Kyle Ann Brooks et al. (2007) International Worm Meeting "Measurement of triglycerides in C. elegans mutants."

Jennifer Watts, Kyle Ann Brooks, John Browse

[International Worm Meeting, 2007]

C. elegans has emerged as a useful model for genetic studies of fat storage. Recently mutants have been reported to possess high fat or low fat stores based on staining with Nile Red and Sudan Black. In order to verify the staining results we measured triglycerides in young adults of various mutants using thin layer chromatography and gas chromatography. Our data show that daf-2(e1370) and daf-7(e1372), mutants in the insulin-signaling and TGF<font face=symbol>b</font>-branches of the dauer formation pathway, exhibit high triglyceride stores in agreement with previously published observations. On the other hand, loss-of-function and gain-of-function mutants in egl-4, a gene encoding a cyclic GMP-dependent kinase, showed triglyceride levels opposite to that predicted by previously published Nile Red staining. We found that slow-growing, eating-defective, gain-of-function egl-4(ad450) mutants have low triglyceride stores even though they exhibit very intense Nile Red staining. The loss-of-function egl-4(n478) mutants have dark intestines and high triglyceride stores. Other mutants will be discussed in the poster as well. Our results indicate that the intensity of Nile Red staining does not always correlate with triglyceride levels.

Kyle Ann Brooks et al. (2008) C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting "Dietary Nutrients Affect Lifespan, Fat Storage, and Feeding Behavior in C. elegans"

Kyle Ann Brooks, Jennifer Watts, Bin Liang, Leon Avery, Young-jai You

[C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting, 2008]

The optimum amounts of macronutrients in human diets is currently a subject of great interest. Diets emphasizing fat restriction, low carbohydrates or high protein content are promoted in popular books, but little is known about their long-term metabolic effects. We found that various E. coli strains commonly used to maintain C. elegans in most laboratory studies have distinct nutrient compositions. Nematodes maintained on these strains show significant differences in lifespan, fat storage, and feeding behavior. While all E. coli strains have a relatively high protein content, carbohydrate content varies in strains depending on whether or not they secrete a polysaccharide capsule. When growing on the capsule-secreting strain HB101, we found that wild type C. elegans show increased quiescence, reduced fat stores, and a shorter lifespan compared to C. elegans growing on the capsule-less strain OP50. Gene expression studies indicate an increase in fat metabolism in C. elegans growing on OP50, which may induce mitochondrial metabolism and a hormetic response that enables an extended lifespan. We find that the differences lifespan among worms grown on the two bacterial strains depends on efficient feeding, since eat-2 mutants show equally extended lifespans on both bacterial strains. We also find that AAK-2, a homolog of the large subunit of AMP-dependent kinase (AMPK), is necessary for the increased lifespan on OP50. Fat storage depends on feeding, since eat-2 shows indistinguishable low fat stores on both bacterial strains. Furthermore, mutants in the peptide transporter encoded by opt-2 store equally high amounts of fat when growing on both bacterial strains. Our studies indicate that various nutrient sensing pathways feed back to influence feeding behavior and metabolism, which in turn affect fat storage and lifespan.

Zetka M-C et al. (1993) Worm Breeder's Gazette "Mapping of the rec-1 Mutation"

Rose AM, Zetka M-C

[Worm Breeder's Gazette, 1993]

MAPPING OF THE rec-1 MUTATION Monique-Claire Zetka and Ann M. Rose, Dept. of Medical Genetics, 6174 University Blvd., University of British Columbia, Vancouver, B.C., V6T lZ3.

Haesemeyer M et al. (2019) Neuron "Convergent Temperature Representations in Artificial and Biological Neural Networks."

Haesemeyer M, Schier AF, Engert F

[Neuron, 2019]

Discoveries in biological neural networks (BNNs) shaped artificial neural networks (ANNs) and computational parallels between ANNs and BNNs have recently been discovered. However, it is unclear to what extent discoveries in ANNs can give insight into BNN function. Here, we designed and trained an ANN to perform heat gradient navigation and found striking similarities in computation and heat representation to a known zebrafish BNN. This included shared ON- and OFF-type representations of absolute temperature and rates of change. Importantly, ANN function critically relied on zebrafish-like units. We furthermore used the accessibility of the ANN to discover anew temperature-responsive cell type in the zebrafish cerebellum. Finally, constraining the ANN by the C.elegans motor repertoire retuned sensory representations indicating that our approach generalizes. Together, these results emphasize convergence of ANNs and BNNs on stereotypical representations and that ANNs form a powerful tool to understand their biological counterparts.

Vaupel JW et al. (1994) Science "Rates of mortality in populations of Caenorhabditis elegans."

Johnson TE, Fukui HH, Curtsinger JW, Capra WB, Vaupel JW, Xiu L, Lithgow GJ, Khazaeli A, Pletcher S, Wang JL, Carey JR, Muller HG

[Science, 1994]

A. Brooks et al. report that mortality increased exponentially for a cohort of 180,000 nematodes of the species Caenorhabditis elegans of the single genotype TJ1060 [spe-9(hc88) fer-15(b26)]. A closer look at the data reveals that from days 5 through 8 mortality increased at a rate of 0.58 +/- 0.0004, which is more than twice the rate thereafter (0.21 +/- 0.02). Such a "biphasic pattern," with death rates increasing rapidly at younger ages and more slowly at older ages, was also found in a genetically heterogeneous population of 79 recombinant-inbred (RI) strains.

