undulation propagation and that the ciliated sensory neurons participated in the joint selection of motion period and undulation-wave velocity. Our results reveal that the control of maximum curvature, at a sensory or mechanical level, is a key ingredient of the locomotion regulation.

Lebois, Felix; Sauvage, Pascal; Py, Charlotte; Cardoso, Olivier; Ladoux, Benoit; Hersen, Pascal; Di Meglio, Jean-Marc

2012-01-01

135

Long noncoding RNAs in C. elegans  

PubMed Central

Thousands of long noncoding RNAs (lncRNAs) have been found in vertebrate animals, a few of which have known biological roles. To better understand the genomics and features of lncRNAs in invertebrates, we used available RNA-seq, poly(A)-site, and ribosome-mapping data to identify lncRNAs of Caenorhabditis elegans. We found 170 long intervening ncRNAs (lincRNAs), which had single- or multiexonic structures that did not overlap protein-coding transcripts, and about sixty antisense lncRNAs (ancRNAs), which were complementary to protein-coding transcripts. Compared to protein-coding genes, the lncRNA genes tended to be expressed in a stage-dependent manner. Approximately 25% of the newly identified lincRNAs showed little signal for sequence conservation and mapped antisense to clusters of endogenous siRNAs, as would be expected if they serve as templates and targets for these siRNAs. The other 75% tended to be more conserved and included lincRNAs with intriguing expression and sequence features associating them with processes such as dauer formation, male identity, sperm formation, and interaction with sperm-specific mRNAs. Our study provides a glimpse into the lncRNA content of a nonvertebrate animal and a resource for future studies of lncRNA function.

Nam, Jin-Wu; Bartel, David P.

2012-01-01

136

Computational insights into Caenorhabditis elegans vulval development  

PubMed Central

Studies of Caenorhabditis elegans vulval development provide a paradigm for pattern formation during animal development. The fates of the six vulval precursor cells are specified by the combined action of an inductive signal that activates the EGF receptor mitogen-activated PK signaling pathway (specifying a primary fate) and a lateral signal mediated by LIN-12/Notch (specifying a secondary fate). Here we use methods devised for the engineering of complex reactive systems to model a biological system. We have chosen the visual formalism of statecharts and use it to formalize Sternberg and Horvitz's 1989 model [Sternberg, P. W. & Horvitz, H. R. (1989) Cell 58, 679–693], which forms the basis for our current understanding of the interaction between these two signaling pathways. The construction and execution of our model suggest that different levels of the inductive signal induce a temporally graded response of the EGF receptor mitogen-activated PK pathway and make explicit the importance of this temporal response. Our model also suggests the existence of an additional mechanism operating during lateral specification that prohibits neighboring vulval precursor cells from assuming the primary fate.

Fisher, Jasmin; Piterman, Nir; Hubbard, E. Jane Albert; Stern, Michael J.; Harel, David

2005-01-01

137

The Caenorhabditis elegans septin complex is nonpolar  

PubMed Central

Septins are conserved GTPases that form heteromultimeric complexes and assemble into filaments that play a critical role in cell division and polarity. Results from budding and fission yeast indicate that septin complexes form around a tetrameric core. However, the molecular structure of the core and its influence on the polarity of septin complexes and filaments is poorly defined. The septin complex of the nematode Caenorhabditis elegans is formed entirely by the core septins UNC-59 and UNC-61. We show that UNC-59 and UNC-61 form a dimer of coiled-coil-mediated heterodimers. By electron microscopy, this heterotetramer appears as a linear arrangement of four densities representing the four septin subunits. Fusion of GFP to the N termini of UNC-59 and UNC-61 and subsequent electron microscopic visualization suggests that the sequence of septin subunits is UNC-59/UNC-61/UNC-61/UNC-59. Visualization of GFP extensions fused to the extremity of the C-terminal coiled coils indicates that these extend laterally from the heterotetrameric core. Together, our study establishes that the septin core complex is symmetric, and suggests that septins form nonpolar filaments.

John, Corinne M; Hite, Richard K; Weirich, Christine S; Fitzgerald, Daniel J; Jawhari, Hatim; Faty, Mahamadou; Schlapfer, Dominik; Kroschewski, Ruth; Winkler, Fritz K; Walz, Tom; Barral, Yves; Steinmetz, Michel O

2007-01-01

138

The Genetics of Feeding in Caenorhabditis Elegans  

PubMed Central

The pharynx of Caenorhabditis elegans is a nearly self-contained neuromuscular organ responsible for feeding. To identify genes involved in the development or function of the excitable cells of the pharynx, I screened for worms with visible defects in pharyngeal feeding behavior. Fifty-two mutations identified 35 genes, at least 22 previously unknown. The genes broke down into three broad classes: 2 pha genes, mutations in which caused defects in the shape of the pharynx, 7 phm genes, mutations in which caused defects in the contractile structures of the pharyngeal muscle, and 26 eat genes, mutants in which had abnormal pharyngeal muscle motions, but had normally shaped and normally birefringent pharynxes capable of vigorous contraction. Although the Eat phenotypes were diverse, most resembled those caused by defects in the pharyngeal nervous system. For some of the eat genes there is direct evidence from previous genetic mosaic and pharmacological studies that they do in fact affect nervous system. In eat-5 mutants the motions of the different parts of the pharynx were poorly synchronized. eat-6 and eat-12 mutants failed to relax their pharyngeal muscles properly. These pharyngeal motion defects are most easily explained as resulting from abnormal electrical excitability of the pharyngeal muscle membrane.

Avery, L.

1993-01-01

139

Hormesis and aging in Caenorhabditis elegans.  

PubMed

Hormesis has emerged as an important manipulation for the study of aging. Although hormesis is manifested in manifold combinations of stress and model organism, the mechanisms of hormesis are only partly understood. The increased stress resistance and extended survival caused by hormesis can be manipulated to further our understanding of the roles of intrinsic and induced stress resistance in aging. Genes of the dauer/insulin/insulin-like signaling (IIS) pathway have well-established roles in aging in Caenorhabditis elegans. Here, we discuss the role of some of those genes in the induced stress resistance and induced life extension attributable to hormesis. Mutations in three genes (daf-16, daf-18, and daf-12) block hormetically induced life extension. However, of these three, only daf-18 appears to be required for a full induction of thermotolerance induced by hormesis, illustrating possible separation of the genetic requirements for stress resistance and life extension. Mutations in three other genes of this pathway (daf-3, daf-5, and age-1) do not block induced life extension or induced thermotolerance; daf-5 mutants may be unusually sensitive to hormetic conditions. PMID:17067771

Cypser, James R; Tedesco, Pat; Johnson, Thomas E

2006-10-01

140

Effect of vitamin D3 on lifespan in Caenorhabditis elegans.  

PubMed

Vitamin D is an essential micronutrient, necessary for human health. To determine if Caenorhabditis elegans (C. elegans) could function as an effective model to study the mechanisms of action of vitamin D, we asked if vitamin D3 affects C. elegans lifespan. Multiple factors positively impact lifespan in this system including dietary restriction and vitamin E. In addition, the C. elegans DAF-12 nuclear hormone receptor is homologous to the vitamin D receptor in humans and is therefore a candidate for a functional vitamin D receptor. It was hypothesized that vitamin D3 supplementation would increase the lifespan of C. elegans in a DAF-12-dependent manner. Dose-response curves were completed, and results indicate that exposure to 1,000 µg/ml vitamin D3 significantly increased the lifespan of wild-type worms by up to 39% (p<0.001). The daf-12 mutants exposed to 1,000 µg/ml vitamin D3 lived significantly longer than daf-12 controls exposed to 0 µg/ml (p<0.001), but among worms exposed to 1,000 µg/ml vitamin D3, wild type lived significantly longer than daf-12 (p<0.01). The data suggest that vitamin D3 can interact with multiple receptors, possibly implicating the NHR family of nuclear hormone receptors related to DAF-12. This research is the first to our knowledge to utilize C. elegans as a model to study the impact of vitamin D3 on longevity and supports the use of this model system to increase our understanding of vitamin D function at the cellular level, its role in cellular health, and its potential medicinal utility in humans. PMID:24304198

Messing, Jennifer A; Heuberger, Roschelle; Schisa, Jennifer A

2013-12-01

141

Sperm and Oocyte Communication Mechanisms Controlling C. elegans Fertility  

PubMed Central

During sexual reproduction in many species, sperm and oocyte secrete diffusible signaling molecules to help orchestrate the biological symphony of fertilization. In the Caenorhabditis elegans gonad, bidirectional signaling between sperm and oocyte is important for guiding sperm to the fertilization site and inducing oocyte maturation. The molecular mechanisms that regulate sperm guidance and oocyte maturation are being delineated. Unexpectedly, these mechanisms are providing insight into human diseases, such as amyotrophic lateral sclerosis, spinal muscular atrophy, and cancer. Here we review sperm and oocyte communication in C. elegans and discuss relationships to human disorders.

Han, Sung Min; Cottee, Pauline A.; Miller, Michael A.

2010-01-01

142

What can Caenorhabditis elegans tell us about the nuclear envelope?  

PubMed

The nuclear envelope (NE) of the eukaryotic cell provides an essential barrier that separates the nuclear compartment from the cytoplasm. In addition, the NE is involved in essential functions such as nuclear stability, regulation of gene expression, centrosome separation and nuclear migration and positioning. In metazoa the NE breaks down and re-assembles around the segregated chromatids during each cell division. In this review we discuss the molecular constituents of the Caenorhabditis elegans NE and describe their role in post-mitotic NE re-formation, as well as the usefulness of C. elegans as an in vivo system for analyzing NE dynamics. PMID:17418822

Gorjánácz, Mátyás; Jaedicke, Andreas; Mattaj, Iain W

2007-06-19

143

A method for culturing embryonic C. elegans cells.  

PubMed

C. elegans is a powerful model system, in which genetic and molecular techniques are easily applicable. Until recently though, techniques that require direct access to cells and isolation of specific cell types, could not be applied in C. elegans. This limitation was due to the fact that tissues are confined within a pressurized cuticle which is not easily digested by treatment with enzymes and/or detergents. Based on early pioneer work by Laird Bloom, Christensen and colleagues developed a robust method for culturing C. elegans embryonic cells in large scale. Eggs are isolated from gravid adults by treatment with bleach/NaOH and subsequently treated with chitinase to remove the eggshells. Embryonic cells are then dissociated by manual pipetting and plated onto substrate-covered glass in serum-enriched media. Within 24 hr of isolation cells begin to differentiate by changing morphology and by expressing cell specific markers. C. elegans cells cultured using this method survive for up 2 weeks in vitro and have been used for electrophysiological, immunochemical, and imaging analyses as well as they have been sorted and used for microarray profiling. PMID:24084243

Sangaletti, Rachele; Bianchi, Laura

2013-01-01

144

Small-molecule mechanism of action studies in Caenorhabditis elegans.  

PubMed

A general protocol for exogenous small-molecule pull-down experiments with Caenorhabditis elegans is described; it provides a link between small-molecule screens in worms and existing mutant and RNAi technologies, thereby enabling organismal mechanism of action studies for the natural product clovanemagnolol. Forward chemical genetic screens followed by mechanism of action studies with C. elegans, when coupled with genetic validation of identified targets to reproduce the small molecule's phenotypic effects, provide a unique platform for discovering the biological targets of compounds that affect multicellular processes. First, the use of an immobilized FK506 derivative and soluble competition experiments with optimally prepared soluble C. elegans proteome successfully identified interactions with FK506 binding proteins 1 to 6. This approach was used to determine an unknown mechanism of action for clovanemagnolol, a small molecule that promotes axonal branching in both primary neuronal cultures and in vivo in C. elegans. Following the synthesis of an appropriately functionalized solid-phase reagent bearing a clovanemagnolol analogue pull-down experiments employing soluble competition identified kinesin light chain-1 (KLC-1), a protein involved in axonal cargo transport, as a putative target. This was corroborated through the use of mutant worms lacking klc-1 and possessing GFP neuronal labeling, reproducing the axonal branching phenotype induced by the small molecule clovanemagnolol. PMID:24123757

Zlotkowski, Katherine; Eliasen, Anders M; Mitra, Aurpon; Siegel, Dionicio

2013-11-25

145

Characterization of the astacin family of metalloproteases in C. elegans  

Microsoft Academic Search

BACKGROUND: Astacins are a large family of zinc metalloproteases found in bacteria and animals. They have diverse roles ranging from digestion of food to processing of extracellular matrix components. The C. elegans genome contains an unusually large number of astacins, of which the majority have not been functionally characterized yet. RESULTS: We analyzed the expression pattern of previously uncharacterized members

Ja-On Park; Jie Pan; Frank Möhrlen; Marcus-Oliver Schupp; Robert Johnsen; David L Baillie; Richard Zapf; Donald G Moerman; Harald Hutter

2010-01-01

146

Caenorhabditis elegans glia modulate neuronal activity and behavior.  

PubMed

Glial cells of Caenorhabditis elegans can modulate neuronal activity and behavior, which is the focus of this review. Initially, we provide an overview of neuroglial evolution, making a comparison between C. elegans glia and their genealogical counterparts. What follows is a brief discussion on C. elegans glia characteristics in terms of their exact numbers, germ layers origin, their necessity for proper development of sensory organs, and lack of their need for neuronal survival. The more specific roles that various glial cells have on neuron-based activity/behavior are succinctly presented. The cephalic sheath glia are important for development, maintenance and activity of central synapses, whereas the amphid glia seem to set the tone of sensory synapses; these glial cell types are ectoderm-derived. Mesoderm-derived Glial-Like cells in the nerve Ring (GLRs) appear to be a part of the circuit for production of motor movement of the worm anterior. Finally, we discuss tools and approaches utilized in studying C. elegans glia, which are assets available for this animal, making it an appealing model, not only in neurosciences, but in biology in general. PMID:24672428

Stout, Randy F; Verkhratsky, Alexei; Parpura, Vladimir

2014-01-01

147

Distribution and Transport of Cholesterol in Caenorhabditis elegans  

Microsoft Academic Search

Cholesterol transport is an essential process in all multicellular organisms. In this study we applied two recently developed approaches to investigate the distribution and molecular mech- anisms of cholesterol transport in Caenorhabditis elegans. The distribution of cholesterol in living worms was studied by imaging its fluorescent analog, dehydroergosterol, which we applied to the animals by feeding. Dehydroergosterol accumulates primarily in

Vitali Matyash; Christian Geier; Annemarie Henske; Sushmita Mukherjee; David Hirsh; Christoph Thiele; Barth Grant; Frederick R. Maxfield; Teymuras V. Kurzchalia

2001-01-01

148

Proteome changes of Caenorhabditis elegans upon a Staphylococcus aureus infection  

Microsoft Academic Search

BACKGROUND: The success of invertebrates throughout evolution is an excellent illustration of the efficiency of their defence strategies. Caenorhabditis elegans has proven to be an appropriate model for transcriptome studies of host-pathogen interactions. The aim of this paper is to complement this knowledge by investigating the worm's response to a Staphylococcus aureus infection through a 2-dimensional differential proteomics approach. RESULTS:

Annelies Bogaerts; Isabel Beets; Liesbet Temmerman; Liliane Schoofs; Peter Verleyen

2010-01-01

149

The worm has turned - microbial virulence modeled in Caenorhabditis elegans  

Microsoft Academic Search

The nematode Caenorhabditis elegans is emerging as a facile and economical model host for the study of evolu- tionarily conserved mechanisms of microbial patho- genesis and innate immunity. A rapidly growing number of human and animal microbial pathogens have been shown to injure and kill nematodes. In many cases, microbial genes known to be important for full virulence in mammalian

Costi D. Sifri; Jakob Begun; Frederick M. Ausubel

2005-01-01

150

Material properties of Caenorhabditis elegans swimming at low Reynolds number.  

PubMed

Undulatory locomotion, as seen in the nematode Caenorhabditis elegans, is a common swimming gait of organisms in the low Reynolds number regime, where viscous forces are dominant. Although the nematode's motility is expected to be a strong function of its material properties, measurements remain scarce. Here, the swimming behavior of C. elegans is investigated in experiments and in a simple model. Experiments reveal that nematodes swim in a periodic fashion and generate traveling waves that decay from head to tail. The model is able to capture the experiments' main features and is used to estimate the nematode's Young's modulus E and tissue viscosity eta. For wild-type C. elegans, we find E approximately 3.77 kPa and eta approximately -860 Pa.s; values of eta for live C. elegans are negative because the tissue is generating rather than dissipating energy. Results show that material properties are sensitive to changes in muscle functional properties, and are useful quantitative tools with which to more accurately describe new and existing muscle mutants. PMID:20159158

Sznitman, J; Purohit, Prashant K; Krajacic, P; Lamitina, T; Arratia, P E

2010-02-17

151

Histidine Protects Against Zinc and Nickel Toxicity in Caenorhabditis elegans  

PubMed Central

Zinc is an essential trace element involved in a wide range of biological processes and human diseases. Zinc excess is deleterious, and animals require mechanisms to protect against zinc toxicity. To identify genes that modulate zinc tolerance, we performed a forward genetic screen for Caenorhabditis elegans mutants that were resistant to zinc toxicity. Here we demonstrate that mutations of the C. elegans histidine ammonia lyase (haly-1) gene promote zinc tolerance. C. elegans haly-1 encodes a protein that is homologous to vertebrate HAL, an enzyme that converts histidine to urocanic acid. haly-1 mutant animals displayed elevated levels of histidine, indicating that C. elegans HALY-1 protein is an enzyme involved in histidine catabolism. These results suggest the model that elevated histidine chelates zinc and thereby reduces zinc toxicity. Supporting this hypothesis, we demonstrated that dietary histidine promotes zinc tolerance. Nickel is another metal that binds histidine with high affinity. We demonstrated that haly-1 mutant animals are resistant to nickel toxicity and dietary histidine promotes nickel tolerance in wild-type animals. These studies identify a novel role for haly-1 and histidine in zinc metabolism and may be relevant for other animals.

Murphy, John T.; Bruinsma, Janelle J.; Schneider, Daniel L.; Collier, Sara; Guthrie, James; Chinwalla, Asif; Robertson, J. David; Mardis, Elaine R.; Kornfeld, Kerry

2011-01-01

152

Caenorhabditis elegans pathways that surveil and defend mitochondria.  

PubMed

Mitochondrial function is challenged by toxic by-products of metabolism as well as by pathogen attack. Caenorhabditis elegans normally responds to mitochondrial dysfunction with activation of mitochondrial-repair, drug-detoxification and pathogen-response pathways. Here, from a genome-wide RNA interference (RNAi) screen, we identified 45 C. elegans genes that are required to upregulate detoxification, pathogen-response and mitochondrial-repair pathways after inhibition of mitochondrial function by drug-induced or genetic disruption. Animals defective in ceramide biosynthesis are deficient in mitochondrial surveillance, and addition of particular ceramides can rescue the surveillance defects. Ceramide can also rescue the mitochondrial surveillance defects of other gene inactivations, mapping these gene activities upstream of ceramide. Inhibition of the mevalonate pathway, either by RNAi or statin drugs, also disrupts mitochondrial surveillance. Growth of C. elegans with a significant fraction of bacterial species from their natural habitat causes mitochondrial dysfunction. Other bacterial species inhibit C. elegans defence responses to a mitochondrial toxin, revealing bacterial countermeasures to animal defence. PMID:24695221

Liu, Ying; Samuel, Buck S; Breen, Peter C; Ruvkun, Gary

2014-04-17

153

The emergence of stereotyped behaviors in C. elegans  

NASA Astrophysics Data System (ADS)

Many organisms, including humans, engage in stereotyped behaviors and these are often attributed to a deterministic command process within the nervous system. Here we use the locomotor dynamics of the nematode C. elegans to suggest an alternative explanation in which stereotyped behavior emerges due to noise within a non-linear dynamical system. In previous work (PLoS Comp Bio 4, e1000028 (2008)) we found that the body shapes of freely-crawling C. elegans are well-captured by four `eigenworms', two of which encode the phase of a locomotory wave that generates forward and backward motion. We also used this representation to infer a non-linear dynamical model for the phase in which forward and backward crawling emerge as attractors of the deterministic dynamics. Here we show that noise induces reversals between forward and backward crawling and that the predicted reversal rate is in good agreement with experiment, with no adjustable parameters. In this model, reversals follow a stereotyped trajectory for the same reason that Brownian escape over a barrier is dominated by a narrowly defined class of trajectories. Stereotypy becomes even clearer in the dynamics with lower noise levels; the real C. elegans is just outside the regime where the reversal rate follows an Arrhenius dependence on the noise level. We discus the implications of our results for C. elegans and other organisms.

Stephens, Greg; Ryu, William; Bialek, William

2010-03-01

154

The C. elegans rab family: identification, classification and toolkit construction.  

PubMed

Rab monomeric GTPases regulate specific aspects of vesicle transport in eukaryotes including coat recruitment, uncoating, fission, motility, target selection and fusion. Moreover, individual Rab proteins function at specific sites within the cell, for example the ER, golgi and early endosome. Importantly, the localization and function of individual Rab subfamily members are often conserved underscoring the significant contributions that model organisms such as Caenorhabditis elegans can make towards a better understanding of human disease caused by Rab and vesicle trafficking malfunction. With this in mind, a bioinformatics approach was first taken to identify and classify the complete C. elegans Rab family placing individual Rabs into specific subfamilies based on molecular phylogenetics. For genes that were difficult to classify by sequence similarity alone, we did a comparative analysis of intron position among specific subfamilies from yeast to humans. This two-pronged approach allowed the classification of 30 out of 31 C. elegans Rab proteins identified here including Rab31/Rab50, a likely member of the last eukaryotic common ancestor (LECA). Second, a molecular toolset was created to facilitate research on biological processes that involve Rab proteins. Specifically, we used Gateway-compatible C. elegans ORFeome clones as starting material to create 44 full-length, sequence-verified, dominant-negative (DN) and constitutive active (CA) rab open reading frames (ORFs). Development of this toolset provided independent research projects for students enrolled in a research-based molecular techniques course at California State University, East Bay (CSUEB). PMID:23185324

Gallegos, Maria E; Balakrishnan, Sanjeev; Chandramouli, Priya; Arora, Shaily; Azameera, Aruna; Babushekar, Anitha; Bargoma, Emilee; Bokhari, Abdulmalik; Chava, Siva Kumari; Das, Pranti; Desai, Meetali; Decena, Darlene; Saramma, Sonia Dev Devadas; Dey, Bodhidipra; Doss, Anna-Louise; Gor, Nilang; Gudiputi, Lakshmi; Guo, Chunyuan; Hande, Sonali; Jensen, Megan; Jones, Samantha; Jones, Norman; Jorgens, Danielle; Karamchedu, Padma; Kamrani, Kambiz; Kolora, Lakshmi Divya; Kristensen, Line; Kwan, Kelly; Lau, Henry; Maharaj, Pranesh; Mander, Navneet; Mangipudi, Kalyani; Menakuru, Himabindu; Mody, Vaishali; Mohanty, Sandeepa; Mukkamala, Sridevi; Mundra, Sheena A; Nagaraju, Sudharani; Narayanaswamy, Rajhalutshimi; Ndungu-Case, Catherine; Noorbakhsh, Mersedeh; Patel, Jigna; Patel, Puja; Pendem, Swetha Vandana; Ponakala, Anusha; Rath, Madhusikta; Robles, Michael C; Rokkam, Deepti; Roth, Caroline; Sasidharan, Preeti; Shah, Sapana; Tandon, Shweta; Suprai, Jagdip; Truong, Tina Quynh Nhu; Uthayaruban, Rubatharshini; Varma, Ajitha; Ved, Urvi; Wang, Zeran; Yu, Zhe

2012-01-01

155

The Fundamental Role of Pirouettes in Caenorhabditis elegans Chemotaxis  

Microsoft Academic Search

To investigate the behavioral mechanism of chemotaxis in Cae- norhabditis elegans, we recorded the instantaneous position, speed, and turning rate of single worms as a function of time during chemotaxis in gradients of the attractants ammonium chloride or biotin. Analysis of turning rate showed that each worm track could be divided into periods of smooth swimming (runs) and periods of

Jonathan T. Pierce-Shimomura; Thomas M. Morse; Shawn R. Lockery

156

The C. elegans Rab Family: Identification, Classification and Toolkit Construction  

PubMed Central

Rab monomeric GTPases regulate specific aspects of vesicle transport in eukaryotes including coat recruitment, uncoating, fission, motility, target selection and fusion. Moreover, individual Rab proteins function at specific sites within the cell, for example the ER, golgi and early endosome. Importantly, the localization and function of individual Rab subfamily members are often conserved underscoring the significant contributions that model organisms such as Caenorhabditis elegans can make towards a better understanding of human disease caused by Rab and vesicle trafficking malfunction. With this in mind, a bioinformatics approach was first taken to identify and classify the complete C. elegans Rab family placing individual Rabs into specific subfamilies based on molecular phylogenetics. For genes that were difficult to classify by sequence similarity alone, we did a comparative analysis of intron position among specific subfamilies from yeast to humans. This two-pronged approach allowed the classification of 30 out of 31 C. elegans Rab proteins identified here including Rab31/Rab50, a likely member of the last eukaryotic common ancestor (LECA). Second, a molecular toolset was created to facilitate research on biological processes that involve Rab proteins. Specifically, we used Gateway-compatible C. elegans ORFeome clones as starting material to create 44 full-length, sequence-verified, dominant-negative (DN) and constitutive active (CA) rab open reading frames (ORFs). Development of this toolset provided independent research projects for students enrolled in a research-based molecular techniques course at California State University, East Bay (CSUEB).

Gallegos, Maria E.; Balakrishnan, Sanjeev; Chandramouli, Priya

2012-01-01

157

Regulatory myosin light-chain genes of Caenorhabditis elegans.  

PubMed Central

We have cloned and analyzed the Caenorhabditis elegans regulatory myosin light-chain genes. C. elegans contains two such genes, which we have designated mlc-1 and mlc-2. The two genes are separated by 2.6 kilobases and are divergently transcribed. We determined the complete nucleotide sequences of both mlc-1 and mlc-2. A single, conservative amino acid substitution distinguishes the sequences of the two proteins. The C. elegans proteins are strongly homologous to regulatory myosin light chains of Drosophila melanogaster and vertebrates and weakly homologous to a superfamily of eucaryotic calcium-binding proteins. Both mlc-1 and mlc-2 encode abundant mRNAs. We mapped the 5' termini of these transcripts by using primer extension sequencing of mRNA templates. mlc-1 mRNAs initiate within conserved hexanucleotides at two different positions, located at -28 and -38 relative to the start of translation. The 5' terminus of mlc-2 mRNA is not encoded in the 4.8-kilobase genomic region upstream of mlc-2. Rather, mlc-2 mRNA contains at its 5' end a short, untranslated leader sequence that is identical to the trans-spliced leader sequence of three C. elegans actin genes. Images

Cummins, C; Anderson, P

1988-01-01

158

Pharmacology of delayed aging and extended lifespan of Caenorhabditis elegans  

Microsoft Academic Search

The identification and analysis of compounds that delay aging and extend lifespan is an important aspect of gerontology research; these studies can test theories of aging, lead to the discovery of endogenous systems that influence aging, and establish the foundation for treatments that might delay normal human aging. Here we review studies using the nematode Caenorhabditis elegans to identify and

James J. Collins; Kimberley Evason; Kerry Kornfeld

2006-01-01

159

Identification of Pseudomonas aeruginosa Phenazines that Kill Caenorhabditis elegans  

PubMed Central

Pathogenic microbes employ a variety of methods to overcome host defenses, including the production and dispersal of molecules that are toxic to their hosts. Pseudomonas aeruginosa, a Gram-negative bacterium, is a pathogen of a diverse variety of hosts including mammals and the nematode Caenorhabditis elegans. In this study, we identify three small molecules in the phenazine class that are produced by P. aeruginosa strain PA14 that are toxic to C. elegans. We demonstrate that 1-hydroxyphenazine, phenazine-1-carboxylic acid, and pyocyanin are capable of killing nematodes in a matter of hours. 1-hydroxyphenazine is toxic over a wide pH range, whereas the toxicities of phenazine-1-carboxylic acid and pyocyanin are pH-dependent at non-overlapping pH ranges. We found that acidification of the growth medium by PA14 activates the toxicity of phenazine-1-carboxylic acid, which is the primary toxic agent towards C. elegans in our assay. Pyocyanin is not toxic under acidic conditions and 1-hydroxyphenazine is produced at concentrations too low to kill C. elegans. These results suggest a role for phenazine-1-carboxylic acid in mammalian pathogenesis because PA14 mutants deficient in phenazine production have been shown to be defective in pathogenesis in mice. More generally, these data demonstrate how diversity within a class of metabolites could affect bacterial toxicity in different environmental niches.

Cezairliyan, Brent; Vinayavekhin, Nawaporn; Grenfell-Lee, Daniel; Yuen, Grace J.; Saghatelian, Alan; Ausubel, Frederick M.

2013-01-01

160

Control of Larval Development by Chemosensory Neurons in Caenorhabditis elegans  

Microsoft Academic Search

Larval development of the nematode Caenorhabditis elegans is controlled by the activities of four classes of chemosensory neurons. The choice between normal development and development into a specialized larval form called a dauer larva is regulated by competing environmental stimuli: food and a dauer pheromone. When the neuron classes ADF, ASG, ASI, and ASJ are killed, animals develop as dauer

Cornelia I. Bargmann; H. Robert Horvitz

1991-01-01

161

A First Version of the Caenorhabditis elegans Promoterome  

PubMed Central

An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such “localizome” maps should provide information on where (in what cells or tissues) and when (at what stage of development or under what conditions) genes are expressed. They should also indicate in what cellular compartments the corresponding proteins are localized. Caenorhabditis elegans is particularly suited for the development of a localizome map since all its 959 adult somatic cells can be visualized by microscopy, and its cell lineage has been completely described. Here we address one of the challenges of C. elegans localizome mapping projects: that of obtaining a genome-wide resource of C. elegans promoters needed to generate transgenic animals expressing localization markers such as the green fluorescent protein (GFP). To ensure high flexibility for future uses, we utilized the newly developed MultiSite Gateway system. We generated and validated “version 1.1” of the Promoterome: a resource of ?6000 C. elegans promoters. These promoters can be transferred easily into various Gateway Destination vectors to drive expression of markers such as GFP, alone (promoter::GFP constructs), or in fusion with protein-encoding open reading frames available in ORFeome resources (promoter::ORF::GFP).

Dupuy, Denis; Li, Qian-Ru; Deplancke, Bart; Boxem, Mike; Hao, Tong; Lamesch, Philippe; Sequerra, Reynaldo; Bosak, Stephanie; Doucette-Stamm, Lynn; Hope, Ian A.; Hill, David E.; Walhout, Albertha J.M.; Vidal, Marc

2004-01-01

162

Putative telomerase catalytic subunits from Giardia lamblia and Caenorhabditis elegans.  

PubMed

Eukaryotic chromosomes end in short nucleotide repeats that are added by the enzyme telomerase. The catalytic subunit of telomerase has been shown to be most closely related in sequence to reverse transcriptases encoded by eukaryotic retrotransposable elements. This raises the question as to whether the telomerase subunit was present in the first eukaryotes or was derived during early eukaryote evolution from the replication machinery of a retrotransposable element. We present the sequence of a putative telomerase catalytic subunit from the diplomonad parasite, Giardia lamblia. The G. lamblia subunit appears to have most of the characteristics of other sequenced telomerases, except that it lacks the conserved telomerase-specific 'T' motif previously identified in other eukaryotic genes. Searching genomic databases with the G. lamblia sequence, we also identified a potential telomerase catalytic subunit from Caenorhabditis elegans. The C. elegans subunit is uncharacteristically short, and lacks several motifs found in all other telomerases. The identification of a G. lamblia telomerase similar to that of most other eukaryotes suggests that telomerase dates back to the earliest extant marker of eukaryotic evolution. The atypical C. elegans telomerase, on the other hand, raises intriguing biochemical questions concerning sub-domains of the telomerase catalytic subunit previously considered indispensable. The enzymatic machinery for telomere formation in C. elegans is likely to differ substantially from that of other eukaryotes. PMID:10876087

Malik, H S; Burke, W D; Eickbush, T H

2000-06-27

163

Material Properties of Caenorhabditis elegans Swimming at Low Reynolds Number  

PubMed Central

Abstract Undulatory locomotion, as seen in the nematode Caenorhabditis elegans, is a common swimming gait of organisms in the low Reynolds number regime, where viscous forces are dominant. Although the nematode's motility is expected to be a strong function of its material properties, measurements remain scarce. Here, the swimming behavior of C. elegans is investigated in experiments and in a simple model. Experiments reveal that nematodes swim in a periodic fashion and generate traveling waves that decay from head to tail. The model is able to capture the experiments' main features and is used to estimate the nematode's Young's modulus E and tissue viscosity ?. For wild-type C. elegans, we find E ? 3.77 kPa and ? ? ?860 Pa·s; values of ? for live C. elegans are negative because the tissue is generating rather than dissipating energy. Results show that material properties are sensitive to changes in muscle functional properties, and are useful quantitative tools with which to more accurately describe new and existing muscle mutants.

Sznitman, J.; Purohit, Prashant K.; Krajacic, P.; Lamitina, T.; Arratia, P.E.

2010-01-01

164

ROS in Aging Caenorhabditis elegans: Damage or Signaling?  

PubMed Central

Many insights into the mechanisms and signaling pathways underlying aging have resulted from research on the nematode Caenorhabditis elegans. In this paper, we discuss the recent findings that emerged using this model organism concerning the role of reactive oxygen species (ROS) in the aging process. The accrual of oxidative stress and damage has been the predominant mechanistic explanation for the process of aging for many years, but reviewing the recent studies in C. elegans calls this theory into question. Thus, it becomes more and more evident that ROS are not merely toxic byproducts of the oxidative metabolism. Rather it seems more likely that tightly controlled concentrations of ROS and fluctuations in redox potential are important mediators of signaling processes. We therefore discuss some theories that explain how redox signaling may be involved in aging and provide some examples of ROS functions and signaling in C. elegans metabolism. To understand the role of ROS and the redox status in physiology, stress response, development, and aging, there is a rising need for accurate and reversible in vivo detection. Therefore, we comment on some methods of ROS and redox detection with emphasis on the implementation of genetically encoded biosensors in C. elegans.

Back, Patricia; Braeckman, Bart P.; Matthijssens, Filip

2012-01-01

165

Targeted gene alteration in Caenorhabditis elegans by gene conversion  

Microsoft Academic Search

Now that some genomes have been completely sequenced, the ability to direct specific mutations into genomes is particularly desirable. Here we present a method to create mutations in the Caenorhabditis elegans genome efficiently through transgene-directed, transposon-mediated gene conversion. Engineered deletions targeted into two genes show that the frequency of obtaining the desired mutation was higher using this approach than using

Peter L Barrett; John T Fleming; Verena Göbel

2004-01-01

166

40 CFR 80.170 - Volumetric additive reconciliation (VAR), equipment calibration, and recordkeeping requirements.  

Code of Federal Regulations, 2013 CFR

... 2013-07-01 false Volumetric additive reconciliation (VAR), equipment calibration...CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Detergent Gasoline § 80.170 Volumetric additive reconciliation (VAR), equipment...

2013-07-01

167

Isolation of Cryptococcus neoformans var. neoformans from canine otitis.  

PubMed

Cryptococcus neoformans was demonstrated in the clinical material of a 15-year-old male dog with a history of chronic otitis externa by employing Helianthus annuus seed agar as a selective medium. The examination of the isolate for sexual compatibility on modified Helianthus annuus seed medium revealed that it belonged to Filobasidiella neoformans var. neoformans 'alpha' mating type. In the authors' view, this appears to be the first report of isolation of Cr. neoformans var. neoformans from diseased ear of a dog. PMID:2093842

Pal, M; Ono, K; Goitsuka, R; Hasegawa, A

1990-01-01

168

varDB: common ground for a shifting landscape  

PubMed Central

Antigenic variation is a phylogenetically widespread phenomenon thought to lead to survival benefits for the pathogen. Although governed by genetic mechanisms, antigenic variation is ultimately manifested in variant proteins. The varDB database is an attempt to gain an overview of common structures and functions of variant proteins related to enhanced survival. varDB provides a wealth of sequence data and several tools to facilitate their analysis, but current limitations preclude achievement of its full promise. A critique of this database and how it could serve the scientific community is provided here.

Allred, David R.; Barbet, Anthony F.; Barry, J. David; Deitsch, Kirk W.

2013-01-01

169

BZ UMa and Var Her 04: Orphan TOADS  

NASA Astrophysics Data System (ADS)

Both BZ UMa and Var Her 04 are cataclysmic variable stars without a home. Neither fit easily into current classification systems so may extend the population distribution of two unique CV types: UGWZ dwarf novae and intermediate polars. New outburst photometry and archival X-Ray data shed some new light on BZ UMa's high energy state and new spectral and IR observations from Spitzer of dust around the newly discovered cataclysmic variable Var Her 04 may help find it a home as well.

Price, A.; Howell, S.

2005-05-01

170

Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans  

PubMed Central

Background Caenorhabditis elegans is an important model for the study of DNA damage and repair related processes such as aging, neurodegeneration, and carcinogenesis. However, DNA repair is poorly characterized in this organism. We adapted a quantitative polymerase chain reaction assay to characterize repair of DNA damage induced by ultraviolet type C (UVC) radiation in C. elegans, and then tested whether DNA repair rates were affected by age in adults. Results UVC radiation induced lesions in young adult C. elegans, with a slope of 0.4 to 0.5 lesions per 10 kilobases of DNA per 100 J/m2, in both nuclear and mitochondrial targets. L1 and dauer larvae were more than fivefold more sensitive to lesion formation than were young adults. Nuclear repair kinetics in a well expressed nuclear gene were biphasic in nongravid adult nematodes: a faster, first order (half-life about 16 hours) phase lasting approximately 24 hours and resulting in removal of about 60% of the photoproducts was followed by a much slower phase. Repair in ten nuclear DNA regions was 15% and 50% higher in more actively transcribed regions in young and aging adults, respectively. Finally, repair was reduced by 30% to 50% in each of the ten nuclear regions in aging adults. However, this decrease in repair could not be explained by a reduction in expression of nucleotide excision repair genes, and we present a plausible mechanism, based on gene expression data, to account for this decrease. Conclusion Repair of UVC-induced DNA damage in C. elegans is similar kinetically and genetically to repair in humans. Furthermore, this important repair process slows significantly in aging C. elegans, the first whole organism in which this question has been addressed.

