In this Issue of Worm

Short Communications: Transitioning from Surf to Turf, pp. 5–11

Animals exhibit, and often adapt, specific behaviors depending on their surrounding environment. In fact, the survival of an animal is dependent on the ability to exhibit the correct behavior in a specific environment. However, how the animal is able to sense its environment and correctly select a certain repertoire of behaviors is not well understood. In this short communication, Vidal-Gadea et al. build on their latest paper, “Caenorhabditis elegans selects distinct crawling and swimming gaits via dopamine and serotonin” (PNAS 2011; PMID: 21969584), and investigate the modulation of motor patterns as an animal transitions from one environment to another. Given a complete map of neuronal wiring and known behaviors, the authors illustrate that C. elegans is an ideal model for the study of mechanisms that drive the coordination of adaptive hierarchical behaviors.

Is Lethargus Sleeping?, pp. 12–4

C. elegans transition through 4 larval stages before reaching adulthood, molting after each stage. Before molting, the worm enters an interesting stage known as Lethargus. This stage resembles sleep in many ways. The animals show homeostasis, an increase in arousal threshold and reversibility. However, reduced muscle contraction and a typical sleep posture, two indicators for a sleep-like state, have not been previously described, until now. In this short communication, Juliane Schwarz, Jan-Philipp Spies and Henrik Bringmann were able to address this question by generating and studying transgenic worms that express the calcium sensor GCaMP3.35 in striated body muscle walls. This calcium sensor allowed for the detection of calcium influx in muscle cells, a sure indicator of muscle activity. The group observed the animals in high resolution over a long period by placing a small number of animals in unique agarose hydrogel microcompartments (J Neurosci Methods 2011; PMID: 21801751). Using these techniques, they were able to determine that Lethargus is indeed a sleep-like state as C. elegans do assume a relaxed posture and a reduction in muscle activity during Lethargus.

Resource: The Ever-Encompassing WormBase, pp. 15–21

Anyone involved in nematode research is probably no stranger to WormBase. WormBase is an extremely useful bioinformatic database full of genomic and genetic information. The database covers around 20 different nematodes with a focus on C. elegans. Not only does it serve as an invaluable resource, it also serves as a central repository for nematode data, ensuring that the information available is up to date. This technical review explains how the large amount of incoming nematode data is annotated and integrated for an optimal and accurate user experience. The authors, Howe et al., also discuss how they approach sequence curation and how this impacts the accuracy of C. elegans gene models. WormBase is a work in progress, constantly adding and integrating new data to create a comprehensive database for C. elegans researchers. Because of its dynamic nature, suggestions and feedback are most welcome!

Methods Paper: Measuring Fatty Acid Oxidation, pp. 26–30

When food is scarce, our bodies begin to release the contents of fat stores, mainly in the form of triacylglycerols, in order to provide energy. Triacylglycerols are then metabolized into fatty acids, ultimately leading to ATP production. This chain of events is highly regulated and dys-regulation of this process can lead to a variety of metabolic disorders. Research in the area of lipid homeostasis is mainly focused on pathways that lead to an accumulation of lipids, whereas little is known about the pathways involved in the degradation of fatty acids. In this methods paper, Elle, Rødkær and Færgeman describe a method in which the oxidation of fatty acids can be observed and measured in living C. elegans. Interestingly, the rate of fatty acid oxidation differs depending on what strain of bacteria the worms are fed. Using their methods, the authors were able to uncover the roles of specific genes in this oxidation process, suggesting that this methodology will uncover many more genes and pathways in the future.

Reviews: Thermotaxis Explains Environmental-Based Behavior, pp. 31–40

The behavior of C. elegans is largely determined by environmental stimuli, such as mechanical stretch, light, temperature and chemicals. The mechanisms that allow the environment to influence behavior, however, are largely unknown. In this review, Tsubasa Kimata, Hiroyuki Sasakura, Noriyuki Ohnishi, Nana Nishio and Ikue Mori explore this question using thermotaxis as a model for how the C. elegans nervous system senses the environment and regulates behavior accordingly. Interestingly, thermosensory neurons are able to memorize surrounding temperatures and this memorization results in experience-dependent behaviors. The authors describe these temperature-regulated behaviors in detail and explain how their study has helped to uncover new mechanisms for how environmental stimuli affect behavior.

Sequencing the Nematoda Phylum, pp. 42–50

It is no surprise that the sequencing of the entire C. elegans genome has had far-reaching effects across many scientific disciplines. Over the past 20 y, it has also motivated the sequencing of other species furthering our knowledge on not just nematodes, but on organisms across the board. Plant, animal and human parasitic nematodes make up a large number of the Nematoda phylum and access to their genomes will undoubtably lead to the development of new ways to control these parasites. With tens of thousands of known nematode species in existence, it goes without saying that much sequencing remains to be done. In this review, Kumar, Koutsovoulos, Kaur and Blaxter discuss the current stages of nematode genome research and actively encourage others to sequence their own “pet” nematode species. The authors hope to ease deep-seated fears about sequencing by explaining not only how cost-effective it has become, but also how easy it is to share data and experiences by using their recently launched wiki, 959 Nematode Genomes initiative. Access to 959 nematode genomes will certainly be a boon for the scientific community.