Avery L (1995) Worm Breeder's Gazette "Effects of Conus venoms on the pharynx"

Avery L

[Worm Breeder's Gazette, 1995]

Cone snails are predatory snails. They harpoon their prey, which may be small fish, marine worms, or other snails, then inject a paralyzing venom through the hollow harpoon (Olivera et al, Science 249: 257). The venom is a complex mixture of tiny peptide toxins, different in each species. Several of these toxins have been shown to act on cell-surface molecules important for nervous system function such as the N-type Ca++ channel or the voltage-gated Na+ channel (Gray et al, Ann Rev Biochem 57: 665).

Park C et al. (2023) Exp Neurobiol "Caenorhabditis elegans Connectomes of both Sexes as Image Classifiers."

Kim JS, Park C

[Exp Neurobiol, 2023]

Connectome, the complete wiring diagram of the nervous system of an organism, is the biological substrate of the mind. While biological neural networks are crucial to the understanding of neural computation mechanisms, recent artificial neural networks (ANNs) have been developed independently from the study of real neural networks. Computational scientists are searching for various ANN architectures to improve machine learning since the architectures are associated with the accuracy of ANNs. A recent study used the hermaphrodite <i>Caenorhabditis elegans</i> (<i>C. elegans</i>) connectome for image classification tasks, where the edge directions were changed to construct a directed acyclic graph (DAG). In this study, we used the whole-animal connectomes of <i>C. elegans</i> hermaphrodite and male to construct a DAG that preserves the chief information flow in the connectomes and trained them for image classification of MNIST and fashion-MNIST datasets. The connectome-inspired neural networks exhibited over 99.5% and 92.6% of accuracy for MNIST and fashion-MNIST datasets, respectively, which increased from the previous study. Together, we conclude that realistic biological neural networks provide the basis of a plausible ANN architecture. This study suggests that biological networks can provide new inspiration to improve artificial intelligences (AIs).

Easton DM (1997) Exp Gerontol "Gompertz growth in number dead confirms medflies and nematodes show excess oldster survival."

Easton DM

[Exp Gerontol, 1997]

A recent report (Easton, 1995) showed that, at least for Mediterranean fruit flies, a Gompertz growth equation based on the increase in number of individuals that die is a better predictor of survival data than is the classical Gompertz survivorship model based on the decrease in number that survive (analysis of medfly data of Carey et al., 1992). In the growth model, the rate of increase of the number dead (i.e., the death rate) decreases exponentially with age. The poor fit of the classical model predicts "excess survival" of older members, but, when the scale of the better-fitting growth model is increased 2400x, such excess is now also evident as a small but distinctly separate cohort of the medfly subjects. The smaller population appears to be about 0.01% of the larger, and the death rate decreases about one-fourth as fast. Survival of the nematode C. elegans (Brooks et al., 1994) is also better predicted by the growth model, which also shows excess survival of the worms at great age.

Tiffany Roby et al. (2002) Mid-west Worm Meeting "Defining Regulatory Regions In Nematode Muscle Genes By Computational And Transgenic Studies."

Gary Stormo, Lawrence Schriefer, Robert Waterston, Tiffany Roby, Michelle Hresko, Debraj GuhaThakurta

[Mid-west Worm Meeting, 2002]

We have initiated experiments designed to understand the regulatory regions of C. elegans genes using known muscle genes of C. elegans as a model(1). Our primary approach is to use a combination of computational methods to identify potential muscle specific regulatory elements from the known set of C. elegans muscle genes. Local multiple sequence alignment methods like Consensus(1), Ann-Spec(2), and Co-Bind(3) are being used to identify these potential regulatory elements. Using the above method we have already identified several potential regulatory elements that show high degree of specificity for the muscle genes. The regulatory elements that these computational methods predict can then be used to screen the C. elegansgenome for new genes that are expressed in muscle cells.

Stewart HI et al. (1996) West Coast Worm Meeting "Rescue of New Essential Genes on LGIII(left), in the Nematode Caenorhabditis elegans."

Stewart HI, Franz NW, Barbazuk BW, Baillie DL, Ha TT

[West Coast Worm Meeting, 1996]

We utilized trangenic strains containing cosmids, sequenced by the sequencing consortium, to rescue the lethal phenotype of several essential genes (See presentation by Diana Janke et al, this session). The rescued genes are positioned on LGIII(left) balanced by the duplication sDp3(see poster; Stewart et al, this session). A set of overlapping deficiencies was utilized to define areas within which to focus our rescue attempts). PCR analysis was utilized to further define the end points of these deficiencies, facilitating our analysis ( see poster ; Norm Franz et al, this session). We concentrated our analysis on areas to the right of dpy-17, in the interval between dpy-17 to dpy-19. Lethals mapping to sDf125 that were not rescued by sDp8 are presented in a poster by Nigel O'Niel et al, this session. We have rescued several essential genes. Our rescues will facilitate the functional analysis of these new genes. These rescues have also helped us to align and correlate the physical and genetic maps. Our estimates are that there will be more than two essential genes per cosmid. A total of 202 recessive lethal mutations have been generated, using EMS as a mutagen. We intend to make molecular assignments of all of these elements, through our cosmid rescue experiments. As we have estimated that there is only a 28% saturation of the area for essential genes, we will be generating more recessive lethal genes, to facilitate this analysis. This work has been funded by grants from the National Institute of Health (N.I.H.), U. S.A. to Ann Rose; D. Riddle and David Baillie and Canadian Genome and Advanced Technologies (C.G.A.T.), Canada to Ann Rose and David Baillie.