Meyer, Joel N; Boyd, Windy A; Azzam, Gregory A; Haugen, Astrid C; Freedman, Jonathan H; Van Houten, Bennett

2007-01-01

171

Recombinational Landscape and Population Genomics of Caenorhabditis elegans  

PubMed Central

Recombination rate and linkage disequilibrium, the latter a function of population genomic processes, are the critical parameters for mapping by linkage and association, and their patterns in Caenorhabditis elegans are poorly understood. We performed high-density SNP genotyping on a large panel of recombinant inbred advanced intercross lines (RIAILs) of C. elegans to characterize the landscape of recombination and, on a panel of wild strains, to characterize population genomic patterns. We confirmed that C. elegans autosomes exhibit discrete domains of nearly constant recombination rate, and we show, for the first time, that the pattern holds for the X chromosome as well. The terminal domains of each chromosome, spanning about 7% of the genome, exhibit effectively no recombination. The RIAILs exhibit a 5.3-fold expansion of the genetic map. With median marker spacing of 61 kb, they are a powerful resource for mapping quantitative trait loci in C. elegans. Among 125 wild isolates, we identified only 41 distinct haplotypes. The patterns of genotypic similarity suggest that some presumed wild strains are laboratory contaminants. The Hawaiian strain, CB4856, exhibits genetic isolation from the remainder of the global population, whose members exhibit ample evidence of intercrossing and recombining. The population effective recombination rate, estimated from the pattern of linkage disequilibrium, is correlated with the estimated meiotic recombination rate, but its magnitude implies that the effective rate of outcrossing is extremely low, corroborating reports of selection against recombinant genotypes. Despite the low population, effective recombination rate and extensive linkage disequilibrium among chromosomes, which are techniques that account for background levels of genomic similarity, permit association mapping in wild C. elegans strains.

Rockman, Matthew V.; Kruglyak, Leonid

2009-01-01

172

Mitochondrial stress extends lifespan in C. elegans through neuronal hormesis.  

PubMed

Progressive neuronal deterioration accompanied by sensory functions decline is typically observed during aging. On the other hand, structural or functional alterations of specific sensory neurons extend lifespan in the nematode Caenorhabditis elegans. Hormesis is a phenomenon by which the body benefits from moderate stress of various kinds which at high doses are harmful. Several studies indicate that different stressors can hormetically extend lifespan in C. elegans and suggest that hormetic effects could be exploited as a strategy to slow down aging and the development of age-associated (neuronal) diseases in humans. Mitochondria play a central role in the aging process and hormetic-like bimodal dose-response effects on C. elegans lifespan have been observed following different levels of mitochondrial stress. Here we tested the hypothesis that mitochondrial stress may hormetically extend C. elegans lifespan through subtle neuronal alterations. In support of our hypothesis we find that life-lengthening dose of mitochondrial stress reduces the functionality of a subset of ciliated sensory neurons in young animals. Notably, the same pro-longevity mitochondrial treatments rescue the sensory deficits in old animals. We also show that mitochondrial stress extends C. elegans lifespan acting in part through genes required for the functionality of those neurons. To our knowledge this is the first study describing a direct causal connection between sensory neuron dysfunction and extended longevity following mitochondrial stress. Our work supports the potential anti-aging effect of neuronal hormesis and open interesting possibility for the development of therapeutic strategy for age-associated neurodegenerative disorders. PMID:24709340

Maglioni, Silvia; Schiavi, Alfonso; Runci, Alessandra; Shaik, Anjumara; Ventura, Natascia

2014-08-01

173

A gene expression fingerprint of C. elegans embryonic motor neurons  

PubMed Central

Background Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model system in which to correlate gene expression with neuron identity. The UNC-4 transcription factor is expressed in thirteen embryonic motor neurons where it specifies axonal morphology and synaptic function. These cells can be marked with an unc-4::GFP reporter transgene. Here we describe a powerful strategy, Micro-Array Profiling of C. elegans cells (MAPCeL), and confirm that this approach provides a comprehensive gene expression profile of unc-4::GFP motor neurons in vivo. Results Fluorescence Activated Cell Sorting (FACS) was used to isolate unc-4::GFP neurons from primary cultures of C. elegans embryonic cells. Microarray experiments detected 6,217 unique transcripts of which ~1,000 are enriched in unc-4::GFP neurons relative to the average nematode embryonic cell. The reliability of these data was validated by the detection of known cell-specific transcripts and by expression in UNC-4 motor neurons of GFP reporters derived from the enriched data set. In addition to genes involved in neurotransmitter packaging and release, the microarray data include transcripts for receptors to a remarkably wide variety of signaling molecules. The added presence of a robust array of G-protein pathway components is indicative of complex and highly integrated mechanisms for modulating motor neuron activity. Over half of the enriched genes (537) have human homologs, a finding that could reflect substantial overlap with the gene expression repertoire of mammalian motor neurons. Conclusion We have described a microarray-based method, MAPCeL, for profiling gene expression in specific C. elegans motor neurons and provide evidence that this approach can reveal candidate genes for key roles in the differentiation and function of these cells. These methods can now be applied to generate a gene expression map of the C. elegans nervous system.

Fox, Rebecca M; Von Stetina, Stephen E; Barlow, Susan J; Shaffer, Christian; Olszewski, Kellen L; Moore, Jason H; Dupuy, Denis; Vidal, Marc; Miller, David M

2005-01-01

174

The VarS/VarA two-component system modulates the activity of the Vibrio cholerae quorum-sensing transcriptional regulator HapR  

PubMed Central

The human pathogen Vibrio cholerae uses quorum sensing to regulate the expression of a number of phenotypes, including virulence factor production, in response to changes in cell density. It produces small molecules called autoinducers that increase in concentration as cell density increases, and these autoinducers bind to membrane sensors once they reach a certain threshold. This binding leads to signalling through a downstream phosphorelay pathway to alter the expression of the transcriptional regulator HapR. Previously, it was shown that the VarS/VarA two-component system acts on a component of the phosphorelay pathway upstream of HapR to regulate HapR expression levels. Here, we show that in addition to this mechanism of regulation, VarS and VarA also indirectly modulate HapR protein activity. This modulation is mediated by the small RNA CsrB but is independent of the known quorum-sensing system that links the autoinducers to HapR. Thus, the VarS/VarA two-component system intersects with the quorum-sensing network at two levels. In both cases, the effect of VarS and VarA on quorum sensing is dependent on the Csr small RNAs, which regulate carbon metabolism, suggesting that V. cholerae may integrate nutrient status and cell density sensory inputs to tailor its gene expression profile more precisely to surrounding conditions.

Tsou, Amy M.; Liu, Zhi; Cai, Tao

2011-01-01

175

A Decline in p38 MAPK Signaling Underlies Immunosenescence in Caenorhabditis elegans  

PubMed Central

The decline in immune function with aging, known as immunosenescence, has been implicated in evolutionarily diverse species, but the underlying molecular mechanisms are not understood. During aging in Caenorhabditis elegans, intestinal tissue deterioration and the increased intestinal proliferation of bacteria are observed, but how innate immunity changes during C. elegans aging has not been defined. Here we show that C. elegans exhibits increased susceptibility to bacterial infection with age, and we establish that aging is associated with a decline in the activity of the conserved PMK-1 p38 mitogen-activated protein kinase pathway, which regulates innate immunity in C. elegans. Our data define the phenomenon of innate immunosenescence in C. elegans in terms of the age-dependent dynamics of the PMK-1 innate immune signaling pathway, and they suggest that a cycle of intestinal tissue aging, immunosenescence, and bacterial proliferation leads to death in aging C. elegans.

Youngman, Matthew J.; Rogers, Zoe N.; Kim, Dennis H.

2011-01-01

176

Global Regulation of Hox Gene Expression in C. elegans by a SAM Domain Protein  

Microsoft Academic Search

Polycomb group (PcG)-mediated repression of C. elegans Hox genes has not been demonstrated, and genes homologous to components of one of the PcG complexes (PRC1) have not been identified in the C. elegans genome. We find that a mechanism of general Hox gene repression exists in C. elegans, carried out in part by SOP-2, a protein related to, but not

Hong Zhang; Ricardo B. R. Azevedo; Robyn Lints; Christina Doyle; Yingqi Teng; Daniel Haber; Scott W. Emmons

2003-01-01

177

The causes of Spanish unemployment: A structural VAR approach  

Microsoft Academic Search

In this paper, we review the main causes of Spanish unemployment and weight them by estimating a simple macroeconomic model using the structural VAR methodology. By using this methodology we associate different causes of unemployment with shocks of different nature which have long-lasting effects due to full hysteresis. We claim that such an extreme assumption on ‘state dependency’ is reasonable,

Juan José Dolado; Juan F. Jimeno

1997-01-01

178

Common cyclical features analysis in VAR models with cointegration  

Microsoft Academic Search

The paper considers n-dimensional VAR models for variables exhibiting cointegration and common cyclical features. Two specific reduced rank vector error correction models are discussed. In one, named the “strong form” and denoted by SF, the collection of all coefficient matrices of a VECM has rank less than n, in the other, named the “weak form” and denoted by WF, the

Alain Hecq; Franz C. Palm; Jean-Pierre Urbain

2006-01-01

179

Brassica oleracea var. Italica: A Nutritional Supplement with Antimicrobial Potential  

Microsoft Academic Search

Two compounds were isolated from the ethyl acetate extract of Brassica oleracea var. Italica (Brassicaceae), which were obtained from successive extraction of broccoli florets. They were nitrogenous compounds, identified by spectroscopic analysis as uridine and uridine 9-acetate. Ethyl acetate and chloroform extracts were found to be effective against Bacillus cereus and Bacillus subtilis, respectively, gram-positive bacteria. Ethyl acetate and ethanol

Fatma Hashem; Hemaia Motawea; Abd El-Rahman El-Shabrawi; Kamel Shaker; Samar El-Sherbini

2012-01-01

180

Major anthocyanin from ripe berries of Cleistocalyx nervosum var. paniala  

Microsoft Academic Search

Cleistocalyx nervosum var. paniala (known as Ma kiang) is found growing in scatter locations in some villages of the northern provinces of Thailand. The rich purplish red color of Ma kiang is characterized by an anthocyanin profile. It is now popular for functional health food, cosmetic ingredients and health drinks. The aim of this study was to identify the anthocyanins

Chalerm Jansom; Sutatip Bhamarapravati; Arunporn Itharat

181

Micropropagation of Mexican redbud, Cercis canadensis var. mexicana  

Microsoft Academic Search

Mexican redbud (Cercis canadensis var. mexicana) shoot cultures were initiated from explants taken from both mature and juvenile stock plants. Culture conditions affecting shoot growth and proliferation and rooting of three clones were investigated. Shoot growth was best on media supplemented with 0.25% activated charcoal and solidified with 0.2% Gelrite. Four commercially available salt formulations (Anderson's rhododendron medium, WPM, MS,

Wayne A. Mackay; Jimmy L. Tipton; Gary A. Thompson

1995-01-01

182

Three Galactose inducible promoters for use in C. neoformans var. grubii  

PubMed Central

Cryptococcus neoformans is the causative agent of cryptococcal meningoencephalitis, most frequently occurring in immunocompromised individuals. There are three varieties of C. neoformans, var. grubii, var. neoformans, and var. gatti. Worldwide var. grubii is the most prevalent clinical isolate. However, few tools for the study of essential genes in var. grubii exist. Here we describe three endogenous inducible promoters for use in the study of this important opportunistic pathogen. We identified eight potential homologs of S. cerevisiae galactose genes in var. grubii. We found that GAL1, GAL7, and UGE2 were regulated by glucose and galactose and can be used successfully during mating. Our analysis indicated these promoters should prove to be excellent tools for analysis of genes in var. grubii.

Ruff, Jack A.; Lodge, Jennifer K.; Baker, Lorina G.

2009-01-01

183

Three galactose inducible promoters for use in C. neoformans var. grubii.  

PubMed

Cryptococcus neoformans is the causative agent of cryptococcal meningoencephalitis, most frequently occurring in immunocompromised individuals. There are three varieties of C. neoformans, var. grubii, var. neoformans, and var. gatti. Worldwide var. grubii is the most prevalent clinical isolate. However, few tools for the study of essential genes in var. grubii exist. Here we describe three endogenous inducible promoters for use in the study of this important opportunistic pathogen. We identified eight potential homologs of S. cerevisiae galactose genes in var. grubii. We found that GAL1, GAL7, and UGE2 were regulated by glucose and galactose and can be used successfully during mating. Our analysis indicated these promoters should prove to be excellent tools for analysis of genes in var. grubii. PMID:18952189

Ruff, Jack A; Lodge, Jennifer K; Baker, Lorina G

2009-01-01

184

Integrated control of protein degradation in C. elegans muscle.  

PubMed

Protein degradation is a fundamental cellular process, the genomic control of which is incompletely understood. The advent of transgene-coded reporter proteins has enabled the development of C. elegans into a model for studying this problem. The regulation of muscle protein degradation is surprisingly complex, integrating multiple signals from hypodermis, intestine, neurons and muscle itself. Within the muscle, degradation is executed by separately regulated autophagy-lysosomal, ubiquitin-proteasome and calpain-mediated systems. The signal-transduction mechanisms, in some instances, involve modules previously identified for their roles in developmental processes, repurposed in terminally differentiated muscle to regulate the activities of pre-formed proteins. Here we review the genes, and mechanisms, which appear to coordinately control protein degradation within C. elegans muscle. We also consider these mechanisms in the context of development, physiology, pathophysiology and disease models. PMID:23457662

Lehmann, Susann; Shephard, Freya; Jacobson, Lewis A; Szewczyk, Nathaniel J

2012-07-01

185

C. elegans epigenetic regulation in development and aging  

PubMed Central

The precise developmental map of the Caenorhabditis elegans cell lineage, as well as a complete genome sequence and feasibility of genetic manipulation make this nematode species highly attractive to study the role of epigenetics during development. Genetic dissection of phenotypical traits, such as formation of egg-laying organs or starvation-resistant dauer larvae, has illustrated how chromatin modifiers may regulate specific cell-fate decisions and behavioral programs. Moreover, the transparent body of C. elegans facilitates non-invasive microscopy to study tissue-specific accumulation of heterochromatin at the nuclear periphery. We also review here recent findings on how small RNA molecules contribute to epigenetic control of gene expression that can be propagated for several generations and eventually determine longevity.

Gonzalez-Aguilera, Cristina; Palladino, Francesca

2014-01-01

186

Variable Pathogenicity Determines Individual Lifespan in Caenorhabditis elegans  

PubMed Central

A common property of aging in all animals is that chronologically and genetically identical individuals age at different rates. To unveil mechanisms that influence aging variability, we identified markers of remaining lifespan for Caenorhabditis elegans. In transgenic lines, we expressed fluorescent reporter constructs from promoters of C. elegans genes whose expression change with age. The expression levels of aging markers in individual worms from a young synchronous population correlated with their remaining lifespan. We identified eight aging markers, with the superoxide dismutase gene sod-3 expression being the best single predictor of remaining lifespan. Correlation with remaining lifespan became stronger if expression from two aging markers was monitored simultaneously, accounting for up to 49% of the variation in individual lifespan. Visualizing the physiological age of chronologically-identical individuals allowed us to show that a major source of lifespan variability is different pathogenicity from individual to individual and that the mechanism involves variable activation of the insulin-signaling pathway.

Sanchez-Blanco, Adolfo; Kim, Stuart K.

2011-01-01

187

Genome-Wide RNAi Longevity Screens in Caenorhabditis elegans  

PubMed Central

Progress in aging research has identified genetic and environmental factors that regulate longevity across species. The nematode worm Caenorhabditis elegans is a genetically tractable model system that has been widely used to investigate the molecular mechanisms of aging, and the development of RNA interference (RNAi) technology has provided a powerful tool for performing large-scale genetic screens in this organism. Genome-wide screens have identified hundreds of genes that influence lifespan, many of which fall into distinct functional classes and pathways. The purpose of this review is to summarize the results of large-scale RNAi longevity screens in C. elegans, and to provide an in-depth comparison and analysis of their methodology and most significant findings.

Yanos, Melana E; Bennett, Christopher F; Kaeberlein, Matt

2012-01-01

188

Aging in the nervous system of Caenorhabditis elegans  

PubMed Central

It has recently been described that aging in C. elegans is accompanied by the progressive development of morphological changes in the nervous system. These include novel outgrowths from the cell body or axonal process, as well as blebbing and beading along the length of the axon. The formation of these structures is regulated by numerous molecular players including members of the well-conserved insulin/insulin growth factor-like (IGF)-1 signaling and mitogen-activated protein (MAP) kinase pathways. This review summarizes the recent literature on neuronal aging in C. elegans, including our own findings, which indicate a role for protein with tau-like repeats (PTL-1), the homolog of mammalian tau and MAP2/4, in maintaining neuronal integrity during aging.

Chew, Yee Lian; Fan, Xiaochen; Gotz, Jurgen; Nicholas, Hannah R.

2013-01-01

189

Sensory regulation of C. elegans male mate-searching behaviour  

PubMed Central

Summary How do animals integrate internal drives and external environmental cues to coordinate behaviours? We address this question studying mate-searching behaviour in C. elegans. C. elgans males explore their environment in search of mates (hermaphrodites) and will leave food if mating partners are absent. However, when mates and food coincide, male exploratory behaviour is suppressed and males are retained on the food source. We show that the drive to explore is stimulated by male specific neurons in the tail, the ray neurons. Periodic contact with the hermaphrodite detected through ray neurons changes the male’s behaviour during periods of no contact and prevents the male from leaving the food source. The hermaphrodite signal is conveyed by male-specific interneurons that are post-synaptic to the rays and that send processes to the major integrative center in the head. This study identifies key parts of the neural circuit that regulates a sexual appetitive behaviour in C. elegans.

Barrios, Arantza; Nurrish, Stephen; Emmons, Scott W.

2009-01-01

190

C. elegans as a model for membrane traffic.  

PubMed

The counterbalancing action of the endocytosis and secretory pathways maintains a dynamic equilibrium that regulates the composition of the plasma membrane, allowing it to maintain homeostasis and to change rapidly in response to alterations in the extracellular environment and/or intracellular metabolism. These pathways are intimately integrated with intercellular signaling systems and play critical roles in all cells. Studies in Caenorhabditis elegans have revealed diverse roles of membrane trafficking in physiology and development and have also provided molecular insight into the fundamental mechanisms that direct cargo sorting, vesicle budding, and membrane fisson and fusion. In this review, we summarize progress in understanding membrane trafficking mechanisms derived from work in C. elegans, focusing mainly on work done in non-neuronal cell-types, especially the germline, early embryo, coelomocytes, and intestine. PMID:24778088

Sato, Ken; Norris, Anne; Sato, Miyuki; Grant, Barth D

2014-01-01

191

Alteration in cellular acetylcholine influences dauer formation in Caenorhabditis elegans.  

PubMed

Altered acetylcholine (Ach) homeostasis is associated with loss of viability in flies, developmental defects in mice, and cognitive deficits in human. Here, we assessed the importance of Ach in Caenorhabditis elegans development, focusing on the role of Ach during dauer formation. We found that dauer formation was disturbed in choline acetyltransferase (cha-1) and acetylcholinesterase (ace) mutants defective in Ach biosynthesis and degradation, respectively. When examined the potential role of G-proteins in dauer formation, goa-1 and egl-30 mutant worms, expressing mutated versions of mammalian G(o) and G(q) homolog, respectively, showed some abnormalities in dauer formation. Using quantitative mass spectrometry, we also found that dauer larvae had lower Ach content than did reproductively grown larvae. In addition, a proteomic analysis of acetylcholinesterase mutant worms, which have excessive levels of Ach, showed differential expression of metabolic genes. Collectively, these results indicate that alterations in Ach release may influence dauer formation in C. elegans. PMID:24219868

Lee, Jeeyong; Kim, Kwang-Youl; Paik, Young-Ki

2014-02-01

192

C. elegans epigenetic regulation in development and aging.  

PubMed

The precise developmental map of the Caenorhabditis elegans cell lineage, as well as a complete genome sequence and feasibility of genetic manipulation make this nematode species highly attractive to study the role of epigenetics during development. Genetic dissection of phenotypical traits, such as formation of egg-laying organs or starvation-resistant dauer larvae, has illustrated how chromatin modifiers may regulate specific cell-fate decisions and behavioral programs. Moreover, the transparent body of C. elegans facilitates non-invasive microscopy to study tissue-specific accumulation of heterochromatin at the nuclear periphery. We also review here recent findings on how small RNA molecules contribute to epigenetic control of gene expression that can be propagated for several generations and eventually determine longevity. PMID:24326118

González-Aguilera, Cristina; Palladino, Francesca; Askjaer, Peter

2014-05-01

193

C. elegans as a model for membrane traffic  

PubMed Central

The counterbalancing action of the endocytosis and secretory pathways maintains a dynamic equilibrium that regulates the composition of the plasma membrane, allowing it to maintain homeostasis and to change rapidly in response to changes in the extracellular environment and/or intracellular metabolism. These pathways are intimately integrated with intercellular signaling systems and play critical roles in all cells. Studies in Caenorhabditis elegans have revealed diverse roles of membrane trafficking in physiology and development and have also provided molecular insight into the fundamental mechanisms that direct cargo sorting, vesicle budding, and membrane fisson and fusion. In this review, we summarize progress in understanding membrane trafficking mechanisms derived from work in C. elegans, focusing mainly on work done in non-neuronal cell-types, especially the germline, early embryo, coelomocytes, and intestine.

Sato, Ken; Norris, Anne; Sato, Miyuki; Grant, Barth D.

2014-01-01

194

SKIP is an indispensable factor for Caenorhabditis elegans development  

PubMed Central

SKI-binding protein (SKIP) is a transcription cofactor present in all eukaryotes. Here we show that SKIP is a unique protein that is required for Caenorhabditis elegans viability and development. Expression of CeSKIP(skp-1) assayed by RT-PCR and by GFP fluorescence in transgenic lines starts in embryos and continues to adulthood. Loss of CeSKIP activity by RNA-mediated inhibition results in early embryonic arrest similar to that seen following inhibition of RNA polymerase II. RNA polymerase II phosphorylation appears normal early in CeSKIP RNA-mediated inhibition treated embryos although the expression of several embryonic GFP reporter genes is severely restricted or absent. Our data suggest that CeSKIP is an essential component of many RNA polymerase II transcription complexes and is indispensable for C. elegans development.

Kostrouchova, Marta; Housa, Daniel; Kostrouch, Zdenek; Saudek, Vladimir; Rall, Joseph Edward

2002-01-01

195

Transcriptional Regulation of Gene Expression in C. elegans  

PubMed Central

Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single cell and minute time scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated protein and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.

Reinke, Valerie; Krause, Michael; Okkema, Peter

2013-01-01

196

Endogenous RNAi and adaptation to environment in C. elegans  

PubMed Central

The contributions of short RNAs to the control of repetitive elements are well documented in animals and plants. Here, the role of endogenous RNAi and AF10 homolog ZFP-1 in the adaptation of C. elegans to the environment is discussed. First, modulation of insulin signaling through regulation of transcription of the PDK-1 kinase (Mansisidor et al., PLoS Genetics, 2011) is reviewed. Second, an siRNA-based natural selection model is proposed in which variation in endogenous siRNA pools between individuals is subject to natural selection similarly to DNA-based genetic variation. The value of C. elegans for the research of siRNA-based epigenetic variation and adaptation is highlighted.

Grishok, Alla

2012-01-01

197

Biotransformation of Malachite Green by the Fungus Cunninghamella elegans  

PubMed Central

The filamentous fungus Cunninghamella elegans ATCC 36112 metabolized the triphenylmethane dye malachite green with a first-order rate constant of 0.029 ?mol h?1 (mg of cells)?1. Malachite green was enzymatically reduced to leucomalachite green and also converted to N-demethylated and N-oxidized metabolites, including primary and secondary arylamines. Inhibition studies suggested that the cytochrome P450 system mediated both the reduction and the N-demethylation reactions.

Cha, Chang-Jun; Doerge, Daniel R.; Cerniglia, Carl E.

2001-01-01

198

A C. elegans model to study human metabolic regulation.  

PubMed

Lipid metabolic disorder is a critical risk factor for metabolic syndrome, triggering debilitating diseases like obesity and diabetes. Both obesity and diabetes are the epicenter of important medical issues, representing a major international public health threat. Accumulation of fat in adipose tissue, muscles and liver and/or the defects in their ability to metabolize fatty acids, results in insulin resistance. This triggers an early pathogenesis of type 2 diabetes (T2D). In mammals, lipid metabolism involves several organs, including the brain, adipose tissue, muscles, liver, and gut. These organs are part of complex homeostatic system and communicate through hormones, neurons and metabolites. Our study dissects the importance of mammalian Krüppel-like factors in over all energy homeostasis. Factors controlling energy metabolism are conserved between mammals and Caenorhabditis elegans providing a new and powerful strategy to delineate the molecular pathways that lead to metabolic disorder. The C. elegans intestine is our model system where genetics, molecular biology, and cell biology are used to identify and understand genes required in fat metabolism. Thus far, we have found an important role of C. elegans KLF in FA biosynthesis, mitochondrial proliferation, lipid secretion, and ?-oxidation. The mechanism by which KLF controls these events in lipid metabolism is unknown. We have recently observed that C. elegans KLF-3 selectively acts on insulin components to regulate insulin pathway activity. There are many factors that control energy homeostasis and defects in this control system are implicated in the pathogenesis of human obesity and diabetes. In this review we are discussing a role of KLF in human metabolic regulation. PMID:23557393

Hashmi, Sarwar; Wang, Yi; Parhar, Ranjit S; Collison, Kate S; Conca, Walter; Al-Mohanna, Futwan; Gaugler, Randy

2013-01-01

199

Caenorhabditis elegans Neuromuscular Junction: GABA Receptors and Ivermectin Action  

PubMed Central

The prevalence of human and animal helminth infections remains staggeringly high, thus urging the need for concerted efforts towards this area of research. GABA receptors, encoded by the unc-49 gene, mediate body muscle inhibition in Caenorhabditis elegans and parasitic nematodes and are targets of anthelmintic drugs. Thus, the characterization of nematode GABA receptors provides a foundation for rational anti-parasitic drug design. We therefore explored UNC-49 channels from C. elegans muscle cultured cells of the first larval stage at the electrophysiological and behavioral levels. Whole-cell recordings reveal that GABA, muscimol and the anthelmintic piperazine elicit macroscopic currents from UNC-49 receptors that decay in their sustained presence, indicating full desensitization. Single-channel recordings show that all drugs elicit openings of ?2.5 pA (+100 mV), which appear either as brief isolated events or in short bursts. The comparison of the lowest concentration required for detectable channel opening, the frequency of openings and the amplitude of macroscopic currents suggest that piperazine is the least efficacious of the three drugs. Macroscopic and single-channel GABA-activated currents are profoundly and apparently irreversibly inhibited by ivermectin. To gain further insight into ivermectin action at C. elegans muscle, we analyzed its effect on single-channel activity of the levamisol-sensitive nicotinic receptor (L-AChR), the excitatory receptor involved in neuromuscular transmission. Ivermectin produces a profound inhibition of the frequency of channel opening without significant changes in channel properties. By revealing that ivermectin inhibits C. elegans muscle GABA and L-AChR receptors, our study adds two receptors to the already known ivermectin targets, thus contributing to the elucidation of its pleiotropic effects. Behavioral assays in worms show that ivermectin potentiates piperazine-induced paralysis, thus suggesting that their combination is a good strategy to overcome the increasing resistance of parasites, an issue of global concern for human and animal health.

Hernando, Guillermina; Bouzat, Cecilia

2014-01-01

200

Genetic Regulation of Unsaturated Fatty Acid Composition in C. elegans  

Microsoft Academic Search

Delta-9 desaturases, also known as stearoyl-CoA desaturases, are lipogenic enzymes responsible for the generation of vital components of membranes and energy storage molecules. We have identified a novel nuclear hormone receptor, NHR-80, that regulates delta-9 desaturase gene expression in Caenorhabditis elegans. Here we describe fatty acid compositions, lifespans, and gene expression studies of strains carrying mutations in nhr-80 and in

Trisha J Brock; John Browse; Jennifer L Watts

2006-01-01

201

RNAi Pathway in C. elegans : The Argonautes and Collaborators  

Microsoft Academic Search

Since Dr. Sidney Brenner first used it as an animal model system, the round worm Caenorhabditis elegans has significantly contributed to our understanding of important biological processes. Among them, the discovery in the 1990s\\u000a of new gene silencing pathways orchestrated by tiny non-coding RNAs created a new field of research in biology. In this review,\\u000a we will discuss the key

Marie-Eve L. Boisvert; Martin J. Simard

202

Genetic Interactions Affecting Touch Sensitivity in Caenorhabditis elegans  

Microsoft Academic Search

At least 13 genes (mec-1, mec-2, mec-4-10, mec-12, mec-14, mec-15, and mec-18) are needed for the response to gentle touch by 6 touch receptor neurons in the nematode Caenorhabditis elegans. Several, otherwise recessive alleles of some of these genes act as dominant enhancer mutations of temperature-sensitive alleles of mec-4, mec-5, mec-6, mec-12, and mec-15. Screens for additional dominant enhancers of

Guoqiang Gu; Guy A. Caldwell; Martin Chalfie

1996-01-01

203

Gene interactions affecting mechanosensory transduction in Caenorhabditis elegans  

Microsoft Academic Search

GENETIC screening has identified a group ofmec (mechanosensory) genes that are required for the function of a set of six touch-receptor neurons in the nematode Caenorhabditis elegans 1,2. Such genes potentially encode components of the mechanosensory apparatus. We have cloned one of these genes, mec-10, which is a member of the degenerin gene family (genes such as mec-4 and deg-1

Mingxia Huang; Martin Chalfie

1994-01-01

204

Fate of the Nuclear Lamina during Caenorhabditis elegans Apoptosis  

Microsoft Academic Search

Invertebrates and in Drosophila, lamins and lamin-associated proteins are primary targets for cleavage by caspases. Eliminating mammalian lamins causes apoptosis, whereas expressing mutant lamins that cannot be cleaved by caspase-6 delay apoptosis. Caenorhabditis elegans has a single lamin protein, Ce-lamin, and a caspase, CED-3, that is responsible for most if not all somatic apoptosis. In this study we show that

Yonatan B. Tzur; Bradley M. Hersh; H. Robert Horvitz; Yosef Gruenbaum

2002-01-01

205

A mutational analysis of Caenorhabditis elegans in space.  

PubMed

The International Caenorhabditis elegans Experiment First Flight (ICE-First) was a project using C. elegans as a model organism to study the biological effects of short duration spaceflight (11 days in the International Space Station). As a member of the ICE-First research team, our group focused on the mutational effects of spaceflight. Several approaches were taken to measure mutational changes that occurred during the spaceflight including measurement of the integrity of poly-G/poly-C tracts, determination of the mutation frequency in the unc-22 gene, analysis of lethal mutations captured by the genetic balancer eT1(III;V), and identification of alterations in telomere length. By comparing the efficiency, sensitivity, and convenience of these methods, we deduced that the eT1 balancer system is well-suited for capturing, maintaining and recovering mutational events that occur over several generations during spaceflight. In the course of this experiment, we have extended the usefulness of the eT1 balancer system by identifying the physical breakpoints of the eT1 translocation and have developed a PCR assay to follow the eT1 chromosomes. C. elegans animals were grown in a defined liquid media during the spaceflight. This is the first analysis of genetic changes in C. elegans grown in the defined media. Although no significant difference in mutation rate was detected between spaceflight and control samples, which is not surprising given the short duration of the spaceflight, we demonstrate here the utility of worms as an integrating biological dosimeter for spaceflight. PMID:16765996

Zhao, Yang; Lai, Kenneth; Cheung, Iris; Youds, Jillian; Tarailo, Maja; Tarailo, Sanja; Rose, Ann

2006-10-10

206

A C. elegans model to study human metabolic regulation  

PubMed Central

Lipid metabolic disorder is a critical risk factor for metabolic syndrome, triggering debilitating diseases like obesity and diabetes. Both obesity and diabetes are the epicenter of important medical issues, representing a major international public health threat. Accumulation of fat in adipose tissue, muscles and liver and/or the defects in their ability to metabolize fatty acids, results in insulin resistance. This triggers an early pathogenesis of type 2 diabetes (T2D). In mammals, lipid metabolism involves several organs, including the brain, adipose tissue, muscles, liver, and gut. These organs are part of complex homeostatic system and communicate through hormones, neurons and metabolites. Our study dissects the importance of mammalian Krüppel-like factors in over all energy homeostasis. Factors controlling energy metabolism are conserved between mammals and Caenorhabditis elegans providing a new and powerful strategy to delineate the molecular pathways that lead to metabolic disorder. The C. elegans intestine is our model system where genetics, molecular biology, and cell biology are used to identify and understand genes required in fat metabolism. Thus far, we have found an important role of C. elegans KLF in FA biosynthesis, mitochondrial proliferation, lipid secretion, and ?-oxidation. The mechanism by which KLF controls these events in lipid metabolism is unknown. We have recently observed that C. elegans KLF-3 selectively acts on insulin components to regulate insulin pathway activity. There are many factors that control energy homeostasis and defects in this control system are implicated in the pathogenesis of human obesity and diabetes. In this review we are discussing a role of KLF in human metabolic regulation.

2013-01-01

207

Calcium signaling surrounding fertilization in the nematode Caenorhabditis elegans.  

PubMed

Calcium plays a prominent role during fertilization in many animals. This review focuses on roles of Ca(2+) during the events around fertilization in the model organism, Caenorhabditis elegans. Specifically, the role of Ca(2+) in sperm, oocytes and the surrounding somatic tissues during fertilization will be discussed, with the focus on sperm activation, meiotic maturation of oocytes, ovulation, sperm-egg interaction and fertilization. PMID:23218668

Singaravelu, Gunasekaran; Singson, Andrew

2013-01-01

208

Targets of TGF-? Signaling in Caenorhabditis elegans Dauer Formation  

Microsoft Academic Search

Caenorhabditis elegans dauer formation is controlled by multiple environmental factors. The chemosensory neuron ASI regulates dauer formation by secretion of DAF-7\\/TGF-?, but the molecular targets of the DAF-7 ligand are incompletely defined and the cellular targets are unknown. We genetically characterized and cloned a putative transducer of DAF-7 signaling called daf-14 and found that it encodes a Smad protein. DAF-14

Takao Inoue; James H Thomas

2000-01-01

209

Improving the Caenorhabditis elegans genome annotation using machine learning.  

PubMed

For modern biology, precise genome annotations are of prime importance, as they allow the accurate definition of genic regions. We employ state-of-the-art machine learning methods to assay and improve the accuracy of the genome annotation of the nematode Caenorhabditis elegans. The proposed machine learning system is trained to recognize exons and introns on the unspliced mRNA, utilizing recent advances in support vector machines and label sequence learning. In 87% (coding and untranslated regions) and 95% (coding regions only) of all genes tested in several out-of-sample evaluations, our method correctly identified all exons and introns. Notably, only 37% and 50%, respectively, of the presently unconfirmed genes in the C. elegans genome annotation agree with our predictions, thus we hypothesize that a sizable fraction of those genes are not correctly annotated. A retrospective evaluation of the Wormbase WS120 annotation [] of C. elegans reveals that splice form predictions on unconfirmed genes in WS120 are inaccurate in about 18% of the considered cases, while our predictions deviate from the truth only in 10%-13%. We experimentally analyzed 20 controversial genes on which our system and the annotation disagree, confirming the superiority of our predictions. While our method correctly predicted 75% of those cases, the standard annotation was never completely correct. The accuracy of our system is further corroborated by a comparison with two other recently proposed systems that can be used for splice form prediction: SNAP and ExonHunter. We conclude that the genome annotation of C. elegans and other organisms can be greatly enhanced using modern machine learning technology. PMID:17319737

Rätsch, Gunnar; Sonnenburg, Sören; Srinivasan, Jagan; Witte, Hanh; Müller, Klaus-R; Sommer, Ralf-J; Schölkopf, Bernhard

2007-02-23

210

Genomic analysis of stress response against arsenic in Caenorhabditis elegans.  

PubMed

Arsenic, a known human carcinogen, is widely distributed around the world and found in particularly high concentrations in certain regions including Southwestern US, Eastern Europe, India, China, Taiwan and Mexico. Chronic arsenic poisoning affects millions of people worldwide and is associated with increased risk of many diseases including arthrosclerosis, diabetes and cancer. In this study, we explored genome level global responses to high and low levels of arsenic exposure in Caenorhabditis elegans using Affymetrix expression microarrays. This experimental design allows us to do microarray analysis of dose-response relationships of global gene expression patterns. High dose (0.03%) exposure caused stronger global gene expression changes in comparison with low dose (0.003%) exposure, suggesting a positive dose-response correlation. Biological processes such as oxidative stress, and iron metabolism, which were previously reported to be involved in arsenic toxicity studies using cultured cells, experimental animals, and humans, were found to be affected in C. elegans. We performed genome-wide gene expression comparisons between our microarray data and publicly available C. elegans microarray datasets of cadmium, and sediment exposure samples of German rivers Rhine and Elbe. Bioinformatics analysis of arsenic-responsive regulatory networks were done using FastMEDUSA program. FastMEDUSA analysis identified cancer-related genes, particularly genes associated with leukemia, such as dnj-11, which encodes a protein orthologous to the mammalian ZRF1/MIDA1/MPP11/DNAJC2 family of ribosome-associated molecular chaperones. We analyzed the protective functions of several of the identified genes using RNAi. Our study indicates that C. elegans could be a substitute model to study the mechanism of metal toxicity using high-throughput expression data and bioinformatics tools such as FastMEDUSA. PMID:23894281

Sahu, Surasri N; Lewis, Jada; Patel, Isha; Bozdag, Serdar; Lee, Jeong H; Sprando, Robert; Cinar, Hediye Nese

2013-01-01

211

Calcium signaling surrounding fertilization in the nematode Caenorhabditis elegans  

PubMed Central

Summary Calcium plays a prominent role during fertilization in many animals. This review focuses on roles of Ca2+ during the events around fertilization in the model organism, Caenorhabditis elegans. Specifically, the role of Ca2+ in sperm, oocytes and the surrounding somatic tissues during fertilization will be discussed, with the focus on sperm activation, meiotic maturation of oocytes, ovulation, sperm-egg interaction and fertilization.

Singaravelu, Gunasekaran; Singson, Andrew

2012-01-01

212

Isotopic ratio outlier analysis global metabolomics of Caenorhabditis elegans.  

