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[
Cell,
1996]
The process of aging influences our poetry, our art, our lifestyle, and our happiness, yet we know surprisingly little about it. Genetics has taught us a great deal about gene regulation, development, and the cell cycle. Can it teach us how we age?
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[
Aging, Metabolism, Stress, Pathogenesis, and Small RNAs, Madison, WI,
2010]
Lifespan in metazoans is regulated by several conserved signaling pathways, including the insulin/insulin-like growth factor and sirtuin pathways. W e have found that components of the dauer pheromone, the ascarosides (Edison 2009), regulate C. elegans adult lifespan and stress resistance. Ascarosides increased lifespan and thermotolerance of wild-type worms by up to 56% and 25%, respectively, without reducing fecundity or feeding rate. These lifespan increases are completely abolished by loss of the histone deacetylase SIR-2.1 or loss of components of peroxisomal fatty acid beta-oxidation, but do not require insulin signaling via the FOXO-homolog DAF-16 or TGF-beta signaling. Our findings establish endogenous small molecules as modulators of sirtuin-dependent pathways that connect longevity and stress resistance with peroxisomal fat metabolism. A. S. Edison, Curr. Opin. Neurobiol. 19(4), 378 (2009).
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[
Aging, Metabolism, Stress, Pathogenesis, and Small RNAs, Madison, WI,
2010]
We investigated whether the ascarosides, major components of the C. elegans dauer pheromone (Edison, 2009), affect stress resistance of adult worms. We found that ascarosides markedly increased survival under oxidative stress and resistance to heat stress (thermotolerance at 35 degC). We further measured pharyngeal pumping rates under heat stress and found that pumping rates of worms on ascaroside plates were significantly higher than on control plates. Next, we asked whether nutritional conditions influence the observed ascaroside-mediated increases of stress resistance. For thermotolerance assays under caloric restriction (CR) conditions, we transferred worms to plates without bacteria before exposure to heat stress. Mean heat stress survival time under CR conditions was higher than for worms with bacteria, in accordance with previous studies demonstrating increased stress resistance under starvation conditions. Notably, addition of ascarosides did not further increase thermotolerance of CR worms. These results show that the worms' metabolic state influences the efficacy of ascarosides in increasing thermotolerance. A. S. Edison, Curr. Opin. Neurobiol. 19(4), 378 (2009).
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[
PLoS Comput Biol,
2017]
Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (
unc-59(
e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant
unc-59(
e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.
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[
Neuronal Development, Synaptic Function, and Behavior Meeting,
2006]
Signals released into the environment by C. elegans hermaphrodites elicit sex-specific social behaviors: males are attracted to the signals and hermaphrodites avoid them. We are interested in the chemical nature of these signals. The purpose of this work is to first purify the factors in hermaphrodite-conditioned media (HCM) that elicit sex-specific attraction and avoidance behaviors, and then determine their chemical structure. Here, we focus on the attraction activity.
Our first purification step used reverse-phase solid phase extraction chromatography (SPEC) to separate based on hydrophobicity. HCM was loaded onto a C18 cartridge and eluted with increasing methanol concentration; fractions were collected and tested for attraction behavior. A single highly hydrophobic fraction showed very strong attraction behavior and no avoidance behavior. A less hydrophobic fraction elicited attraction behavior and a mild avoidance response. Second, we used ion-exchange SPEC to further separate the active C18 fractions. Coupled cation and anion exchange cartridges were loaded with the active hydrophobic fraction. We collected the flow-through as a neutral fraction, and then decoupled the cartridges and eluted them separately with increasing potassium chloride concentration. Two ion-exchange fractions specifically gave strong attraction behavior: a fraction from the cation-exchange cartridge that eluted at 250mM KCl, and the neutral fraction that was not retained by either cartridge. Third, reverse-phase high performance liquid chromatography (HPLC) coupled with mass spectroscopy (MS) was used to analyze both active and inactive ion-exchange fractions. We detected unique species in active fractions that are not present in the inactive fractions. We will continue our purification until we detect activities in single HPLC fractions that correspond to a single species by MS. Structures will be determined by magnetic resonance spectroscopy. To summarize our current results, it seems likely that more than one factor that can elicit the attraction behavior in C. elegans, and they can be separated into distinct fractions based on hydrophobicity and charge.
