Table of Contents

Volume 1, Issue 1

  January/February/March 2012

  Pages 1 - 89

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EDITOR'S CORNERS

Open Access Article

Introducing Worm: The journal

Harald Hutter
Page 1
http://dx.doi.org/10.4161/worm.19560
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Open Access Article

In this Issue of Worm

Elaine Ellerton
Pages 2 - 4
http://dx.doi.org/10.4161/worm.19394
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SHORT COMMUNICATIONS

Open Access Article

Coordination of behavioral hierarchies during environmental transitions in Caenorhabditis elegans

Andrés G. Vidal-Gadea, Scott Davis, Lindsay Becker and Jonathan T. Pierce-Shimomura
Pages 5 - 11
http://dx.doi.org/10.4161/worm.19148
Abstract | Full Text | PDF

For animals inhabiting multiple environments, the ability to select appropriate behaviors is crucial as their adaptability is often context dependent. Caenorhabditis elegans uses distinct gaits to move on land and in water. Gait transitions can potentially coordinate behaviors associated with distinct environments. We investigated whether land and water differentially affect the behavioral repertoire of C. elegans. Swimming worms interrupted foraging, feeding, egg-laying and defecation. Exogenous dopamine induced bouts of these land-associated behaviors in water. Our finding that worms do not drink fluid while immersed may explain why higher drug doses are required in water than on land to elicit the same effects. C. elegans is a valid model to study behavioral hierarchies and how environmental pressures alter their balance.

Open Access Article

Reduced muscle contraction and a relaxed posture during sleep-like Lethargus

Juliane Schwarz, Jan-Philipp Spies and Henrik Bringmann
Pages 12 - 14
http://dx.doi.org/10.4161/worm.19499
Abstract | Full Text | PDF

Sleep is characterized by reduced muscle activity resulting in reduced movement and a typical posture compatible with relaxed muscles. Prior to each molt, C. elegans larvae go through a phase of behavioral quiescence called Lethargus. Lethargus has sleep-like properties, but a specific posture has not yet been described. Do C. elegans larvae relax their muscles during sleep and do they assume a typical posture? We measured worm posture and body wall muscle activity using calcium imaging across the sleep-wake-like cycle. We found that worms were less curved and had less muscle activity during the sleep-like state. We conclude that during Lethargus, muscle activity is reduced, resulting in a relaxed body posture typical for a sleep-like state.




RESOURCES

Open Access Article

WormBase: Annotating many nematode genomes

Kevin Howe, Paul Davis, Michael Paulini, Mary Ann Tuli, Gary Williams, Karen Yook, Richard Durbin, Paul Kersey and Paul Sternberg
Pages 15 - 21
http://dx.doi.org/10.4161/worm.19574
Abstract | Full Text | PDF

WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase’s role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

Open Access Article

New techniques and tools in 2011

Elaine Ellerton and Harald Hutter
Pages 22 - 25
http://dx.doi.org/10.4161/worm.19575
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METHODS PAPER

Open Access Article

A method for measuring fatty acid oxidation in C. elegans

Ida Coordt Elle, Steven Vestergaard Rødkær, Julius Fredens and Nils Joakim Færgeman
Pages 26 - 30
http://dx.doi.org/10.4161/worm.19564
Abstract | Full Text | PDF

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 β-oxidation in C. elegans.




REVIEWS

Open Access Article

Thermotaxis of C. elegans as a model for temperature perception, neural information processing and neural plasticity

Tsubasa Kimata, Hiroyuki Sasakura, Noriyuki Ohnishi, Nana Nishio and Ikue Mori
Pages 31 - 41
http://dx.doi.org/10.4161/worm.19504
Abstract | Full Text | PDF

Thermotaxis is a model to elucidate how nervous systems sense and memorize environmental conditions to regulate behavioral strategies in Caenorhabditis elegans. The genetic and neural imaging analyses revealed molecular and cellular bases of this experience-dependent behavior. Surprisingly, thermosensory neurons themselves memorize the sensed temperatures. Recently developed techniques for optical manipulation of neuronal activity have facilitated the revelation that there is a sophisticated information flow between sensory neurons and interneurons. Further studies on thermotaxis will allow us to understand the fundamental logics of neural processing from sensory perceptions to behavioral outputs.