PubMed

We demonstrate the global metabolic analysis of Caenorhabditis elegans stress responses using a mass-spectrometry-based technique called isotopic ratio outlier analysis (IROA). In an IROA protocol, control and experimental samples are isotopically labeled with 95 and 5% (13)C, and the two sample populations are mixed together for uniform extraction, sample preparation, and LC-MS analysis. This labeling strategy provides several advantages over conventional approaches: (1) compounds arising from biosynthesis are easily distinguished from artifacts, (2) errors from sample extraction and preparation are minimized because the control and experiment are combined into a single sample, (3) measurement of both the molecular weight and the exact number of carbon atoms in each molecule provides extremely accurate molecular formulas, and (4) relative concentrations of all metabolites are easily determined. A heat-shock perturbation was conducted on C. elegans to demonstrate this approach. We identified many compounds that significantly changed upon heat shock, including several from the purine metabolism pathway. The metabolomic response information by IROA may be interpreted in the context of a wealth of genetic and proteomic information available for C. elegans . Furthermore, the IROA protocol can be applied to any organism that can be isotopically labeled, making it a powerful new tool in a global metabolomics pipeline. PMID:24274725

Stupp, Gregory S; Clendinen, Chaevien S; Ajredini, Ramadan; Szewc, Mark A; Garrett, Timothy; Menger, Robert F; Yost, Richard A; Beecher, Chris; Edison, Arthur S

2013-12-17

213

Function and Regulation of Lipid Biology in Caenorhabditis elegans Aging  

PubMed Central

Rapidly expanding aging populations and a concomitant increase in the prevalence of age-related diseases are global health problems today. Over the past three decades, a large body of work has led to the identification of genes and regulatory networks that affect longevity and health span, often benefiting from the tremendous power of genetics in vertebrate and invertebrate model organisms. Interestingly, many of these factors appear linked to lipids, important molecules that participate in cellular signaling, energy metabolism, and structural compartmentalization. Despite the putative link between lipids and longevity, the role of lipids in aging remains poorly understood. Emerging data from the model organism Caenorhabditis elegans suggest that lipid composition may change during aging, as several pathways that influence aging also regulate lipid metabolism enzymes; moreover, some of these enzymes apparently play key roles in the pathways that affect the rate of aging. By understanding how lipid biology is regulated during C. elegans aging, and how it impacts molecular, cellular, and organismal function, we may gain insight into novel ways to delay aging using genetic or pharmacological interventions. In the present review we discuss recent insights into the roles of lipids in C. elegans aging, including regulatory roles played by lipids themselves, the regulation of lipid metabolic enzymes, and the roles of lipid metabolism genes in the pathways that affect aging.

Hou, Nicole Shangming; Taubert, Stefan

2012-01-01

214

Analyzing cell physiology in C. elegans with fluorescent ratiometric reporters.  

PubMed

Ratiometric fluorescent reporters have recently emerged a new technique to non-invasively measure aspects of cell physiology such as redox status, calcium levels, energy production, and NADH levels. These reporters consist of either a single or pair of fluorophores along with specific modifications, such as the addition of a protein domain which binds to a metabolite of interest, thereby producing gradual alterations in fluorescence in response to changes in the measured parameter. Measurement of the changes in fluorescence produces a quantitative read-out of the cellular environment. While these reporters were initially developed to easily visualize and track changes in cultured cells, several groups have adapted these reporters to use in Caenorhabditis elegans which opens a new avenue through which to explore cell physiology during development or aging, in response to changes in external environment, or in response to genetic manipulation. These reporters have the advantage of being easily targeted to any part of the worm, and because C. elegans is transparent both the reporters and changes in their fluorescence can be clearly observed in vivo. Here we discuss the application of ratiometric reporters to C. elegans, and outline a method to quantitatively measure changes in intracellular peroxide levels using the HyPer ratiometric reporter. However, these principles can be applied to alternate ratiometric reporters which are designed to measure either other chemical species or other cellular parameters. PMID:24915644

Wang, Hongning; Karadge, Uma; Humphries, William H; Fisher, Alfred L

2014-08-01

215

Automated lineage and expression profiling in live Caenorhabditis elegans embryos.  

PubMed

Describing gene expression during animal development requires a way to quantitatively measure expression levels with cellular resolution and to describe how expression changes with time. Fluorescent protein reporters make it possible to measure expression dynamics in live cells by time-lapse microscopy, but it can be challenging to identify expressing cells in complex tissues and to compare expression across organisms. This protocol describes how to use automated lineage analysis to identify cells in Caenorhabditis elegans embryos expressing fluorescent reporters and how to quantify that expression with cellular resolution. Because C. elegans develops through an invariant pattern of cell divisions, every cell's identity and future fate can be predicted from its pattern of previous cell divisions. Automated analysis of images collected from embryos expressing a fluorescent histone transgene in all cells allows lineage tracing and cell identification. This provides a scaffold with which to describe expression of a second color reporter such as a fusion of a second fluorescent protein to a gene of interest or its regulatory sequences. These methods can also be used for analysis of reporter expression, cell division timing, and cell position in genetically perturbed embryos. The protocol describes how to prepare C. elegans strains containing nuclear-expressed fluorescent reporters, collect images of appropriate quality from embryos, perform automated lineage analysis, manually edit and curate the lineage, and, finally, extract and display reporter signals. PMID:22854571

Murray, John Isaac; Bao, Zhirong

2012-08-01

216

Optical Silencing of C. elegans Cells with Arch Proton Pump  

PubMed Central

Background Optogenetic techniques using light-driven ion channels or ion pumps for controlling excitable cells have greatly facilitated the investigation of nervous systems in vivo. A model organism, C. elegans, with its small transparent body and well-characterized neural circuits, is especially suitable for optogenetic analyses. Methodology/Principal Findings We describe the application of archaerhodopsin-3 (Arch), a recently reported optical neuronal silencer, to C. elegans. Arch::GFP expressed either in all neurons or body wall muscles of the entire body by means of transgenes were localized, at least partially, to the cell membrane without adverse effects, and caused locomotory paralysis of worms when illuminated by green light (550 nm). Pan-neuronal expression of Arch endowed worms with quick and sustained responsiveness to such light. Worms reliably responded to repeated periods of illumination and non-illumination, and remained paralyzed under continuous illumination for 30 seconds. Worms expressing Arch in different subsets of motor neurons exhibited distinct defects in the locomotory behavior under green light: selective silencing of A-type motor neurons affected backward movement while silencing of B-type motor neurons affected forward movement more severely. Our experiments using a heat-shock-mediated induction system also indicate that Arch becomes fully functional only 12 hours after induction and remains functional for more than 24 hour. Conclusions/Sgnificance Arch can be used for silencing neurons and muscles, and may be a useful alternative to currently widely used halorhodopsin (NpHR) in optogenetic studies of C. elegans.

Okazaki, Ayako; Sudo, Yuki; Takagi, Shin

2012-01-01

217

Aluminium exposure disrupts elemental homeostasis in Caenorhabditis elegans  

PubMed Central

Aluminium (Al) is highly abundant in the environment and can elicit a variety of toxic responses in biological systems. Here we characterize the effects of Al on Caenorhabditis elegans by identifying phenotypic abnormalities and disruption in whole-body metal homeostasis (metallostasis) following Al exposure in food. Widespread changes to the elemental content of adult nematodes were observed when chronically exposed to Al from the first larval stage (L1). Specifically, we saw increased barium, chromium, copper and iron content, and a reduction in calcium levels. Lifespan was decreased in worms exposed to low levels of Al, but unexpectedly increased when the Al concentration reached higher levels (4.8 mM). This bi-phasic phenotype was only observed when Al exposure occurred during development, as lifespan was unaffected by Al exposure during adulthood. Lower levels of Al slowed C. elegans developmental progression, and reduced hermaphrodite self-fertility and adult body size. Significant developmental delay was observed even when Al exposure was restricted to embryogenesis. Similar changes in Al have been noted in association with Al toxicity in humans and other mammals, suggesting that C. elegans may be of use as a model for understanding the mechanisms of Al toxicity in mammalian systems.

Page, Kathryn E.; White, Keith N.; McCrohan, Catherine R.

2013-01-01

218

Undulatory locomotion of Caenorhabditis elegans on wet surfaces.  

PubMed

The physical and biomechanical principles that govern undulatory movement on wet surfaces have important applications in physiology, physics, and engineering. The nematode Caenorhabditis elegans, with its highly stereotypical and functionally distinct sinusoidal locomotory gaits, is an excellent system in which to dissect these properties. Measurements of the main forces governing the C. elegans crawling gait on lubricated surfaces have been scarce, primarily due to difficulties in estimating the physical features at the nematode-gel interface. Using kinematic data and a hydrodynamic model based on lubrication theory, we calculate both the surface drag forces and the nematode's bending force while crawling on the surface of agar gels within a preexisting groove. We find that the normal and tangential surface drag coefficients during crawling are ?222 and 22, respectively, and the drag coefficient ratio is ?10. During crawling, the calculated internal bending force is time-periodic and spatially complex, exhibiting a phase lag with respect to the nematode's body bending curvature. This phase lag is largely due to viscous drag forces, which are higher during crawling as compared to swimming in an aqueous buffer solution. The spatial patterns of bending force generated during either swimming or crawling correlate well with previously described gait-specific features of calcium signals in muscle. Further, our analysis indicates that one may be able to control the motility gait of C. elegans by judiciously adjusting the magnitude of the surface drag coefficients. PMID:22735527

Shen, X N; Sznitman, J; Krajacic, P; Lamitina, T; Arratia, P E

2012-06-20

219

Assaying ?-amyloid Toxicity using a Transgenic C. elegans Model  

PubMed Central

Accumulation of the ?-amyloid peptide (A?) is generally believed to be central to the induction of Alzheimer's disease, but the relevant mechanism(s) of toxicity are still unclear. A? is also deposited intramuscularly in Inclusion Body Myositis, a severe human myopathy. The intensely studied nematode worm Caenorhabditis elegans can be transgenically engineered to express human A?. Depending on the tissue or timing of A? expression, transgenic worms can have readily measurable phenotypes that serve as a read-out of A? toxicity. For example, transgenic worms with pan-neuronal A? expression have defects is associative learning (Dosanjh et al. 2009), while transgenic worms with constitutive muscle-specific expression show a progressive, age-dependent paralysis phenotype (Link, 1995; Cohen et al. 2006). One particularly useful C. elegans model employs a temperature-sensitive mutation in the mRNA surveillance system to engineer temperature-inducible muscle expression of an A? transgene, resulting in a reproducible paralysis phenotype upon temperature upshift (Link et al. 2003). Treatments that counter A? toxicity in this model [e.g., expression of a protective transgene (Hassan et al. 2009) or exposure to Ginkgo biloba extracts (Wu et al. 2006)] reproducibly alter the rate of paralysis induced by temperature upshift of these transgenic worms. Here we describe our protocol for measuring the rate of paralysis in this transgenic C. elegans model, with particular attention to experimental variables that can influence this measurement.

Dostal, Vishantie; Link, Christopher D.

2010-01-01

220

Control of Oocyte Growth and Meiotic Maturation in C. elegans  

PubMed Central

In sexually reproducing animals, oocytes arrest at diplotene or diakinesis and resume meiosis (meiotic maturation) in response to hormones. Chromosome segregation errors in female meiosis I are the leading cause of human birth defects, and age-related changes in the hormonal environment of the ovary are a suggested cause. C. elegans is emerging as a genetic paradigm for studying hormonal control of meiotic maturation. The meiotic maturation processes in C. elegans and mammals share a number of biological and molecular similarities. Major sperm protein (MSP) and luteinizing hormone (LH), though unrelated in sequence, both trigger meiotic resumption using somatic G?s-adenylate cyclase pathways and soma-germline gap-junctional communication. At a molecular level, the oocyte responses apparently involve the control of conserved protein kinase pathways and post-transcriptional gene regulation in the oocyte. At a cellular level, the responses include cortical cytoskeletal rearrangement, nuclear envelope breakdown, assembly of the acentriolar meiotic spindle, chromosome segregation, and likely changes important for fertilization and the oocyte-to-embryo transition. This chapter focuses on signaling mechanisms required for oocyte growth and meiotic maturation in C. elegans and discusses how these mechanisms coordinate the completion of meiosis and the oocyte-to-embryo transition.

Kim, Seongseop; Spike, Caroline; Greenstein, David

2013-01-01

221

A method for measuring fatty acid oxidation in C. elegans  

PubMed Central

The nematode C. elegans has during the past decade proven to be a valuable model organism to identify and examine molecular mechanisms regulating lipid storage and metabolism. While the primary approach has been to identify genes and pathways conferring alterations in lipid accumulation, only a few recent studies have recognized the central role of fatty acid degradation in cellular lipid homeostasis. In the present study, we show how complete oxidation of fatty acids can be determined in live C. elegans by examining oxidation of tritium-labeled fatty acids to tritiated H2O that can be measured by scintillation counting. Treating animals with sodium azide, an inhibitor of the electron transport chain, reduced 3H2O production to approximately 15%, while boiling of animals prior to assay completely blocked the production of labeled water. We demonstrate that worms fed different bacterial strains exhibit different fatty acid oxidation rates. We show that starvation results in increased fatty acid oxidation, which is independent of the transcription factor NHR-49. On the contrary, fatty acid oxidation is reduced to approximately 70% in animals lacking the worm homolog of the insulin receptor, DAF-2. Hence, the present methodology can be used to delineate the role of specific genes and pathways in the regulation of ?-oxidation in C. elegans.

Elle, Ida Coordt; R?dkaer, Steven Vestergaard; Fredens, Julius; Faergeman, Nils Joakim

2012-01-01

222

The Redox System in C. elegans, a Phylogenetic Approach  

PubMed Central

Oxidative stress is a toxic state caused by an imbalance between the production and elimination of reactive oxygen species (ROS). ROS cause oxidative damage to cellular components such as proteins, lipids, and nucleic acids. While the role of ROS in cellular damage is frequently all that is noted, ROS are also important in redox signalling. The “Redox Hypothesis" has been proposed to emphasize a dual role of ROS. This hypothesis suggests that the primary effect of changes to the redox state is modified cellular signalling rather than simply oxidative damage. In extreme cases, alteration of redox signalling can contribute to the toxicity of ROS, as well as to ageing and age-related diseases. The nematode species Caenorhabditis elegans provides an excellent model for the study of oxidative stress and redox signalling in animals. We use protein sequences from central redox systems in Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae to query Genbank for homologous proteins in C. elegans. We then use maximum likelihood phylogenetic analysis to compare protein families between C. elegans and the other organisms to facilitate future research into the genetics of redox biology.

Johnston, Andrew D.; Ebert, Paul R.

2012-01-01

223

Serotonin Control of Thermotaxis Memory Behavior in Nematode Caenorhabditis elegans  

PubMed Central

Caenorhabditis elegans is as an ideal model system for the study of mechanisms underlying learning and memory. In the present study, we employed C. elegans assay system of thermotaxis memory to investigate the possible role of serotonin neurotransmitter in memory control. Our data showed that both mutations of tph-1, bas-1, and cat-4 genes, required for serotonin synthesis, and mutations of mod-5 gene, encoding a serotonin reuptake transporter, resulted in deficits in thermotaxis memory behavior. Exogenous treatment with serotonin effectively recovered the deficits in thermotaxis memory of tph-1 and bas-1 mutants to the level of wild-type N2. Neuron-specific activity assay of TPH-1 suggests that serotonin might regulate the thermotaxis memory behavior by release from the ADF sensory neurons. Ablation of ADF sensory neurons by expressing a cell-death activator gene egl-1 decreased the thermotaxis memory, whereas activation of ADF neurons by expression of a constitutively active protein kinase C homologue (pkc-1(gf)) increased the thermotaxis memory and rescued the deficits in thermotaxis memory in tph-1 mutants. Moreover, serotonin released from the ADF sensory neurons might act through the G-protein-coupled serotonin receptors of SER-4 and SER-7 to regulate the thermotaxis memory behavior. Genetic analysis implies that serotonin might further target the insulin signaling pathway to regulate the thermotaxis memory behavior. Thus, our results suggest the possible crucial role of serotonin and ADF sensory neurons in thermotaxis memory control in C. elegans.

Guo, Yuling; Wang, Daoyong; Li, Chaojun; Wang, Dayong

2013-01-01

224

Undulatory Locomotion of Caenorhabditis elegans on Wet Surfaces  

PubMed Central

The physical and biomechanical principles that govern undulatory movement on wet surfaces have important applications in physiology, physics, and engineering. The nematode Caenorhabditis elegans, with its highly stereotypical and functionally distinct sinusoidal locomotory gaits, is an excellent system in which to dissect these properties. Measurements of the main forces governing the C. elegans crawling gait on lubricated surfaces have been scarce, primarily due to difficulties in estimating the physical features at the nematode-gel interface. Using kinematic data and a hydrodynamic model based on lubrication theory, we calculate both the surface drag forces and the nematode's bending force while crawling on the surface of agar gels within a preexisting groove. We find that the normal and tangential surface drag coefficients during crawling are ?222 and 22, respectively, and the drag coefficient ratio is ?10. During crawling, the calculated internal bending force is time-periodic and spatially complex, exhibiting a phase lag with respect to the nematode's body bending curvature. This phase lag is largely due to viscous drag forces, which are higher during crawling as compared to swimming in an aqueous buffer solution. The spatial patterns of bending force generated during either swimming or crawling correlate well with previously described gait-specific features of calcium signals in muscle. Further, our analysis indicates that one may be able to control the motility gait of C. elegans by judiciously adjusting the magnitude of the surface drag coefficients.

Shen, X.N.; Sznitman, J.; Krajacic, P.; Lamitina, T.; Arratia, P.E.

2012-01-01

225

Caenorhabditis elegans Innate Immune Response Triggered by Salmonella enterica Requires Intact LPS and Is Mediated by a MAPK Signaling Pathway  

Microsoft Academic Search

Compared to mammals, insects, and plants, relatively little is known about innate immune responses in the nematode Caenorhabditis elegans. Previous work showed that Salmonella enterica serovars cause a persistent infection in the C. elegans intestine [1, 2] that triggers gonadal programmed cell death (PCD) and that C. elegans cell death (ced) mutants are more susceptible to Salmonella-mediated killing [3]. To

Alejandro Aballay; Eliana Drenkard; Layla R. Hilbun; Frederick M. Ausubel

2003-01-01

226

Changes in Nuclear Receptor and Vitellogenin Gene Expression in Response to Steroids and Heavy Metal in Caenorhabditis elegans  

Microsoft Academic Search

SYNOPSIS. To gain basic understanding of the reproductive and developmental effects of endocrine dis- rupting chemicals in invertebrates, we have used C. elegans as an animal model. The completion of the C. elegans genome sequence brings to bear microarray analysis as a tool for these studies. We previously showed that the C. elegans genome was responsive to vertebrate steroid hormones,

APOLONIA NOVILLO; S EUNG-JAE WON; IAN P. C ALLARD

2005-01-01

227

An in vivo and in vitro model of Plasmodium falciparum rosetting and autoagglutination mediated by varO, a group A var gene encoding a frequent serotype.  

PubMed

In the Saimiri sciureus monkey, erythrocytes infected with the varO antigenic variant of the Plasmodium falciparum Palo Alto 89F5 clone bind uninfected red blood cells (rosetting), form autoagglutinates, and have a high multiplication rate, three phenotypic characteristics that are associated with severe malaria in human patients. We report here that varO parasites express a var gene having the characteristics of group A var genes, and we show that the varO Duffy binding-like 1alpha(1) (DBL1alpha(1)) domain is implicated in the rosetting of both S. sciureus and human erythrocytes. The soluble varO N-terminal sequence (NTS)-DBL1alpha(1) recombinant domain, produced in a baculovirus-insect cell system, induced high titers of antibodies that reacted with varO-infected red blood cells and disrupted varO rosettes. varO parasites were culture adapted in vitro using human erythrocytes. They formed rosettes and autoagglutinates, and they had the same surface serotype and expressed the same varO gene as the monkey-propagated parasites. To develop an in vitro model with highly homogeneous varO parasites, rosette purification was combined with positive selection by panning with a varO NTS-DBL1alpha(1)-specific mouse monoclonal antibody. The single-variant, clonal parasites were used to analyze seroprevalence for varO at the village level in a setting where malaria is holoendemic (Dielmo, Senegal). We found 93.6% (95% confidence interval, 89.7 to 96.4%) seroprevalence for varO surface-reacting antibodies and 86.7% (95% confidence interval, 82.8 to 91.6%) seroprevalence for the recombinant NTS-DBL1alpha(1) domain, and virtually all permanent residents had seroconverted by the age of 5 years. These data imply that the varO model is a relevant in vivo and in vitro model for rosetting and autoagglutination that can be used for rational development of vaccine candidates and therapeutic strategies aimed at preventing malaria pathology. PMID:18809668

Vigan-Womas, Inès; Guillotte, Micheline; Le Scanf, Cécile; Igonet, Sébastien; Petres, Stéphane; Juillerat, Alexandre; Badaut, Cyril; Nato, Farida; Schneider, Achim; Lavergne, Anne; Contamin, Hugues; Tall, Adama; Baril, Laurence; Bentley, Graham A; Mercereau-Puijalon, Odile

2008-12-01

228

Automated quantification of synaptic fluorescence in C. elegans.  

PubMed

Synapse strength refers to the amplitude of postsynaptic responses to presynaptic neurotransmitter release events, and has a major impact on overall neural circuit function. Synapse strength critically depends on the abundance of neurotransmitter receptors clustered at synaptic sites on the postsynaptic membrane. Receptor levels are established developmentally, and can be altered by receptor trafficking between surface-localized, subsynaptic, and intracellular pools, representing important mechanisms of synaptic plasticity and neuromodulation. Rigorous methods to quantify synaptically-localized neurotransmitter receptor abundance are essential to study synaptic development and plasticity. Fluorescence microscopy is an optimal approach because it preserves spatial information, distinguishing synaptic from non-synaptic pools, and discriminating among receptor populations localized to different types of synapses. The genetic model organism Caenorhabditis elegans is particularly well suited for these studies due to the small size and relative simplicity of its nervous system, its transparency, and the availability of powerful genetic techniques, allowing examination of native synapses in intact animals. Here we present a method for quantifying fluorescently-labeled synaptic neurotransmitter receptors in C. elegans. Its key feature is the automated identification and analysis of individual synapses in three dimensions in multi-plane confocal microscope output files, tabulating position, volume, fluorescence intensity, and total fluorescence for each synapse. This approach has two principal advantages over manual analysis of z-plane projections of confocal data. First, because every plane of the confocal data set is included, no data are lost through z-plane projection, typically based on pixel intensity averages or maxima. Second, identification of synapses is automated, but can be inspected by the experimenter as the data analysis proceeds, allowing fast and accurate extraction of data from large numbers of synapses. Hundreds to thousands of synapses per sample can easily be obtained, producing large data sets to maximize statistical power. Considerations for preparing C. elegans for analysis, and performing confocal imaging to minimize variability between animals within treatment groups are also discussed. Although developed to analyze C. elegans postsynaptic receptors, this method is generally useful for any type of synaptically-localized protein, or indeed, any fluorescence signal that is localized to discrete clusters, puncta, or organelles. The procedure is performed in three steps: 1) preparation of samples, 2) confocal imaging, and 3) image analysis. Steps 1 and 2 are specific to C. elegans, while step 3 is generally applicable to any punctate fluorescence signal in confocal micrographs. PMID:22907390

Sturt, Brianne L; Bamber, Bruce A

2012-01-01

229

Comparative genomics and functional study of lipid metabolic genes in Caenorhabditis elegans  

PubMed Central

Background Animal models are indispensable to understand the lipid metabolism and lipid metabolic diseases. Over the last decade, the nematode Caenorhabditis elegans has become a popular animal model for exploring the regulation of lipid metabolism, obesity, and obese-related diseases. However, the genomic and functional conservation of lipid metabolism from C. elegans to humans remains unknown. In the present study, we systematically analyzed genes involved in lipid metabolism in the C. elegans genome using comparative genomics. Results We built a database containing 471 lipid genes from the C. elegans genome, and then assigned most of lipid genes into 16 different lipid metabolic pathways that were integrated into a network. Over 70% of C. elegans lipid genes have human orthologs, with 237 of 471 C. elegans lipid genes being conserved in humans, mice, rats, and Drosophila, of which 71 genes are specifically related to human metabolic diseases. Moreover, RNA-mediated interference (RNAi) was used to disrupt the expression of 356 of 471 lipid genes with available RNAi clones. We found that 21 genes strongly affect fat storage, development, reproduction, and other visible phenotypes, 6 of which have not previously been implicated in the regulation of fat metabolism and other phenotypes. Conclusions This study provides the first systematic genomic insight into lipid metabolism in C. elegans, supporting the use of C. elegans as an increasingly prominent model in the study of metabolic diseases.

2013-01-01

230

Mode of bacterial pathogenesis determines phenotype in elt-2 and elt-7 RNAi Caenorhabditis elegans  

Microsoft Academic Search

Caenorhabditis elegans has become a useful model for studying innate immunity. ELT-2, which is homologous to human GATA-4, -5 and -6, is considered the primary GATA transcription factor controlling intestinal immunity in C. elegans. In this study, we characterize the timeline of intestinal distension in nematodes where ELT-2 and another intestinal GATA transcription factor, ELT-7, are abrogated by RNAi using

Samantha L. Elliott; Craig R. Sturgeon; Deborah M. Travers; Madeline C. Montgomery

2011-01-01

231

Molecular and functional analysis of apical junction formation in the gut epithelium of Caenorhabditis elegans  

Microsoft Academic Search

The Caenorhabditis elegans intestine is a simple and accessible model system to analyze the mechanism of junction assembly. In comparison to Drosophila and vertebrates, the C. elegans apical junction is remarkable because a single electron-dense structure is implicated in complex processes such as epithelial tightness, vectorial transport and cell adhesion. Here we present evidence in support of a heterogeneous molecular

Christoph Segbert; Kevin Johnson; Carin Theres; Daniela van Fürden; Olaf Bossinger

2004-01-01

232

A Decline in p38 MAPK Signaling Underlies Immunosenescence in Caenorhabditis elegans  

Microsoft Academic Search

The decline in immune function with aging, known as immunosenescence, has been implicated in evolutionarily diverse species, but the underlying molecular mechanisms are not understood. During aging in Caenorhabditis elegans, intestinal tissue deterioration and the increased intestinal proliferation of bacteria are observed, but how innate immunity changes during C. elegans aging has not been defined. Here we show that C.

Matthew J. Youngman; Zoë N. Rogers; Dennis H. Kim

2011-01-01

233

Distinct Pathogenesis and Host Responses during Infection of C. elegans by P. aeruginosa and S. aureus  

Microsoft Academic Search

The genetically tractable model host Caenorhabditis elegans provides a valuable tool to dissect host-microbe interactions in vivo. Pseudomonas aeruginosa and Staphylococcus aureus utilize virulence factors involved in human disease to infect and kill C. elegans. Despite much progress, virtually nothing is known regarding the cytopathology of infection and the proximate causes of nematode death. Using light and electron microscopy, we

Javier E. Irazoqui; Emily R. Troemel; Rhonda L. Feinbaum; Lyly G. Luhachack; Brent O. Cezairliyan; Frederick M. Ausubel

2010-01-01

234

Evolution of host innate defence: insights from Caenorhabditis elegans and primitive invertebrates  

Microsoft Academic Search

The genetically tractable model organism Caenorhabditis elegans was first used to model bacterial virulence in vivo a decade ago. Since then, great strides have been made in identifying the host response pathways that are involved in its defence against infection. Strikingly, C. elegans seems to detect, and respond to, infection without the involvement of its homologue of Toll-like receptors, in

Javier E. Irazoqui; Jonathan M. Urbach; Frederick M. Ausubel

2010-01-01

235

The Impact of Bacterial Diet on the Migration and Navigation of Caenorhabditis elegans  

Microsoft Academic Search

Can diet have a significant impact on the ability of organisms to sense and locate food? Focusing on the bacterial feeder Caenorhabditis elegans, we investigated what effect preconditioning on a range of bacterial substrates had on the subsequent chemotaxis process involved in the nematode locating other bacterial populations. Remarkably, we found that C. elegans, initially fed on a diet of

S. Rodger; B. S. Griffiths; J. W. McNicol; R. W. Wheatley; I. M. Young

2004-01-01

236

Salmonella typhimurium proliferates and establishes a persistent infection in the intestine of Caenorhabditis elegans  

Microsoft Academic Search

Genetic analysis of host–pathogen interactions has been hampered by the lack of genetically tractable models of such interactions. We showed previously that the human opportunistic pathogen Pseudomonas aeruginosa kills Caenorhabditis elegans, that P. aeruginosa and C. elegans genes can be identified that affect this killing, and that most of these P. aeruginosa genes are also important for mammalian pathogenesis. Here,

Alejandro Aballay; Peter Yorgey; Frederick M. Ausubel

2000-01-01

237

Locomotion of C. elegans: A Piecewise-Harmonic Curvature Representation of Nematode Behavior  

Microsoft Academic Search

Caenorhabditis elegans, a free-living soil nematode, displays a rich variety of body shapes and trajectories during its undulatory locomotion in complex environments. Here we show that the individual body postures and entire trails of C. elegans have a simple analytical description in curvature representation. Our model is based on the assumption that the curvature wave is generated in the head

Venkat Padmanabhan; Zeina S. Khan; Deepak E. Solomon; Andrew Armstrong; Kendra P. Rumbaugh; Siva A. Vanapalli; Jerzy Blawzdziewicz

2012-01-01

238

Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements  

Microsoft Academic Search

The availability of completely sequenced genomes from eight species of nematodes has provided an opportunity to identify novel cis-regulatory elements in the promoter regions of Caenorhabditis elegans transcripts using comparative genomics. We deter- mined orthologues for C. elegans transcripts in C. briggsae, C. remanei, C. brenneri, C. japonica, Pristionchus pacificus, Brugia malayi and Trichinella spiralis using the WABA alignment algorithm.

Monica C. Sleumer; Gordon Robertson; Nina Thiessen; Steven J. M. Jones

2009-01-01

239

Selection of Reliable Reference Genes in Caenorhabditis elegans for Analysis of Nanotoxicity  

Microsoft Academic Search

Despite rapid development and application of a wide range of manufactured metal oxide nanoparticles (NPs), the understanding of potential risks of using NPs is less completed, especially at the molecular level. The nematode Caenorhabditis elegans (C.elegans) has been emerging as an environmental model to study the molecular mechanism of environmental contaminations, using standard genetic tools such as the real-time quantitative

Yanqiong Zhang; Dongliang Chen; Michael A. Smith; Baohong Zhang; Xiaoping Pan

2012-01-01

240

Mapping a Mutation in "Caenorhabditis elegans" Using a Polymerase Chain Reaction-Based Approach  

ERIC Educational Resources Information Center

Many single nucleotide polymorphisms (SNPs) have been identified within the "Caenorhabditis elegans" genome. SNPs present in the genomes of two isogenic "C. elegans" strains have been routinely used as a tool in forward genetics to map a mutation to a particular chromosome. This article describes a laboratory exercise in which…

Myers, Edith M.

2014-01-01

241

Visualization of synaptic specializations in live C. elegans with synaptic vesicle protein-GFP fusions  

Microsoft Academic Search

Synaptic specializations are difficult to visualize at the light microscope level in living preparations. To circumvent this problem, synaptic vesicle proteins were fused to green fluorescent protein (GFP) and expressed in C. elegans neurons. C. elegans synaptobrevin-GFP and synaptogyrin-GFP fusion proteins were observed to target to synaptic sites. This localization allowed the visualization of synaptic specializations in living animals with

Michael L. Nonet

1999-01-01

242

A SURVEY OF THE LAND WINKLE POMATIAS ELEGANS (MU LLER, 1774) IN THE BURREN, CO. CLARE  

Microsoft Academic Search

The first Irish colony of the land winkle Pomatias elegans was found in the Burren, Co. Clare, in 1976, but the site was never surveyed. From the 28 July to the 7 August 2000 the extent and abundance of the P. elegans population was established in this locality. Standard searches by three people for five minutes each were used to

Elizabeth Platts; Stuart Bailey; David McGrath; Grainne McGeough

243

A Neural Network Model of Chemotaxis Predicts Functions of Synaptic Connections in the Nematode Caenorhabditis elegans  

Microsoft Academic Search

The anatomical connectivity of the nervous system of the nematode Caenorhabditis elegans has been almost completely described, but determination of the neurophysiological basis of behavior in this sys- tem is just beginning. Here we used an optimization algorithm to search for patterns of connectivity suffi- cient to compute the sensorimotor transformation underlying C. elegans chemotaxis, a simple form of spatial

Nathan A. Dunn; Shawn R. Lockery; Jonathan T. Pierce-shimomura; John S. Conery

2004-01-01

244

Chemical structure and biological activity of the Caenorhabditis elegans dauer-inducing pheromone  

Microsoft Academic Search

Pheromones are cell type-specific signals used for communication between individuals of the same species. When faced with overcrowding or starvation, Caenorhabditis elegans secrete the pheromone daumone, which facilitates communication between individuals for adaptation to adverse environmental stimuli. Daumone signals C. elegans to enter the dauer stage, an enduring and non-ageing stage of the nematode life cycle with distinctive adaptive features

Pan-Young Jeong; Mankil Jung; Yong-Hyeon Yim; Heekyeong Kim; Eunmi Hong; Weontae Lee; Young Hwan Kim; Kun Kim; Young-Ki Paik

2005-01-01

245

Using RNAi in C. "elegans" to Demonstrate Gene Knockdown Phenotypes in the Undergraduate Biology Lab Setting  

ERIC Educational Resources Information Center

RNA interference (RNAi) is a powerful technology used to knock down genes in basic research and medicine. In 2006 RNAi technology using "Caenorhabditis elegans" ("C. elegans") was awarded the Nobel Prize in medicine and thus students graduating in the biological sciences should have experience with this technology. However,…

Roy, Nicole M.

2013-01-01

246

Galactose-Inducible promoters in Cryptococcus neoformans var. grubii.  

PubMed

Inducible promoters are invaluable tools for modulating gene expression (turning transcription on or off) and have been a key approach for ascertaining gene essentiality in Cryptococcus neoformans. Galactose-inducible promoters have been successfully used in Saccharomyces cerevisiae to manipulate heterologous gene expression. Utilizing S. cerevisiae galactose-inducible genes in a BLAST search of the sequenced C. neoformans var. grubii genome, we found three potential galactose-inducible promoters, P(GAL1), P(GAL7), and P(UGE2) that are induced by galactose and repressed by glucose in this variety. This chapter describes how to make a fusion of these promoters with heterologous genes, how to insert the fused gene back into the genome, and how to induce expression during asexual and sexual growth in C. neoformans var. grubii. PMID:22328377

Baker, Lorina G; Lodge, Jennifer K

2012-01-01

247

Yield, Essential Oil Content and Composition of Coriandrum sativum Varieties (var. vulgare Alef and var. microcarpum DC.) Grown in Two Different Locations  

Microsoft Academic Search

Coriander (Coriandrum sativum L.) has two varieties (var. vulgare Alef. and var. microcarpum DC.) in the populations of Turkey. Field experiments were conducted during 2000 and 2001 in two different locations (Tokat and Diyarbakir) in order to investigate yield, oil content and composition of the varieties. The oil composition of the varieties was analyzed by GC and GC\\/MS. Ecological variation

Isa Telci; Ozlem Gul Toncer; Nermin Sahbaz

2006-01-01

248

Effects of municipal reclaimed wastewater on the macro- and micro-elements status of soil and of Brassica oleracea var. Italica, and B. oleracea var. Gemmifera  

Microsoft Academic Search

An experiment was conducted in a greenhouse, located in Agrinion, Greece, where the effect of treated municipal wastewater (TMWW), compared to the ordinary irrigation water, was studied by means of a randomized block statistical design, on the macro- and micro-element and heavy metal content of Brassica oleracea var. Italica (Broccoli), and B. oleracea var. Gemmifera (Brussels sprouts) plants, as well

I. K. Kalavrouziotis; P. Robolas; P. H. Koukoulakis; A. H. Papadopoulos

2008-01-01

249

Effects of temperature, water activity and gas atmosphere on mycelial growth of tempe fungi Rhizopus microsporus var. microsporus and R. microsporus var. oligosporus  

Microsoft Academic Search

Rhizopus microsporus var. microsporus and var. oligosporus are used in the manufacture of various Asian fermented foods (tempe, black oncom, sufu). In view of solid-substrate fermentation (SSF) control, mycelial growth of strains of both varieties was tested for sensitivity to fluctuations of temperature, water activity and interstitial gas composition. This was achieved by measuring radial growth as well as biomass

B. Z. Han; M. J. R. Nout

2001-01-01

250

Evaluation of morphological and molecular variation in Plantago asiatica var. densiuscula, with special reference to the systematic treatment of Plantago asiatica var. yakusimensis.  

PubMed

Morphological and molecular variations in Plantago asiatica L. var. densiuscula Pilg. were analyzed to evaluate the genetic basis for recognizing the dwarf variety P. asiatica var. yakusimensis (Masam.) Ohwi. Considerable variation in the leaf size of P. asiatica var. densiuscula was observed, and no morphological discontinuities were found between the dwarf types of P. asiatica var. densiuscula and P. asiatica var. yakusimensis. Morphological analysis of plants grown under standardized conditions revealed that both environmental plasticity and genetic differentiation contributed to the dwarfisms. Molecular phylogenetic analysis of rDNA internal transcribed spacer (ITS) regions and the SUC1 locus encoding a sucrose transporter revealed that P. asiatica var. yakusimensis was genetically unique although the differentiation level was low. From the above results, we concluded that P. asiatica var. yakusimensis should be reduced to a form of P. asiatica var. densiuscula. Furthermore, the geographic distribution of the SUC1 genotype suggested multiple origins of dwarves, and possible hypotheses for the origins of dwarves are discussed. PMID:16773281

Ishikawa, Naoko; Yokoyama, Jun; Ikeda, Hiroshi; Takabe, Eriko; Tsukaya, Hirokazu

2006-07-01

251

Phenolic glycosides from the leaves of Alangium platanifolium var. platanifolium.  

PubMed

Chemical investigation of Alangium platanifolium var. platanifolium has resulted in the isolation of nine phenolic glycosides that were identified by means of 1D and 2D NMR experiments. Among them, catechol and salicinol O- and 1-O-beta-D-(6-O-beta-D-apiofuranosyl)glucopyranosides, respectively 1 and 2, and two compounds characterized as adducts of 2, 6-dihydroxybenzoic acid with salicin (plataplatanoside, 3) and 4-hydroxysalicin (4-hydroxyalangifolioside, 4) were determined structurally as new compounds. PMID:11076566

Tamaki, A; Ide, T; Otsuka, H

2000-10-01

252

Isolation and characterisation of Gaeumannomyces graminis var. graminis melanin mutants  

Microsoft Academic Search

Gaeumannomyces graminis var. graminis produces 1,8-dihydroxynaphthalene (DHN) melanin in its hyphal and hyphopodial cell walls. We isolated G. graminis mutants that were aected in their melanin biosynthesis. One was unable to synthesize DHN-melanin and, because it accumulated 2-hydroxyjuglone, a DHN melanin pathway shunt product, it is most likely to be defective in the reductase that catalyzes the conversion of 1,3,8-trihydroxynaphthalene

B. A. Frederick; T.-C. Caesar-Tonthat; M. H. Wheeler; K. B. Sheehan; W. A. Edens; J. M. Henson

1999-01-01

253

Triterpenoid biosynthesis in tissue cultures of Glycyrrhiza glabra var. glandulifera  

Microsoft Academic Search

The incorporation of [1-14C]acetate and [214 C]mevalonate into free and esterified triterpen-3-ols was examined in original plant organs and tissue cultures of Glycyrrhiza glabra var. glandulifera. Both substrates labeled ß-amyrin, an oleanane-type triterpene, and cycloartenol and 24-methylenecycloartanol, both of which are intermediates of phytosterol biosynthesis. The label in esterified triterpenes was distributed mainly in phytosterol intermediates, but not in ß-amyrin.