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[
International C. elegans Meeting,
1995]
We have sequenced an Ascaris suum gene encoding six peptides related to molluscan FMRFamide neuropeptides (Edison et al., in preparation). As in other FMRFamide-like genes, the peptides are processed from a precursor protein containing multiple peptides. We compared the A. suum sequence to other available FMRFamide-like sequences. Although the sequences of the A. suum and Caenorhabtidis elegans peptides are similar, a phylogenetic analysis of the genes finds no evidence of homology. These and other FMRFamide-like genes appear to have evolved independently through internal reiterations rather than by gene duplication. This study reveals potential patterns of functional diversification in nematode neuropeptides.
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[
Conf Proc IEEE Eng Med Biol Soc,
2015]
Registration is difficult when images to be registered contain sparse but large-valued differences. We present a method for robust registration that ignores some fraction of large differences, while constraining the sparseness of these errors. We apply the method to stabilize microscopy videos of C. elegans tissues, in which bright moving filaments and tissue wounding appear as sparse large-valued differences. We demonstrate the advantage of the method on both synthetic and real data compared to state-of-the-art methods.
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[
Biotechniques,
2019]
We report a generic smartphone app for quantitative annotation of complex images. The app is simple enough to be used by children, and annotation tasks are distributed across app users, contributing to efficient annotation. We demonstrate its flexibility and speed by annotating >30,000 images, including features of rice root growth and structure, stem cell aggregate morphology, and complex worm (<i>Caenorhabditis elegans</i>) postures, for which we show that the speed of annotation is >130-fold faster than state-of-the-art techniques with similar accuracy.
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[
BioData Min,
2021]
BACKGROUND: The data explosion caused by unprecedented advancements in the field of genomics is constantly challenging the conventional methods used in the interpretation of the human genome. The demand for robust algorithms over the recent years has brought huge success in the field of Deep Learning (DL) in solving many difficult tasks in image, speech and natural language processing by automating the manual process of architecture design. This has been fueled through the development of new DL architectures. Yet genomics possesses unique challenges that requires customization and development of new DL models. METHODS: We proposed a new model, DASSI, by adapting a differential architecture search method and applying it to the Splice Site (SS) recognition task on DNA sequences to discover new high-performance convolutional architectures in an automated manner. We evaluated the discovered model against state-of-the-art tools to classify true and false SS in Homo sapiens (Human), Arabidopsis thaliana (Plant), Caenorhabditis elegans (Worm) and Drosophila melanogaster (Fly). RESULTS: Our experimental evaluation demonstrated that the discovered architecture outperformed baseline models and fixed architectures and showed competitive results against state-of-the-art models used in classification of splice sites. The proposed model - DASSI has a compact architecture and showed very good results on a transfer learning task. The benchmarking experiments of execution time and precision on architecture search and evaluation process showed better performance on recently available GPUs making it feasible to adopt architecture search based methods on large datasets. CONCLUSIONS: We proposed the use of differential architecture search method (DASSI) to perform SS classification on raw DNA sequences, and discovered new neural network models with low number of tunable parameters and competitive performance compared with manually engineered architectures. We have extensively benchmarked DASSI model with other state-of-the-art models and assessed its computational efficiency. The results have shown a high potential of using automated architecture search mechanism for solving various problems in the field of genomics.
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[
WormBook,
2006]
The simple and well-defined structure of the C. elegans nervous system has made it an attractive model for studying the neural and genetic basis of behavior. However, the wider use physiological methods for monitoring neural activity in vivo or determining the effects of specific ion channels on neuronal function has been a relatively recent development. This chapter presents a compendium of protocols and technical reports on the current state of the art in C. elegans electrophysiology and neuroimaging. These include methods for calcium imaging in intact animals, in situ electrical recording from neurons and muscle cells, and in vitro recording from cultured neurons and oocytes.