Chavez-Perez, Carlos et al. (2021) MicroPubl Biol

Keenan, Brendan T, Raizen, David M, Jafari, Niusha, Rohacek, Alex M, Chavez-Perez, Carlos

[MicroPubl Biol, 2021]

Like other animals, the nematode C. elegans exhibits reduced movement and sleep in response to sickness, which can be induced by exposure to high temperatures (Hill et al. 2014; Nelson et al. 2014) ultraviolet light (DeBardeleben et al. 2017), and other stressful exposures (Hill et al. 2014; Goetting et al. 2020). This response has been termed Stress/Sickness-Induced Sleep (SIS) (Hill et al. 2014; Trojanowski and Raizen 2016). Exposure to the stressor leads to quiescence in part via release of the cytokine Epidermal Growth Factor (EGF) (Hill et al. 2014; Konietzka et al. 2020), which is encoded by the gene lin-3 (Hill and Sternberg 1992). EGF activates the ALA and RIS neurons, which then release their respective neuropeptides to effect reduced movement and behavioral quiescence (Konietzka et al. 2020).

Gray JM et al. (2005) Proc Natl Acad Sci U S A "A circuit for navigation in Caenorhabditis elegans."

Gray JM, Bargmann CI, Hill JJ

[Proc Natl Acad Sci U S A, 2005]

This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected on April 29, 2003. Caenorhabditis elegans explores its environment by interrupting its forward movement with occasional turns and reversals. Turns and reversals occur at stable frequencies but irregular intervals, producing probabilistic exploratory behaviors. Here we dissect the roles of individual sensory neurons, interneurons, and motor neurons in exploratory behaviors under different conditions. After animals are removed from bacterial food, they initiate a local search behavior consisting of reversals and deep omega-shaped turns triggered by AWC olfactory neurons, ASK gustatory neurons, and AIB interneurons. Over the following 30 min, the animals disperse as reversals and omega turns are suppressed by ASI gustatory neurons and AIY interneurons. Interneurons and motor neurons downstream of AIB and AIY encode specific aspects of reversal and turn frequency, amplitude, and directionality. SMD motor neurons help encode the steep amplitude of omega turns, RIV motor neurons specify the ventral bias of turns that follow a reversal, and SMB motor neurons set the amplitude of sinusoidal movement. Many of these sensory neurons, interneurons, and motor neurons are also implicated in chemotaxis and thermotaxis. Thus, this circuit may represent a common substrate for multiple navigation behaviors.

Hill RJ et al. (1992) Nature "The gene lin-3 encodes an inductive signal for vulval development in C. elegans."

Hill RJ, Sternberg PW

[Nature, 1992]

The lin-3 gene is necessary for induction of the Caenorhabditis elegans vulva by the anchor cell. It encodes a molecule similar to epidermal growth factor and to transforming growth factor-alpha and acts through the epidermal growth factor receptor homologue let-23. Expression of lin-3 in the anchor cell stimulates vulval induction; lin-3 may encode the vulval inducing signal.AD - Howard Hughes Medical Institute, California Institute of Technology, Pasadena 91125.FAU - Hill, R JAU - Hill RJFAU - Sternberg, P WAU - Sternberg PWLA - engPT - Journal ArticleCY - ENGLANDTA - NatureJID - 0410462RN - 0 (Helminth Proteins)RN - 0 (Recombinant Fusion Proteins)RN - 148412-70-8 (Lin 3 protein)RN - 62229-50-9 (Epidermal Growth Factor)SB - IM

Michael A Beer (2005) International Worm Meeting "Systematic genome-wide identification of transcriptional cis-regulatory logic in C. elegans."

Michael A Beer

[International Worm Meeting, 2005]

