BX106

Caenorhabditis elegans

Zhang W et al. (2015) Chem Commun (Camb) "Elucidating the relationship between superoxide anion levels and lifespan using an enhanced two-photon fluorescence imaging probe."

Wang H, Zhang W, Wang X, Tang B, Li P, Huang F

[Chem Commun (Camb), 2015]

We report a new reversible fluorescent two-photon (TP) probe (PY-CA) with high TP absorption cross section and pH-independent fluorescence response, which allow monitoring of O2(-) fluxes dynamically, selectively and sensitively. The imaging results indicate that O2(-) at high levels can shorten the life of Caenorhabditis elegans.

Wang L et al. (2010) BMC Bioinformatics "Localizing triplet periodicity in DNA and cDNA sequences."

Wang L, Stein LD

[BMC Bioinformatics, 2010]

BACKGROUND: The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is divided into small segments and a Fourier Transform is applied on each segment, a strong peak at frequency 1/3 is typically observed in the Fourier spectrum of coding segments, but not in non-coding regions. This property has been used in identifying the locations of protein-coding genes in unannotated sequence. The method is fast and requires no training. However, the need to compute the Fourier Transform across a segment (window) of arbitrary size affects the accuracy with which one can localize TP boundaries. Here, we report a technique that provides higher-resolution identification of these boundaries, and use the technique to explore the biological correlates of TP regions in the genome of the model organism C. elegans. RESULTS: Using both simulated TP signals and the real C. elegans sequence F56F11 as an example, we demonstrate that, (1) Modified Wavelet Transform (MWT) can better define the boundary of TP region than the conventional Short Time Fourier Transform (STFT); (2) The scale parameter (a) of MWT determines the precision of TP boundary localization: bigger values of a give sharper TP boundaries but result in a lower signal to noise ratio; (3) RNA splicing sites have weaker TP signals than coding region; (4) TP signals in coding region can be destroyed or recovered by frame-shift mutations; (5) 6 bp periodicities in introns and intergenic region can generate false positive signals and it can be removed with 6 bp MWT. CONCLUSIONS: MWT can provide more precise TP boundaries than STFT and the boundaries can be further refined by bigger scale MWT. Subtraction of 6 bp periodicity signals reduces the number of false positives. Experimentally-introduced frame-shift mutations help recover TP signal that have been lost by possible ancient frame-shifts. More importantly, TP signal has the potential to be used to detect the splice junctions in fully spliced mRNA sequence.

Yin H et al. (2015) Sci Rep "Tea polyphenols as an antivirulence compound Disrupt Quorum-Sensing Regulated Pathogenicity of Pseudomonas aeruginosa."

Wang H, Chu W, Zhuang X, Deng Y, Yin H, Liu W

[Sci Rep, 2015]

Green tea, a water extract of non-fermented leaves of Camellia sinensis L., is one of the nonalcoholic beverages in China. It is becoming increasingly popular worldwide, because of its refreshing, mild stimulant and medicinal properties. Here we examined the quorum sensing inhibitory potentials of tea polyphenols (TP) as antivirulence compounds both in vitro and in vivo. Biosensor assay data suggested minimum inhibitory concentrations (MICs) of TP against selected pathogens were 6.25~12.5mg/mL. At sub-MIC, TP can specifically inhibit the production of violacein in Chromobacterium violaceum 12472 with almost 98% reduction at 3.125mg/mL without affecting its growth rate. Moreover, TP exhibited inhibitory effects on virulence phenotypes regulated by QS in Pseudomonas aeruginosa. The total proteolytic activity, elastase, swarming motility and biofilm formation were reduced in a concentration-dependent manner. In vivo, TP treatment resulted in the reduction of P. aeruginosa pathogenicity in Caenorhabditis elegans. When its concentration was 3.125mg/mL, the survival rate reached 63.3%. In the excision wound infection model, the wound contraction percentage in treatment groups was relatively increased and the colony-forming units (CFU) in the wound area were significantly decreased. These results suggested that TP could be developed as a novel non-antibiotic QS inhibitor without killing the bacteria but as an antivirulence compound to control bacterial infection.

Liang S et al. (2016) Colloids Surf B Biointerfaces "A water-soluble and biocompatible polymeric nanolabel based on naphthalimide grafted poly(acrylic acid) for the two-photon fluorescence imaging of living cells and C. elegans."