Commentaries: Sizing the Glial Compartment, pp. 51–5

Glia, such as oligodendrocytes in the CNS and Schwann cells in the PNS, are cells that surround neuronal endings. These cells are essential to a nervous system and their correct size is imperative for this system to function correctly. It turns out that the glia?s associated axon is what determines its size. C. elegans also have glia and many neuronal endings lie in specialized compartments created by glia. How these compartments are sized and formed, however, is unknown. In this commentary, Grigorios Oikonomou and Shai Shaham use the amphid, the main sensory organ of C. elegans, to address this question. The authors found that the growth, and therefore size of the glia compartment, is determined by a struggle between two molecules, LIT-1 and DAF-6 (PLoS Biol. 2011; 9:e1001121). LIT-1, a nemo-like kinase, promotes compartmental growth via interaction with the cytoskeleton, while the Patched-related transmembrane protein, DAF-6, keeps a tight rein on the overall size. The authors discuss in depth how secretion defines the glial compartment shape.

Worms May Help Explain Why Obesity is so Hard to Fight, pp. 56–60

The quest for food is undeniably one of the strongest and most important urges that an animal has. It's survival depends on it. It is no surprise that staying away from those extra calories is exceptionally difficult. After all, it is hardwired into our nervous systems. In mammals, behavioral responses to food restriction are mediated via signaling molecules that act on G-proteins of the Gαi/o family. In this commentary, Catherin Hofler and Michael Koelle describe recent findings that C. elegans also use Gαo signaling, activated by the G Protein Regulator domain protein AGS-3 and RIC-8, to mediate behavior after food restriction (J Neurosci 2011; PMID:21832186). Interestingly, these proteins are also found in the human brain. The conservation of these proteins across species makes C. elegans an excellent model to study the molecular mechanisms underpinning hunger induced behavior. With obesity on the rise, insights to why we are so drawn to eat not just one, but the entire bag of chips, is in great demand.

Worms without Water, pp. 61–5

Life, as we know it, cannot exist without water. However, some animals are able to survive extended periods of time in a desiccated, or anhydrobiotic, state. Although this has been discovered more than 300 y ago, little is known about this peculiar process. Many nematode species are able to survive in a desiccated state, but a lack of genetic tools has hampered further study. Armed with this knowledge, Erkut et al. turned to one of the best known model organisms, C. elegans, discovering that the dauer larva of C. elegans were indeed, anhydrobiotic. In this commentary, Erkut et al. summarize findings from their recent publication on the desiccation tolerance of the dauer larva, emphasizing the protective role of trehalose on membranes (Curr Biol. 2011; PMID:21782434). The authors also provide a putative mechanism driving the anhydriotic process.

Tallying up Proteins with a New Technique, pp. 66–71

A good step toward understanding how processes in a cell are regulated is to first identify the resident proteins. To get a fuller understanding, however, the quantification of each protein is important. The increased use of quantitative proteomics now provides this valuable insight for many organisms. Unfortunately, quantifying proteins in C. elegans has proven to be a difficult task due to a lack of reliable protein labeling techniques. In this commentary, Julius Fredens and Nils Faergeman discuss a recently developed technique that can reliably label proteins in C. elegans. The authors discuss how this technique, which tags amino acids with a heavily-labeled lysine, has successfully quantified proteins in an RNAi mediated knock-down of the transcription factor NHR-49 (Nat Methods 2011; PMID:21874006). The use of both stable-isotope lysine labeling along with RNAi gene knock-down may be a key to understanding C. elegans at a cellular level.

Organelles Can Go Both Ways, at the Same Time, pp. 72–6

A properly functioning cell is reliant on the precise organization of its cellular components. Even a spindle out of place could have disastrous results. Active force generators, such as molecular motors and the cytoskeleton, provide the usual mechanics that correctly position organelles within the cell. However, there may be another way. In this commentary, Ritsuya Niwayama and Akatsuki Kimura discuss their recent findings that organelles can also be positioned using a funicular-like coupling that can simultaneously exert movement in two separate directions (Proc Natl Acad Sci USA 2011; 108:11900–5; PMID:21730185). The authors further speculate on the significance and potential advantages that this unusual organelle transporting mechanism may have over the usual uni-directional forces.

An Inheritable Epigenome? pp. 77–81

Many of us expect that our time on this earth is somewhat dependent on the genes that were passed on to us. In fact, this may be only one part of the story. It is possible that other inherited mechanisms may be influencing our life spans. Recently, a study by Greer et al. showed that a reliance on not only genetics, but epigenetics as well, can determine longevity (Aging Cell 2011; PMID:21834846). This means that some observable traits of our ancestors can be heritably passed down to their offspring without any changes to the DNA sequence. Even more surprising, the transference of these traits can span more than one generation. In this commentary, Be´re´nice A. Benayoun and Anne Brunet examine the possible implications epigenetic memory may have on longevity and also provide potential mechanisms for this transgenerational epigenetic inheritance. Although these studies were conducted in C. elegans, it is intriguing to think that this may also be the case for humans as well.

But Wait, There's More: Multiplying β-Catenins, pp. 82–9

The Wnt signaling pathway is highly conserved across species, with most species carrying only a single β-catenin gene. As with most rules, there is always at least one exception and in this case the exception turns out to be C. elegans. In fact, not even two but four separate β-catenins have been discovered in this outlying worm. In this commentary, Scott Robertson and Rueyling Lin discuss their recent paper describing the functional divergence of worm β-catenins (Development 2011; PMID:21852394). The authors explain the mutually inhibitory effects of the multiple β-catenins and their different binding specificities. The authors also speculate on what evolutionary forces could have resulted in the proliferation of β-catenin genes in this worm and how they combine and contribute to Wnt activation and signaling.