S. Ayabe; H. Takano; To Fujita; T. Furuya; H. Hirota; T. Takahashi

1990-01-01

254

Production of Kestoses (Fructosylsucroses) by Phytophthora parasitica var. nicotianae  

PubMed Central

The synthesis of kestoses (trisaccharides composed of two fructose units and one glucose unit) by races 0 and 1 of Phytophthora parasitica var. nicotianae is shown. The trisaccharide is found in culture filtrates of isolates grown in liquid media containing 3% sucrose. The utilization of sucrose and trisaccharide formation by the organisms over a 16-day period is described. The kestoses were identified by chemical and enzymatic analysis, and two of three possible isomers were found.

Hankin, Lester; McIntyre, John L.

1977-01-01

255

The thermostability of purified isoperoxidases from Brassica oleracea VAR. gemmifera  

Microsoft Academic Search

The thermostabilities of four previously purified isoperoxidases from Brussels sprouts (Brassica oleracea VAR. gemmifera.)have been determined. The heating time periods selected (10 s – 0.5 min intervals) are comparable to those used during commercial blanching. Non-linear regression (NLR) equation fitting, using common goodness of fit criteria (low chi-squared value, high regression coefficient and low residuals) points to a mechanism of

J. L. Forsyth; R. K. Owusu Apenten; D. S. Robinson

1999-01-01

256

Composition of the essential oil of Pogostemon travancoricus var. travancoricus.  

PubMed

The essential oil of Pogostemon travancoricus Bedd. var. travancoricus collected from the Agasthyamalai region of Tamil Nadu, India was analyzed by GC and GC-MS. The major components of the oil were bicyclogermacrene (16.0%), cis-calamenene (6.3%), germacrene B (11.1%), spathulenol (7.6%), viridiflorol (5.8%), alpha-cadinol (4.2%) and pogostone (9.9%). PMID:22428255

Murugan, Ramar; Mallavarapu, Gopal Rao

2012-01-01

257

New clerodane diterpenes from Tinospora sagittata var. yunnanensis.  

PubMed

Four new clerodane diterpenes, namely sagittatayunnanosides A-D (1-4), were isolated from the roots of Tinospora sagittata var. yunnanensis, together with two known compounds, tinospinoside C (5) and tinospinoside E (6). The structures of the four new compounds were well elucidated by extensive analyses of the MS, IR, and 1D and 2D?NMR data. The cytotoxic and antifouling activities of compounds 1-6 were evaluated. PMID:24634023

Jiang, Zhi-Yong; Li, Wen-Juan; Jiao, Li-Xiang; Guo, Jun-Ming; Tian, Kai; Yang, Chun-Tao; Huang, Xiang-Zhong

2014-03-01

258

Sporulation and regeneration efficiency of phosphobacteria ( Bacillus megaterium var phosphaticum )  

Microsoft Academic Search

Sporulation in Bacillus megaterium var phosphaticum (PB — 1) was induced using modified nutrient media. This modified medium induced sporulation within 36 h. After spore induction\\u000a the spores were kept under refrigerated (5?C) and room temperature (32?C) for five months and survival of spores was studied\\u000a at 15 days intervals by plating them in nutrient agar medium. It was observed

M. Gomathy; M. Thangaraju; S. Gunasekaran; N. O. Gopal

2007-01-01

259

Synthesis of Calocybe indica var. APK2 polysaccharide repeating unit.  

PubMed

The first total synthesis of p-methoxyphenyl ?-l-fucopyranosyl-(1?6)-?-d-galactopyranosyl-(1?4)-?-d-glucopyranosyl-(1?6)-?-d-glucopyranosyl-(1?6)-?-d-glucopyranoside (2) was achieved starting from five monosaccharide building blocks. This structure represents the repeating unit of the polysaccharide isolated from edible mushroom Calocybe indica var. APK2, and was synthesized in high overall yield via a convergent '3+2' glycosylation strategy. PMID:24785386

Zhang, Lei; Zhu, Xiangming

2014-06-01

260

Autofluorescence of the fungus Morchella conica var. rigida  

Microsoft Academic Search

Autofluorescence (primary fluorescence (AF)) of fruiting bodies and stems of the fungus Morchella conica var. rigida was studied by fluorescence microscopy including sporangia and ascospores. The ascospores were characterized by a weak green–yellow\\u000a AF at blue excitation. Using a green excitation, no AF was observed. The hyphae located under the layer of asci with ascospores\\u000a exhibited a higher primary fluorescence,

Z. Žižka; J. Gabriel

2011-01-01

261

New neohopane triterpenoidal saponin glycosides from Glimus lotoids var. Dectamnoids  

Microsoft Academic Search

Two neohopane triterpenoidal saponins(glinusides D and E) were isolated from the n-butanol fraction of Glinus lotoids var. dectammoids, their structures elucidated as 3-O-? -L-arabinopyranosyl -22-O- ? -D-glucopyranosyl (4 ? 1)-?-L-rhamnopyranosyl-16- ? - hydroxy-5- ? -neohoane and 3-O-? -larabinopyranosyl -22-O-? -D-glucopyransyl(4 ? 1)- ? -D-glucopyranosyl-16- ? -5- ? -neohopane respectively by means of spectral data, especially NMR includin8 COSY, HMQC, HMBC,

Arafa I. Hamed; Nasr A. El-Emary

1999-01-01

262

Transcribed var Genes Associated with Placental Malaria in Malawian Women  

Microsoft Academic Search

Determining the diversity of PfEMP1 sequences expressed by Plasmodium falciparum-infected erythrocytes isolated from placentas is important for attempts to develop a pregnancy-specific malaria vaccine. The DBL and var2csa DBL3x domains of PfEMP1 molecules are believed to mediate placental sequestration of infected erythrocytes, so the sequences encoding these domains were amplified from the cDNAs of placental parasites by using degenerate oligonucleotides.

Michael F. Duffy; Aphrodite Caragounis; Rintis Noviyanti; Helen M. Kyriacou; Ee Ken Choong; Katja Boysen; Julie Healer; J. Alexandra Rowe; Malcolm E. Molyneux; Graham V. Brown; Stephen J. Rogerson

2006-01-01

263

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes  

PubMed Central

The nematode Caenorhabditis elegans is a popular model system in genetics, not least because a majority of human disease genes are conserved in C. elegans. To generate a comprehensive inventory of its expressed proteome, we performed extensive shotgun proteomics and identified more than half of all predicted C. elegans proteins. This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins. Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster). We found that the abundances of orthologous proteins in metazoans correlate remarkably well, better than protein abundance versus transcript abundance within each organism or transcript abundances across organisms; this suggests that changes in transcript abundance may have been partially offset during evolution by opposing changes in protein abundance.

Schrimpf, Sabine P; Weiss, Manuel; Reiter, Lukas; Ahrens, Christian H; Jovanovic, Marko; Malmstrom, Johan; Brunner, Erich; Mohanty, Sonali; Lercher, Martin J; Hunziker, Peter E; Aebersold, Ruedi; von Mering, Christian; Hengartner, Michael O

2009-01-01

264

Role of phosphatidylinositol-4-phosphate 5? kinase (ppk-1) in ovulation of Caenorhabditis elegans  

PubMed Central

During C. elegans ovulation, the somatic gonad integrates signals from germ cells and propels a mature oocyte into the spermatheca for fertilization. Previous work suggests that phosphoinositide signaling plays important roles in C. elegans fertility. To fully understand inositol-1,4,5-trisphosphate (IP3) signaling in ovulation, we have examined the function of phosphatidylinositol-4-phosphate 5? kinase (PIP5K) in C. elegans. Our results show that the C. elegans PIP5K homolog, ppk-1, is essential for ovulation in C. elegans; ppk-1 is mainly expressed in somatic gonad, and depletion of ppk-1 expression causes defective ovulation, reduced gonad sheath contractility, and sterility. Increased IP3 signaling compensates for ppk-1 (RNAi)-induced sterility, suggesting that ppk-1 is linked to IP3 signaling. These results demonstrate that ppk-1 plays an essential role in IP3 signaling and cytoskeleton organization in somatic gonad.

Xu, Xiaojian; Guo, Haisu; Wycuff, Diane L.; Lee, Myeongwoo

2007-01-01

265

Biological activity of Bacillus thuringiensis (Bacillales: Bacillaceae) chitinase against Caenorhabditis elegans (Rhabditida: Rhabditidae).  

PubMed

In addition to being used increasingly as a model system in modern molecular biology studies, the free-living nematode Caenorhabditis elegans (Maupas, 1900) is an important pathogen in fungi and straw mushrooms. In this study, Bacillus thuringiensis strain 010 was found to have significantly detrimental activity against C. elegans. To further characterize this activity, the toxicological mechanism was elucidated at molecular level. Genes encoding for crystal protein and chitinase were isolated, cloned, and sequenced. However, the toxicity was detected only in the chitinase. Under transmission electron microscopy, change in the body wall and gut structures of C. elegans was observed, and thus degeneration of body wall and gut in the worms was also investigated. Further bioassay also confirmed the mortality of C. elegans fed with Escherichia coli TB1 strain. These observations suggest great potential for B. thuringiensis 010 as a biocontrol agent against C. elegans and other nematodes. PMID:24772534

Zhang, Lingling; Yu, Jie; Xie, Yufei; Lin, Hongli; Huang, Zhipeng; Xu, Lei; Gelbic, Ivan; Guan, Xiong

2014-04-01

266

Sporulation and regeneration efficiency of phosphobacteria (Bacillus megaterium var phosphaticum).  

PubMed

Sporulation in Bacillus megaterium var phosphaticum (PB - 1) was induced using modified nutrient media. This modified medium induced sporulation within 36 h. After spore induction the spores were kept under refrigerated (5°C) and room temperature (32°C) for five months and survival of spores was studied at 15 days intervals by plating them in nutrient agar medium. It was observed that there was not much variation in the storage temperature (5°C & 32°C). The spore cells of Bacillus megaterium var phosphaticum (PB - 1) were observed up to five months of storage under refrigerated (5°C) and room temperature (32°C). Regeneration of spore cells into vegetative cells was studied in tap water, rice gruel, nutrient broth, sterile lignite and sterile water at different concentrations of spore inoculum. The multiplication of sporulated Bacillus megaterium var phosphaticum culture was fast and reached its maximum (29.5 × 10(8) cfu ml(-1)) in nutrient broth containing 5 per cent inoculum level. PMID:23100674

Gomathy, M; Thangaraju, M; Gunasekaran, S; Gopal, N O

2007-09-01

267

Caenorhabditis elegans-based Model Systems for Antifungal Drug Discovery  

PubMed Central

The substantial morbidity and mortality associated with invasive fungal infections constitute undisputed tokens of their severity. The continued expansion of susceptible population groups (such as immunocompromised individuals, patients undergoing extensive surgery, and those hospitalized with serious underlying diseases especially in the intensive care unit) and the limitations of current antifungal agents due to toxicity issues or to the development of resistance, mandate the development of novel antifungal drugs. Currently, drug discovery is transitioning from the traditional in vitro large-scale screens of chemical libraries to more complex bioassays, including in vivo studies on whole animals; invertebrates, such as Caenorhabditis elegans, are thus gaining momentum as screening tools. Key pathogenesis features of fungal infections, including filament formation, are expressed in certain invertebrate and mammalian hosts; among the various potential hosts, C. elegans provides an attractive platform both for the study of host-pathogen interactions and the identification of new antifungal agents. Advantages of compound screening in this facile, relatively inexpensive and not as ethically challenged whole-animal context, include the simultaneous assessment of antifungal efficacy and toxicity that could result in the identification of compounds with distinct mechanisms of action, for example by promoting host immune responses or by impeding fungal virulence factors. With the recent advent of using predictive models to screen for compounds with improved chances of bioavailability in the nematode a priori, high-throughput screening of chemical libraries using the C. elegans-c. albicans antifungal discovery assay holds even greater promise for the identification of novel antifungal agents in the near future.

Anastassopoulou, Cleo G.; Fuchs, Beth Burgwyn; Mylonakis, Eleftherios

2013-01-01

268

Mechanism underlying prolongevity induced by bifidobacteria in Caenorhabditis elegans.  

PubMed

Lactobacilli and bifidobacteria are probiotic bacteria that modify host defense systems and have the ability to extend the lifespan of the nematode Caenorhabditis elegans. Here, we attempted to elucidate the mechanism by which bifidobacteria prolong the lifespan of C. elegans. When the nematode was fed Bifidobacterium infantis (BI) mixed at various ratios with the standard food bacterium Escherichia coli strain OP50 (OP), the mean lifespan of worms was extended in a dose-dependent manner. Worms fed BI displayed higher locomotion and produced more offspring than control worms. The growth curves of nematodes were similar regardless of the amount of BI mixed with OP, suggesting that BI did not induce prolongevity effects through caloric restriction. Notably, feeding worms the cell wall fraction of BI alone was sufficient to promote prolongevity. The accumulation of protein carbonyls and lipofuscin, a biochemical marker of aging, was also lower in worms fed BI; however, the worms displayed similar susceptibility to heat, hydrogen peroxide, and paraquat, an inducer of free radicals, as the control worms. As a result of BI feeding, loss-of-function mutants of daf-16, jnk-1, aak-2, tol-1, and tir-1 exhibited a longer lifespan than OP-fed control worms, but BI failed to extend the lifespan of pmk-1, skn-1, and vhp-1 mutants. As skn-1 induces phase 2 detoxification enzymes, our findings suggest that cell wall components of bifidobacteria increase the average lifespan of C. elegans via activation of skn-1, regulated by the p38 MAPK pathway, but not by general activation of the host defense system via DAF-16. PMID:23291976

Komura, Tomomi; Ikeda, Takanori; Yasui, Chikako; Saeki, Shigeru; Nishikawa, Yoshikazu

2013-02-01

269

Global remodeling of nucleosome positions in C. elegans  

PubMed Central

Background Eukaryotic chromatin architecture is affected by intrinsic histone-DNA sequence preferences, steric exclusion between nucleosome particles, formation of higher-order structures, and in vivo activity of chromatin remodeling enzymes. Results To disentangle sequence-dependent nucleosome positioning from the other factors, we have created two high-throughput maps of nucleosomes assembled in vitro on genomic DNA from the nematode worm Caenorhabditis elegans. A comparison of in vitro nucleosome positions with those observed in a mixed-stage, mixed-tissue population of C. elegans cells reveals that in vivo sequence preferences are modified on the genomic scale. Indeed, G/C dinucleotides are predicted to be most favorable for nucleosome formation in vitro but not in vivo. Nucleosome sequence read coverage in vivo is distinctly lower in chromosome arms than in central regions; the observed changes in apparent nucleosome sequence specificity, likely due to genome-wide chromatin remodeler activity, contribute to the formation of these megabase-scale chromatin domains. We also observe that the majority of well-positioned in vivo nucleosomes do not occupy thermodynamically favorable sequences observed in vitro. Finally, we find that exons are intrinsically more amenable to nucleosome formation compared to introns. Nucleosome occupancy of introns and exons consistently increases with G/C content in vitro but not in vivo, in agreement with our observation that G/C dinucleotide enrichment does not strongly promote in vivo nucleosome formation. Conclusions Our findings highlight the importance of both sequence specificity and active nucleosome repositioning in creating large-scale chromatin domains, and the antagonistic roles of intrinsic sequence preferences and chromatin remodelers in C. elegans. Sequence read data has been deposited into Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra; accession number SRA050182). Additional data, software and computational predictions are available on the Nucleosome Explorer website (http://nucleosome.rutgers.edu).

2013-01-01

270

Proteome changes of Caenorhabditis elegans upon a Staphylococcus aureus infection  

PubMed Central

Background The success of invertebrates throughout evolution is an excellent illustration of the efficiency of their defence strategies. Caenorhabditis elegans has proven to be an appropriate model for transcriptome studies of host-pathogen interactions. The aim of this paper is to complement this knowledge by investigating the worm's response to a Staphylococcus aureus infection through a 2-dimensional differential proteomics approach. Results Different types of growth media in combination with either E. coli OP50 or Staphylococcus aureus were tested for an effect on the worm's lifespan. LB agar was chosen and C. elegans samples were collected 1 h, 4 h, 8 h and 24 h post S. aureus infection or E. coli incubation. Proteomics analyses resulted in the identification of 130 spots corresponding to a total of 108 differentially expressed proteins. Conclusions Exploring four time-points discloses a dynamic insight of the reaction against a gram-positive infection at the level of the whole organism. The remarkable upregulation after 8 h and 24 h of many enzymes involved in the citric acid cycle might illustrate the cost of fighting off an infection. Intriguing is the downregulation of chaperone molecules, which are presumed to serve a protective role. A comparison with a similar experiment in which C. elegans was infected with the gram-negative Aeromonas hydrophila reveals that merely 9% of the identified spots, some of which even exhibiting an opposite regulation, are present in both studies. Hence, our findings emphasise the complexity and pathogen-specificity of the worm's immune response and form a firm basis for future functional research. Reviewers This article was reviewed by Itai Yanai, Dieter Wolf and Torben Luebke (nominated by Walter Lutz).

2010-01-01

271

Caenorhabditis elegans: a model to monitor bacterial air quality  

PubMed Central

Background Low environmental air quality is a significant cause of mortality and morbidity and this question is now emerging as a main concern of governmental authorities. Airborne pollution results from the combination of chemicals, fine particles, and micro-organisms quantitatively or qualitatively dangerous for health or for the environment. Increasing regulations and limitations for outdoor air quality have been decreed in regards to chemicals and particles contrary to micro-organisms. Indeed, pertinent and reliable tests to evaluate this biohazard are scarce. In this work, our purpose was to evaluate the Caenorhaditis elegans killing test, a model considered as an equivalent to the mouse acute toxicity test in pharmaceutical industry, in order to monitor air bacterial quality. Findings The present study investigates the bacterial population in dust clouds generated during crop ship loading in harbor installations (Rouen harbor, Normandy, France). With a biocollector, airborne bacteria were impacted onto the surface of agar medium. After incubation, a replicate of the colonies on a fresh agar medium was done using a velvet. All the replicated colonies were pooled creating the "Total Air Sample". Meanwhile, all the colonies on the original plate were isolated. Among which, five representative bacterial strains were chosen. The virulence of these representatives was compared to that of the "Total Air Sample" using the Caenorhaditis elegans killing test. The survival kinetic of nematodes fed with the "Total Air Sample" is consistent with the kinetics obtained using the five different representatives strains. Conclusions Bacterial air quality can now be monitored in a one shot test using the Caenorhaditis elegans killing test.

2011-01-01

272

Drug Absorption Efficiency in Caenorhbditis elegans Delivered by Different Methods  

PubMed Central

Background Caenorhbditis elegans has being vigorously used as a model organism in many research fields and often accompanied by administrating with various drugs. The methods of delivering drugs to worms are varied from one study to another, which make difficult in comparing results between studies. Methodology/Principal Findings We evaluated the drug absorption efficiency in C. elegans using five frequently used methods with resveratrol with low aqueous solubility and water-soluble 5-Fluoro-2?-deoxyuridine (FUDR) as positive compounds. The drugs were either applied to the LB medium with bacteria OP50, before spreading onto Nematode Growth Medium (NGM) plates (LB medium method), or to the NGM with live (NGM live method) or dead bacteria (NGM dead method), or spotting the drug solution to the surface of plates directly (spot dead method), or growing the worms in liquid medium (liquid growing method). The concentration of resveratrol and FUDR increased gradually within C. elegans and reached the highest during 12 hours to one day and then decreased slowly. At the same time point, the higher the drug concentration, the higher the metabolism rate. The drug concentrations in worms fed with dead bacteria were higher than with live bacteria at the same time point. Consistently, the drug concentration in medium with live bacteria decreased much faster than in medium with dead bacteria, reach to about half of the original concentration within 12 hours. Conclusion Resveratrol with low aqueous solubility and water-soluble FUDR have the same absorption and metabolism pattern. The drug metabolism rate in worms was both dosage and time dependent. NGM dead method and liquid growing method achieved the best absorption efficiency in worms. The drug concentration within worms was comparable with that in mice, providing a bridge for dose translation from worms to mammals.

Zheng, Shan-Qing; Ding, Ai-Jun; Li, Guo-Ping; Wu, Gui-Sheng; Luo, Huai-Rong

2013-01-01

273

Characterisation of Caenorhabditis elegans sperm transcriptome and proteome  

PubMed Central

Background Although sperm is transcriptionally and translationally quiescent, complex populations of RNAs, including mRNAs and non-coding RNAs, exist in sperm. Previous microarray analysis of germ cell mutants identified hundreds of sperm genes in Caenorhabditis elegans. To take a more comprehensive view on C. elegans sperm genes, here, we isolate highly pure sperm cells and employ high-throughput technologies to obtain sperm transcriptome and proteome. Results First, sperm transcriptome consists of considerable amounts of non-coding RNAs, many of which have not been annotated and may play functional roles during spermatogenesis. Second, apart from kinases/phosphatases as previously reported, ion binding proteins are also enriched in sperm, underlying the crucial roles of intracellular ions in post-translational regulation in sperm. Third, while the majority of sperm genes/proteins have low abundance, a small number of sperm genes/proteins are hugely enriched in sperm, implying that sperm only rely on a small set of proteins for post-translational regulation. Lastly, by extensive RNAi screening of sperm enriched genes, we identified a few genes that control fertility. Our further analysis reveals a tight correlation between sperm transcriptome and sperm small RNAome, suggesting that the endogenous siRNAs strongly repress sperm genes. This leads to an idea that the inefficient RNAi screening of sperm genes, a phenomenon currently with unknown causes, might result from the competition between the endogenous RNAi pathway and the exogenous RNAi pathway. Conclusions Together, the obtained sperm transcriptome and proteome serve as valuable resources to systematically study spermatogenesis in C. elegans.

2014-01-01

274

Diurnal ventilatory patterns in the garter snake, Thamnophis elegans  

Microsoft Academic Search

Garter snakes,Thamnophis elegans, were entrained to a 14L (06.30–20.30 h) 10D (20.30–06.30 h) cycle for five weeks at 25 °C. Following entrainment, simultaneous measurements of ventilation and oxygen uptake were made. Pulmonary oxygen uptake (\\u000a$$\\\\dot V_{O_2 } $$\\u000a) exhibited a diurnal rhythm with minimum values of\\u000a$$\\\\dot V_{O_2 } $$\\u000a occurring during 10D. The diurnal rhythm persisted during

James W. Hicks; Marvin L. Riedesel

1983-01-01

275

Folate status of gut microbiome affects Caenorhabditis elegans lifespan  

PubMed Central

In a paper in BMC Biology Virk et al. show that Caenorhabditis elegans lifespan is extended in response to a diet of folate-deficient Escherichia coli. The deficiencies in folate biosynthesis were due to an aroD mutation, or treatment of E. coli with sulfa drugs, which are mimics of the folate precursor para-aminobenzoic acid. This study suggests that pharmacological manipulation of the gut microbiome folate status may be a viable approach to slow animal aging, and raises questions about folate supplementation. See research article http://www.http://www.biomedcentral.com/1741-7007/10/67

2012-01-01

276

Google matrix analysis of C.elegans neural network  

NASA Astrophysics Data System (ADS)

We study the structural properties of the neural network of the C.elegans (worm) from a directed graph point of view. The Google matrix analysis is used to characterize the neuron connectivity structure and node classifications are discussed and compared with physiological properties of the cells. Our results are obtained by a proper definition of neural directed network and subsequent eigenvector analysis which recovers some results of previous studies. Our analysis highlights particular sets of important neurons constituting the core of the neural system. The applications of PageRank, CheiRank and ImpactRank to characterization of interdependency of neurons are discussed.

Kandiah, V.; Shepelyansky, D. L.

2014-05-01

277

Caenorhabditis elegans - A model system for space biology studies  

NASA Technical Reports Server (NTRS)

The utility of the nematode Caenorhabditis elegans in studies spanning aspects of development, aging, and radiobiology is reviewed. These topics are interrelated via cellular and DNA repair processes especially in the context of oxidative stress and free-radical metabolism. The relevance of these research topics to problems in space biology is discussed and properties of the space environment are outlined. Exposure to the space-flight environment can induce rapid changes in living systems that are similar to changes occurring during aging; manipulation of these environmental parameters may represent an experimental strategy for studies of development and senescence. The current and future opportunities for such space-flight experimentation are presented.

Johnson, Thomas E.; Nelson, Gregory A.

1991-01-01

278

Molecular epidemiology of Italian clinical Cryptococcus neoformans var. grubii isolates.  

PubMed

Cryptococcus neoformans variety grubii is the major etiological agent of cryptococcal meningitis in both immunocompromised and immunocompetent patients. The current PCR-based molecular methods are not sufficient to discriminate among the different populations of this yeast. Therefore, the aim of the present study was to investigate the genotypes of the Italian clinical C. neoformans var. grubii isolates by multilocus sequence typing (MLST). A total of 53 isolates, each representative of a single case, were studied. Genotyping was performed using the ISHAM Cryptococcus MLST consensus scheme and the results were compared to the publically available global C. neoformans var. grubii MLST dataset. A total of 16 genotypes were identified; 14 were new genotypes, one was identical to sequence type (ST) ST81, which had been previously reported from Thailand, and one to ST23 already identified in Uganda, the USA and Korea. Sequence type ST61 was the most numerous, including 16 isolates. Network phylogenetic analysis showed that the Italian isolates could be divided into at least three clusters with similarities with those recovered in Africa, Asia and Americas. Distribution of the STs among the isolates could not be correlated to the hospital in which they were recovered or to the HIV status of the patients. The majority of the isolates belonged to the molecular type VNI; three belonged to the rare molecular type VNII and one to the VNB group, which until now had not been described in Europe. The results reveal that the Italian C. neoformans var. grubii population presents a distinct variability, displaying a high number of new genotypes, and probably recombines sexually. PMID:23286351

Cogliati, Massimo; Zamfirova, Ralika R; Tortorano, Anna Maria; Viviani, Maria Anna

2013-07-01

279

Evolution of host innate defence: insights from C. elegans and primitive invertebrates  

PubMed Central

Preface The genetically tractable model organism Caenorhabditis elegans was first used to model bacterial virulence in vivo a decade ago. Since then, great strides have been made in the identification of host response pathways that are involved in the defence against infection. Strikingly, C. elegans seems to detect and respond to infection without the involvement of its Toll-like receptor homologue, in contrast to the well-established role for these proteins in innate immunity in mammals. What, therefore, do we know about host defence mechanisms in C. elegans, and what can they tell us about innate immunity in higher organisms?

Irazoqui, Javier E.; Urbach, Jonathan M.; Ausubel, Frederick M.

2010-01-01

280

Sesquiterpenoids from Tanacetum argenteum subsp. canum var. canum  

Microsoft Academic Search

Aerial parts of Tanacetum argenteum subsp. canum var. canum afforded fourteen sesquiterpene lactones, two of them being new. The new compounds 1?-hydroxy-6?-angeloyloxygermacra-4(5),10(14),11(13)-trien-8,12-olide and 1?,4?-dihydroxy-6?-isobutyloxyeudesm-11(13)-en-8,12-olide, as well as the known ones: parthenolide, peroxyparthenolide, dihyroparthenolide, 1-epi-tatridin B, sivasinolide, flabellin, 1?,4?-dihydroxy-6?-angeloyloxyeudesm-11(13)-en-8,12-olide, 1?-hydroxy-6?-angeloyloxyeudesm-4(15),11(13)-dien-8,12-olide, michelenolide, magnograndiolide, santamarin and douglanin, were identified by spectral methods.

Nezhun Gören; Elif Tahtasakal

1997-01-01

281

[Study on chemical constituents of Drosera peltata var. multisepala].  

PubMed

Chemical investigatation of Drosera peltata var. multisepala led to the isolation of eleven compounds using various chromatographic techniques. The structures of these compounds were elucidated as isoshinanolone-4-O-beta-D-glucoside (1), isoshinanolone (2), epi-isoshinanolone (3), plumbagin (4), droserone (5), droserone-5-O-glucoside (6), quercetin (7), kaempferol (8) , gossypetin-8-O-glucoside (9), 3,3'-dimethoxy ellagic acid (10), and ellagic acid (11) by their physicochemical properties and spectral data analysis. Compound 1 was a new compound. Compounds 3, 8, 10, and 11 were isolated from this plant for the first time. PMID:22737855

Li, Lin; Huang, Jin; Xu, Xianghua; Zhang, Yao; Cheng, Kejun; Yu, Peizhong

2012-01-01

282

Triterpenoid saponins from Polycarpaea corymbosa Lamk. var. eriantha Hochst.  

PubMed

Four triterpenoid saponins (1-4) were isolated from Polycarpaea corymbosa Lamk. var. eriantha Hochst along with the known apoanagallosaponin IV (5). Their structures were elucidated by spectroscopic data analysis. Among the compounds 1, 3-5 which were evaluated for their cytotoxicity against three tumor cell lines (SW480, DU145 and EMT6), compound 1 exhibited cytotoxicity with IC50 values ranging from 4.61 to 22.61 ?M, which was greater than that of etoposide. Compound 2 was tested only against SW480 and a cardiomyoblast cell line (H9c2), and was inactive. PMID:24507482

Manase, Mahenina Jaovita; Mitaine-Offer, Anne-Claire; Miyamoto, Tomofumi; Tanaka, Chiaki; Delemasure, Stéphanie; Dutartre, Patrick; Lacaille-Dubois, Marie-Aleth

2014-04-01

283

Sesquiterpenes and other constituents from Dendranthema zawadskii var. latilobum.  

PubMed

Six new germacranolides, zawadskinolides A-F (1-6), and a new eudesmane glucoside, chrysantiloboside (7) were isolated from the aerial parts of Dendranthema zawadskii var. latilobum, along with thirteen known constituents. Their structures were elucidated by means of spectroscopic evidence. Bioassay showed that flavonoids such as apigenin (9), (-)-eriodictyol (10) and nepetin (12), as well as the sesquiterpene lactone, zawadskinolide F (6), inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophage cells with IC50 values of 66.15, 132.55, 35.44, and 91.32??M, respectively. PMID:22382409

Shin, Hyun Jung; Lee, So Young; Kim, Ju Sun; Lee, Sanghyun; Choi, Ran Joo; Chung, Ha Sook; Kim, Yeong Shik; Kang, Sam Sik

2012-01-01

284

Amino acid sequence of ferredoxin from Physalis alkekengi var. francheti.  

PubMed

The complete amino acid sequence of [2Fe-2S] ferredoxin from Physalis alkekengi var. francheti has been determined by automated Edman degradation of the entire Cm-protein and of the peptides obtained by trypsin and endoproteinase Asp-N digestions. This ferredoxin exhibited ten, ten, and nine differences respectively in the amino acid sequence, when compared with the ferredoxins of Datura stramonium, D. metel, and D. arborea, but 21-28 differences for other angiosperms, and 34-37 differences for fern and horsetails. These results are in harmony with the taxonomic position for these plants. PMID:9862138

Mino, Y; Yasuda, K

1998-11-01

285

[Chemical constituents from roots of Chirita longgangensis var. hongyao].  

PubMed

To study the chemical constituents from the roots of Chirita longgangensis var. hongyao. The methanol extract was isolated and purified by silica gel, Sephadex LH-20 and preparative HPLC. Their structures were elucidated by MS and spectral data (1H, 13C-NMR). Seven compounds were isolated and identified as plantainoside A (1), plantainoside B (2), calcedarioside C (3), calcedarioside D (4), platyphylloside (5), hirsutanonol (6), and hirsutanonol-5-O-beta-D-glucopyranoside (7). Compounds 5-7 were isolated for the first time from the family Gesneriaceae. PMID:24956847

Huang, Hai-Jiang; He, Lan-Yun

2014-03-01

286

Neural integrity is maintained by dystrophin in C. elegans.  

PubMed

The dystrophin protein complex (DPC), composed of dystrophin and associated proteins, is essential for maintaining muscle membrane integrity. The link between mutations in dystrophin and the devastating muscle failure of Duchenne's muscular dystrophy (DMD) has been well established. Less well appreciated are the accompanying cognitive impairment and neuropsychiatric disorders also presented in many DMD patients, which suggest a wider role for dystrophin in membrane-cytoskeleton function. This study provides genetic evidence of a novel role for DYS-1/dystrophin in maintaining neural organization in Caenorhabditis elegans. This neuronal function is distinct from the established role of DYS-1/dystrophin in maintaining muscle integrity and regulating locomotion. SAX-7, an L1 cell adhesion molecule (CAM) homologue, and STN-2/?-syntrophin also function to maintain neural integrity in C. elegans. This study provides biochemical data that show that SAX-7 associates with DYS-1 in an STN-2/?-syntrophin-dependent manner. These results reveal a recruitment of L1CAMs to the DPC to ensure neural integrity is maintained. PMID:21242290

Zhou, Shan; Chen, Lihsia

2011-01-24

287

Transformation of 1- and 2-methylnaphthalene by Cunninghamella elegans.  

PubMed Central

Cunninghamella elegans metabolized 1- and 2-methylnaphthalene primarily at the methyl group to form 1- and 2-hydroxymethylnaphthalene, respectively. Other compounds isolated and identified were 1- and 2-naphthoic acids, 5-hydroxy-1-naphthoic acid, 5-hydroxy-2-naphthoic acid, 6-hydroxy-2-naphthoic acid, and phenolic derivatives of 1- and 2-methylnaphthalene. The metabolites were isolated by thin-layer and reverse-phase high-pressure liquid chromatography and characterized by the application of UV-visible absorption, 1H nuclear magnetic resonance, and mass spectral techniques. Experiments with [8-14C]2-methylnaphthalene indicated that over a 72-h period, 9.8% of 2-methylnaphthalene was oxidized to metabolic products. The ratio of organic-soluble in water-soluble metabolites at 2 h was 92:8, and at 72 h it was 41:59. Enzymatic treatment of the 48-h aqueous phase with either beta-glucuronidase or arylsulfatase released 60% of the metabolites of 2-methylnaphthalene that were extractable with ethyl acetate. In both cases, the major conjugates released were 5-hydroxy-2-naphthoic acid and 6-hydroxy-2-naphthoic acid. The ratio of the water-soluble glucuronide conjugates to sulfate conjugates was 1:1. Incubation of C. elegans with 2-methylnaphthalene under an 18O2 atmosphere and subsequent mass spectral analysis of 2-hydroxymethylnaphthalene indicated that hydroxylation of the methyl group is catalyzed by a monooxygenase.

Cerniglia, C E; Lambert, K J; Miller, D W; Freeman, J P

1984-01-01

288

Emergence of long timescales and stereotyped behaviors in Caenorhabditis elegans  

PubMed Central

Animal behaviors often are decomposable into discrete, stereotyped elements, well separated in time. In one model, such behaviors are triggered by specific commands; in the extreme case, the discreteness of behavior is traced to the discreteness of action potentials in the individual command neurons. Here, we use the crawling behavior of the nematode Caenorhabditis elegans to demonstrate the opposite view, in which discreteness, stereotypy, and long timescales emerge from the collective dynamics of the behavior itself. In previous work, we found that as C. elegans crawls, its body moves through a “shape space” in which four dimensions capture approximately 95% of the variance in body shape. Here we show that stochastic dynamics within this shape space predicts transitions between attractors corresponding to abrupt reversals in crawling direction. With no free parameters, our inferred stochastic dynamical system generates reversal timescales and stereotyped trajectories in close agreement with experimental observations. We use the stochastic dynamics to show that the noise amplitude decreases systematically with increasing time away from food, resulting in longer bouts of forward crawling and suggesting that worms can use noise to modify their locomotory behavior.

Stephens, Greg J.; Bueno de Mesquita, Matthew; Ryu, William S.; Bialek, William

2011-01-01

289

Genetic Analysis of the Caenorhabditis elegans pax-6 Locus  

PubMed Central

PAX-6 proteins are involved in eye and brain development in many animals. In the nematode Caenorhabditis elegans the pax-6 locus encodes multiple PAX-6 isoforms both with and without a paired domain. Mutations in the C. elegans pax-6 locus can be grouped into three classes. Mutations that affect paired domain-containing isoforms cause defects in epidermal morphogenesis, epidermal cell fates, and gonad cell migration and define the class I (vab-3) complementation group. The class II mutation mab-18(bx23) affects nonpaired domain-containing isoforms and transforms the fate of a sensory organ in the male tail. Class III mutations affect both paired domain and nonpaired domain isoforms; the most severe class III mutations are candidate null mutations in pax-6. Class III mutant phenotypes do not resemble a simple sum of class I and class II phenotypes. A comparison of class I and class III phenotypes indicates that PAX-6 isoforms can interact additively, synergistically, or antagonistically, depending on the cellular context.

Cinar, Hediye Nese; Chisholm, Andrew D.

2004-01-01

290

Mitochondrial efficiency is increased in axenically cultured Caenorhabditis elegans.  

PubMed

Culturing Caenorhabditis elegans in axenic medium leads to a twofold increase in lifespan and considering the similar phenotypical traits with dietary restricted animals, it is referred to as axenic dietary restriction (ADR). The free radical theory of aging has suggested a pivotal role for mitochondria in the aging process and previous findings established that culture in axenic medium increases metabolic rate. We asked whether axenic culture induces changes in mitochondrial functionality of C. elegans. We show that ADR induces increased electron transport chain (ETC) capacity, enhanced coupling efficiency and reduced leakiness of the mitochondria of young adult worms but not a decrease of ROS production capacity and in vivo H2O2 levels. The age-dependent increase in leak respiration and decrease in coupling efficiency is repressed under ADR conditions. Although ADR mitochondria experience a decrease in ETC capacity with age, they succeed to maintain highly efficient and well-coupled function compared to fully fed controls. This might be mediated by combination of a limited increase in supercomplex abundance and decreased individual CIV abundance, facilitating electron transport and ultimately leading to increased mitochondrial efficiency. PMID:24556280

Castelein, Natascha; Muschol, Michael; Dhondt, Ineke; Cai, Huaihan; De Vos, Winnok H; Dencher, Norbert A; Braeckman, Bart P

2014-08-01

291

Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans  

NASA Astrophysics Data System (ADS)

It has been theorized for decades that mitochondria act as the biological clock of ageing, but the evidence is incomplete. Here we show a strong coupling between mitochondrial function and ageing by in vivo visualization of the mitochondrial flash (mitoflash), a frequency-coded optical readout reflecting free-radical production and energy metabolism at the single-mitochondrion level. Mitoflash activity in Caenorhabditis elegans pharyngeal muscles peaked on adult day 3 during active reproduction and on day 9 when animals started to die off. A plethora of genetic mutations and environmental factors inversely modified the lifespan and the day-3 mitoflash frequency. Even within an isogenic population, the day-3 mitoflash frequency was negatively correlated with the lifespan of individual animals. Furthermore, enhanced activity of the glyoxylate cycle contributed to the decreased day-3 mitoflash frequency and the longevity of daf-2 mutant animals. These results demonstrate that the day-3 mitoflash frequency is a powerful predictor of C. elegans lifespan across genetic, environmental and stochastic factors. They also support the notion that the rate of ageing, although adjustable in later life, has been set to a considerable degree before reproduction ceases.