Liang S, Yang F, Liu Y, Chen X, Fu T, Yan G

[Colloids Surf B Biointerfaces, 2016]

Polymeric nanoparticles (NPs) with two-photon (TP) activity were prepared by grafting a naphthalimide fluorophore onto poly(acrylic acid) to yield an amphiphilic polymer, which self-assembled in water. The NPs were characterized using various analytical techniques such as transmission electron microscopy, dynamic light scattering and spectroscopic measurements. The in vitro and in vivo biocompatibilities of the NPs were assessed by a cytotoxicity assay using HeLa cells and a feeding assay using Caenorhabditis elegans (C. elegans) as a small animal model, respectively. Finally, TP fluorescence imaging (FI) of living cells and C. elegans labelled with the NPs were observed by TP confocal microscopy. The experimental outcomes demonstrated that the NPs had sufficient water-dispersity and biocompatibility, had TP fluorescence activity, were resistant to pH variation and illumination, and were physically stable. TP FI revealed that the NPs could enter living cells and were primarily located in the cytoplasm. In addition, the NPs were ingested by C. elegans during the feeding process and were recognized and taken up by the active transport system of the intestinal cells. These findings indicated the feasibility of using the developed NPs as a nanolabel for TP FI. Moreover, with numerous modifiable carboxyl groups on its surface, the NPs could act as a platform to build multifunctional probes for potential applications in biosensing and assay labeling.

Douglas A Fantz et al. (2001) International C. elegans Meeting "Docking sites on substrate proteins direct extracellular signal-regulated kinase (ERK) to phosphorylate specific residues."

Kerry Kornfeld, Dave Jacobs, Douglas A Fantz, Danielle Glossip

[International C. elegans Meeting, 2001]

During vulval development the primary cell fate is induced by a signaling pathway that includes mpk-1 , the C. elegans homolog of extracellular signal-regulated kinase (ERK), a member of the mitogen activated protein (MAP) kinase family. ERK phosphorylates S/TP sites in many different protein substrates including C. elegans LIN-1. We identified gain-of-function mutations in lin-1 that affect an FQFP motif that functions as a docking site for ERK. We characterized the sequence of amino acids that can constitute the FXFP motif using peptide and protein substrates. Substitutions of the phenylalanines at positions 1 and 3 had significant effects, indicating that these phenylalanines provide substantial binding affinity, whereas substitutions of the residues at positions 2 and 4 had less effect. LIN-1 also contains a different ERK docking site called the D-domain. The FXFP and D-domain docking sites were analyzed in a variety of positions and arrangements in the proteins Elk-1 (a vertebrate homolog of C. elegans LIN-1) and C. elegans KSR-1. Our results indicate that the FXFP and D-domain docking sites form a flexible, modular system that has two functions. First, the affinity of a substrate for ERK can be regulated by the number, type, position, and arrangement of docking sites. Second, in substrates with multiple potential phosphorylation sites, docking sites can direct phosphorylation of specific S/TP residues. In particular, the FQFP motif of Elk-1 is necessary and sufficient to direct phosphorylation of serine 383, a residue that is important for Elk-1 transcriptional activation, whereas the D-domain directs phosphorylation of other S/TP sites in Elk-1.

Pooranachithra M et al. (2019) Life Sci "Unravelling the wound healing ability and mode of action of pyridine carboxamide oxime using Caenorhabditis elegans as potential prescreen wound model."

Pooranachithra M, Venkateswaran K, Sekhar DS, Gnanasekaran J, Balamurugan K, Deepa M, Prabhanand BJ

[Life Sci, 2019]

AIM: In the current scenario of ethical issues related to animal usage in research, the present study was intended to explore the proficient utility of nematode, Caenorhabditis elegans as wound model in preliminary screening of wound healing therapeutics. MAIN METHODS: In this study, a new wounding protocol and quantitative assessment strategies for various healing parameters [survival, Reactive Oxygen Species (ROS), calcium signals, F-actin dynamics, new collagen synthesis and wound induced anti-microbial peptides] were developed and used for preliminary screening of wound healing actives from natural sources. Wound healing ability of positive lead Tridax procumbens (TP) and its major phytocompounds [Octa decenoic acid (ODA), Pyridine carboxamide oxime, known as Nicotinamide (NA) and Dimethyl Benz[c]acridine (DMB)] were assessed using C. elegans wound model and cell lines scratch wound healing assay. Mode of action of active lead was elucidated using metabolome analysis coupled with MALDI-MS followed by molecular docking. KEY FINDINGS: From the four tested methanolic extracts, TP was chosen as positive lead compared to control, Benzalkonium chloride (BKC) based on survival and new collagen synthesis analyses. Results indicated that the wound healing ability of TP was majorly contributed by NA. Further, it was found that NA acts in chloromethyl nicotinamide derivative form by interacting with the known wound healing biomarker, glycogen synthase kinase 3 (GSK-3) to exert wound healing ability. SIGNIFICANCE: The study evidenced that C. elegans, could be a reliable wound model for high-throughput screening of wound healing actives and to identify their possible mode of action.

Wender, Nora et al. (2011) International Worm Meeting "Analysis of cellular toxicity mechanisms of alpha-synuclein in C. elegans."