We have developed a systematic approach for inferring cis-regulatory logic from whole-genome microarray expression data.[1] This approach identifies local DNA sequence elements and the combinatorial and positional constraints that determine their context-dependent role in transcriptional regulation. We use a Bayesian probabilistic framework that relates general DNA sequence features to mRNA expression patterns. By breaking the expression data into training and test sets of genes, we are able to evaluate the predictive accuracy of our inferred Bayesian network. Applied to S. cerevisiae, our inferred combinatorial regulatory rules correctly predict expression patterns for most of the genes. Applied to microarray data from C. elegans[2], we identify novel regulatory elements and combinatorial rules that control the phased temporal expression of transcription factors, histones, and germline specific genes during embryonic and larval development. While many of the DNA elements we find in S. cerevisiae are known transcription factor binding sites, the vast majority of the DNA elements we find in C. elegans and the inferred regulatory rules are novel, and provide focused mechanistic hypotheses for experimental validation. Successful DNA element detection is a limiting factor in our ability to infer predictive combinatorial rules, and the larger regulatory regions in C. elegans make this more challenging than in yeast. Here we extend our previous algorithm to explicitly use conservation of regulatory regions in C. briggsae to focus the search for DNA elements. In addition, we expand the range of regulatory programs we identify by applying to more diverse microarray datasets.[3] 1. Beer MA and Tavazoie S. Cell 117, 185-198 (2004). 2. Baugh LR, Hill AA, Slonim DK, Brown EL, and Hunter, CP. Development 130, 889-900 (2003); Hill AA, Hunter CP, Tsung BT, Tucker-Kellogg G, and Brown EL. Science 290, 809812 (2000). 3. Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, Slonim DK, Brown EL, and Hunter, CP. Development 132, 1843-1854 (2005); Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, Ahringer J, Li H, and Kenyon C. Nature 424 277-283 (2003); Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, and Kim SK. Mol Cell 6 605-616 (2000).

Hooper C (1991) The Journal of NIH Research "Old-aged mutant ninja nematodes' cool anti-age gene."

Hooper C

[The Journal of NIH Research, 1991]

Cowabugna, dudes! Those lean, gene-revealing machines have scored a most totally excellent victory in the battle to understand aging. We are, of course, talking about mutant ninja nematodes here. At a conference on aging in January at Cold Spring Harbor's Banbury Center, Thomas Johnson of the Institute for Behavioral Genetics at the University of Colorado in Boulder brought some dudes and dudettes from Capitol Hill up to date on the latest awesome achievements of the bodacious beasts know as Caenorhabditis elegans.

Herman RK (1992) Nature "Developmental biology. Inducing concentric worm holes."

Herman RK

[Nature, 1992]

Induction is the process in development in which the fate of one cell mass is determined by another. A simple example occurs during vulval development in the nematode Caenorhabditis elegans: a gonadal cell called the anchor cell induces three neighbouring cells to embark on a programme of cell division and morphogenesis, which culminates, in a few hours, in the formation of a vulva. On page 470 of this issue, Hill and Sternberg report strong evidence that they have identified the anchor-cell signalling molecule, which they find is a member of the EGF (epidermal growth factor) group of growth factors.

Van Buskirk, C.L. et al. (2019) International Worm Meeting "Identification of components of stress-induced sleep (SIS) in an undergraduate laboratory course."

Van Buskirk, C.L., Full Immersion Research Experience, Students of BIOL447\/FIRE:

[International Worm Meeting, 2019]

Animals from cnidarians to vertebrates engage in sleep - quickly reversible periods of behavioral quiescence that are associated with reduced sensory responsiveness. Though the cellular function of sleep is of debate, its benefit is inarguable, and sleep loss is associated with a wide range of adverse effects from impairments in cognitive function to death. Interestingly, sleep in C. elegans does not appear to fall under circadian regulation. This nematode sleeps at the end of each larval molt during a period known as developmentally-timed sleep (DTS) or lethargus (Raizen et al., 2008). C. elegans also sleeps during recovery from exposure to damaging conditions - a phenomenon referred to as stress-induced sleep (SIS) (Hill et al., 2014; Nelson et al., 2014). Despite their phenotypic similarity, DTS and SIS are regulated by largely independent genetic and neural circuits (Trojanowski and Raizen, 2015). DTS is linked to the molting cycle and depends on the release of sleep-promoting flp-11 neuropeptides from the RIS interneuron (Turek et al., 2016). By contrast, SIS is triggered by conditions that cause cellular damage and is dependent on EGF signaling within the peptidergic ALA neuron and the collective action of a distinct set of ALA-expressed neuropeptides (Hill et al., 2014, Nelson et al., 2014, Nath et al., 2016). Engagement in SIS appears to be beneficial, as sleep-defective mutants are impaired for recovery following exposure to damaging conditions (Hill et al., 2014; Fry et al., 2016). We posit that SIS reveals a deeply conserved phenomenon, and that a core function of sleep is to repair cellular damage that accrues during wakefulness. In support of this notion, recent studies in zebrafish have shown that the number of double-strand breaks (DSBs) in neuronal nuclei increases during the day and that sleep promotes chromosome dynamics that are required for DSB repair (Zada et al., 2019). We are therefore interested in identifying additional components of SIS in C. elegans, with the goal of characterizing this potentially deeply conserved phenomenon. To this end, we are performing forward genetic screens for SIS-defective mutants, and we are doing this within the context of an undergraduate laboratory course at CSUN called BIOL447: FIRE (Full Immersion Research Experience). We will present several SIS components that we have identified thus far through mapping and whole-genome sequencing of our SIS-defective mutants.