Shen, En-Zhi; Song, Chun-Qing; Lin, Yuan; Zhang, Wen-Hong; Su, Pei-Fang; Liu, Wen-Yuan; Zhang, Pan; Xu, Jiejia; Lin, Na; Zhan, Cheng; Wang, Xianhua; Shyr, Yu; Cheng, Heping; Dong, Meng-Qiu

2014-04-01

292

The Rich Club of the C. elegans Neuronal Connectome  

PubMed Central

There is increasing interest in topological analysis of brain networks as complex systems, with researchers often using neuroimaging to represent the large-scale organization of nervous systems without precise cellular resolution. Here we used graph theory to investigate the neuronal connectome of the nematode worm Caenorhabditis elegans, which is defined anatomically at a cellular scale as 2287 synaptic connections between 279 neurons. We identified a small number of highly connected neurons as a rich club (N = 11) interconnected with high efficiency and high connection distance. Rich club neurons comprise almost exclusively the interneurons of the locomotor circuits, with known functional importance for coordinated movement. The rich club neurons are connector hubs, with high betweenness centrality, and many intermodular connections to nodes in different modules. On identifying the shortest topological paths (motifs) between pairs of peripheral neurons, the motifs that are found most frequently traverse the rich club. The rich club neurons are born early in development, before visible movement of the animal and before the main phase of developmental elongation of its body. We conclude that the high wiring cost of the globally integrative rich club of neurons in the C. elegans connectome is justified by the adaptive value of coordinated movement of the animal. The economical trade-off between physical cost and behavioral value of rich club organization in a cellular connectome confirms theoretical expectations and recapitulates comparable results from human neuroimaging on much larger scale networks, suggesting that this may be a general and scale-invariant principle of brain network organization.

Vertes, Petra E.; Ahnert, Sebastian E.; Schafer, William R.; Bullmore, Edward T.

2013-01-01

293

Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans  

PubMed Central

In recent years, the Piwi pathway has been shown to regulate the silencing of mobile genetic elements. However, we know little about how Piwi pathways impose silencing and even less about trans-generational stability of Piwi-induced silencing. We demonstrate that the Caenorhabditis elegans Piwi protein PRG-1 can initiate an extremely stable form of gene silencing on a transgenic, single-copy target. This type of silencing is faithfully maintained over tens of generations in the absence of a functional Piwi pathway. Interestingly, RNAi can also trigger permanent gene silencing of a single-copy transgene and the phenomenon will be collectively referred to as RNA-induced epigenetic silencing (RNAe). RNAe can act in trans and is dependent on endogenous RNAi factors. The involvement of factors known to act in nuclear RNAi and the fact that RNAe is accompanied by repressive chromatin marks indicate that RNAe includes a transcriptional silencing component. Our results demonstrate that, at least in C. elegans, the Piwi pathway can impose a state of gene silencing that borders on ‘permanently silent'. Such a property may be more widely conserved among Piwi pathways in different animals.

Luteijn, Maartje J; van Bergeijk, Petra; Kaaij, Lucas J T; Almeida, Miguel Vasconcelos; Roovers, Elke F; Berezikov, Eugene; Ketting, Rene F

2012-01-01

294

3-D Worm Tracker for Freely Moving C. elegans  

PubMed Central

The manner in which the nervous system regulates animal behaviors in natural environments is a fundamental issue in biology. To address this question, C. elegans has been widely used as a model animal for the analysis of various animal behaviors. Previous behavioral assays have been limited to two-dimensional (2-D) environments, confining the worm motion to a planar substrate that does not reflect three-dimensional (3-D) natural environments such as rotting fruits or soil. Here, we develop a 3-D worm tracker (3DWT) for freely moving C. elegans in 3-D environments, based on a stereoscopic configuration. The 3DWT provides us with a quantitative trajectory, including the position and movement direction of the worm in 3-D. The 3DWT is also capable of recording and visualizing postures of the moving worm in 3-D, which are more complex than those in 2-D. Our 3DWT affords new opportunities for understanding the nervous system function that regulates animal behaviors in natural 3-D environments.

Kwon, Namseop; Pyo, Jaeyeon; Lee, Seung-Jae; Je, Jung Ho

2013-01-01

295

Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behaviour.  

PubMed

Animals locate and track chemoattractive gradients in the environment to find food. With its small nervous system, Caenorhabditis elegans is a good model system in which to understand how the dynamics of neural activity control this search behaviour. Extensive work on the nematode has identified the neurons that are necessary for the different locomotory behaviours underlying chemotaxis through the use of laser ablation, activity recording in immobilized animals and the study of mutants. However, we do not know the neural activity patterns in C. elegans that are sufficient to control its complex chemotactic behaviour. To understand how the activity in its interneurons coordinate different motor programs to lead the animal to food, here we used optogenetics and new optical tools to manipulate neural activity directly in freely moving animals to evoke chemotactic behaviour. By deducing the classes of activity patterns triggered during chemotaxis and exciting individual neurons with these patterns, we identified interneurons that control the essential locomotory programs for this behaviour. Notably, we discovered that controlling the dynamics of activity in just one interneuron pair (AIY) was sufficient to force the animal to locate, turn towards and track virtual light gradients. Two distinct activity patterns triggered in AIY as the animal moved through the gradient controlled reversals and gradual turns to drive chemotactic behaviour. Because AIY neurons are post-synaptic to most chemosensory and thermosensory neurons, it is probable that these activity patterns in AIY have an important role in controlling and coordinating different taxis behaviours of the animal. PMID:23000898

Kocabas, Askin; Shen, Ching-Han; Guo, Zengcai V; Ramanathan, Sharad

2012-10-11

296

A Distributed Chemosensory Circuit for Oxygen Preference in C. elegans  

PubMed Central

The nematode Caenorhabditis elegans has complex, naturally variable behavioral responses to environmental oxygen, food, and other animals. C. elegans detects oxygen through soluble guanylate cyclase homologs (sGCs) and responds to it differently depending on the activity of the neuropeptide receptor NPR-1: npr-1(lf) and naturally isolated npr-1(215F) animals avoid high oxygen and aggregate in the presence of food; npr-1(215V) animals do not. We show here that hyperoxia avoidance integrates food with npr-1 activity through neuromodulation of a distributed oxygen-sensing network. Hyperoxia avoidance is stimulated by sGC-expressing oxygen-sensing neurons, nociceptive neurons, and ADF sensory neurons. In npr-1(215V) animals, the switch from weak aerotaxis on food to strong aerotaxis in its absence requires close regulation of the neurotransmitter serotonin in the ADF neurons; high levels of ADF serotonin promote hyperoxia avoidance. In npr-1(lf) animals, food regulation is masked by increased activity of the oxygen-sensing neurons. Hyperoxia avoidance is also regulated by the neuronal TGF-? homolog DAF-7, a secreted mediator of crowding and stress responses. DAF-7 inhibits serotonin synthesis in ADF, suggesting that ADF serotonin is a convergence point for regulation of hyperoxia avoidance. Coalitions of neurons that promote and repress hyperoxia avoidance generate a subtle and flexible response to environmental oxygen.

Chang, Andy J; Chronis, Nikolas; Karow, David S; Marletta, Michael A; Bargmann, Cornelia I

2006-01-01

297

Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans.  

PubMed

It has been theorized for decades that mitochondria act as the biological clock of ageing, but the evidence is incomplete. Here we show a strong coupling between mitochondrial function and ageing by in vivo visualization of the mitochondrial flash (mitoflash), a frequency-coded optical readout reflecting free-radical production and energy metabolism at the single-mitochondrion level. Mitoflash activity in Caenorhabditis elegans pharyngeal muscles peaked on adult day 3 during active reproduction and on day 9 when animals started to die off. A plethora of genetic mutations and environmental factors inversely modified the lifespan and the day-3 mitoflash frequency. Even within an isogenic population, the day-3 mitoflash frequency was negatively correlated with the lifespan of individual animals. Furthermore, enhanced activity of the glyoxylate cycle contributed to the decreased day-3 mitoflash frequency and the longevity of daf-2 mutant animals. These results demonstrate that the day-3 mitoflash frequency is a powerful predictor of C.?elegans lifespan across genetic, environmental and stochastic factors. They also support the notion that the rate of ageing, although adjustable in later life, has been set to a considerable degree before reproduction ceases. PMID:24522532

Shen, En-Zhi; Song, Chun-Qing; Lin, Yuan; Zhang, Wen-Hong; Su, Pei-Fang; Liu, Wen-Yuan; Zhang, Pan; Xu, Jiejia; Lin, Na; Zhan, Cheng; Wang, Xianhua; Shyr, Yu; Cheng, Heping; Dong, Meng-Qiu

2014-04-01

298

Molecular signatures of cell migration in C. elegans Q neuroblasts  

PubMed Central

Metazoan cell movement has been studied extensively in vitro, but cell migration in living animals is much less well understood. In this report, we have studied the Caenorhabditis elegans Q neuroblast lineage during larval development, developing live animal imaging methods for following neuroblast migration with single cell resolution. We find that each of the Q descendants migrates at different speeds and for distinct distances. By quantitative green fluorescent protein imaging, we find that Q descendants that migrate faster and longer than their sisters up-regulate protein levels of MIG-2, a Rho family guanosine triphosphatase, and/or down-regulate INA-1, an integrin ? subunit, during migration. We also show that Q neuroblasts bearing mutations in either MIG-2 or INA-1 migrate at reduced speeds. The migration defect of the mig-2 mutants, but not ina-1, appears to result from a lack of persistent polarization in the direction of cell migration. Thus, MIG-2 and INA-1 function distinctly to control Q neuroblast migration in living C. elegans.

Ou, Guangshuo

2009-01-01

299

Axons degenerate in the absence of mitochondria in C. elegans.  

PubMed

Many neurodegenerative disorders are associated with mitochondrial defects [1-3]. Mitochondria can play an active role in degeneration by releasing reactive oxygen species and apoptotic factors [4-7]. Alternatively, mitochondria can protect axons from stress and insults, for example by buffering calcium [8]. Recent studies manipulating mitochondria lend support to both of these models [9-13]. Here, we identify a C. elegans mutant, ric-7, in which mitochondria are unable to exit the neuron cell bodies, similar to the kinesin-1/unc-116 mutant. When axons lacking mitochondria are cut with a laser, they rapidly degenerate. Some neurons even spontaneously degenerate in ric-7 mutants. Degeneration can be suppressed by forcing mitochondria into the axons of the mutants. The protective effect of mitochondria is also observed in the wild-type: a majority of axon fragments containing a mitochondrion survive axotomy, whereas those lacking mitochondria degenerate. Thus, mitochondria are not required for axon degeneration and serve a protective role in C. elegans axons. PMID:24631238

Rawson, Randi L; Yam, Lung; Weimer, Robby M; Bend, Eric G; Hartwieg, Erika; Horvitz, H Robert; Clark, Scott G; Jorgensen, Erik M

2014-03-31

300

PTL-1 regulates neuronal integrity and lifespan in C. elegans  

PubMed Central

Summary Protein with tau-like repeats (PTL-1) is the sole Caenorhabditis elegans homolog of tau and MAP2, which are members of the mammalian family of microtubule-associated proteins (MAPs). In mammalian neurons, tau and MAP2 are segregated, with tau being mainly localised to the axon and MAP2 mainly to the dendrite. In particular, tau plays a crucial role in pathology, as elevated levels lead to the formation of tau aggregates in many neurodegenerative conditions including Alzheimer's disease. We used PTL-1 in C. elegans to model the biological functions of a tau-like protein without the complication of functional redundancy that is observed among the mammalian MAPs. Our findings indicate that PTL-1 is important for the maintenance of neuronal health as animals age, as well as in the regulation of whole organism lifespan. In addition, gene dosage of PTL-1 is crucial because variations from wild-type levels are detrimental. We also observed that human tau is unable to robustly compensate for loss of PTL-1, although phenotypes observed in tau transgenic worms are dependent on the presence of endogenous PTL-1. Our data suggest that some of the effects of tau pathology result from the loss of physiological tau function and not solely from a toxic gain-of-function due to accumulation of tau.

Chew, Yee Lian; Fan, Xiaochen; Gotz, Jurgen; Nicholas, Hannah R.

2013-01-01

301

A sexually conditioned switch of chemosensory behavior in C. elegans.  

PubMed

In sexually reproducing animals, mating is essential for transmitting genetic information to the next generation and therefore animals have evolved mechanisms for optimizing the chance of successful mate location. In the soil nematode C. elegans, males approach hermaphrodites via the ascaroside pheromones, recognize hermaphrodites when their tails contact the hermaphrodites' body, and eventually mate with them. These processes are mediated by sensory signals specialized for sexual communication, but other mechanisms may also be used to optimize mate location. Here we describe associative learning whereby males use sodium chloride as a cue for hermaphrodite location. Both males and hermaphrodites normally avoid sodium chloride after associative conditioning with salt and starvation. However, we found that males become attracted to sodium chloride after conditioning with salt and starvation if hermaphrodites are present during conditioning. For this conditioning, which we call sexual conditioning, hermaphrodites are detected by males through pheromonal signaling and additional cue(s). Sex transformation experiments suggest that neuronal sex of males is essential for sexual conditioning. Altogether, these results suggest that C. elegans males integrate environmental, internal and social signals to determine the optimal strategy for mate location. PMID:23861933

Sakai, Naoko; Iwata, Ryo; Yokoi, Saori; Butcher, Rebecca A; Clardy, Jon; Tomioka, Masahiro; Iino, Yuichi

2013-01-01

302

Aging and resistance to oxidative damage in Caenorhabditis elegans.  

PubMed

The dauer larva state and the age-1 mutation, both of which extend life-span in Caenorhabditis elegans, were tested for hyperresistance to cellular damage that may be relevant to aging. The age-1 strain TJ401 displayed hyperresistance to oxidative stress relative to its parental strain. The activities of two enzymes that protect cells from oxidative damage, superoxide dismutase (SOD) and catalase, showed an age-dependent increase in mutant animals, which was not seen in the parental strain. These increases in activities paralleled the time course of the hyperresistance. The results are consistent with the age-1 gene product functioning as a negative regulator of SOD and catalase activities. In wild-type and age-1 dauer larvae, elevated levels of SOD activity, but not of catalase activity, were present when compared with young adults. The common increase in SOD activity prompted cloning the C. elegans Cu/Zn SOD gene. Its position on the physical map of the genome was in the region to which the age-1 gene has been genetically mapped, but it is unlikely that a mutation at the SOD locus confers the Age phenotype. Results support the free radical theory of aging by suggesting that the increased resistance to oxidative stress may be among the causes of increased longevity in both strain TJ401 and in the dauer larva. PMID:8415630

Larsen, P L

1993-10-01

303

Gait Modulation in C. elegans: An Integrated Neuromechanical Model  

PubMed Central

Equipped with its 302-cell nervous system, the nematode Caenorhabditis elegans adapts its locomotion in different environments, exhibiting so-called swimming in liquids and crawling on dense gels. Recent experiments have demonstrated that the worm displays the full range of intermediate behaviors when placed in intermediate environments. The continuous nature of this transition strongly suggests that these behaviors all stem from modulation of a single underlying mechanism. We present a model of C. elegans forward locomotion that includes a neuromuscular control system that relies on a sensory feedback mechanism to generate undulations and is integrated with a physical model of the body and environment. We find that the model reproduces the entire swim-crawl transition, as well as locomotion in complex and heterogeneous environments. This is achieved with no modulatory mechanism, except via the proprioceptive response to the physical environment. Manipulations of the model are used to dissect the proposed pattern generation mechanism and its modulation. The model suggests a possible role for GABAergic D-class neurons in forward locomotion and makes a number of experimental predictions, in particular with respect to non-linearities in the model and to symmetry breaking between the neuromuscular systems on the ventral and dorsal sides of the body.

Boyle, Jordan H.; Berri, Stefano; Cohen, Netta

2012-01-01

304

Selenium induces cholinergic motor neuron degeneration in Caenorhabditis elegans.  

PubMed

Selenium is an essential micronutrient required for cellular antioxidant systems, yet at higher doses it induces oxidative stress. Additionally, in vertebrates environmental exposures to toxic levels of selenium can cause paralysis and death. Here we show that selenium-induced oxidative stress leads to decreased cholinergic signaling and degeneration of cholinergic neurons required for movement and egg-laying in Caenorhabditis elegans. Exposure to high levels of selenium leads to proteolysis of a soluble muscle protein through mechanisms suppressible by two pharmacological agents, levamisole and aldicarb which enhance cholinergic signaling in muscle. In addition, animals with reduction-of-function mutations in genes encoding post-synaptic levamisole-sensitive acetylcholine receptor subunits or the vesicular acetylcholine transporter developed impaired forward movement faster during selenium-exposure than normal animals, again confirming that selenium reduces cholinergic signaling. Finally, the antioxidant reduced glutathione, inhibits selenium-induced reductions in egg-laying through a cellular protective mechanism dependent on the C. elegans glutaredoxin, GLRX-21. These studies provide evidence that the environmental toxicant selenium induces neurodegeneration of cholinergic neurons through depletion of glutathione, a mechanism linked to the neuropathology of Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. PMID:22560997

Estevez, Annette O; Mueller, Catherine L; Morgan, Kathleen L; Szewczyk, Nathaniel J; Teece, Luke; Miranda-Vizuete, Antonio; Estevez, Miguel

2012-10-01

305

3-D worm tracker for freely moving C. elegans.  

PubMed

The manner in which the nervous system regulates animal behaviors in natural environments is a fundamental issue in biology. To address this question, C. elegans has been widely used as a model animal for the analysis of various animal behaviors. Previous behavioral assays have been limited to two-dimensional (2-D) environments, confining the worm motion to a planar substrate that does not reflect three-dimensional (3-D) natural environments such as rotting fruits or soil. Here, we develop a 3-D worm tracker (3DWT) for freely moving C. elegans in 3-D environments, based on a stereoscopic configuration. The 3DWT provides us with a quantitative trajectory, including the position and movement direction of the worm in 3-D. The 3DWT is also capable of recording and visualizing postures of the moving worm in 3-D, which are more complex than those in 2-D. Our 3DWT affords new opportunities for understanding the nervous system function that regulates animal behaviors in natural 3-D environments. PMID:23437394

Kwon, Namseop; Pyo, Jaeyeon; Lee, Seung-Jae; Je, Jung Ho

2013-01-01

306

Microbeam irradiation of C. elegans nematode in microfluidic channels.  

PubMed

To perform high-throughput studies on the biological effects of ionizing radiation in vivo, we have implemented a microfluidic tool for microbeam irradiation of Caenorhabditis elegans. The device allows the immobilization of worms with minimal stress for a rapid and controlled microbeam irradiation of multiple samples in parallel. Adapted from an established design, our microfluidic clamp consists of 16 tapered channels with 10-?m-thin bottoms to ensure charged particle traversal. Worms are introduced into the microfluidic device through liquid flow between an inlet and an outlet, and the size of each microchannel guarantees that young adult worms are immobilized within minutes without the use of anesthesia. After site-specific irradiation with the microbeam, the worms can be released by reversing the flow direction in the clamp and collected for analysis of biological endpoints such as repair of radiation-induced DNA damage. For such studies, minimal sample manipulation and reduced use of drugs such as anesthetics that might interfere with normal physiological processes are preferable. By using our microfluidic device that allows simultaneous immobilization and imaging for irradiation of several whole living samples on a single clamp, here we show that 4.5-MeV proton microbeam irradiation induced DNA damage in wild-type C. elegans, as assessed by the formation of Rad51 foci that are essential for homologous repair of radiation-induced DNA damage. PMID:23942865

Buonanno, M; Garty, G; Grad, M; Gendrel, M; Hobert, O; Brenner, D J

2013-11-01

307

Phylogenetic analysis of cryptic speciation in the polychaete Pygospio elegans  

PubMed Central

Development in marine invertebrate species can take place through a variety of modes and larval forms, but within a species, developmental mode is typically uniform. Poecilogony refers to the presence of more than one mode of development within a single species. True poecilogony is rare, however, and in some cases, apparent poecilogony is actually the result of variation in development mode among recently diverged cryptic species. We used a phylogenetic approach to examine whether poecilogony in the marine polychaete worm, Pygospio elegans, is the result of cryptic speciation. Populations of worms identified as P. elegansooded, and intermediate larvae; these modes are found both within and among populations. We examined sequence variation among partial mitochondrial cytochrome c oxidase subunit I sequences obtained for 279 individual worms sampled across broad geographic and environmental scales. Despite a large number of unique haplotypes (121 haplotypes from 279 individuals), sequence divergence among European samples was low (1.7%) with most of the sequence variation observed within populations, relative to the variation among regions. More importantly, we observed common haplotypes that were widespread among the populations we sampled, and the two most common haplotypes were shared between populations differing in developmental mode. Thus, our results support an earlier conclusion of poecilogony in P elegans. In addition, predominantly planktonic populations had a larger number of population-specific low-frequency haplotypes. This finding is largely consistent with interspecies comparisons showing high diversity for species with planktonic developmental modes in contrast to low diversity in species with brooded developmental modes.

Kesaniemi, J E; Rawson, P D; Lindsay, S M; Knott, K E

2012-01-01

308

Economic Growth and Threatened and Endangered Species Listings: A VAR Analysis  

Microsoft Academic Search

We conduct several analyses to examine the link between threatened and endangered species listings and macroeconomic activity. Preliminary tests using ordinary least squares are run on both time series data on the national level and cross sectional data at the state level. The analysis is then extended using vector autoregressive (VAR) techniques. VAR results, impulse response functions and variance decompositions

Catherine M. Chambers; Paul E. Chambers; John C. Whitehead

2008-01-01

309

Polimorfismo en Phaseolus vulgaris var. aborigineus (Fabaceae). Evidencias que indican hibridación natural  

Microsoft Academic Search

A polymorphic population of Phaseolus vulgaris var. aborigineus growing at the Northwest of Argentina was studied. In order to know the origin of this polymorphism, some plants belonging to the var. abo- rigineus, other plants showing floral dimorphism and other individuals with particular characters were collect- ed. Their seeds, obtained after field-work treatments of autogamy and free pollination, were sown

Patricia S. Hoc; Shirley M. Espert; Susana I. Drewes; Alicia D. Burghardt

310

Infection caused by Cryptococcus neoformans var. gattii serotype B in an AIDS patient in India.  

PubMed

Cryptococcus neoformans is an opportunistic pathogen infecting AIDS patients. However, infection caused by C. neoformans var. gattii in AIDS patients is reportedly rare. We report herein the first culture proven C. neoformans var. gattii serotype B infection in an AIDS patient in India. PMID:9292426

Abraham, M; Mathews, V; Ganesh, A; John, T J; Mathews, M S

1997-01-01

311

Sexual Cycle of Cryptococcus neoformans var. grubii and Virulence of Congenic a and   Isolates  

Microsoft Academic Search

Cryptococcus neoformans is a human-pathogenic fungus that has evolved into three distinct varieties that infect most prominently the central nervous system. A sexual cycle involving haploid cells of a and mating types has been reported for two varieties (C. neoformans var. neoformans, serotype D, and C. neoformans var. gattii, serotypes B and C), yet the vast majority of infections involve

Kirsten Nielsen; Gary M. Cox; Ping Wang; Dena L. Toffaletti; John R. Perfect; Joseph Heitman

2003-01-01

312

Modeling and application studies for a modern static VAr system installation  

Microsoft Academic Search

This paper presents a description of modeling and application studies related to a modern static VAr system (SVS) installation in a utility grid. The SVS incorporates a fully integrated static VAr compensator (SVC) and coordinated, automatically switched capacitor banks using a sophisticated control system. The capacitor banks are switched by individual circuit breakers. Descriptions are provided for the SVC control

Pouyan Pourbeik; Anders Boström; Bhaskar Ray

2006-01-01

313

A Control System for Static VAr Compensator Based on a Digitally Controlled Oscillator  

Microsoft Academic Search

This article deals with the design, construction, and testing of a new control system for a static VAr compensator. The new control system is based on monitoring reactive power, which is used as the only feedback variable for a digitally controlled oscillator. In addition to synchronizing the static VAr compensator with the AC system, the digitally controlled oscillator also schedules

S. Calderón-Fernández; M. Hernández-Ángeles; J. L. Guardado; V. Venegas-Rebollar

2012-01-01

314

Expression of var genes located within polymorphic subtelomeric domains of Plasmodium falciparum chromosomes.  

PubMed Central

Plasmodium falciparum var genes encode a diverse family of proteins, located on the surfaces of infected erythrocytes, which are implicated in the pathology of human malaria through antigenic variation and adhesion of infected erythrocytes to the microvasculature. We have constructed a complete representative telomere-to-telomere yeast artificial chromosome (YAC) contig map of the P. falciparum chromosome 8 for studies on the chromosomal organization, distribution, and expression of var genes. Three var gene loci were identified on chromosome 8, two of which map close to the telomeres at either end of the chromosome. Analysis of the previously described chromosome 2 contig map and random P. falciparum telomeric YAC clones revealed that most, if not all, 14 P. falciparum chromosomes contain var genes in a subtelomeric location. Mapping the chromosomal location of var genes expressed in a long-term culture of the P. falciparum isolate Dd2 revealed that four of the five different expressed var genes identified map within subtelomeric locations. Expression of var genes from a chromosomal domain known for frequent rearrangements has important implications for the mechanism of var gene switching and the generation of novel antigenic and adhesive phenotypes.

Fischer, K; Horrocks, P; Preuss, M; Wiesner, J; Wunsch, S; Camargo, A A; Lanzer, M

1997-01-01

315

The guideline and procedures for constructing quality control charts with VAR models  

Microsoft Academic Search

To construct multivariate control charts for serially correlated process, a number of very detailed problems are overcome. We suggest guidelines for construction of control charts for vector autoregressive (VAR) residuals. We discuss the use of VAR models to approximate multivariate serially correlated processes, residual estimation, selecting the number of variables, and selecting appropriate orders, among other issues. In addition, we

J. Jarrett

2006-01-01

316

A Field Test of Power Swing Damping by Static Var Compensator  

Microsoft Academic Search

This paper presents the results of a field test conducted for a static var compensator installed at a 500 kV substation. The static var compensator with a damping control function improved power system damping performance significantly by increasing the synchronizing and damping torques. Frequency response analysis was employed for examining the synchronizing and damping torques. Simulations of the test cases

T. Sawa; Y. Shirai; T. Michigami; Y. Sakanaka; Y. Uemura

1989-01-01

317

Puccinia jaceae var. solstitialis teliospore priming on yellow starthistle.  

PubMed

Following the introduction of Puccinia jaceae var. solstitialis to California for biological control of yellow starthistle (Centaurea solstitialis, Asteraceae), teliospores, pycnia, and multiple urediniospore generations have been observed in the field. Because urediniospores have a relatively short life span in the field, functioning teliospores are expected to be necessary for the permanent establishment of P. jaceae var. solstitialis in California. To determine if conditions in California were conducive to this, teliospore emergence and priming were evaluated in the field. A factorial experiment in the laboratory with five incubation times and three incubation temperatures was used to determine teliospore priming requirements. Teliospore production coincided with plant senescence in August and September at two sites in 2 years; fewer teliospores were produced in 2006, suggesting inconsistent teliospore production may limit population growth and contribute to local extinctions in some areas. When teliospores were primed in the field, germination was low through the fall and abruptly peaked in January during both years. In the laboratory, teliospore germination increased as incubation time increased from 2 to 6 weeks and temperatures decreased from 12 to 4 degrees C. A degree-hour model derived from laboratory data accurately predicts when teliospores are primed for germination in the field. Based on the results obtained in this study, it is apparent that teliospore germination can occur over a range of priming conditions. However, lower temperatures and longer incubation periods are superior in breaking teliospore dormancy. PMID:19055436

Fisher, A J; Aegerter, B J; Gordon, T R; Smith, L; Woods, D M

2009-01-01

318

Baccharis megapotamica var. weirii poisoning in water buffalo (Bubalus bubalis).  

PubMed

An outbreak of an acute disease in buffalo (Bubalus bubalis) caused by the ingestion of Baccharis megapotamica var. weirii occurred in the southern region of Brazil. Ten out of 50 buffalo died 24-48 hr after being introduced into a pasture containing abundant amounts of the plant. Factors influencing the ingestion of the plant and consequent toxicosis included hunger, stress caused by shipment, and unfamiliarity with the plant. Clinical signs included serous ocular discharge, incoordination, mild bloat, and muscle trembling. One buffalo was necropsied. Gross findings included dehydration, abundant liquid in the rumen, reddening of the mucosa of forestomachs, abomasum, and intestine, and edema of the wall of the rumen. The main histologic lesions were superficial to full thickness degeneration and necrosis of the stratified epithelium lining the forestomachs, necrosis of the intestinal mucosa, and widespread lymphoid necrosis. A calf (Bos taurus) was fed a single dose of 5 g/kg/body weight of B. megapotamica var. weirii harvested from the same site where the buffalo died. Twenty hours after the administration of the plant this calf died with clinical signs and lesions similar to those observed in the naturally poisoned buffalo. PMID:21908301

Oliveira-Filho, José C; Carmo, Priscila M S; Lucena, Ricardo B; Pierezan, Felipe; Barros, Claudio S L

2011-05-01

319

Metabolic and bioactivity insights into Brassica oleracea var. acephala.  

PubMed

Seeds of Brassica oleracea var. acephala (kale) were analyzed by HPLC/UV-PAD/MSn-ESI. Several phenolic acids and flavonol derivatives were identified. The seeds of this B. oleracea variety exhibited more flavonol derivatives than those of tronchuda cabbage (Brassica oleracea var. costata), also characterized in this paper. Quercetin and isorhamnetin derivatives were found only in kale seeds. Oxalic, aconitic, citric, pyruvic, malic, quinic, shikimic, and fumaric acids were the organic acids present in these matrices, malic acid being predominant in kale and citric acid in tronchuda cabbage seeds. Acetylcholinesterase (AChE) inhibitory activity was determined in aqueous extracts from both seeds. Kale leaves and butterflies, larvae, and excrements of Pieris brassicae reared on kale were also evaluated. Kale seeds were the most effective AChE inhibitor, followed by tronchuda cabbage seeds and kale leaves. With regard to P. brassicae material, excrements exhibited stronger inhibitory capacity. These results may be explained by the presence of sinapine, an analogue of acetylcholine, only in seed materials. A strong concentration-dependent antioxidant capacity against DPPH, nitric oxide, and superoxide radicals was observed for kale seeds. PMID:19722523

Ferreres, Federico; Fernandes, Fátima; Sousa, Carla; Valentão, Patrícia; Pereira, José A; Andrade, Paula B

2009-10-14

320

Molecular structures of fructans from Agave tequilana Weber var. azul.  

PubMed

Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought. PMID:14690361

Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

2003-12-31

321

Effects of temperature, water activity and gas atmosphere on mycelial growth of tempe fungi Rhizopus microsporus var. microsporus and R. microsporus var. oligosporus  

Microsoft Academic Search

Rhizopus microsporus var. microsporus and var. oligosporus are used in the manufacture of various Asian fermented foods (tempe, black oncom, sufu). In view of solid-substrate fermentation\\u000a (SSF) control, mycelial growth of strains of both varieties was tested for sensitivity to fluctuations of temperature, water\\u000a activity and interstitial gas composition. This was achieved by measuring radial growth as well as biomass

Bei-Zhong Han; Robert M. J. Nout

2000-01-01

322

1-MCP is more effective on a floral brassica ( Brassica oleracea var. italica L.) than a leafy brassica ( Brassica rapa var. chinensis)  

Microsoft Academic Search

Florets of broccoli (Brassica oleracea var. italica L.) and the youngest fully expanded leaf detached from pak choy (Brassica rapa var. chinensis) were treated with 1-methylcyclopropene (1-MCP) overnight (16 h) and then stored at supermarket retail temperature (10°C). A concentration of 12 ?l l?1 was considered optimal for both pak choy leaves and broccoli florets. 1-MCP increased shelf life of

Amanda J Able; Lung Sing Wong; Amikha Prasad; Timothy J O'Hare

2002-01-01

323

Intestinal autophagy activity is essential for host defense against Salmonella typhimurium infection in Caenorhabditis elegans.  

PubMed

Salmonella typhimurium infects both intestinal epithelial cells and macrophages. Autophagy is a lysosomal degradation pathway that is present in all eukaryotes. Autophagy has been reported to limit the Salmonella replication in Caenorhabditis elegans and in mammals. However, it is unknown whether intestinal autophagy activity plays a role in host defense against Salmonella infection in C. elegans. In this study, we inhibited the autophagy gene bec-1 in different C. elegans tissues and examined the survival of these animals following Salmonella infection. Here we show that inhibition of the bec-1 gene in the intestine but not in other tissues confers susceptibility to Salmonella infection, which is consistent with recent studies in mice showing that autophagy is involved in clearance of Salmonella in the intestinal epithelial cells. Therefore, the intestinal autophagy activity is essential for host defense against Salmonella infection from C. elegans to mice, perhaps also in humans. PMID:24674884

Curt, Alexander; Zhang, Jiuli; Minnerly, Justin; Jia, Kailiang

2014-08-01

324

The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans.  

PubMed

Autophagy is a cellular recycling process that has an important anti-aging role, but the underlying molecular mechanism is not well understood. The mammalian transcription factor EB (TFEB) was recently shown to regulate multiple genes in the autophagy process. Here we show that the predicted TFEB orthologue HLH-30 regulates autophagy in Caenorhabditis elegans and, in addition, has a key role in lifespan determination. We demonstrate that hlh-30 is essential for the extended lifespan of Caenorhabditis elegans in six mechanistically distinct longevity models, and overexpression of HLH-30 extends lifespan. Nuclear localization of HLH-30 is increased in all six Caenorhabditis elegans models and, notably, nuclear TFEB levels are augmented in the livers of mice subjected to dietary restriction, a known longevity-extending regimen. Collectively, our results demonstrate a conserved role for HLH-30 and TFEB in autophagy, and possibly longevity, and identify HLH-30 as a uniquely important transcription factor for lifespan modulation in Caenorhabditis elegans. PMID:23925298

Lapierre, Louis R; De Magalhaes Filho, C Daniel; McQuary, Philip R; Chu, Chu-Chiao; Visvikis, Orane; Chang, Jessica T; Gelino, Sara; Ong, Binnan; Davis, Andrew E; Irazoqui, Javier E; Dillin, Andrew; Hansen, Malene

2013-01-01

325

RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans  

PubMed Central

Here we take advantage of the well-characterized and simple nervous system of Caenorhabditis elegans to further our understanding of the functions of RNA editing. We describe the two C.elegans ADAR genes, adr-1 and adr-2, and characterize strains containing homozygous deletions in each, or both, of these genes. We find that adr-1 is expressed in most, if not all, cells of the C.elegans nervous system and also in the developing vulva. Using chemotaxis assays, we show that both ADARs are important for normal behavior. Biochemical, molecular and phenotypic analyses indicate that ADR-1 and ADR-2 have distinct roles in C.elegans, but sometimes act together.

Tonkin, Leath A.; Saccomanno, Lisa; Morse, Daniel P.; Brodigan, Thomas; Krause, Michael; Bass, Brenda L.

2002-01-01

326

The neural circuits and sensory channels mediating harsh touch sensation in C. elegans  

PubMed Central

Most animals can distinguish two distinct types of touch stimuli: gentle (innocuous) and harsh (noxious/painful) touch, but the underlying mechanisms are not well understood. C. elegans is a highly successful model for the study of gentle touch sensation. However, little is known about harsh touch sensation in this organism. Here we characterize harsh touch sensation in C. elegans. We show that C. elegans exhibits differential behavioral responses to harsh touch and gentle touch. Laser ablations identify distinct sets of sensory neurons and interneurons required for harsh touch sensation at different body segments. Optogenetic stimulation of the circuitry can drive behavior. Patch-clamp recordings reveal that TRP family and amiloride-sensitive Na+ channels mediate touch-evoked currents in different sensory neurons. Our work identifies the neural circuits and characterizes the sensory channels mediating harsh touch sensation in C. elegans, establishing it as a genetic model for studying this sensory modality.

Li, Wei; Kang, Lijun; Piggott, Beverly J.; Feng, Zhaoyang; Shawn Xu, X. Z.

2011-01-01

327

Mode of bacterial pathogenesis determines phenotype in elt-2 and elt-7 RNAi Caenorhabditis elegans.  

PubMed

Caenorhabditis elegans has become a useful model for studying innate immunity. ELT-2, which is homologous to human GATA-4, -5 and -6, is considered the primary GATA transcription factor controlling intestinal immunity in C. elegans. In this study, we characterize the timeline of intestinal distension in nematodes where ELT-2 and another intestinal GATA transcription factor, ELT-7, are abrogated by RNAi using two different models: colonization and toxin-based infections by Pseudomonas aeruginosa. We show that both ELT-2 and ELT-7 are important for survival of C. elegans exposed to P. aeruginosa. Intestinal distension is accelerated in elt-2 RNAi nematodes, and is observed in colonization but not toxin-based Pseudomonas infection. Upon onset of intestinal distension, nematodes die within 24 h, regardless of experimental treatment. These data provide new insight into the role of ELT-2 and ELT-7 in protecting C. elegans against P. aeruginosa infection. PMID:21168435

Elliott, Samantha L; Sturgeon, Craig R; Travers, Deborah M; Montgomery, Madeline C

2011-05-01

328

Toxic effects of acetochlor on mortality, reproduction and growth of Caenorhabditis elegans and Pristionchus pacificus.  