Wender, Nora, Hegermann, Jan, Eimer, Stefan

[International Worm Meeting, 2011]

Aggregation of a-synuclein (aS) in Lewy bodies is one of the pathological hallmarks of Parkinson's disease (PD). Mutations in aS as well as increased aS expression levels have been associated with PD. As the PD mutants of aS are more prone to forming fibrillar aggregates, these fibrils were initially considered to be causing toxicity. However, in different model systems no clear correlation between toxicity and fibril formation was found. This indicates that small oligomeric precursors rather than fibrils might be the toxic species. In order to investigate which form of aS is causing toxicity, we were making use of a designed variant of aS that stops at the stage of soluble oligomers. This variant is called TP aS (triple proline aS) as it was derived from wt aS by introduction of three proline residues. In vitro NMR studies as well as in vivo analysis of the aggregation of aS variants tagged with YFP in C. elegans muscle cells confirmed that the occurrence of aS fibrils was strongly reduced in TP aS. Next we were assessing toxicity of TP aS in comparison to wt aS as well as PD mutants of aS by investigation of neurite degeneration and impairment of dopamine-associated behavior upon expression of different aS variants in C. elegans dopaminergic neurons. We found that TP is the most toxic aS variant, exhibiting the most severe effects on dopaminergic neuron morphology and function. This suggests that indeed the small oligomers rather than aS fibrils are causing toxicity. So far, the cellular function of aS and the mechanisms causing toxicity remain unclear. It is known that aS binds to intracellular membranes including the mitochondrial membrane. Furthermore, mitochondrial impairment upon expression of wt and mutant aS was reported. Recently it has been reported that several PD-associated genes play a role in mitochondrial dynamics and that loss of function or overexpression leads to morphological changes in the mitochondrial network. Therefore we aimed in understanding how expression of different variants of aS affects mitochondrial dynamics. Thus we were analyzing mitochondrial morphology and distribution by Electron Microscopy as well as Spinning Disk Microscopy. We found that expression of aS in C. elegans muscles and neurons leads to mitochondrial fragmentation and severe changes in mitochondrial morphology. Remarkably, similar changes could be observed in aged worms not expressing aS. It is therefore tempting to suggest that increased expression levels of aS accelerate mitochondrial aging.

Gadagkar R (1999) Trends in Ecology & Evolution "Caenorhabditis and the cost of sex - Reply."

Gadagkar R

[Trends in Ecology & Evolution, 1999]

In a recent TREE news & comment, Gadagkar made some useful comments on LaMunyon and Ward's interesting study on sexual reproduction in nematodes. I think, however, that he - and LaMunyon and Ward - have confused the benefits of sex for species or demes with those for individuals or genes. For females and hermaphrodites (but not for species or demes), the twofold cost of sexual reproduction or producing males' in Maynard Smith's sense implies the cost of producing offspring that have only half of the hermaphrodite parent's genome set - not directly that of producing males. An offspring of a hermaphrodite Caenorhabditis briggsae inherits half, not more, of each parental genome set. The hermaphrodite parent still pays the two fold cost of sexual reproduction in the same way as

Jones AK et al. (2011) J Biol Chem "A Cys-loop mutation in the Caenorhabditis elegans nicotinic receptor subunit UNC-63 impairs but does not abolish channel function."

Maynard TP, Buckingham SD, Jones AK, Sattelle DB, Hernando G, Rayes D, Bouzat CB, Jones R, Al-Diwani A

[J Biol Chem, 2011]

The nematode Caenorhabditis elegans is an established model organism for studying neurobiology. UNC-63 is a C. elegans nicotinic acetylcholine receptor (nAChR) -subunit. It is an essential component of the levamisole-sensitive muscle nAChR (L-nAChR) and therefore plays an important role in cholinergic transmission at the nematode neuromuscular junction. Here, we show that worms with the unc-63(x26) allele, with its C151Y mutation disrupting the Cys-loop, have deficient muscle function reflected by impaired swimming (thrashing). Single-channel recordings from cultured muscle cells from the mutant strain showed a 100-fold reduced frequency of opening events and shorter channel openings of L-nAChRs compared with those of wild-type worms. Anti-UNC-63 antibody staining in both cultured adult muscle and embryonic cells showed that L-nAChRs were expressed at similar levels in the mutant and wild-type cells, suggesting that the functional changes in the receptor, rather than changes in expression, are the predominant effect of the mutation. The kinetic changes mimic those reported in patients with fast-channel congenital myasthenic syndromes. We show that pyridostigmine bromide and 3,4-diaminopyridine, which are drugs used to treat fast-channel congenital myasthenic syndromes, partially rescued the motility defect seen in unc-63(x26). The C. elegans unc-63(x26) mutant may therefore offer a useful model to assist in the development of therapies for syndromes produced by altered function of human nAChRs.