Open Access Article

Toward 959 nematode genomes

Sujai Kumar, Georgios Koutsovoulos, Gaganjot Kaur and Mark Blaxter
Pages 42 - 50
http://dx.doi.org/10.4161/worm.19046
Abstract | Full Text | PDF

The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism. The success of the C. elegans genome sequencing project also inspired communities working on other organisms to approach genome sequencing of their species. The phylum Nematoda is rich and diverse and of interest to a wide range of research fields from basic biology through ecology and parasitic disease. For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases. The advent of second-generation sequencing technologies, improvements in computing algorithms and infrastructure and growth in bioinformatics and genomics literacy is making the addition of genome sequencing to the research goals of any nematode research program a less daunting prospect. To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/). Just as the deciphering of the developmental lineage of the 959 cells of the adult hermaphrodite C. elegans was the gateway to broad advances in biomedical science, we hope that a nematode phylogeny with (at least) 959 sequenced species will underpin further advances in understanding the origins of parasitism, the dynamics of genomic change and the adaptations that have made Nematoda one of the most successful animal phyla.




COMMENTARIES

Open Access Article

On the morphogenesis of glial compartments in the sensory organs of Caenorhabditis elegans

Grigorios Oikonomou and Shai Shaham
Pages 51 - 55
http://dx.doi.org/10.4161/worm.19343
Abstract | Full Text | PDF

Glial cells surround neuronal endings and isolate them within specialized compartments. This architecture is found at synapses in the central nervous system, as well as at receptive endings of sensory neurons. Recent studies are beginning to uncover the contributions of glial compartments to the functions of the ensheathed neurons. However, the cellular and molecular processes that guide compartment morphogenesis remain unknown. The main sensory organ of Caenorhabditis elegans, the amphid, provides an experimentally tractable setting in which to address the mechanisms underlying glial compartment formation. Amphid development is stereotyped and amphid structure is easily assayed. We recently uncovered a molecular tug of war that regulates the size of the amphid sensory compartment. The Nemo-like kinase LIT-1 interacts with the glial cytoskeleton to promote compartment growth, a process that also involves components of the retromer complex, while the Patched-related transmembrane protein DAF-6 keeps this expansion in check. Here we discuss how regulation of secretion by the cytoskeleton could guide the sculpting of glial compartments.

Open Access Article

The G protein regulator AGS-3 allows C. elegans to alter behaviors in response to food deprivation

Catherine Hofler and Michael Koelle
Pages 56 - 60
http://dx.doi.org/10.4161/worm.19042
Abstract | Full Text | PDF

Behavioral responses to food deprivation are a fundamental aspect of nervous system function in all animals. In humans, these behavioral responses prevent dieting from being an effective remedy for obesity. Several signaling molecules in the mammalian brain act through G proteins of the Gα_i/o family to mediate responses to food restriction. The mechanisms for neural response to food deprivation may be conserved across species, allowing the power of genetic model organisms to generate insights relevant to the problem of human obesity. In a recent study, we found that C. elegans uses Gα_o signaling to mediate a number of behavioral changes that occur after food deprivation. Food deprivation causes biochemical changes in the G Protein Regulator (GPR) domain protein AGS-3 and AGS-3, together with the guanine nucleotide exchange factor RIC-8, activates Gα_o signaling to alter food-seeking behavior. These proteins are all conserved in the human brain. Thus the study of behavioral responses to food deprivation in C. elegans may reveal the details of conserved molecular mechanisms underlying neural responses to food deprivation.

Open Access Article

How worms survive desiccation: Trehalose pro water

Cihan Erkut, Sider Penkov, Karim Fahmy and Teymuras Kurzchalia
Pages 61 - 65
http://dx.doi.org/10.4161/worm.19040
Abstract | Full Text | PDF

While life requires water, many organisms, known as anhydrobiotes, can survive in the absence of water for extended periods of time. Although discovered 300 years ago, we know very little about the fascinating phenomenon of anhydrobiosis. In this paper, we summarize our previous findings on the desiccation tolerance of the Caenorhabditis elegans dauer larva. A special emphasis is given to the role of trehalose in protecting membranes against desiccation. We also propose a simple mechanism for this process.