PubMed

The effects of acetochlor on the mortality, growth and reproduction of two nematode species were assessed. The LC50 values for Caenorhabditis elegans and Pristionchus pacificus were 1,296 and 210.7 mg/L at 24 h, and 540.0 and 126.4 mg/L at 48 h exposure, respectively. In three succession generations, reproductive capacity was more sensitive in P. pacificus than in C. elegans. Moreover, the sublethal test endpoint of final length was more sensitive with P. pacificus. This study suggested that acetochlor had no long-term effects on C. elegans at lower concentrations. The higher concentrations of acetochlor (from 40 to 160 mg/L) revealed sublethal toxicity to the two tested species, with P. pacificus being more sensitive than C. elegans. PMID:23212891

Zhang, Jingnan; Liang, Wenju; Wu, Xia; Jiang, Siwei; Li, Qi

2013-03-01

329

Reserpine can confer stress tolerance and lifespan extension in the nematode C. elegans.  

PubMed

Though the lifespan extension mechanism is partly understood from C. elegans to mice, a viable pharmacological intervention is not yet feasible. Here, we report that reserpine largely known as an antipsychotic-antihypertensive drug, can extend C. elegans lifespan. Chronic reserpine treatment from embryo stage or young adults extends the C. elegans lifespan robustly at 25 degrees C. Most importantly, the reserpine treated long lived worms are active (locomotion and pharyngeal pumping) for a long time thereby conferring high quality throughout life. Reserpine mediated lifespan extension is independent of the daf-16 pathway and partly requires serotonin. Reserpine treatment makes the worms highly thermotolerant. Thus, in addition to its known function, reserpine is able to provide stress tolerance and lifespan extension in C. elegans. PMID:18409080

Srivastava, Deepti; Arya, Upasna; SoundaraRajan, Thangavelu; Dwivedi, Hemalata; Kumar, Sandeep; Subramaniam, Jamuna R

2008-10-01

330

Monitoring the Clearance of Apoptotic and Necrotic Cells in the Nematode Caenorhabditis elegans  

PubMed Central

The nematode Caenorhabditis elegans is an excellent model organism for studying the mechanisms controlling cell death, including apoptosis, a cell suicide event, and necrosis, pathological cell deaths caused by environmental insults or genetic alterations. C. elegans has also been established as a model for understanding how dying cells are cleared from animal bodies. In particular, the transparent nature of worm bodies and eggshells make C. elegans particularly amenable for live-cell microscopy. Here we describe methods for identifying apoptotic and necrotic cells in living C. elegans embryos, larvae, and adults and for monitoring their clearance during development. We further discuss specific methods to distinguish engulfed from unengulfed apoptotic cells, and methods to monitor cellular and molecular events occurring during phagosome maturation. These methods are based on Differential Interference Contrast (DIC) microscopy or fluorescence microscopy using GFP-based reporters.

Li, Zao; Lu, Nan; He, Xiangwei; Zhou, Zheng

2014-01-01

331

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

PubMed Central

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.

Bokov, Alex F.; Hakala, Kevin W.; Weintraub, Susan T.; Rea, Shane L.

2012-01-01

332

Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris  

PubMed Central

Background VAR2CSA is the main candidate for a vaccine against pregnancy-associated malaria, but vaccine development is complicated by the large size and complex disulfide bonding pattern of the protein. Recent X-ray crystallographic information suggests that domain boundaries of VAR2CSA Duffy binding-like (DBL) domains may be larger than previously predicted and include two additional cysteine residues. This study investigated whether longer constructs would improve VAR2CSA recombinant protein secretion from Pichia pastoris and if domain boundaries were applicable across different VAR2CSA alleles. Methods VAR2CSA sequences were bioinformatically analysed to identify the predicted C11 and C12 cysteine residues at the C-termini of DBL domains and revised N- and C-termimal domain boundaries were predicted in VAR2CSA. Multiple construct boundaries were systematically evaluated for protein secretion in P. pastoris and secreted proteins were tested as immunogens. Results From a total of 42 different VAR2CSA constructs, 15 proteins (36%) were secreted. Longer construct boundaries, including the predicted C11 and C12 cysteine residues, generally improved expression of poorly or non-secreted domains and permitted expression of all six VAR2CSA DBL domains. However, protein secretion was still highly empiric and affected by subtle differences in domain boundaries and allelic variation between VAR2CSA sequences. Eleven of the secreted proteins were used to immunize rabbits. Antibodies reacted with CSA-binding infected erythrocytes, indicating that P. pastoris recombinant proteins possessed native protein epitopes. Conclusion These findings strengthen emerging data for a revision of DBL domain boundaries in var-encoded proteins and may facilitate pregnancy malaria vaccine development.

Avril, Marion; Hathaway, Marianne J; Cartwright, Megan M; Gose, Severin O; Narum, David L; Smith, Joseph D

2009-01-01

333

The stn- 1 Syntrophin Gene of C. elegans is Functionally Related to Dystrophin and Dystrobrevin  

Microsoft Academic Search

Syntrophins are a family of PDZ domain-containing adaptor proteins required for receptor localization. Syntrophins are also associated with the dystrophin complex in muscles. We report here the molecular and functional characterization of the Caenorhabditis elegans gene stn-1 (F30A10.8), which encodes a syntrophin with homology to vertebrate alpha and beta-syntrophins. stn-1 is expressed in neurons and in muscles of C.elegans. stn-1

Karine Grisoni; Kathrin Gieseler; Marie-Christine Mariol; Edwige Martin; Maité Carre-Pierrat; Gary Moulder; Robert Barstead; Laurent Ségalat

2003-01-01

334

Identification of a gonadotropin-releasing hormone receptor orthologue in Caenorhabditis elegans  

Microsoft Academic Search

BACKGROUND: The Caenorhabditis elegans genome is known to code for at least 1149 G protein-coupled receptors (GPCRs), but the GPCR(s) critical to the regulation of reproduction in this nematode are not yet known. This study examined whether GPCRs orthologous to human gonadotropin-releasing hormone receptor (GnRHR) exist in C. elegans. RESULTS: Our sequence analyses indicated the presence of two proteins in

Sivan Vadakkadath Meethal; Miguel J Gallego; Ryan J Haasl; Stephen J Petras; Jean-Yves Sgro; Craig S Atwood

2006-01-01

335

Caenorhabditis elegans HCF1 Functions in Longevity Maintenance as a DAF-16 Regulator  

Microsoft Academic Search

The transcription factor DAF-16\\/forkhead box O (FOXO) is a critical longevity determinant in diverse organisms, however the molecular basis of how its transcriptional activity is regulated remains largely unknown. We report that the Caenorhabditis elegans homolog of host cell factor 1 (HCF-1) represents a new longevity modulator and functions as a negative regulator of DAF-16. In C. elegans, hcf-1 inactivation

Ji Li; Atsushi Ebata; Yuqing Dong; Gizem Rizki; Terri Iwata; Siu Sylvia Lee

2008-01-01

336

Hydrogen Sulfide Is an Endogenous Regulator of Aging in Caenorhabditis elegans.  

PubMed

Abstract Aims: To investigate the role of endogenous hydrogen sulfide (H2S) in the control of aging and healthspan of Caenorhabditis elegans. Results: We show that the model organism, C. elegans, synthesizes H2S. Three H2S-synthesizing enzymes are present in C. elegans, namely cystathionine ? lyase (CSE), cystathionine ? synthetase, and 3-mercaptopyruvate transferase (MPST or 3-MST). Genetic deficiency of mpst-1 (3-MST orthologue 1), but not cth-2 (CSE orthologue), reduced the lifespan of C. elegans. This effect was reversed by a pharmacological H2S donor (GYY4137). GYY4137 also reduced detrimental age-dependent changes in a range of physiological indices, including pharyngeal contraction and defecation. Treatment of C. elegans with GYY4137 increased the expression of several age-related, stress response, and antioxidant genes, whereas MitoSOX Red fluorescence, indicative of reactive oxygen species generation, was increased in mpst-1 knockouts and decreased by GYY4137 treatment. GYY4137 additionally increased the lifespan in short-lived mev-1 mutants with elevated oxidative stress and protected wild-type C. elegans against paraquat poisoning. The lifespan-prolonging and health-promoting effects of H2S in C. elegans are likely due to the antioxidant action of this highly cell-permeable gas. Innovation: The possibility that novel pharmacological agents based on the principle of H2S donation may be able to retard the onset of age-related disease by slowing the aging process warrants further study. Conclusion: Our results show that H2S is an endogenous regulator of oxidative damage, metabolism, and aging in C. elegans and provide new insight into the mechanisms, which control aging in this model organism. Antioxid. Redox Signal. 20, 2621-2630. PMID:24093496

Qabazard, Bedoor; Li, Ling; Gruber, Jan; Peh, Meng Teng; Ng, Li Fang; Kumar, Srinivasan Dinesh; Rose, Peter; Tan, Choon-Hong; Dymock, Brian W; Wei, Feng; Swain, Suresh C; Halliwell, Barry; Stürzenbaum, Stephen R; Moore, Philip K

2014-06-01

337

Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics  

Microsoft Academic Search

Background  The recent availability of genome sequences of multiple related Caenorhabditis species has made it possible to identify, using comparative genomics, similarly transcribed genes in Caenorhabditis elegans and its sister species. Taking this approach, we have identified numerous novel ciliary genes in C. elegans, some of which may be orthologs of unidentified human ciliopathy genes.\\u000a \\u000a \\u000a \\u000a \\u000a Results  By screening for genes possessing canonical

Nansheng Chen; Allan Mah; Oliver E Blacque; Jeffrey Chu; Kiran Phgora; Mathieu W Bakhoum; C Rebecca Hunt Newbury; Jaswinder Khattra; Susanna Chan; Anne Go; Evgeni Efimenko; Robert Johnsen; Prasad Phirke; Peter Swoboda; Marco Marra; Donald G Moerman; Michel R Leroux; David L Baillie; Lincoln D Stein

2007-01-01

338

Impact of Cigarette Smoke Exposure on Innate Immunity: A Caenorhabditis elegans Model  

Microsoft Academic Search

BackgroundCigarette smoking is the major cause of chronic obstructive pulmonary disease (COPD) and lung cancer. Respiratory bacterial infections have been shown to be involved in the development of COPD along with impaired airway innate immunity.Methodology\\/Principal FindingsTo address the in vivo impact of cigarette smoke (CS) exclusively on host innate defense mechanisms, we took advantage of Caenorhabditis elegans (C. elegans), which

Rebecca M. Green; Fabienne Gally; Jonathon G. Keeney; Scott Alper; Bifeng Gao; Min Han; Richard J. Martin; Andrew R. Weinberger; Stephanie R. Case; Maisha N. Minor; Hong Wei Chu; Carol Feghali-Bostwick

2009-01-01

339

C. elegans ATAD-3 Is Essential for Mitochondrial Activity and Development  

Microsoft Academic Search

BackgroundMammalian ATAD3 is a mitochondrial protein, which is thought to play an important role in nucleoid organization. However, its exact function is still unresolved.ResultsHere, we characterize the Caenorhabditis elegans (C. elegans) ATAD3 homologue (ATAD-3) and investigate its importance for mitochondrial function and development. We show that ATAD-3 is highly conserved among different species and RNA mediated interference against atad-3 causes

Michael Hoffmann; Nadège Bellance; Rodrigue Rossignol; Werner J. H. Koopman; Peter H. G. M. Willems; Ertan Mayatepek; Olaf Bossinger; Felix Distelmaier; Thomas Zwaka

2009-01-01

340

A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans  

Microsoft Academic Search

While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and\\/or RNA-sequencing, we have characterized the genome-wide transcriptional changes that

Ilka Engelmann; Aurélien Griffon; Laurent Tichit; Frédéric Montañana-Sanchis; Guilin Wang; Valerie Reinke; Robert H. Waterston; LaDeana W. Hillier; Jonathan J. Ewbank

2011-01-01

341

Caenorhabditis elegans Survives Atmospheric Breakup of STS107, Space Shuttle Columbia  

Microsoft Academic Search

The nematode Caenorhabditis elegans, a popular organism for biological studies, is being developed as a model system for space biology. The chemically defined liquid medium, C. elegans Maintenance Medium (CeMM), allows axenic cultivation and automation of experiments that are critical for spaceflight research. To validate CeMM for use during spaceflight, we grew animals using CeMM and standard laboratory conditions onboard

Nathaniel J. Szewczyk; Rocco L. Mancinelli; William McLamb; David Reed; Baruch S. Blumberg; Catharine A. Conley

2005-01-01

342

Characterizing the transcriptional regulation of let-721 , a Caenorhabditis elegans homolog of human electron flavoprotein dehydrogenase  

Microsoft Academic Search

LET-721 is the Caenorhabditis elegans ortholog of electron-transferring flavoprotein dehydrogenase (ETFDH). We are studying this protein in C. elegans in order to establish a tractable model system for further exploration of ETFDH structure and function. ETFDH is an inner\\u000a mitochondrial membrane localized enzyme that plays a key role in the beta-oxidation of fatty acids and catabolism of amino\\u000a acids and

Derek S. Chew; Allan K. Mah; David L. Baillie

2009-01-01

343

The KLP-6 Kinesin Is Required for Male Mating Behaviors and Polycystin Localization in Caenorhabditis elegans  

Microsoft Academic Search

Background: Male mating behavior of the nematode Caenorhabditis elegans offers an intriguing model to study the genetics of sensory behavior, cilia function, and autosomal dominant polycystic kidney disease (ADPKD). The C. elegans polycystins LOV-1 and PKD-2 act in male-specific sensory cilia required for response and vulva-location mating behaviors.Results: Here, we identify and characterize a new mating mutant, sy511. sy511 behavioral

Erik M. Peden; Maureen M. Barr

2005-01-01

344

A Discrete Time Model for the Analysis of Medium-Throughput C. elegans Growth Data  

Microsoft Academic Search

BackgroundAs part of a program to predict the toxicity of environmental agents on human health using alternative methods, several in vivo high- and medium-throughput assays are being developed that use C. elegans as a model organism. C. elegans-based toxicological assays utilize the COPAS Biosort flow sorting system that can rapidly measure size, extinction (EXT) and time-of-flight (TOF), of individual nematodes.

Marjolein V. Smith; Windy A. Boyd; Grace E. Kissling; Julie R. Rice; Daniel W. Snyder; Christopher J. Portier; Jonathan H. Freedman; Anne C. Hart

2009-01-01

345

The Influence of Bacterial Diet on Fat Storage in C. elegans  

Microsoft Academic Search

BackgroundThe nematode Caenorhabditis elegans has emerged as an important model for studies of the regulation of fat storage. C. elegans feed on bacteria, and various strains of E. coli are commonly used in research settings. However, it is not known whether particular bacterial diets affect fat storage and metabolism.Methodology\\/Principal FindingsFat staining of fixed nematodes, as well as biochemical analysis of

Kyleann K. Brooks; Bin Liang; Jennifer L. Watts; Simon Melov

2009-01-01

346

Effects induced by keV low-energy ion irradiation in the nematode Caenorhabditis elegans  

Microsoft Academic Search

The nematode Caenorhabditis elegans is an excellent model organism with which to study the biological effects and mechanisms of ionizing irradiation. In this\\u000a study, using C. elegans as a model, the effects of keV low-energy argon ion irradiation were investigated, by examining cuticle damage, worm survival,\\u000a brood size, life span, and germ cell death. The surface etching of worm cuticle

Xuelan Liu; Kezhou Cai; Huiyun Feng; Hang Yuan; Mingguang Kong; Lijun Wu; Yuejin Wu; Zengliang Yu

2007-01-01

347

Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development  

Microsoft Academic Search

A number of studies showed that the development and the lifespan of Caenorhabditis elegans is dependent on mitochondrial function. In this study, we addressed the role of mitochondrial DNA levels and mtDNA maintenance in development of C. elegans by analyzing deletion mutants for mito- chondrial polymerase gamma (polg-1(ok1548)). Surprisingly, even though previous studies in other model organisms showed necessity of

Ivana Bratic; J urgen Hench; Johan Henriksson; Adam Antebi; Thomas R Burglin; Aleksandra Trifunovic

2009-01-01

348

Effects of resveratrol on lifespan in Drosophila melanogaster and Caenorhabditis elegans  

Microsoft Academic Search

It was recently reported that the plant polyphenol resveratrol, found, e.g., in grape berry skins, extended lifespan in the fruit fly Drosophila melanogaster and the nematode worm Caenorhabditis elegans. This lifespan extension was dependent on an NAD+-dependent histone deacetylase, Sir2 in Drosophila and SIR-2.1 in C. elegans. The extension of lifespan appeared to occur through a mechanism related to dietary

Timothy M. Bass; David Weinkove; Koen Houthoofd; David Gems; Linda Partridge

2007-01-01

349

Perineural spread of rhino-orbitocerebral mucormycosis caused by Apophysomyces elegans  

PubMed Central

Rhino-orbitocerebral mucormycosis (ROCM) is a fungal infection commonly affecting individuals with diabetes and those in immunocompromised states. However, infections caused by Apophysomyces elegans can involve immunocompetent individuals. The invasion pattern of cerebral mucormycosis is somewhat predictable and may occur by direct invasion or hematogenous spread. Perineural spread of the disease is unusual. Here, we report the first case of perineural extension of ROCM caused by A. elegans along the trigeminal nerve in a 25-year-old immunocompetent, nondiabetic individual.

Parsi, Kirti; Itgampalli, Raghavendra K.; Vittal, R.; Kumar, Anjani

2013-01-01

350

Monascus-Fermented Dioscorea Enhances Oxidative Stress Resistance via DAF-16/FOXO in Caenorhabditis elegans  

PubMed Central

Background Monascus-fermented products are mentioned in an ancient Chinese pharmacopoeia of medicinal food and herbs. Monascus-fermented products offer valuable therapeutic benefits and have been extensively used in East Asia for several centuries. Several biological activities of Monascus-fermented products were recently described, and the extract of Monascus-fermented products showed strong antioxidant activity of scavenging DPPH radicals. To evaluate whether Monascus-fermented dioscorea products have potential as nutritional supplements, Monascus-fermented dioscorea’s modulation of oxidative-stress resistance and associated regulatory mechanisms in Caenorhabditis elegans were investigated. Principal Findings We examined oxidative stress resistance of the ethanol extract of red mold dioscorea (RMDE) in C. elegans, and found that RMDE-treated wild-type C. elegans showed an increased survival during juglone-induced oxidative stress compared to untreated controls, whereas the antioxidant phenotype was absent from a daf-16 mutant. In addition, the RMDE reduced the level of intracellular reactive oxygen species in C. elegans. Finally, the RMDE affected the subcellular distribution of the FOXO transcription factor, DAF-16, in C. elegans and induced the expression of the sod-3 antioxidative gene. Conclusions These findings suggest that the RMDE acts as an antioxidative stress agent and thus may have potential as a nutritional supplement. Further studies in C. elegans suggest that the antioxidant effect of RMDE is mediated via regulation of the DAF-16/FOXO-dependent pathway.

Shi, Yeu-Ching; Yu, Chan-Wei; Liao, Vivian Hsiu-Chuan; Pan, Tzu-Ming

2012-01-01

351

Stimulation of Host Immune Defenses by a Small Molecule Protects C. elegans from Bacterial Infection  

PubMed Central

The nematode Caenorhabditis elegans offers currently untapped potential for carrying out high-throughput, live-animal screens of low molecular weight compound libraries to identify molecules that target a variety of cellular processes. We previously used a bacterial infection assay in C. elegans to identify 119 compounds that affect host-microbe interactions among 37,214 tested. Here we show that one of these small molecules, RPW-24, protects C. elegans from bacterial infection by stimulating the host immune response of the nematode. Using transcriptome profiling, epistasis pathway analyses with C. elegans mutants, and an RNAi screen, we show that RPW-24 promotes resistance to Pseudomonas aeruginosa infection by inducing the transcription of a remarkably small number of C. elegans genes (?1.3% of all genes) in a manner that partially depends on the evolutionarily-conserved p38 MAP kinase pathway and the transcription factor ATF-7. These data show that the immunostimulatory activity of RPW-24 is required for its efficacy and define a novel C. elegans–based strategy to identify compounds with activity against antibiotic-resistant bacterial pathogens.

Pukkila-Worley, Read; Feinbaum, Rhonda; Kirienko, Natalia V.; Larkins-Ford, Jonah; Conery, Annie L.; Ausubel, Frederick M.

2012-01-01

352

Excessive folate synthesis limits lifespan in the C. elegans: E. coli aging model  

PubMed Central

Background Gut microbes influence animal health and thus, are potential targets for interventions that slow aging. Live E. coli provides the nematode worm Caenorhabditis elegans with vital micronutrients, such as folates that cannot be synthesized by animals. However, the microbe also limits C. elegans lifespan. Understanding these interactions may shed light on how intestinal microbes influence mammalian aging. Results Serendipitously, we isolated an E. coli mutant that slows C. elegans aging. We identified the disrupted gene to be aroD, which is required to synthesize aromatic compounds in the microbe. Adding back aromatic compounds to the media revealed that the increased C. elegans lifespan was caused by decreased availability of para-aminobenzoic acid, a precursor to folate. Consistent with this result, inhibition of folate synthesis by sulfamethoxazole, a sulfonamide, led to a dose-dependent increase in C. elegans lifespan. As expected, these treatments caused a decrease in bacterial and worm folate levels, as measured by mass spectrometry of intact folates. The folate cycle is essential for cellular biosynthesis. However, bacterial proliferation and C. elegans growth and reproduction were unaffected under the conditions that increased lifespan. Conclusions In this animal:microbe system, folates are in excess of that required for biosynthesis. This study suggests that microbial folate synthesis is a pharmacologically accessible target to slow animal aging without detrimental effects.

2012-01-01

353

?High Resolution-Magic-Angle Spinning NMR Spectroscopy for Metabolic Phenotyping of Caenorhabditis elegans.  

PubMed

Analysis of model organisms, such as the submillimeter-size Caenorhabditis elegans, plays a central role in understanding biological functions across species and in characterizing phenotypes associated with genetic mutations. In recent years, metabolic phenotyping studies of C. elegans based on (1)H high-resolution magic-angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy have relied on the observation of large populations of nematodes, requiring labor-intensive sample preparation that considerably limits high-throughput characterization of C. elegans. In this work, we open new platforms for metabolic phenotyping of C. elegans mutants. We determine rich metabolic profiles (31 metabolites identified) from samples of 12 individuals using a (1)H NMR microprobe featuring high-resolution magic-angle coil spinning (HR-MACS), a simple conversion of a standard HR-MAS probe to ?HR-MAS. In addition, we characterize the metabolic variations between two different strains of C. elegans (wild-type vs slcf-1 mutant). We also acquire a NMR spectrum of a single C. elegans worm at 23.5 T. This study represents the first example of a metabolomic investigation carried out on a small number of submillimeter-size organisms, demonstrating the potential of NMR microtechnologies for metabolomics screening of small model organisms. PMID:24897622

Wong, Alan; Li, Xiaonan; Molin, Laurent; Solari, Florence; Elena-Herrmann, Bénédicte; Sakellariou, Dimitris

2014-06-17

354

Caenorhabditis elegans RNA-processing Protein TDP-1 Regulates Protein Homeostasis and Life Span*?  

PubMed Central

Transactive response DNA-binding protein (TARDBP/TDP-43), a heterogeneous nuclear ribonucleoprotein (hnRNP) with diverse activities, is a common denominator in several neurodegenerative disorders, including amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Orthologs of TDP-43 exist in animals ranging from mammals to invertebrates. Here, we systematically studied mutant Caenorhabditis elegans lacking the nematode TDP-43 ortholog, TDP-1. Heterologous expression of human TDP-43 rescued the defects in C. elegans lacking TDP-1, suggesting their functions are conserved. Although the tdp-1 mutants exhibited deficits in fertility, growth, and locomotion, loss of tdp-1 attenuated defects in several C. elegans models of proteotoxicity. Loss of tdp-1 suppressed defects in transgenic C. elegans expressing TDP-43 or CuZn superoxide dismutase, both of which are associated with proteotoxicity in neurodegenerative diseases. Loss of tdp-1 also reduced defects in mutant animals lacking the heat shock factor HSF-1. Transcriptional profiling demonstrated that the loss of TDP-1 altered expression of genes functioning in RNA processing and protein folding. Furthermore, the absence of tdp-1 extended the life span in C. elegans. The life span extension required a FOXO transcriptional factor DAF-16 but not HSF-1. These results suggest that the C. elegans TDP-1 has a role in the regulation of protein homeostasis and aging.

Zhang, Tao; Hwang, Ho-Yon; Hao, Haiping; Talbot, Conover; Wang, Jiou

2012-01-01

355

Radiation-induced gene expression in the nematode Caenorhabditis elegans  

NASA Technical Reports Server (NTRS)

We used the nematode C. elegans to characterize the genotoxic and cytotoxic effects of ionizing radiation in a simple animal model emphasizing the unique effects of charged particle radiation. Here we demonstrate by RT-PCR differential display and whole genome microarray hybridization experiments that gamma rays, accelerated protons and iron ions at the same physical dose lead to unique transcription profiles. 599 of 17871 genes analyzed (3.4%) showed differential expression 3 hrs after exposure to 3 Gy of radiation. 193 were up-regulated, 406 were down-regulated and 90% were affected only by a single species of radiation. A novel statistical clustering technique identified the regulatory relationships between the radiation-modulated genes and showed that genes affected by each radiation species were associated with unique regulatory clusters. This suggests that independent homeostatic mechanisms are activated in response to radiation exposure as a function of track structure or ionization density.

Nelson, Gregory A.; Jones, Tamako A.; Chesnut, Aaron; Smith, Anna L.

2002-01-01

356

Cryopreservation of nematode Caenorhabditis elegans in the adult stage.  

PubMed

Cryopreservation of nematode Caenorhabditis elegans in the adult stage is of importance as the nematode is a powerful research model organism. In this study, we applied the protocol previously established for cryopreservation of the L4 nematode to the adult one, and achieved a survival rate of 84%. When ice seeding was induced with bacteria P. syringae directly added to the nematode suspension instead of using a pre-cooled steel sticking needle, comparable survival rate was obtained after thawing. Moreover, a simple freezing device composed of a polystyrene foam box surrounded by a Dewar vessel put in a deep freezer was developed for a practical use. This simple method obtained a survival rate of 69 ± 4% for the adult nematode after thawing. PMID:23995406

Hayashi, M; Amino, H; Kita, K; Murase, N

2013-01-01

357

The epipharyngeal sensilla of the damselfly Ischnura elegans (Odonata, Coenagrionidae).  

PubMed

The knowledge on Odonata adult mouthparts sensilla is scanty and, notwithstanding the epipharynx in the labrum is considered an organ of taste, no ultrastructural investigation has been performed so far on this structure in Odonata. The labrum of the adult of the damselfly Ischnura elegans (Odonata, Coenagrionidae) shows on its ventral side the epipharynx with sensilla represented by articulated hairs and by small pegs located at the apex of slightly raised domes. Under scanning and transmission electron microscope, the articulated hairs, with a well developed socket and tubular body, have the typical structure of bristles, the most common type of insect mechanoreceptors, usually responding to direct touch; the pegs, showing an apical pore together with a variable number of sensory neurons (from two to five), the outer dendritic segments of which show a dendrite sheath stopping along their length, have features typical of contact chemoreceptors. PMID:25080274

Rebora, Manuela; Gaino, Elda; Piersanti, Silvana

2014-11-01

358

X-chromosome silencing in the germline of C. elegans  

PubMed Central

SUMMARY Germline maintenance in the nematode C. elegans requires global repressive mechanisms that involve chromatin organization. During meiosis, the X chromosome in both sexes exhibits a striking reduction of histone modifications that correlate with transcriptional activation when compared with the genome as a whole. The histone modification spectrum on the X chromosome corresponds with a lack of transcriptional competence, as measured by reporter transgene arrays. The X chromosome in XO males is structurally analogous to the sex body in mammals, contains a histone modification associated with heterochromatin in other species and is inactivated throughout meiosis. The synapsed X chromosomes in hermaphrodites also appear to be silenced in early meiosis, but genes on the X chromosome are detectably expressed at later stages of oocyte meiosis. Silencing of the sex chromosome during early meiosis is a conserved feature throughout the nematode phylum, and is not limited to hermaphroditic species.

Kelly, William G.; Schaner, Christine E.; Dernburg, Abby F.; Lee, Min-Ho; Kim, Stuart K.; Villeneuve, Anne M.; Reinke, Valerie

2014-01-01

359

C. elegans Nuclear Receptors: Insights into Life Traits  

PubMed Central

Nuclear receptors (NRs) are a class of hormone-gated transcription factors found in metazoans that regulate global changes in gene expression when bound to their cognate ligands. Despite species diversification, NRs act similarly across taxa to play fundamental roles in detecting intrinsic and environmental signals, and subsequently in coordinating transcriptional cascades that direct reproduction, development, metabolism, and homeostasis. These endocrine receptors function in vivo in part as molecular switches and timers that regulate transcriptional cascades. Here we discuss in detail how several C. elegans NRs integrate intrinsic and extrinsic signals to regulate the dauer diapause and longevity, molting, and heterochronic circuits of development, and draw parallels to similar in vivo endocrine regulated processes in other animals.

Magner, Daniel B.; Antebi, Adam

2009-01-01

360

How Does C. elegans Respond to Altered Gravity?  

NASA Technical Reports Server (NTRS)

All organisms on Earth have evolved at unit gravity (1xG), and thus are probably adapted to function optimally at 1xG. However, with the advent of space exploration, it has been shown that organisms are capable of surviving at much less than 1xG, as well as at greater than 1xG. Organisms subjected to increased G levels exhibit alterations in physiological processes that compensate for novel environmental stresses, such as increased weight and density-driven sedimentation. These physiological adaptations illustrate the plasticity of organisms when presented with environmental conditions in which they could not possibly have evolved. Investigating the mechanism(s) behind these adaptations may uncover biological pathways that have not previously been identified. An easily-cultured and well-studied organism, such as C. elegans, would be a desirable model system for these studies. Additional information is contained in the original extended abstract.

Conley, Catharine A.; Udranszky, Ingrid; Hoffman, David; Kim, Stuart K.

2001-01-01

361

Complexin maintains vesicles in the primed state in C. elegans  

PubMed Central

Summary Background Complexin binds the SNARE complex at synapses and regulates exocytosis, but genetic studies indicate contradictory roles: in flies it predominantly inhibits synaptic vesicle fusion, whereas in mice it promotes evoked responses. Results Here we characterize the complexin mutant in the nematode Caenorhabditis elegans and reveal bipolar functions in neurotransmission: complexin inhibits spontaneous fusion of synaptic vesicles but is also essential for evoked responses. Complexin mutants exhibit a doubling of vesicle fusion in the absence of extracellular calcium. Even more profoundly, mutants exhibit an almost complete loss of evoked responses, current amplitudes are reduced by 94%. One possible interpretation is that spontaneous fusion leads to a severe depletion of primed vesicles and thereby eliminates the readily releasable pool. Consistent with this hypothesis, docked synaptic vesicles are reduced by 70% in complexin-1 mutants. Conclusion These data suggest that the main function of complexin is to maintain the docked state both by inhibiting fusion as well as by promoting priming.

Hobson, Robert J.; Liu, Qiang; Watanabe, Shigeki; Jorgensen, Erik M.

2011-01-01

362

Axon regeneration genes identified by RNAi screening in C. elegans.  

PubMed

Axons of the mammalian CNS lose the ability to regenerate soon after development due to both an inhibitory CNS environment and the loss of cell-intrinsic factors necessary for regeneration. The complex molecular events required for robust regeneration of mature neurons are not fully understood, particularly in vivo. To identify genes affecting axon regeneration in Caenorhabditis elegans, we performed both an RNAi-based screen for defective motor axon regeneration in unc-70/?-spectrin mutants and a candidate gene screen. From these screens, we identified at least 50 conserved genes with growth-promoting or growth-inhibiting functions. Through our analysis of mutants, we shed new light on certain aspects of regeneration, including the role of ?-spectrin and membrane dynamics, the antagonistic activity of MAP kinase signaling pathways, and the role of stress in promoting axon regeneration. Many gene candidates had not previously been associated with axon regeneration and implicate new pathways of interest for therapeutic intervention. PMID:24403161

Nix, Paola; Hammarlund, Marc; Hauth, Linda; Lachnit, Martina; Jorgensen, Erik M; Bastiani, Michael

2014-01-01

363

Experimental determination of invasive fitness in Caenorhabditis elegans.  

PubMed

Estimation of fitness is a key step in experimental evolution studies. However, no established methods currently exist to specifically estimate how successful new alleles are in invading populations. The main reason is that most assays do not accurately reflect the randomness associated with the first stages of the invasion, when invaders are rare and extinctions are frequent. In this protocol, I describe how such experiments can be done in an effective way. By using the nematode model, Caenorhabditis elegans, a large number of invasion experiments are set up, whereby invading individuals carrying a visual marker are introduced into populations in very low numbers. The number of invaders counted in consecutive generations, together with the number of extinctions, is then used in the context of individual-based computer simulations to provide likelihood (Lk) estimates for fitness. This protocol can take up to five generations of experimental invasions and a few hours of computer processing time. PMID:24853925

Chelo, Ivo M

2014-06-01

364

Trimethylpsoralen induces small deletion mutations in Caenorhabditis elegans.  

PubMed Central

To examine the mutagenic spectrum of 4,5',8-trimethylpsoralen (TMP) in Caenorhabditis elegans, we isolated mutations in the unc-22 and pal-1 genes following TMP mutagenesis and analyzed them for restriction fragment length polymorphisms by Southern blot. Eleven of 21 unc-22 mutations exhibited restriction fragment length polymorphisms, 8 of which were deletions of between 0.10 and 15 kb in length. Both of two pal-1 mutations were also small deletions within this size range. Comparison of our results with previous studies on mutagenesis by gamma-rays and x-rays suggests that the mutagenic spectrum of TMP may be similar. TMP should be useful in generating mutations that cause complete loss of function of single genes and that are likely to result in allele-specific DNA polymorphisms. Images

Yandell, M D; Edgar, L G; Wood, W B

1994-01-01

365

Crossover suppressors and balanced recessive lethals in Caenorhabditis elegans.  

PubMed

Two dominant suppressors of crossing over have been identified following X-ray treatment of the small nematode C. elegans. They suppress crossing over in linkage group II (LGII) about 100-fold and 50-fold and are both tightly linked to LGII markers. One, called C1, segregates independently of all other linkage groups and is homozygous fertile. The other is a translocation involving LGII and X. The translocation also suppresses crossing over along the right half of X and is homozygous lethal. C1 has been used as a balancer of LGII recessive lethal and sterile mutations induced by EMS. The frequencies of occurrence of lethals and steriles were approximately equal. Fourteen mutations were assigned to complementation groups and mapped. They tended to map in the same region where LGII visibles are clustered. PMID:631558

Herman, R K

1978-01-01

366

Axon Regeneration Genes Identified by RNAi Screening in C. elegans  

PubMed Central

Axons of the mammalian CNS lose the ability to regenerate soon after development due to both an inhibitory CNS environment and the loss of cell-intrinsic factors necessary for regeneration. The complex molecular events required for robust regeneration of mature neurons are not fully understood, particularly in vivo. To identify genes affecting axon regeneration in Caenorhabditis elegans, we performed both an RNAi-based screen for defective motor axon regeneration in unc-70/?-spectrin mutants and a candidate gene screen. From these screens, we identified at least 50 conserved genes with growth-promoting or growth-inhibiting functions. Through our analysis of mutants, we shed new light on certain aspects of regeneration, including the role of ?-spectrin and membrane dynamics, the antagonistic activity of MAP kinase signaling pathways, and the role of stress in promoting axon regeneration. Many gene candidates had not previously been associated with axon regeneration and implicate new pathways of interest for therapeutic intervention.

Nix, Paola; Hammarlund, Marc; Hauth, Linda; Lachnit, Martina; Jorgensen, Erik M.

2014-01-01

367

Is dauer pheromone of Caenorhabditis elegans really a pheromone?  

NASA Astrophysics Data System (ADS)

Animals respond to signals and cues in their environment. The difference between a signal (e.g. a pheromone) and a cue (e.g. a waste product) is that the information content of a signal is subject to natural selection, whereas that of a cue is not. The model free-living nematode Caenorhabditis elegans forms an alternative developmental morph (the dauer larva) in response to a so-called `dauer pheromone', produced by all worms. We suggest that the production of `dauer pheromone' has no fitness advantage for an individual worm and therefore we propose that `dauer pheromone' is not a signal, but a cue. Thus, it should not be called a pheromone.

Viney, M. E.; Franks, N. R.

368

High-Throughput Behavioral Analysis in C. elegans  

PubMed Central

We have designed a real-time computer vision system, the Multi-Worm Tracker (MWT), that can simultaneously quantify the behavior of dozens of Caenorhabditis elegans on a traditional petri plate at video rates. Three traditional behavioral paradigms are examined using this system: spontaneous movement on food, where the behavior changes over tens of minutes; chemotaxis, where turning events must be detected accurately to determine strategy; and habituation of response to tap, where the response is stochastic and changes over time. In each case, manual analysis or automated single-worm tracking would be tedious and time-consuming, but the MWT system allows rapid quantification of behavior with minimal human effort. Thus, this system will enablelarge scale forward and reverse genetic screens for complex behaviors.

Swierczek, Nicholas A.; Giles, Andrew C.; Rankin, Catharine H.; Kerr, Rex A.

2011-01-01

369

Genome-wide analysis of condensin binding in Caenorhabditis elegans  

PubMed Central

Background Condensins are multi-subunit protein complexes that are essential for chromosome condensation during mitosis and meiosis, and play key roles in transcription regulation during interphase. Metazoans contain two condensins, I and II, which perform different functions and localize to different chromosomal regions. Caenorhabditis elegans contains a third condensin, IDC, that is targeted to and represses transcription of the X chromosome for dosage compensation. Results To understand condensin binding and function, we performed ChIP-seq analysis of C. elegans condensins in mixed developmental stage embryos, which contain predominantly interphase nuclei. Condensins bind to a subset of active promoters, tRNA genes and putative enhancers. Expression analysis in kle-2-mutant larvae suggests that the primary effect of condensin II on transcription is repression. A DNA sequence motif, GCGC, is enriched at condensin II binding sites. A sequence extension of this core motif, AGGG, creates the condensin IDC motif. In addition to differences in recruitment that result in X-enrichment of condensin IDC and condensin II binding to all chromosomes, we provide evidence for a shared recruitment mechanism, as condensin IDC recruiter SDC-2 also recruits condensin II to the condensin IDC recruitment sites on the X. In addition, we found that condensin sites overlap extensively with the cohesin loader SCC-2, and that SDC-2 also recruits SCC-2 to the condensin IDC recruitment sites. Conclusions Our results provide the first genome-wide view of metazoan condensin II binding in interphase, define putative recruitment motifs, and illustrate shared loading mechanisms for condensin IDC and condensin II.