Mansfield, R. et al. (2015) International Worm Meeting "Disruption of cellular proteostasis drives sleep behavior in C. elegans."

Van Buskirk, C., Mansfield, R.

[International Worm Meeting, 2015]

Sleep is widely regarded to be a restorative state, and the physiological perturbations associated with sleep deprivation are extensive. Despite intensive study, none of these perturbations has in turn been shown to drive sleep. Recently our lab has shown that in C. elegans, environmental stressors such as heat, cold and toxins induce a sleep-like state (Hill et al., 2014). As noxious environmental stressors are known to interrupt normal proteostasis, the existence of a subsequent sleep state suggests that sleep serves to assist in the restoration of normal proteostasis. This idea is supported by our observation that sleepless animals have impaired survival following severe stress (Hill et al., 2014). Further, we have found that chaperone response defective mutants display exaggerated sleep responses. These mutants include animals lacking the stress-induced transcription factors hsf-1/HSF-1, daf-16/FOXO and a component of the endoplasmic reticulum stress-response pathway hsp-4/BiP. We are testing site-of-action for this effect by examining strains with tissue-specific rescue of HSF-1. In addition, we are using pharmacological inhibitors of the proteasome to test whether direct inhibition of the proteostasis machinery can trigger sleep. Last, we are performing RNAi against both positive and negative regulators of the heat shock transcriptional response, and screening for sleep phenotypes. The results of these efforts will be presented.Hill AJ, Mansfield R, Lopez JMG, Raizen DM, Van Buskirk C (2014) Cellular stress induces a protective sleep-like state in C. elegans. Curr Bio 24:1-7.Zimmerman JE, Naidoo N, Raizen DM, Pack AI (2008) Conservation of sleep: insights from non-mammalian model systems. Trends Neurosci 31:371-6.

David S Peal et al. (2001) International C. elegans Meeting "Chemical and Genetic Inhibition of Sulfation in C. elegans"

David S Peal, Laura L Kiessling

[International C. elegans Meeting, 2001]

In order to examine the process of sulfation in C. elegans, sulfation was inhibited chemically using sodium chlorate, and genetically using the process of RNA-mediated interference (RNAi). Sodium chlorate inhibition during early larval stages resulted in a dose-dependant developmental delay. BLAST searches of characterized sulfotransferases against the worm genome resulted in the identification of 4 putative sulfotransferases: C34F6.4 and F08B4.6 (previously identified: [1] and [2]), F40H3.5, and Y34B4A.e. RNAi of the putative N-deacetylase/N-sulfotransferase F08B4.6 resulted in "stacking" of eggs in the gonad, along with eggs laid at the 2- and 4-celled stage. RNAi of the putative hexuronic 2-O sulfotransferase C34F6.4 resulted in a shortened, bulbous gonad. These initial results indicate that sulfation may be important during development of C. elegans. [1] Shworak, NW, Liu, J, Fritze, LMS, Schwartz, JJ, Zhang, L, Logeart, D, Rosenberg, RD. JBC 272: 28008-19 (1997). [2] Kobayashi, M, Sugumaran, G, Liu, J, Shworak, NW, Silbert, JE, Rosenberg, RD. JBC 274: 10474-80 (1999).

Klopfenstein DR et al. (2002) Cell "Role of phosphatidylinositol(4,5)bisphosphate organization in membrane transport by the Unc104 kinesin motor."

Vale RD, Stuurman N, Klopfenstein DR, Tomishige M

[Cell, 2002]

Unc104 (KIF1A) kinesin transports membrane vesicles along microtubules in lower and higher eukaryotes. Using an in vitro motility assay, we show that Unc104 uses a lipid binding pleckstrin homology (PH) domain to dock onto membrane cargo. Through its PH domain, Unc104 can transport phosphatidylinositol(4,5)bisphosphate (PtdIns(4,5)P2)-containing liposomes with similar properties to native vesicles. Interestingly, liposome movement by monomeric Unc104 motors shows a very steep dependence on PtdIns(4,5)P2 concentration (Hill coefficient of approximately 20), even though liposome binding is noncooperative. This switch-like transition for movement can be shifted to lower PtdIns(4,5)P2 concentrations by the addition of cholesterol/sphingomyelin or GM1 ganglioside/cholera toxin, conditions that produce raft-like behavior of Unc104 bound to lipid bilayers. These studies suggest that clustering of Unc104 in PtdIns(4,5)P2-containing rafts provides a trigger for membrane transport.