Open Access Article

Quantitative proteomics by amino acid labeling identifies novel NHR-49 regulated proteins in C. elegans

Julius Fredens and Nils J. Færgeman
Pages 66 - 71
http://dx.doi.org/10.4161/worm.19044
Abstract | Full Text | PDF

Stable isotope labeling by amino acids combined with mass spectrometry is a widely used methodology to quantitatively examine metabolic and signaling pathways in yeast, fruit flies, plants, cell cultures and mice. However, only metabolic labeling using ¹⁵N has been applied to examine such events in the nematode Caenorhabditis elegans. We have recently shown that C. elegans can be completely labeled with heavy-labeled lysine by feeding worms on prelabeled lysine auxotroph Escherichia coli for just one generation. We applied this methodology to examine the organismal response to functional loss or RNAi mediated knock down of the transcription factor NHR-49, and found numerous proteins involved in lipid metabolism to be downregulated, which is consistent with its previously proposed function as a transcriptional regulator of fatty acid metabolism. The combined use of quantitative proteomics and selective gene knockdown by RNAi provides a powerful tool with broad implications for C. elegans biology.

Open Access Article

A cellular funicular: A hydrodynamic coupling between the anterior- and posterior-directed cytoplasmic flows

Ritsuya Niwayama and Akatsuki Kimura
Pages 72 - 76
http://dx.doi.org/10.4161/worm.19039
Abstract | Full Text | PDF

Organelles inside cells move to position themselves at the right place at the right time. A mechanism for generating active force exists for each of such directed organelle movements. In our recent study on cytoplasmic streaming in the Caenorhabditis elegans one-cell embryo, we demonstrated that an anterior-directed force generated by myosin could drive not only anterior-directed cortical flow but also posterior-directed cytoplasmic flow. This coupling of flows in opposing directions is mediated by the hydrodynamic properties of the cytoplasm. This work provided a good example of an active force generation mechanism that drives organelle movements in two opposite directions inside the cell, just as a funicular moves up and down a slope. Interestingly, the funicular-like coupling of intracellular movements is also seen in our recent studies on centrosome positioning in the C. elegans embryo and on interkinetic nuclear movement during mouse neurogenesis. Thus, funicular-like coupling may be a general strategy used repeatedly in cells. The use of the funicular-like coupling seems advantageous because it is efficient, as one active force generation mechanism can drive movements in two directions, and also because the two movements can be coordinated to have similar speeds.

Open Access Article

Epigenetic memory of longevity in Caenorhabditis elegans

Bérénice A. Benayoun and Anne Brunet
Pages 77 - 81
http://dx.doi.org/10.4161/worm.19157
Abstract | Full Text | PDF

A recent study by Greer et al. in the nematode C. elegans has shown transgenerational epigenetic inheritance of longevity in the descendants of worms deficient for subunits of a complex responsible for histone H3 lysine 4 trimethylation (H3K4me3). In this commentary, we discuss the implications of this epigenetic memory of longevity and the potential mechanisms underlying this phenomenon. The transgenerational inheritance of longevity could result from heritable depletion of H3K4me3 at particular aging-regulating gene loci that would only be progressively replenished. The epigenetic memory of longevity could also be explained by the transgenerational transmission of other molecules, for example other proteins or non-coding RNAs. The discovery of an epigenetic memory of longevity in worms raises the intriguing possibility that environmental cues modulating longevity in ancestors might affect subsequent generations in a non-Mendelian manner. Another remaining intriguing question is whether transgenerational inheritance of longevity also exists in other species, including mammals.

Open Access Article

Our evolving view of Wnt signaling in C. elegans: If two’s company and three’s a crowd, is four really necessary?

Scott Robertson and Rueyling Lin
Pages 82 - 89
http://dx.doi.org/10.4161/worm.19156
Abstract | Full Text | PDF

In this commentary, we discuss how our recent paper by Yang et al. contributes a new wrinkle to the already somewhat curious Wnt signaling pathway in C. elegans. We begin with a historical perspective on the Wnt pathway in the worm, followed by a summary of the key salient point from Yang et al., 2011, namely demonstration of mutually inhibitory binding of a β-catenin SYS-1 to the N-terminus and another β-catenin WRM-1 to the C-terminus of the TCF protein POP-1, and a plausible structural explanation for these differential binding specificities. The mutually inhibitory binding creates one population of POP-1 that is bound by WRM-1, phosphorylated by the NLK kinase and exported from the nucleus, and another bound by coactivator SYS-1 that remains in the nucleus. We speculate on the evolutionary history of the four β-catenins in C. elegans and suggest a possible link between multiple β-catenin gene duplications and the requirement to reduce nuclear POP-1 levels to activate Wnt target genes.