2013-01-01

370

Identification of a Nuclear Carbonic Anhydrase in Caenorhabditis elegans  

PubMed Central

Background Carbonic anhydrases (CA) catalyze the inter-conversion of CO2 with HCO3 and H+, and are involved in a wide variety of physiologic processes such as anion transport, pH regulation, and water balance. In mammals there are sixteen members of the classical ?-type CA family, while the simple genetic model organism C. elegans codes for six ?CA isoforms (cah-1 through cah-6). Methods Fluorescent reporter constructs were used to analyze gene promoter usage, splice variation, and protein localization in transgenic worms. Catalytic activity of recombinant CA proteins was assessed using Hanssons histochemistry. CA’s ability to regulate pH as a function of CO2 and HCO3 was measured using dynamic fluorescent imaging of genetically-targeted biosensors. Results Each of the six CA genes was found to be expressed in a distinct repertoire of cell types. Surprisingly, worms also expressed a catalytically-active CA splice variant, cah-4a, in which an alternative first exon targeted the protein to the nucleus. Cah-4a expression was restricted mainly to the nervous system, where it was found in nearly all neurons, and recombinant CAH-4A protein could regulate pH in the nucleus. Conclusions In addition to establishing C. elegans as a platform for studying ?CA function, this is the first example of a nuclear-targeted ?CA in any organism to date. General Significance A classical ?CA isoform is targeted exclusively to the nucleus where its activity may impact nuclear physiologic and pathophysiologic responses.

Sherman, Teresa A.; Rongali, Sharath; Matthews, Tori A.; Pfeiffer, Jason; Nehrke, Keith

2012-01-01

371

Benzophenones from Hypericum elegans with antioxidant and acetylcholinesterase inhibitory potential  

PubMed Central

Background: Hypericum elegans is used in Bulgarian folk medicine for treatment of wounds, depression, gastrointestinal and bacterial diseases. Objective: Recently, new natural benzophenones: Elegaphenone and O-glycosides: Hypericophenonoside, Neoannulatophenonoside and Elegaphenonoside as well as already known 7-Epiclusianone were isolated from the titled species. The aim of the present study was to evaluate the antioxidant and acetyl cholinesterase inhibitory potential of the isolated compounds. Materials and Methods: 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) di-ammonium salt (ABTS) free radicals, ferric reducing antioxidant power (FRAP) assay as well as inhibition of lipid peroxidation in linoleic acid system were used for determination of antioxidant activity. Modified Ellman's colorimetric method was carried out to assess the acetyl cholinesterase inhibition potential. Hyperoside and Galantamine hydrobromide were used as positive controls. Results: Hypericophenonoside was found to possess the strongest DPPH radical scavenging activity (IC50 = 181.85 ± 6.82 ?M), while Neoannulatophenonoside showed the highest ABTS (IC50 = 0.25 ± 0.005 ?M) and lipid peroxidation inhibitor activity. FRAP activity was demonstrated only by prenylated aglycones – Elegaphenone [942.16 ± 4.03 ?M Trolox Equivalent (TE)] and 7-Epiclusianone (642.95 ± 3.95 ?M TE) and was stronger compared to the control Hyperoside (421.75 ± 9.29 ?M TE). Elegaphenone and 7-Epiclusianone were found to possess moderate acetyl cholinesterase inhibitory potential with IC50 values of 192.19 ± 3.54 ?M and 142.97 ± 4.62 ?M, respectively. Conclusion: The results obtained revealed that H. elegans is a potential natural source of bioactive compounds and benzophenones could be useful in therapy of free radical pathologies and neurodegenerative disorders.

Zheleva-Dimitrova, Dimitrina; Nedialkov, Paraskev; Momekov, Georgi

2013-01-01

372

Isolation and Culture of Larval Cells from C. elegans  

PubMed Central

Cell culture is an essential tool to study cell function. In C. elegans the ability to isolate and culture cells has been limited to embryonically derived cells. However, cells or blastomeres isolated from mixed stage embryos terminally differentiate within 24 hours of culture, thus precluding post-embryonic stage cell culture. We have developed an efficient and technically simple method for large-scale isolation and primary culture of larval-stage cells. We have optimized the treatment to maximize cell number and minimize cell death for each of the four larval stages. We obtained up to 7.8×104 cells per microliter of packed larvae, and up to 97% of adherent cells isolated by this method were viable for at least 16 hours. Cultured larval cells showed stage-specific increases in both cell size and multinuclearity and expressed lineage- and cell type-specific reporters. The majority (81%) of larval cells isolated by our method were muscle cells that exhibited stage-specific phenotypes. L1 muscle cells developed 1 to 2 wide cytoplasmic processes, while L4 muscle cells developed 4 to 14 processes of various thicknesses. L4 muscle cells developed bands of myosin heavy chain A thick filaments at the cell center and spontaneously contracted ex vivo. Neurons constituted less than 10% of the isolated cells and the majority of neurons developed one or more long, microtubule-rich protrusions that terminated in actin-rich growth cones. In addition to cells such as muscle and neuron that are high abundance in vivo, we were also able to isolate M-lineage cells that constitute less than 0.2% of cells in vivo. Our novel method of cell isolation extends C. elegans cell culture to larval developmental stages, and allows use of the wealth of cell culture tools, such as cell sorting, electrophysiology, co-culture, and high-resolution imaging of subcellular dynamics, in investigation of post-embryonic development and physiology.

Zhang, Sihui; Banerjee, Diya; Kuhn, Jeffrey R.

2011-01-01

373

Transgenerational epigenetics in the germline cycle of Caenorhabditis elegans.  

PubMed

Epigenetic mechanisms create variably stable changes in gene expression through the establishment of heritable states of chromatin architecture. While many epigenetic phenomena are, by definition, heritably passed through cell division during animal and plant development, evidence suggests that 'epigenetic states' may also be inherited across multiple generations. Work in the nematode Caenorhabditis elegans has uncovered a number of mechanisms that participate in regulating the transgenerational passage of epigenetic states. These mechanisms include some that establish and maintain heritable epigenetic information in the form of histone modifications, as well as those that filter the epigenetic information that is stably transmitted. The information appears to influence and help guide or regulate gene activity and repression in subsequent generations. Genome surveillance mechanisms guided by small RNAs appear to be involved in identifying and directing heritable repression of genomic elements, and thus may participate in filtering information that is inappropriate for stable transmission. This review will attempt to summarize recent findings that illustrate this simple nematode to be a truly elegant resource for defining emerging biological paradigms.As the cell lineage that links generations, the germline is the carrier of both genetic and epigenetic information. Like genetic information, information in the epigenome can heritably affect gene regulation and phenotype; yet unlike genetic information, the epigenome of the germ lineage is highly modified within each generation. Despite such alterations, some epigenetic information is highly stable across generations, leading to transgenerationally stable phenotypes that are unlinked to genetic changes. Studies in the nematode C. elegans have uncovered mechanisms that contribute to transgenerational repression as well as to the expression of genes that rely on histone modifying machinery and/or non-coding RNA-based mechanisms. These studies indicate that epigenetic mechanisms operating within the germ cell cycle of this organism filter and maintain an epigenetic memory that is required for germ cell function and can also influence gene expression in somatic lineages. PMID:24678826

Kelly, William G

2014-01-01

374

Mechanisms of plasticity in a Caenorhabditis elegans mechanosensory circuit  

PubMed Central

Despite having a small nervous system (302 neurons) and relatively short lifespan (14–21 days), the nematode Caenorhabditis elegans has a substantial ability to change its behavior in response to experience. The behavior discussed here is the tap withdrawal response, whereby the worm crawls backwards a brief distance in response to a non-localized mechanosensory stimulus from a tap to the side of the Petri plate within which it lives. The neural circuit that underlies this behavior is primarily made up of five sensory neurons and four pairs of interneurons. In this review we describe two classes of mechanosensory plasticity: adult learning and memory and experience dependent changes during development. As worms develop through young adult and adult stages there is a shift toward deeper habituation of response probability that is likely the result of changes in sensitivity to stimulus intensity. Adult worms show short- intermediate- and long-term habituation as well as context dependent habituation. Short-term habituation requires glutamate signaling and auto-phosphorylation of voltage-dependent potassium channels and is modulated by dopamine signaling in the mechanosensory neurons. Long-term memory (LTM) for habituation is mediated by down-regulation of expression of an AMPA-type glutamate receptor subunit. Intermediate memory involves an increase in release of an inhibitory neuropeptide. Depriving larval worms of mechanosensory stimulation early in development leads to fewer synaptic vesicles in the mechanosensory neurons and lower levels of an AMPA-type glutamate receptor subunit in the interneurons. Overall, the mechanosensory system of C. elegans shows a great deal of experience dependent plasticity both during development and as an adult. The simplest form of learning, habituation, is not so simple and is mediated and/or modulated by a number of different processes, some of which we are beginning to understand.

Bozorgmehr, Tahereh; Ardiel, Evan L.; McEwan, Andrea H.; Rankin, Catharine H.

2012-01-01

375

A spatial and temporal map of C. elegans gene expression  

PubMed Central

The C. elegans genome has been completely sequenced, and the developmental anatomy of this model organism is described at single-cell resolution. Here we utilize strategies that exploit this precisely defined architecture to link gene expression to cell type. We obtained RNAs from specific cells and from each developmental stage using tissue-specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA-tagging method. We then generated gene expression profiles of more than 30 different cells and developmental stages using tiling arrays. Machine-learning–based analysis detected transcripts corresponding to established gene models and revealed novel transcriptionally active regions (TARs) in noncoding domains that comprise at least 10% of the total C. elegans genome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell types. Examination of known tissue- and cell-specific transcripts validates these data sets and suggests that newly identified TARs may exercise cell-specific functions. Additionally, we used self-organizing maps to define groups of coregulated transcripts and applied regulatory element analysis to identify known transcription factor– and miRNA-binding sites, as well as novel motifs that likely function to control subsets of these genes. By using cell-specific, whole-genome profiling strategies, we have detected a large number of novel transcripts and produced high-resolution gene expression maps that provide a basis for establishing the roles of individual genes in cellular differentiation.

Spencer, W. Clay; Zeller, Georg; Watson, Joseph D.; Henz, Stefan R.; Watkins, Kathie L.; McWhirter, Rebecca D.; Petersen, Sarah; Sreedharan, Vipin T.; Widmer, Christian; Jo, Jeanyoung; Reinke, Valerie; Petrella, Lisa; Strome, Susan; Von Stetina, Stephen E.; Katz, Menachem; Shaham, Shai; Ratsch, Gunnar; Miller, David M.

2011-01-01

376

Isoflurane Selectively Inhibits Distal Mitochondrial Complex I in Caenorhabditis Elegans  

PubMed Central

BACKGROUND Complex I of the electron transport chain (ETC) is a possible target of volatile anesthetics (VAs). Complex I enzymatic activities are inhibited by VAs, and dysfunction of complex I can lead to hypersensitivity to VAs in worms and in people. Mutant analysis in Caenorhabditis (C.) elegans suggests that VAs may specifically interfere with complex I function at the binding site for its substrate ubiquinone. We hypothesized that isoflurane inhibits electron transport by competing with ubiquinone for binding to complex I. METHODS Wildtype and mutant C. elegans were used to study the effects of isoflurane on isolated mitochondria. Enzymatic activities of the ETC were assayed and dose-response curves determined using established techniques. Two-dimensional native gels of mitochondrial proteins were performed after exposure of mitochondria to isoflurane. RESULTS Complex I is the most sensitive component of the ETC to isoflurane inhibition; however the proximal portion of complex I (the flavoprotein) is relatively insensitive to isoflurane. Isoflurane and quinone do not compete for a common binding site on complex I. The absolute rate of complex I enzymatic activity in vitro does not predict immobilization of the animal by isoflurane. Isoflurane had no measurable effect on stability of mitochondrial supercomplexes. Reduction of ubiquinone by complex I displayed positive cooperative kinetics not disrupted by isoflurane. CONCLUSIONS Isoflurane directly inhibits complex I at a site distal to the flavoprotein subcomplex. However, we have excluded our original hypothesis that isoflurane and ubiquinone compete for a common hydrophobic binding site on complex I. In addition, immobilization of the nematode by isoflurane is not due to limiting absolute amounts of complex I electron transport as measured in isolated mitochondria.

Kayser, Ernst-Bernhard; Suthammarak, Wichit; Morgan, Phil G.; Sedensky, Margaret M.

2011-01-01

377

Malate and fumarate extend lifespan in Caenorhabditis elegans.  

PubMed

Malate, the tricarboxylic acid (TCA) cycle metabolite, increased lifespan and thermotolerance in the nematode C. elegans. Malate can be synthesized from fumarate by the enzyme fumarase and further oxidized to oxaloacetate by malate dehydrogenase with the accompanying reduction of NAD. Addition of fumarate also extended lifespan, but succinate addition did not, although all three intermediates activated nuclear translocation of the cytoprotective DAF-16/FOXO transcription factor and protected from paraquat-induced oxidative stress. The glyoxylate shunt, an anabolic pathway linked to lifespan extension in C. elegans, reversibly converts isocitrate and acetyl-CoA to succinate, malate, and CoA. The increased longevity provided by malate addition did not occur in fumarase (fum-1), glyoxylate shunt (gei-7), succinate dehydrogenase flavoprotein (sdha-2), or soluble fumarate reductase F48E8.3 RNAi knockdown worms. Therefore, to increase lifespan, malate must be first converted to fumarate, then fumarate must be reduced to succinate by soluble fumarate reductase and the mitochondrial electron transport chain complex II. Reduction of fumarate to succinate is coupled with the oxidation of FADH2 to FAD. Lifespan extension induced by malate depended upon the longevity regulators DAF-16 and SIR-2.1. Malate supplementation did not extend the lifespan of long-lived eat-2 mutant worms, a model of dietary restriction. Malate and fumarate addition increased oxygen consumption, but decreased ATP levels and mitochondrial membrane potential suggesting a mild uncoupling of oxidative phosphorylation. Malate also increased NADPH, NAD, and the NAD/NADH ratio. Fumarate reduction, glyoxylate shunt activity, and mild mitochondrial uncoupling likely contribute to the lifespan extension induced by malate and fumarate by increasing the amount of oxidized NAD and FAD cofactors. PMID:23472183

Edwards, Clare B; Copes, Neil; Brito, Andres G; Canfield, John; Bradshaw, Patrick C

2013-01-01

378

Secondary metabolites from Opuntia ficus-indica var. saboten.  

PubMed

A butanol fraction, from the methanolic extract of Opuntia ficus-indica var. saboten, on purification either by preparative TLC or reversed phase HPLC, yielded three chemical components: isorhamnetin 3-O-(6''-O-E-feruloyl)neohesperidoside (1), (6R)-9,10-dihydroxy-4,7-megastigmadien-3-one-9-O-beta-D-glucopyranoside (2) and (6S)-9,10-dihydroxy-4,7-megastigmadien-3-one-9-O-beta-D-glucopyranoside (3) along with 15 known compounds. Structures of compounds (1-3) were elucidated by aid of spectroscopic analyses. The absolute stereochemistry in compounds 2 and 3 was established with the help of CD data analysis and comparison with the literature data. In a DPPH radical scavenging assay, compound 1 showed moderate inhibitory activity (IC50 = 45.58 microg/ml). PMID:16762382

Saleem, Muhammad; Kim, Hyoung Ja; Han, Chang Kyun; Jin, Changbae; Lee, Yong Sup

2006-07-01

379

Alkaloid content of the seeds from Erythroxylum Coca var. Coca.  

PubMed

Alkaloid extracts from the seeds of Erythroxylum Coca var. Coca grown in the Chapare Valley of Bolivia were subjected to gas and liquid chromatographic-mass spectrometric analyses. Several alkaloids from these seeds were detected and characterized, including methylecgonidine, tropine, 3alpha-acetoxytropane, ecgonine methyl ester, cuscohygrine, N-norbenzoyltropine, benzoyltropine, hexanoylecgonine methyl ester, cocaine, cis-cinnamoylcocaine, and trans-cinnamoylcocaine. Methylecgonidine was determined to be the primary constituent and not an analytical artifact. Additionally, two significant new uncharacterized alkaloids were established as present. Recent evidence suggests that some cocaine processors are adding this seed extraction material to cocaine extracted from coca leaf and may impact cocaine impurity signature profiles. PMID:16382835

Casale, John F; Toske, Steven G; Colley, Valerie L

2005-11-01

380

Antiplasmodial sesquiterpenes from the seeds of Salacia longipes var. camerunensis.  

PubMed

Phytochemical investigation of the seeds of Salacia longipes var. camerunensis led to the isolation of four sesquiterpenoid derivatives, salaterpene A (1) (1?,2?,8?-triacetoxy-6?,9?-dibenzoyloxy-4?-hydroxy-dihydro-?-agarofuran), salaterpene B (2) (1?,2?,8?-triacetoxy-9?-benzoyloxy-6?-cinnamoyloxy-4?-hydroxy-dihydro-?-agarofuran), salaterpene C (3) (1?,2?-diacetoxy-6?,9?-dibenzoyloxy-4?-hydroxy-dihydro-?-agarofuran) and salaterpene D (4) (2?-acetoxy-1?,6?-dibenzoyloxy-4?-hydroxy-9?-nicotinoyloxy-dihydro-?-agarofuran) together with two known compounds (5 and 6). The structures of the compounds were established by means of NMR spectroscopy. Compounds 1-4 and 6 were tested in vitro for their antiplasmodial activity against Plasmodium falciparum chloroquine-resistant strain W2. All the tested compounds exhibited a moderate potency with IC50 below 2.7 ?M. PMID:23863332

Mba'ning, Brice M; Lenta, Bruno N; Noungoué, Diderot T; Antheaume, Cyril; Fongang, Yanick F; Ngouela, Silvère A; Boyom, Fabrice F; Rosenthal, Philip J; Tsamo, Etienne; Sewald, Norbert; Laatsch, Hartmut

2013-12-01

381

Anti-adipogenic effects of extracts of Ficus deltoidea var. deltoidea and var. angustifolia on 3T3-L1 adipocytes*  

PubMed Central

Objective: This study examined the anti-adipogenic effects of extracts of Ficus deltoidea var. deltoidia and var. angustifolia, a natural slimming aid, on 3T3-L1 adipocytes. Methods: Methanol and water extracts of leaves of the F. deltoidea varieties were analyzed to determine their total flavonoid content (TFC) and total phenolic content (TPC), respectively. The study was initiated by determining the maximum non-toxic dose (MNTD) of the methanol and water extracts for 3T3-L1 preadipocytes. Possible anti-adipogenic effects were then examined by treating 2-d post confluent 3T3-L1 preadipocytes with either methanol extract or water extract at MNTD and half MNTD (½MNTD), after which the preadipocytces were induced to form mature adipocytes. Visualisation and quantification of lipid content in mature adipocytes were carried out through oil red O staining and measurement of optical density (OD) at 520 nm, respectively. Results: The TFCs of the methanol extracts were 1.36 and 1.97 g quercetin equivalents (QE)/100 g dry weight (DW), while the TPCs of the water extracts were 5.61 and 2.73 g gallic acid equivalents (GAE)/100 g DW for var. deltoidea and var. angustilofia, respectively. The MNTDs determined for methanol and water extracts were (300.0±28.3) and (225.0±21.2) ?g/ml, respectively, for var. deltoidea, while much lower MNTDs [(60.0±2.0) ?g/ml for methanol extracts and (8.0±1.0) ?g/ml for water extracts] were recorded for var. angustifolia. Studies revealed that the methanol extracts of both varieties and the water extracts of var. angustifolia at either MNTD or ½MNTD significantly inhibited the maturation of preadipocytes. Conclusions: The inhibition of the formation of mature adipocytes indicated that leaf extracts of F. deltoidea could have potential anti-obesity effects.

Woon, Shiau Mei; Seng, Yew Wei; Ling, Anna Pick Kiong; Chye, Soi Moi; Koh, Rhun Yian

2014-01-01

382

Chemistry and biological activities of Tanacetum chiliophyllum var. oligocephalum extracts.  

PubMed

Tanacetum chiliophyllum (Fisch. & Mey.) var. oligocephalum (D.C.) Sosn. collected in Turkey was subjected to phytochemical and biological evaluations in this study. Pure compounds were obtained from ethyl acetate extracts of the stems of the plant material. Structures of isolated compounds were determined using spectral methods. Seven known flavones, i.e., 5-hydroxy-3',4',6,7-tetramethoxyflavone, eupatilin (6-hydroxyluteolin-6,3',4'-trimethylether), cirsimaritin (scuttellarin-6,7-dimethylether), cirsilineol, 5-hydroxy-3',4',7-trimethoxy flavone, desmethoxy-centaureidin, and jaceosidin and one known triterpene, taraxasterol acetate, were identified from the ethyl acetate extracts. The first seven compounds, as well as the ethyl acetate and methanol extracts, were also investigated for their insecticidal, antimicrobial, and 1,1-diphenyl-2-picrylhydrazil radical (DPPH)-scavenging activities. The insecticidal contact toxicity of the extracts were evaluated on Sitophilus granarius. The ethyl acetate (81.8%) and methanol (88.4%) extracts of T. chiliophyllum var. oligocephalum showed high toxicity against this pest. Most promising antimicrobial activity was observed for ethyl acetate extracts of the stems against Bacillus cereus. This extract showed the same inhibition concentration (125 microL/mg) with the positive control chloramphenicol. The ethyl acetate (91.9%) and methanol (93%) extracts of the stems showed significant DPPH-scavenging activity compared with the positive controls alpha-tocopherol (94.5%) and butylated hydroxytoluene (92.9%) at 10 mg/mL concentration. Among the isolated compounds, the highest DPPH-scavenging activity was observed for jaceosidin at 1 mg/mL concentration (81.5%). PMID:24645497

Polato?lu, Kaan; Karakoç, Omer Cem; Demirci, Fatih; Gökçe, Ayhan; Gören, Nezhun

2013-01-01

383

Origin of Cryptococcus neoformans var. neoformans Diploid Strains  

PubMed Central

The basidiomycetous yeast Cryptococcus neoformans is an important human fungal pathogen. Two varieties, C. neoformans var. neoformans and C. neoformans var. gattii, have been identified. Both are heterothallic with two mating types, MATa and MAT?. Some rare isolates are self-fertile and are considered occasional diploid or aneuploid strains. In the present study, 133 isolates, mostly from Italian patients, were investigated to detect the presence of diploid strains in the Igiene Università Milano culture collection. All of the diploid isolates were further investigated by different methods to elucidate their origins. Forty-nine diploid strains were identified by flow cytometry. PCR fingerprinting using the (GACA)4 primer showed that the diploid state was associated with two specific genotypes identified as VN3 and VN4. Determination of mating type on V8 juice medium confirmed that the majority of the strains were sterile. PCR and dot blotting using the two pheromone genes (MFa and MF?) as probes identified 36 of the 49 diploid isolates as MATa/?. The results of pheromone gene sequencing showed that two allelic MF? genes exist and are distinct for serotypes A and D. In contrast, the MFa gene sequence was conserved in both serotype alleles. Amplification of serotype-specific STE20 alleles demonstrated that the diploid strains contained one mating locus inherited from a serotype A parent and one inherited from a serotype D parent. The present results suggest that diploid isolates may be common among the C. neoformans population and that in Italy and other European countries serotype A and D populations are not genetically isolated but are able to recombine by sexual reproduction.

Cogliati, Massimo; Esposto, Maria C.; Clarke, David L.; Wickes, Brian L.; Viviani, Maria A.

2001-01-01

384

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.  

PubMed

HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology and ethnic occurrence, accompanied by mutation frequencies and references. Here, we report updates to >600 HbVar entries, inclusion of population-specific data for 28 populations and 27 ethnic groups for ?-, and ?-thalassemias and additional querying options in the HbVar query page. HbVar content was also inter-connected with two other established genetic databases, namely FINDbase (http://www.findbase.org) and Leiden Open-Access Variation database (http://www.lovd.nl), which allows comparative data querying and analysis. HbVar data content has contributed to the realization of two collaborative projects to identify genomic variants that lie on different globin paralogs. Most importantly, HbVar data content has contributed to demonstrate the microattribution concept in practice. These updates significantly enriched the database content and querying potential, enhanced the database profile and data quality and broadened the inter-relation of HbVar with other databases, which should increase the already high impact of this resource to the globin and genetic database community. PMID:24137000

Giardine, Belinda; Borg, Joseph; Viennas, Emmanouil; Pavlidis, Cristiana; Moradkhani, Kamran; Joly, Philippe; Bartsakoulia, Marina; Riemer, Cathy; Miller, Webb; Tzimas, Giannis; Wajcman, Henri; Hardison, Ross C; Patrinos, George P

2014-01-01

385

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations  

PubMed Central

HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology and ethnic occurrence, accompanied by mutation frequencies and references. Here, we report updates to >600 HbVar entries, inclusion of population-specific data for 28 populations and 27 ethnic groups for ?-, and ?-thalassemias and additional querying options in the HbVar query page. HbVar content was also inter-connected with two other established genetic databases, namely FINDbase (http://www.findbase.org) and Leiden Open-Access Variation database (http://www.lovd.nl), which allows comparative data querying and analysis. HbVar data content has contributed to the realization of two collaborative projects to identify genomic variants that lie on different globin paralogs. Most importantly, HbVar data content has contributed to demonstrate the microattribution concept in practice. These updates significantly enriched the database content and querying potential, enhanced the database profile and data quality and broadened the inter-relation of HbVar with other databases, which should increase the already high impact of this resource to the globin and genetic database community.

Giardine, Belinda; Borg, Joseph; Viennas, Emmanouil; Pavlidis, Cristiana; Moradkhani, Kamran; Joly, Philippe; Bartsakoulia, Marina; Riemer, Cathy; Miller, Webb; Tzimas, Giannis; Wajcman, Henri; Hardison, Ross C.; Patrinos, George P.

2014-01-01

386

Cloning of the repertoire of individual Plasmodium falciparum var genes using transformation associated recombination (TAR).  

PubMed

One of the major virulence factors of the malaria causing parasite is the Plasmodium falciparum encoded erythrocyte membrane protein 1 (PfEMP1). It is translocated to It the membrane of infected erythrocytes and expressed from approximately 60 var genes in a mutually exclusive manner. Switching of var genes allows the parasite to alter functional and antigenic properties of infected erythrocytes, to escape the immune defense and to establish chronic infections. We have developed an efficient method for isolating VAR genes from telomeric and other genome locations by adapting transformation-associated recombination (TAR) cloning, which can then be analyzed and sequenced. For this purpose, three plasmids each containing a homologous sequence representing the upstream regions of the group A, B, and C var genes and a sequence homologous to the conserved acidic terminal segment (ATS) of var genes were generated. Co-transfection with P. falciparum strain ITG2F6 genomic DNA in yeast cells yielded 200 TAR clones. The relative frequencies of clones from each group were not biased. Clones were screened by PCR, as well as Southern blotting, which revealed clones missed by PCR due to sequence mismatches with the primers. Selected clones were transformed into E. coli and further analyzed by RFLP and end sequencing. Physical analysis of 36 clones revealed 27 distinct types potentially representing 50% of the var gene repertoire. Three clones were selected for sequencing and assembled into single var gene containing contigs. This study demonstrates that it is possible to rapidly obtain the repertoire of var genes from P. falciparum within a single set of cloning experiments. This technique can be applied to individual isolates which will provide a detailed picture of the diversity of var genes in the field. This is a powerful tool to overcome the obstacles with cloning and assembly of multi-gene families by simultaneously cloning each member. PMID:21408186

Gaida, Annette; Becker, Marion M; Schmid, Christoph D; Bühlmann, Tobias; Louis, Edward J; Beck, Hans-Peter

2011-01-01

387

Cryptococcus neoformans var. grubii: Separate Varietal Status for Cryptococcus neoformans Serotype A Isolates  

PubMed Central

Cryptococcus neoformans var. neoformans presently includes isolates which have been determined by the immunologic reactivity of their capsular polysaccharides to be serotype A and those which have been determined to be serotype D. However, recent analyses of the URA5 sequences and DNA fingerprinting patterns suggest significant genetic differences between the two serotypes. Therefore, we propose to recognize these genotypic distinctions, as well as previously reported phenotypic differences, by restricting C. neoformans var. neoformans to isolates which are serotype D and describing a new variety, C. neoformans var. grubii, for serotype A isolates.

Franzot, Sarah P.; Salkin, Ira F.; Casadevall, Arturo

1999-01-01

388

Restriction analysis of an amplified rodA gene fragment to distinguish Aspergillus fumigatus var. ellipticus from Aspergillus fumigatus var. fumigatus.  

PubMed

A previous multidisciplinary study indicated that gliotoxin-producing Aspergillus fumigatus Fresen. isolates from silage commodities mostly belonged to its variant A. fumigatus var. ellipticus Raper & Fennell. Sequence analysis revealed the presence of a single nucleotide polymorphism at five positions in a fragment of the rodA gene (coding for a hydrophobin rodletA protein) between Aspergillus fumigatus var. fumigatus and Aspergillus fumigatus var. ellipticus. A method was developed to distinguish these two types of isolates based on restriction analysis of this rodA gene fragment using the HinfI restriction enzyme. In addition, in silico analysis of 113 rodA gene fragments retrieved from GenBank was performed and confirmed the suitability of this method. In conclusion, the method developed in this study allows easy distinction between A. fumigatus var. fumigatus and its variant ellipticus. In combination with the earlier developed PCR-restriction fragment length polymorphism method of Staab et al. (2009, J Clin Microbiol 47: 2079), this method is part of a sequencing-independent identification scheme that allows for rapid distinction between similar species/variants within Aspergillus section Fumigati, specifically A. fumigatus, A. fumigatus var. ellipticus, Aspergillus lentulus Balajee & K.A. Marr, Neosartorya pseudofischeri S.W. Peterson and Neosartorya udagawae Y. Horie, Miyaji & Nishim. PMID:22670589

Van Pamel, Els; Daeseleire, Els; De Clercq, Nikki; Herman, Lieve; Verbeken, Annemieke; Heyndrickx, Marc; Vlaemynck, Geertrui

2012-08-01

389

Burkholderia pseudomallei kills Caenorhabditis elegans through virulence mechanisms distinct from intestinal lumen colonization.  

PubMed

The nematode Caenorhabditis elegans is hypersusceptible to Burkholderia pseudomallei infection. However, the virulence mechanisms underlying rapid lethality of C. elegans upon B. pseudomallei infection remain poorly defined. To probe the host-pathogen interaction, we constructed GFP-tagged B. pseudomallei and followed bacterial accumulation within the C. elegans intestinal lumen. Contrary to slow-killing by most bacterial pathogens, B. pseudomallei caused fairly limited intestinal lumen colonization throughout the period of observation. Using grinder-defective mutant worms that allow the entry of intact bacteria also did not result in full intestinal lumen colonization. In addition, we observed a significant decline in C. elegans defecation and pharyngeal pumping rates upon B. pseudomallei infection. The decline in defecation rates ruled out the contribution of defecation to the limited B. pseudomallei colonization. We also demonstrated that the limited intestinal lumen colonization was not attributed to slowed host feeding as bacterial loads did not change significantly when feeding was stimulated by exogenous serotonin. Both these observations confirm that B. pseudomallei is a poor colonizer of the C. elegans intestine. To explore the possibility of toxin-mediated killing, we examined the transcription of the C. elegans ABC transporter gene, pgp-5, upon B. pseudomallei infection of the ppgp-5::gfp reporter strain. Expression of pgp-5 was highly induced, notably in the pharynx and intestine, compared with Escherichia coli-fed worms, suggesting that the host actively thwarted the pathogenic assaults during infection. Collectively, our findings propose that B. pseudomallei specifically and continuously secretes toxins to overcome C. elegans immune responses. PMID:23076282

Ooi, Soon-Keat; Lim, Tian-Yeh; Lee, Song-Hua; Nathan, Sheila

2012-10-01

390

Multilevel voltage-source inverter with separate dc sources for static var generation.  

National Technical Information Service (NTIS)

A new multilevel voltage-source inverter with a separate dc sources is proposed for high-voltage, high-power applications, such as flexible ac transmission systems (FACTS) including static var generation (SVG), power line conditioning, series compensation...

F. Z. Peng J. S. Lai J. McKeever J. VanCoevering

1995-01-01

391

CO 2 enrichment in vitro. Effect on autotrophic and heterotrophic cultures of Nicotiana tabacum (var. Samsun )  

Microsoft Academic Search

Summary Plantlets of Nicotiana tabacum (var. Samsun) were grown under CO2 enriched air supplied by a Warburg buffer. Growth of all plant parts was enhanced. The maximum growth increase was found for roots (120%).

Marianne Mousseau

1986-01-01

392

Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant.  

National Technical Information Service (NTIS)

Background: Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptat...

C. Chapman H. Daligault H. S. Gibbons L. A. McNew S. M. Broomall

2011-01-01

393

Phytoremediation of cadmium-contaminated farmland soil by the hyperaccumulator Beta vulgaris L. var. cicla.  

PubMed

A field study was conducted to evaluate the phytoremediation efficiency of cadmium (Cd) contaminated soil utilizing the Cd hyperaccumulator Beta vulgaris L. var. cicla during one growing season (about 2 months) on farmland in Zhangshi Irrigation Area, the representative wastewater irrigation area in China. Results showed that B. vulgaris L. var. cicla is a promising plant in the phytoremediation of Cd contaminated farmland soil. The maximum of Cd phytoremediation efficiency by B. vulgaris L. var. cicla reached 144.6 mg/ha during one growing season. Planting density had a significant effect on the plant biomass and the overall Cd phytoremediation efficiency (p < 0.05). The amendment of organic manure promoted the biomass increase of B. vulgaris L. var. cicla (p < 0.05) but inhibited the Cd phytoremediation efficiency. PMID:22286610

Song, Xueying; Hu, Xiaojun; Ji, Puhui; Li, Yushuang; Chi, Guangyu; Song, Yufang

2012-04-01

394

Identification of a gonadotropin-releasing hormone receptor orthologue in Caenorhabditis elegans  

PubMed Central

Background The Caenorhabditis elegans genome is known to code for at least 1149 G protein-coupled receptors (GPCRs), but the GPCR(s) critical to the regulation of reproduction in this nematode are not yet known. This study examined whether GPCRs orthologous to human gonadotropin-releasing hormone receptor (GnRHR) exist in C. elegans. Results Our sequence analyses indicated the presence of two proteins in C. elegans, one of 401 amino acids [GenBank: NP_491453; WormBase: F54D7.3] and another of 379 amino acids [GenBank: NP_506566; WormBase: C15H11.2] with 46.9% and 44.7% nucleotide similarity to human GnRHR1 and GnRHR2, respectively. Like human GnRHR1, structural analysis of the C. elegans GnRHR1 orthologue (Ce-GnRHR) predicted a rhodopsin family member with 7 transmembrane domains, G protein coupling sites and phosphorylation sites for protein kinase C. Of the functionally important amino acids in human GnRHR1, 56% were conserved in the C. elegans orthologue. Ce-GnRHR was actively transcribed in adult worms and immunoanalyses using antibodies generated against both human and C. elegans GnRHR indicated the presence of a 46-kDa protein, the calculated molecular mass of the immature Ce-GnRHR. Ce-GnRHR staining was specifically localized to the germline, intestine and pharynx. In the germline and intestine, Ce-GnRHR was localized specifically to nuclei as revealed by colocalization with a DNA nuclear stain. However in the pharynx, Ce-GnRHR was localized to the myofilament lattice of the pharyngeal musculature, suggesting a functional role for Ce-GnRHR signaling in the coupling of food intake with reproduction. Phylogenetic analyses support an early evolutionary origin of GnRH-like receptors, as evidenced by the hypothesized grouping of Ce-GnRHR, vertebrate GnRHRs, a molluscan GnRHR, and the adipokinetic hormone receptors (AKHRs) and corazonin receptors of arthropods. Conclusion This is the first report of a GnRHR orthologue in C. elegans, which shares significant similarity with insect AKHRs. In vertebrates, GnRHRs are central components of the reproductive endocrine system, and the identification of a GnRHR orthologue in C. elegans suggests the potential use of C. elegans as a model system to study reproductive endocrinology.

Vadakkadath Meethal, Sivan; Gallego, Miguel J; Haasl, Ryan J; Petras, Stephen J; Sgro, Jean-Yves; Atwood, Craig S

2006-01-01

395

Microtubules and microtubule-associated proteins from the nematode Caenorhabditis elegans: periodic cross-links connect microtubules in vitro  

Microsoft Academic Search

The nematode Caenorhabditis elegans should be an excellent model system in which to study the role of microtubules in mitosis, embryogenesis, morphogenesis, and nerve function. It may be studied by the use of biochemical, genetic, molecular biologi- cal, and cell biological approaches. We have purified microtubules and microtubule-associated proteins (MAPs) from C. elegans by the use of the anti-tumor drug

Eric J. Aamodt; Joseph G. Culotti

1986-01-01

396

Programmed cell death mediated by ced-3 and ced-4 protects Caenorhabditis elegans from Salmonella typhimurium-mediated killing  

Microsoft Academic Search

Programmed cell death (PCD) in mammals has been implicated in several disease states including cancer, autoimmune disease, and neurodegenerative disease. In Caenorhabditis elegans, PCD is a normal component of development. We find that Salmonella typhimurium colonization of the C. elegans intestine leads to an increased level of cell death in the worm gonad. S. typhimurium-mediated germ-line cell death is not

Alejandro Aballay; Frederick M. Ausubel

2001-01-01

397

Maintenance of the intestinal tube in Caenorhabditis elegans: the role of the intermediate filament protein IFC2  

Microsoft Academic Search

The Caenorhabditis elegans intestinal lumen is surrounded by a dense cytoplasmic network that is laterally attached to the junctional complex and is referred to as the endotube. It localizes to the terminal web region which anchors the microvillar actin filament bundles and is particularly rich in intermediate filaments. To examine their role in intestinal morphogenesis and function, C. elegans reporter

Katrin Hüsken; Tobias Wiesenfahrt; Christian Abraham; Reinhard Windoffer; Olaf Bossinger; Rudolf E. Leube

2008-01-01

398

Fluoxetine-Resistance Genes in Caenorhabditis elegans Function in the Intestine and May Act in Drug Transport  

Microsoft Academic Search

Fluoxetine (Prozac) is one of the most widely prescribed pharmaceuticals, yet important aspects of its mechanism of action remain unknown. We previously reported that fluoxetine and related antidepressants induce nose muscle contraction ofC.elegans. We also reported the identification and initial characterization of mutations in seven C. elegans genes that cause defects in this response (Nrf, nose resistant to f luoxetine).

Robert K. M. Choy; John M. Kemner; James H. Thomas

2006-01-01

399

Virulence of Leucobacter chromiireducens subsp. solipictus to Caenorhabditis elegans: Characterization of a Novel Host-Pathogen Interaction  

Microsoft Academic Search

We describe the pathogenic interaction between a newly described gram-positive bacterium, Leucobacter chromiireducens subsp. solipictus strain TAN 31504, and the nematode Caenorhabditis elegans. TAN 31504 pathogenesis on C. elegans is exerted primarily through infection of the adult nematode uterus. TAN 31504 enters the uterus through the external vulval opening, and the ensuing uterine infection is strongly correlated with a significant

Rachel E. Muir; Man-Wah Tan

2008-01-01

400

Caenorhabditis elegans b -G Spectrin Is Dispensable for Establishment of Epithelial Polarity, but Essential for Muscular and Neuronal Function  

Microsoft Academic Search

The Caenorhabditis elegans genome encodes one a spectrin subunit, a b spectrin subunit ( b -G), and a b -H spectrin subunit. Our experiments show that the phenotype resulting from the loss of the C. elegans a spectrin is reproduced by tandem depletion of both b -G and b -H spectrins. We propose that a spectrin combines with the b

Suraj Moorthy; Lihsia Chen; Vann Bennett

401

Identification of 1088 new transposon insertions of Caenorhabditis elegans: a pilot study toward large-scale screens.  

PubMed Central

We explored the feasibility of a strategy based on transposons to generate identified mutants of most Caenorhabditis elegans genes. A total of 1088 random new insertions of C. elegans transposons Tc1, Tc3, and Tc5 were identified by anchored PCR, some of which result in a mutant phenotype.

Martin, Edwige; Laloux, Helene; Couette, Gaelle; Alvarez, Thierry; Bessou, Catherine; Hauser, Oliver; Sookhareea, Satis; Labouesse, Michel; Segalat, Laurent

2002-01-01

402

Homologs of genes expressed in Caenorhabditis elegans GABAergic neurons are also found in the developing mouse forebrain  

Microsoft Academic Search

BACKGROUND: In an effort to identify genes that specify the mammalian forebrain, we used a comparative approach to identify mouse homologs of transcription factors expressed in developing Caenorhabditis elegans GABAergic neurons. A cell-specific microarray profiling study revealed a set of transcription factors that are highly expressed in embryonic C. elegans GABAergic neurons. RESULTS: Bioinformatic analyses identified mouse protein homologs of

Elizabeth AD Hammock; Kathie L Eagleson; Susan Barlow; Laurie R Earls; David M Miller; Pat Levitt

2010-01-01

403

A Comparative Study of Fat Storage Quantitation in Nematode Caenorhabditis elegans Using Label and Label-Free Methods  

Microsoft Academic Search

The nematode Caenorhabditis elegans has been employed as a model organism to study human obesity due to the conservation of the pathways that regulate energy metabolism. To assay for fat storage in C. elegans, a number of fat-soluble dyes have been employed including BODIPY, Nile Red, Oil Red O, and Sudan Black. However, dye-labeled assays produce results that often do

Kelvin Yen; Thuc T. Le; Ankita Bansal; Sri Devi Narasimhan; Ji-Xin Cheng; Heidi A. Tissenbaum; Simon Melov

2010-01-01

404

Mitochondrial DNA reveals the genealogical history of the snake-eyed lizards ( Ophisops elegans and O. occidentalis) (Sauria: Lacertidae)  

Microsoft Academic Search

The snake-eyed lizards of the genus Ophisops (Lacertidae) have been through a series of taxonomical revisions, but still their phylogenetic relationships remain uncertain. In the present study we estimate the phylogeographic structure of O. elegans across its distributional range and we evaluate the relationships between O. elegans and the sympatric, in North Africa, species O. occidentalis, using partial mtDNA sequences

P. Kyriazi; N. Poulakakis; A. Parmakelis; P. A. Crochet; J. Moravec; N. Rastegar-Pouyani; C. S. Tsigenopoulos; A. Magoulas; M. Mylonas; P. Lymberakis

2008-01-01

405

Identification of Virulence Properties in Salmonella Typhimurium DT104 Using Caenorhabditis elegans  

PubMed Central

Salmonella enterica serover Typhimurium definitive phage type DT104, resistant to multiple antibiotics, is one of the most widespread Salmonella species in human infection worldwide. Although several cohort studies indicate that DT104 carrying the multidrug resistance (MDR) locus on salmonella genomic island 1 is a possible hyper-virulent strain compared to DT104 strains without MDR, or other Salmonella enterica serotypes, existing experimental evidence regarding virulence properties associated with the MDR region is controversial. To address this question, we constructed an isogenic MDR deletion (?MDR) mutant strain of DT104, SNS12, by allelic exchange and used Caenorhabditis elegans as a host model to assess differences in virulence between these two strains. SNS12 exhibited decreased virulence in C. elegans, and we observed increased colonization and proliferation of the intestine of C. elegans by DT104. The immune response against MDR-carrying DT104 appears to function through a non-canonical Unfolded Protein Response (UPR) pathway, namely prion-like-(QN-rich)-domain-bearing protein pathway (PQN), in a ced-1 dependent manner in C. elegans. Further, we also demonstrate that genes of the PQN pathway and antimicrobial peptide gene abf-2, are expressed at higher transcriptional levels in worms immediately following exposure to DT104, in comparison with worms exposed to SNS12. Altogether, our results suggest that the MDR region of Salmonella Typhimurium DT104 has a direct role in virulence against Caenorhabditis elegans.

Sahu, Surasri N.; Anriany, Yuda; Grim, Christopher J.; Kim, Sungji; Chang, Zenas; Joseph, Sam W.; Cinar, Hediye N.

2013-01-01

406

Identification of virulence properties in Salmonella Typhimurium DT104 using Caenorhabditis elegans.  

PubMed

Salmonella enterica serover Typhimurium definitive phage type DT104, resistant to multiple antibiotics, is one of the most widespread Salmonella species in human infection worldwide. Although several cohort studies indicate that DT104 carrying the multidrug resistance (MDR) locus on salmonella genomic island 1 is a possible hyper-virulent strain compared to DT104 strains without MDR, or other Salmonella enterica serotypes, existing experimental evidence regarding virulence properties associated with the MDR region is controversial. To address this question, we constructed an isogenic MDR deletion (?MDR) mutant strain of DT104, SNS12, by allelic exchange and used Caenorhabditis elegans as a host model to assess differences in virulence between these two strains. SNS12 exhibited decreased virulence in C. elegans, and we observed increased colonization and proliferation of the intestine of C. elegans by DT104. The immune response against MDR-carrying DT104 appears to function through a non-canonical Unfolded Protein Response (UPR) pathway, namely prion-like-(QN-rich)-domain-bearing protein pathway (PQN), in a ced-1 dependent manner in C. elegans. Further, we also demonstrate that genes of the PQN pathway and antimicrobial peptide gene abf-2, are expressed at higher transcriptional levels in worms immediately following exposure to DT104, in comparison with worms exposed to SNS12. Altogether, our results suggest that the MDR region of Salmonella Typhimurium DT104 has a direct role in virulence against Caenorhabditis elegans. PMID:24124587

Sahu, Surasri N; Anriany, Yuda; Grim, Christopher J; Kim, Sungji; Chang, Zenas; Joseph, Sam W; Cinar, Hediye N

2013-01-01

407

Understanding the molecular basis of Alzheimer's disease using a Caenorhabditis elegans model system  

PubMed Central

Alzheimer’s disease (AD) is the major cause of dementia in the United States. At the cellular level, the brains of AD patients are characterized by extracellular dense plaques and intracellular neurofibrillary tangles whose major components are the ?-amyloid peptide and tau, respectively. The ?-amyloid peptide is a cleavage product of the amyloid precursor protein (APP); mutations in APP have been correlated with a small number of cases of familial Alzheimer’s disease. APP is the canonical member of the APP family, whose functions remain unclear. The nematode Caenorhabditis elegans, one of the premier genetic workhorses, is being used in a variety of ways to address the functions of APP and determine how the ?-amyloid peptide and tau can induce toxicity. First, the function of the C. elegans APP-related gene, apl-1, is being examined. Although different organisms may use APP and related proteins, such as APL-1, in different functional contexts, the pathways in which they function and the molecules with which they interact are usually conserved. Second, components of the ?-secretase complex and their respective functions are being revealed through genetic analyses in C. elegans. Third, to address questions of toxicity, onset of degeneration, and protective mechanisms, different human ?-amyloid peptide and tau variants are being introduced into C. elegans and the resultant transgenic lines examined. Here, we summarize how a simple system such as C. elegans can be used as a model to understand APP function and suppression of ?-amyloid peptide and tau toxicity in higher organisms.

Ewald, Collin Y.; Li, Chris

2013-01-01

408

Modeling Molecular and Cellular Aspects of Human Disease using the Nematode Caenorhabditis elegans  

PubMed Central

As an experimental system, Caenorhabditis elegans, offers a unique opportunity to interrogate in vivo the genetic and molecular functions of human disease-related genes. For example, C. elegans has provided crucial insights into fundamental biological processes such as cell death and cell fate determinations, as well as pathological processes such as neurodegeneration and microbial susceptibility. The C. elegans model has several distinct advantages including a completely sequenced genome that shares extensive homology with that of mammals, ease of cultivation and storage, a relatively short lifespan and techniques for generating null and transgenic animals. However, the ability to conduct unbiased forward and reverse genetic screens in C. elegans remains one of the most powerful experimental paradigms for discovering the biochemical pathways underlying human disease phenotypes. The identification of these pathways leads to a better understanding of the molecular interactions that perturb cellular physiology, and forms the foundation for designing mechanism-based therapies. To this end, the ability to process large numbers of isogenic animals through automated work stations suggests that C. elegans, manifesting different aspects of human disease phenotypes, will become the platform of choice for in vivo drug discovery and target validation using high-throughput/content screening technologies.

Silverman, Gary A.; Luke, Cliff J.; Bhatia, Sangeeta R.; Long, Olivia S.; Vetica, Anne C.; Perlmutter, David H.; Pak, Stephen C.

2009-01-01

409

Deletion of Thioredoxin Reductase and Effects of Selenite and Selenate Toxicity in Caenorhabditis elegans  

PubMed Central

Thioredoxin reductase-1 (TRXR-1) is the sole selenoprotein in C. elegans, and selenite is a substrate for thioredoxin reductase, so TRXR-1 may play a role in metabolism of selenium (Se) to toxic forms. To study the role of TRXR in Se toxicity, we cultured C. elegans with deletions of trxr-1, trxr-2, and both in axenic media with increasing concentrations of inorganic Se. Wild-type C. elegans cultured for 12 days in Se-deficient axenic media grow and reproduce equivalent to Se-supplemented media. Supplementation with 0–2 mM Se as selenite results in inverse, sigmoidal response curves with an LC50 of 0.20 mM Se, due to impaired growth rather than reproduction. Deletion of trxr-1, trxr-2 or both does not modulate growth or Se toxicity in C. elegans grown axenically, and 75Se labeling showed that TRXR-1 arises from the trxr-1 gene and not from bacterial genes. Se response curves for selenide (LC50 0.23 mM Se) were identical to selenite, but selenate was 1/4th as toxic (LC50 0.95 mM Se) as selenite and not modulated by TRXR deletion. These nutritional and genetic studies in axenic media show that Se and TRXR are not essential for C. elegans, and that TRXR alone is not essential for metabolism of inorganic Se to toxic species.

Boehler, Christopher J.; Raines, Anna M.; Sunde, Roger A.

2013-01-01

410

Extension of Lifespan in C. elegans by Naphthoquinones That Act through Stress Hormesis Mechanisms  

PubMed Central

Hormesis occurs when a low level stress elicits adaptive beneficial responses that protect against subsequent exposure to severe stress. Recent findings suggest that mild oxidative and thermal stress can extend lifespan by hormetic mechanisms. Here we show that the botanical pesticide plumbagin, while toxic to C. elegans nematodes at high doses, extends lifespan at low doses. Because plumbagin is a naphthoquinone that can generate free radicals in vivo, we investigated whether it extends lifespan by activating an adaptive cellular stress response pathway. The C. elegans cap‘n’collar (CNC) transcription factor, SKN-1, mediates protective responses to oxidative stress. Genetic analysis showed that skn-1 activity is required for lifespan extension by low-dose plumbagin in C. elegans. Further screening of a series of plumbagin analogs identified three additional naphthoquinones that could induce SKN-1 targets in C. elegans. Naphthazarin showed skn-1dependent lifespan extension, over an extended dose range compared to plumbagin, while the other naphthoquinones, oxoline and menadione, had differing effects on C. elegans survival and failed to activate ARE reporter expression in cultured mammalian cells. Our findings reveal the potential for low doses of naturally occurring naphthoquinones to extend lifespan by engaging a specific adaptive cellular stress response pathway.

Wilson, Mark A.; Yu, Quian-Sheng; Wood, William H.; Zhang, Yongqing; Becker, Kevin G.; Greig, Nigel H.; Mattson, Mark P.; Camandola, Simonetta; Wolkow, Catherine A.

2011-01-01

411

Deletion of thioredoxin reductase and effects of selenite and selenate toxicity in Caenorhabditis elegans.  

PubMed

Thioredoxin reductase-1 (TRXR-1) is the sole selenoprotein in C. elegans, and selenite is a substrate for thioredoxin reductase, so TRXR-1 may play a role in metabolism of selenium (Se) to toxic forms. To study the role of TRXR in Se toxicity, we cultured C. elegans with deletions of trxr-1, trxr-2, and both in axenic media with increasing concentrations of inorganic Se. Wild-type C. elegans cultured for 12 days in Se-deficient axenic media grow and reproduce equivalent to Se-supplemented media. Supplementation with 0-2 mM Se as selenite results in inverse, sigmoidal response curves with an LC50 of 0.20 mM Se, due to impaired growth rather than reproduction. Deletion of trxr-1, trxr-2 or both does not modulate growth or Se toxicity in C. elegans grown axenically, and (75)Se labeling showed that TRXR-1 arises from the trxr-1 gene and not from bacterial genes. Se response curves for selenide (LC50 0.23 mM Se) were identical to selenite, but selenate was 1/4(th) as toxic (LC50 0.95 mM Se) as selenite and not modulated by TRXR deletion. These nutritional and genetic studies in axenic media show that Se and TRXR are not essential for C. elegans, and that TRXR alone is not essential for metabolism of inorganic Se to toxic species. PMID:23936512

Boehler, Christopher J; Raines, Anna M; Sunde, Roger A

2013-01-01

412

Nanosilver suppresses growth and induces oxidative damage to DNA in Caenorhabditis elegans.  

PubMed

Studies on the effects of nanomaterial exposure in mammals are limited, and new methods for rapid risk assessment of nanomaterials are urgently required. The utility of Caenorhabditis elegans cultured in axenic liquid media was evaluated as an alternative in vivo model for the purpose of screening nanomaterials for toxic effects. Spherical silver nanoparticles of 10?nm diameter (10nmAg) were used as a test material, and ionic silver from silver acetate as a positive control. Silver uptake and localization, larval growth, morphology and DNA damage were utilized as endpoints for toxicity evaluation. Confocal reflection analysis indicated that 10nmAg localized to the lumen and tissues of the digestive tract of C. elegans. 10nmAg at 10?µg?ml(-1) reduced the growth of C. elegans larvae, and induced oxidative damage to DNA as measured by 8-OH guanine levels. Consistent with previously published studies using mammalian models, ionic silver suppressed growth in C. elegans larvae to a greater extent than 10nmAg. Our data suggest that medium-throughput growth screening and DNA damage analysis along with morphology assessments in C. elegans could together provide powerful tools for rapid toxicity screening of nanomaterials. PMID:23636779

Hunt, Piper Reid; Marquis, Bryce J; Tyner, Katherine M; Conklin, Sean; Olejnik, Nicholas; Nelson, Bryant C; Sprando, Robert L

2013-10-01

413

The wounded worm: Using C. elegans to understand the molecular basis of skin wound healing.  

PubMed

The ability to heal wounds is an ancient and conserved function of epidermal epithelial layers. The importance of skin wound healing to human life and biology has long been evident, however many of the molecular mechanisms underlying wound repair remain little understood. In the past several years, analysis of the C. elegans innate immune response to fungal infection of the epidermis has led to investigations of the ability of the C. elegans skin to respond to damage. In a recent paper we used live imaging to investigate the cell biological basis of wound repair in the adult C. elegans epidermis. We found that needle or laser injury of the skin triggers a large and sustained increase in epidermal calcium. Epidermal calcium signals appear to specifically promote actin-dependent processes of wound closure. The innate immune and wound closure responses act in parallel to promote survival after injury. Our findings indicate that wounding triggers multiple signals in the C. elegans skin. C. elegans offers a tractable model to dissect how epidermal epithelia activate coordinated responses to repair damage. PMID:24058838

Xu, Suhong; Hsiao, Tiffany I; Chisholm, Andrew D

2012-04-01

414

hunchback and Ikaros-like zinc finger genes control reproductive system development in C. elegans  

PubMed Central

Here we provide evidence for a C2H2 zinc finger gene family with similarity to Ikaros and hunchback. The founding member of this family is C. elegans ehn-3, which has important and poorly understood functions in somatic gonad development. We examined the expression and function of four additional hunchback/Ikaros-like (HIL) genes in C. elegans reproductive system development. Two genes, ehn-3 and R08E3.4, are expressed in somatic gonadal precursors (SGPs) and have overlapping functions in their development. In ehn-3; R08E3.4 double mutants, we find defects in the generation of distal tip cells, anchor cells, and spermatheca; three of the five tissues derived from the SGPs. We provide in vivo evidence that C. elegans HIL proteins have functionally distinct zinc finger domains, with specificity residing in the N-terminal set of four zinc fingers and a likely protein-protein interaction domain provided by the C-terminal pair of zinc fingers. In addition, we find that a chimeric human Ikaros protein containing the N-terminal zinc fingers of EHN-3 functions in C. elegans. Together, these results lend support to the idea that the C. elegans HIL genes and Ikaros have similar functional domains. We propose that hunchback, Ikaros, and the HIL genes arose from a common ancestor that was present prior to the divergence of protostomes and deuterostomes

Large, Edward E.; Mathies, Laura D.

2013-01-01

415

A HIGH-THROUGHPUT METHOD FOR ASSESSING CHEMICAL TOXICITY USING A CAENORHABDITIS ELEGANS REPRODUCTION ASSAY  

PubMed Central

The National Research Council has outlined the need for non-mammalian toxicological models to test the potential health effects of a large number of chemicals while also reducing the use of traditional animal models. The nematode Caenorhabditis elegans is an attractive alternative model because of its well-characterized and evolutionarily-conserved biology, low cost, and ability to be used in high-throughput screening. A high-throughput method is described for quantifying the reproductive capacity of C. elegans exposed to chemicals for 48 h from the last larval stage (L4) to adulthood using a COPAS Biosort. Initially, the effects of exposure conditions that could influence reproduction were defined. Concentrations of DMSO vehicle ? 1% did not affect reproduction. Previous studies indicated that C. elegans may be influenced by exposure to low pH conditions. At pHs greater than 4.5, C. elegans reproduction was not affected, however below this pH there was a significant decrease in the number of offspring. Cadmium chloride was chosen as a model toxicant to verify that automated measurements were comparable to those of traditional observational studies. EC50 values for cadmium for automated measurements (176-192 ?M) were comparable to those previously reported for a 72-h exposure using manual counting (151 ?M). The toxicity of seven test toxicants on C. elegans reproduction was highly correlative with rodent lethality suggesting that this assay may be useful in predicting the potential toxicity of chemicals in other organisms.

Boyd, Windy A.; McBride, Sandra J.; Rice, Julie R.; Snyder, Daniel W.; Freedman, Jonathan H.

2010-01-01

416

Cytoplasmic Expression of Mouse Prion Protein Causes Severe Toxicity in C. elegans  

PubMed Central

To test if Caenorhabditis elegans could be established as a model organism for prion study, we created transgenic C. elegans expressing the cytosolic form of the mouse prion .protein, MoPrP(23-231), which lacks the N-terminal signal sequence and the C-terminal glycosylphosphatidylinisotol (GPI) anchor site. We report here that transgenic worms expressing MoPrP(23-231)–CFP exhibited a wide range of distinct phenotypes: from normal growth and development, reduced mobility and development delay, complete paralysis and development arrest, to embryonic lethality. Similar levels of MoPrP (23-231)-CFP were produced in animals exhibiting these distinct phenotypes, suggesting that MoPrP (23-231)-CFP might have misfolded into distinct toxic species. In combining with the observation that mutations in PrP that affect prion pathogenesis also affect the toxic phenotypes in C. elegans, we conclude that the prion protein folding mechanism is similar in mammals and C. elegans. Thus, C. elegans can be a useful model organism for prion research.

Park, Kyung-Won; Li, Liming

2008-01-01

417

abf-1 and abf-2, ASABF-type antimicrobial peptide genes in Caenorhabditis elegans.  

PubMed Central

Two genes encoding the ASABF (Ascaris suum antibacterial factor)-type antimicrobial peptide, abf-1 and abf-2, were identified in Caenorhabditis elegans. Recombinant ABF-2 exhibited potent microbicidal activity against Gram-positive and Gram-negative bacteria, and yeasts. The tissue-specific distribution estimated by immunofluorescence staining and transgenic analysis of a gfp fusion gene (where GFP corresponds to green fluorescent protein) suggested that ABF-2 contributes to surface defence in the pharynx. abf-1 contains a single intron at a conserved position, suggesting that asabf and abf originated from a common ancestor. Both transcripts for abf-1 and abf-2 were detected as two distinct forms, i.e. spliced leader (SL)1-trans-spliced with a long 5'-untranslated region (UTR) and SL-less with a short 5'-UTR. A polycistronic precursor RNA encoding ABF-1 and ABF-2 was detected, suggesting that these genes form an operon. An 'opportunistic operon' model for regulation of abf genes, including the generation of short SL-less transcripts, is proposed. In conclusion, C. elegans should have an immune defence system due to the antimicrobial peptides. C. elegans can be a novel model for innate immunity. Furthermore, the combination of biochemical identification in Ascaris suum and homologue hunting in C. elegans should be a powerful method of finding rapidly evolved proteins, such as some immune-related molecules in C. elegans.

Kato, Yusuke; Aizawa, Tomoyasu; Hoshino, Hirokazu; Kawano, Keiichi; Nitta, Katsutoshi; Zhang, Hong

2002-01-01

418

Inducible and titratable silencing of Caenorhabditis elegans neurons in vivo with histamine-gated chloride channels.  

PubMed

Recent progress in neuroscience has been facilitated by tools for neuronal activation and inactivation that are orthogonal to endogenous signaling systems. We describe here a chemical-genetic approach for inducible silencing of Caenorhabditis elegans neurons in intact animals, using the histamine-gated chloride channel HisCl1 from Drosophila and exogenous histamine. Administering histamine to freely moving C. elegans that express HisCl1 transgenes in neurons leads to rapid and potent inhibition of neural activity within minutes, as assessed by behavior, functional calcium imaging, and electrophysiology of neurons expressing HisCl1. C. elegans does not use histamine as an endogenous neurotransmitter, and exogenous histamine has little apparent effect on wild-type C. elegans behavior. HisCl1-histamine silencing of sensory neurons, interneurons, and motor neurons leads to behavioral effects matching their known functions. In addition, the HisCl1-histamine system can be used to titrate the level of neural activity, revealing quantitative relationships between neural activity and behavioral output. We use these methods to dissect escape circuits, define interneurons that regulate locomotion speed (AVA, AIB) and escape-related omega turns (AIB), and demonstrate graded control of reversal length by AVA interneurons and DA/VA motor neurons. The histamine-HisCl1 system is effective, robust, compatible with standard behavioral assays, and easily combined with optogenetic tools, properties that should make it a useful addition to C. elegans neurotechnology. PMID:24550306

Pokala, Navin; Liu, Qiang; Gordus, Andrew; Bargmann, Cornelia I

2014-02-18

419

Extension of lifespan in C. elegans by naphthoquinones that act through stress hormesis mechanisms.  

PubMed

Hormesis occurs when a low level stress elicits adaptive beneficial responses that protect against subsequent exposure to severe stress. Recent findings suggest that mild oxidative and thermal stress can extend lifespan by hormetic mechanisms. Here we show that the botanical pesticide plumbagin, while toxic to C. elegans nematodes at high doses, extends lifespan at low doses. Because plumbagin is a naphthoquinone that can generate free radicals in vivo, we investigated whether it extends lifespan by activating an adaptive cellular stress response pathway. The C. elegans cap'n'collar (CNC) transcription factor, SKN-1, mediates protective responses to oxidative stress. Genetic analysis showed that skn-1 activity is required for lifespan extension by low-dose plumbagin in C. elegans. Further screening of a series of plumbagin analogs identified three additional naphthoquinones that could induce SKN-1 targets in C. elegans. Naphthazarin showed skn-1dependent lifespan extension, over an extended dose range compared to plumbagin, while the other naphthoquinones, oxoline and menadione, had differing effects on C. elegans survival and failed to activate ARE reporter expression in cultured mammalian cells. Our findings reveal the potential for low doses of naturally occurring naphthoquinones to extend lifespan by engaging a specific adaptive cellular stress response pathway. PMID:21765926

Hunt, Piper R; Son, Tae Gen; Wilson, Mark A; Yu, Quian-Sheng; Wood, William H; Zhang, Yongqing; Becker, Kevin G; Greig, Nigel H; Mattson, Mark P; Camandola, Simonetta; Wolkow, Catherine A

2011-01-01

420

The insecticidal crystal protein gene is expressed in vegetative cells of Bacillus thuringiensis var. tenebrionis  

Microsoft Academic Search

The time of appearance of the insecticidal crystal protein (ICP) transcript and the corresponding crystal antigen of the coleopteran-toxicBacillus thuringiensis var.tenebrionis was determined. The results indicate that inB. thuringiensis var.tenebrionis, unlike otherB. thuringiensis varieties, the ICP antigen and the ICP transcript are made at detectable levels in vegetative cells. The expression of the ICP gene increases dramatically and reaches a

Vaithilingam Sekar

1988-01-01

421

[Actinomyces fulvoviolaceus ver. achromogenes var. nov., a producer of the new heptaene complex, fulvomycin].  

PubMed

An actinomycetous culture designated as LIA-0721 was isolated from a soil sample. It was close to Act. fulvoviolaceus by its morphologo-cultural features and differed from it in production of melanoid pigments and the spectrum of carbohydrate assimilation. This justified its classification as Act. fulvoviolaceus var. achromogenes var. nov. The culture produced new aromatic heptaens, i. e. fulvomycins A, B and C. Their physico- chemical and biological characteristics are presented. PMID:1225210

Tsyganov, V A; Iakovleva, E P; Kruglikova, L F; Shenin, Iu D; Etingov, E D

1975-06-01

422

Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris  

Microsoft Academic Search

BACKGROUND: VAR2CSA is the main candidate for a vaccine against pregnancy-associated malaria, but vaccine development is complicated by the large size and complex disulfide bonding pattern of the protein. Recent X-ray crystallographic information suggests that domain boundaries of VAR2CSA Duffy binding-like (DBL) domains may be larger than previously predicted and include two additional cysteine residues. This study investigated whether longer

Marion Avril; Marianne J Hathaway; Megan M Cartwright; Severin O Gose; David L Narum; Joseph D Smith

2009-01-01

423

Free Radical Scavenging Activity of Aqueous and Ethanolic Extract of Brassica oleracea L. var. italica  

Microsoft Academic Search

In this study, antioxidant activities of aqueous and ethanolic extracts of Brassica oleracea L. var. italica were investigated. The antioxidant properties of both extracts of Brassica oleracea L. var. italica were evaluated using different antioxidant tests, including 1, 1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, superoxide\\u000a radical scavenging, inhibition of microsomal lipid peroxidation, reduction of power, and metal ion chelating activities. Inhibition\\u000a of

Abdul Mueed Bidchol; A. Wilfred; P. Abhijna; R. Harish

424

Soil bio-functioning under Acacia nilotica var. tomentosa protected forest along the Senegal River  

Microsoft Academic Search

Acacia nilotica var. tomentosa trees from the Diarra protected forest located in the Senegal River valley were identified for the assessment of both biological\\u000a nitrogen fixation, using the natural abundance method, and soil bio-functioning parameters (nodulation, root biomass, total\\u000a microbial biomass, and potential N mineralization). The presence and the genetic diversity of indigenous rhizobia nodulating\\u000a A. nilotica var. tomentosa was also

Aliou Faye; Saidou Sall; Jean-Luc Chotte; Didier Lesueur

2007-01-01

425

Physiological and Biochemical Effects of Simulated Acid Rain on Phaseolus Vulgaris Var. HUR-15  

Microsoft Academic Search

Pot experiments were performed to determine the effects of simulated acid rain on Phaseolus vulgaris var. HUR-15. Seeds of Phaseolus vulgaris var. HUR-15 were exposed to simulated acid rain at pH values of 5.1, 4.1, 3.1, 2.1 and 1.1 and a control level of pH 6.8. Plants were harvested at three stages, i.e. pre, peak and post-flowering stages. Seedlings succumbed

T. I. Khan; Shikha Devpura

2004-01-01

426

Weinmannia marquesana var. angustifolia (Cunoniaceae), a new variety from the Marquesas Islands  

PubMed Central

Abstract Weinmannia marquesana F. Br. var. angustifolia Lorence & W. L. Wagner, var. nov., a new variety with narrow, simple leaves endemic to Tahuata, Marquesas Islands (French Polynesia) is described and its affinities and conservation status are discussed. It is similar to the other two varieties of this species by having simple leaves, but this new variety has much narrower leaf blades, and it resembles Weinmannia tremuloides in having narrow leaf blades but differs by having simple, not trifoliolate leaves.

Lorence, David H.; Wagner, Warren L.

2011-01-01

427

Biological control of grapevine crown gall by nonpathogenic Agrobacterium vitis strain VAR03-1  

Microsoft Academic Search

A nonpathogenic strain of Agrobacterium vitis VAR03-1 was tested as a biological control agent against crown gall of grapevine (Vitis vinifera L.). A mixture of the nonpathogenic strain VAR03-1 and a tumorigenic strain G-Ag-27 of A. vitis at cell ratios of 1?:?1, 3?:?1, 9?:?1, and 99?:?1 significantly inhibited gall formation and size on stems of tomato (Lycopersicon esculentum Mill.). Strain

Akira Kawaguchi; Koji Inoue; Hideo Nasu

2007-01-01

428

Semi-nonparametric VaR forecasts for hedge funds during the recent crisis  

NASA Astrophysics Data System (ADS)

The need to provide accurate value-at-risk (VaR) forecasting measures has triggered an important literature in econophysics. Although these accurate VaR models and methodologies are particularly demanded for hedge fund managers, there exist few articles specifically devoted to implement new techniques in hedge fund returns VaR forecasting. This article advances in these issues by comparing the performance of risk measures based on parametric distributions (the normal, Student’s t and skewed-t), semi-nonparametric (SNP) methodologies based on Gram-Charlier (GC) series and the extreme value theory (EVT) approach. Our results show that normal-, Student’s t- and Skewed t- based methodologies fail to forecast hedge fund VaR, whilst SNP and EVT approaches accurately success on it. We extend these results to the multivariate framework by providing an explicit formula for the GC copula and its density that encompasses the Gaussian copula and accounts for non-linear dependences. We show that the VaR obtained by the meta GC accurately captures portfolio risk and outperforms regulatory VaR estimates obtained through the meta Gaussian and Student’s t distributions.

Del Brio, Esther B.; Mora-Valencia, Andrés; Perote, Javier

2014-05-01

429

Reduced order POD/DEIM 4-D Var data assimilation  

NASA Astrophysics Data System (ADS)

The computational cost of realistic ensemble and hybrid variational/ensemble data assimilation is typically dominated by the cost of ensemble forecasting. The high computational cost of ensemble forecasting limits the number of ensembles, eventually creating a severe rank reduction. Consequently, the efficiency and quality of ensemble-based data assimilation are greatly reduced. With the ever-increasing spatiotemporal resolution and complexity of numerical weather prediction (NWP) models, the room for ensemble forecasting is getting even smaller, creating a paradox: Although the NWP generally benefits from increased resolution and complexity of the models, the quality of their data assimilation is getting worse due to additional computational restrictions. We propose POD model order reduction substantially improving computational efficiency of NWP models. We present recent advances in this domain and the state-of the art of hyper reduction addressing issues of turbulence closure and nonlinearities allowing CPU speed -ups of orders of magnitude, reduced order 4-D VAR and future prospects of implementation to operational NMP models.

Navon, Michael; Stefanescu, Razvan

2014-05-01

430

Acylated iridoids from the roots of Valeriana officinalis var. latifolia.  

PubMed

Phytochemical investigation of the roots of Valeriana officinalis var. latifolia resulted in the isolation and characterization of six new acylated iridoids, (5S,7S,8S,9S)-7-hydroxy-8-isovaleroyloxy-??,¹¹-dihyronepetalactone (1), (5S,7S,8S,9S)-7-hydroxy-10-isovaleroyloxy-??,¹¹-dihyronepetalactone (2), (5S,8S,9S)-10-isovaleroyloxy-??,¹¹-dihyronepetalactone (3), (5S,6S,8S,9R)-6-isovaleroyloxy-??,¹¹-1,3-diol (4), (5S,6S,8S,9R)-1,3-isovaleroxy-?4,11-1,3-diol (5), and (5S,6S,8S,9R)-3-isovaleroxy-6-isovaleroyloxy-??,¹¹-1,3-diol (6). Their structures were determined mainly by 1D and 2D?NMR spectroscopic techniques. We also report herein for the first time the single crystal X-ray structure of compound 1. In addition, the cytotoxic activities of compounds 1-6 were evaluated against A549 (human lung adenocarcinoma), HCT116 (human colon carcinoma), SK-BR-3 (human breast carcinoma), and HepG2 (human hepatoma) cell lines. Compound 6 showed weak cell growth inhibition of A549, HCT116, SK-BR-3, and HepG2 cells. PMID:22872588

Han, Zhu-zhen; Yan, Zhao-hui; Liu, Qing-xin; Hu, Xian-qing; Ye, Ji; Li, Hui-liang; Zhang, Wei-dong

2012-10-01

431

Three new clerodane diterpenes from Polyalthia longifolia var. pendula.  

PubMed

Three new clerodane diterpenes, (4?2)-abeo-cleroda-2,13E-dien-2,14-dioic acid (1), (4?2)-abeo-2,13-diformyl-cleroda-2,13E-dien-14-oic acid (2), and 16(R&S)- methoxycleroda-4(18),13-dien-15,16-olide (3), were isolated from the unripe fruit of Polyalthia longifolia var. pendula (Annonaceae) together with five known compounds (4-8). The structures of all isolates were determined by spectroscopic analysis. The anti-inflammatory activity of the isolates was evaluated by testing their inhibitory effect on NO production in LPS-stimulated RAW 264.7 macrophages. Among the isolated compounds, 16-hydroxycleroda-3,13-dien-15,16-olide (6) and 16-oxocleroda-3,13-dien-15-oic acid (7) showed promising NO inhibitory activity at 10 µg/mL, with 81.1% and 86.3%, inhibition, respectively. PMID:24531220

Wu, Tung-Ho; Cheng, Yung-Yi; Chen, Chao-Jung; Ng, Lean-Teik; Chou, Li-Chen; Huang, Li-Jiau; Chen, Yung-Husan; Kuo, Sheng-Chu; El-Shazly, Mohamed; Wu, Yang-Chang; Chang, Fang-Rong; Liaw, Chih-Chuang

2014-01-01

432

Decarboxylation of ?-Keto Acids by Streptococcus lactis var. maltigenes1  

PubMed Central

Decarboxylation rates for a series of C-3 to C-6 ?-keto acids were determined in the presence of resting cells and cell-free extracts of Streptococcus lactis var. maltigenes. The C-5 and C-6 acids branched at the penultimate carbon atom were converted most rapidly to the respective aldehydes in the manner described for ?-carboxylases. Pyruvate and ?-ketobutyrate did not behave as ?-carboxylase substrates, in that O2 was absorbed when they were reacted with resting cells. The same effect with pyruvate was noted in a nonmalty S. lactis, accounting for CO2 produced by some “homofermentative” streptococci. Mixed substrate reactions indicated that the same enzyme was responsible for decarboxylation of ?-ketoisocaproate and ?-ketoisovalerate, but it appeared unlikely that this enzyme was responsible for the decarboxylation of pyruvate. Ultrasonic disruption of cells of the malty culture resulted in an extract inactive for decarboxylation of pyruvate in the absence of ferricyanide. Dialyzed cell-free extracts were inactive against all keto acids and could not be reactivated.

Tucker, J. S.; Morgan, M. E.

1967-01-01

433

Long-Term Imaging of Caenorhabditis elegans Using Nanoparticle-Mediated Immobilization  

PubMed Central

One advantage of the nematode Caenorhabditis elegans as a model organism is its suitability for in vivo optical microscopy. Imaging C. elegans often requires animals to be immobilized to avoid movement-related artifacts. Immobilization has been performed by application of anesthetics or by introducing physical constraints using glue or specialized microfluidic devices. Here we present a method for immobilizing C. elegans using polystyrene nanoparticles and agarose pads. Our technique is technically simple, does not expose the worm to toxic substances, and allows recovery of animals. We evaluate the method and show that the polystyrene beads increase friction between the worm and agarose pad. We use our method to quantify calcium transients and long-term regrowth in single neurons following axotomy by a femtosecond laser.

Kim, Eric; Sun, Lin; Gabel, Christopher V.; Fang-Yen, Christopher

2013-01-01

434

Latrophilin is required for toxicity of black widow spider venom in Caenorhabditis elegans.  

PubMed Central

Black widow spider venom (BWSV) kills Caenorhabditis elegans after injection owing to the presence of heat- and detergent-sensitive components, which are high-molecular-mass latrotoxins. A C. elegans homologue of latrophilin/CIRL (calcium-independent receptor for latrotoxin), B0457.1, was identified and shown to have five conserved domains. RNAi (RNA interference) of this gene rendered C. elegans resistant to BWSV, whereas RNAi for CYP37A1 or a neurexin I homologue, and a deletion mutant of the related B0286.2 gene, had no effect on BWSV toxicity. The latrophilin RNAi mutants exhibit changes in defaecation cycle and alterations in drug sensitivity. These results demonstrate that latrophilin mediates the toxicity of BWSV and provide evidence for a physiological function of this receptor.

Mee, Christopher J; Tomlinson, Simon R; Perestenko, Pavel V; De Pomerai, David; Duce, Ian R; Usherwood, Peter N R; Bell, David R

2004-01-01

435

Excision Repair of Uv Radiation-Induced DNA Damage in Caenorhabditis Elegans  

PubMed Central

Radioimmunoassays were used to monitor the removal of antibody-binding sites associated with the two major UV radiation-induced DNA photoproducts [cyclobutane dimers and (6-4) photoproducts]. Unlike with