Wang N et al. (2017) Int J Nanomedicine "Toxicity evaluation of boron nitride nanospheres and water-soluble boron nitride in Caenorhabditis elegans."

Tang C, Wang H, Wang N, Wang L, Lei S, Wang G, Shen W, Wang Z, Wang C

[Int J Nanomedicine, 2017]

Boron nitride (BN) nanomaterials have been increasingly explored for potential biological applications. However, their toxicity remains poorly understood. Using Caenorhabditis elegans as a whole-animal model for toxicity analysis of two representative types of BN nanomaterials - BN nanospheres (BNNSs) and highly water-soluble BN nanomaterial (named BN-800-2) - we found that BNNSs overall toxicity was less than soluble BN-800-2 with irregular shapes. The concentration thresholds for BNNSs and BN-800-2 were 100 g-mL(-1) and 10 g-mL(-1), respectively. Above this concentration, both delayed growth, decreased life span, reduced progeny, retarded locomotion behavior, and changed the expression of phenotype-related genes to various extents. BNNSs and BN-800-2 increased oxidative stress levels in C. elegans by promoting reactive oxygen species production. Our results further showed that oxidative stress response and MAPK signaling-related genes, such as GAS1, SOD2, SOD3, MEK1, and PMK1, might be key factors for reactive oxygen species production and toxic responses to BNNSs and BN-800-2 exposure. Together, our results suggest that when concentrations are lower than 10 g-mL(-1), BNNSs are more biocompatible than BN-800-2 and are potentially biocompatible material.

van den Ecker D et al. (2010) Anal Biochem "Blue native electrophoresis to study mitochondrial complex I in C. elegans."

van den Brand MA, Nijtmans LG, Distelmaier F, van den Ecker D, Bossinger O, Mayatepek E

[Anal Biochem, 2010]

Blue native polyacrylamide gel electrophoresis (BN-PAGE) is an essential tool for investigating mitochondrial respiratory chain complexes. However, with current BN-PAGE protocols for Caenorhabditis elegans (C. elegans), large worm amounts and high quantities of mitochondrial protein are required to yield clear results. Here, we present an efficient approach to isolate mitochondrial complex I (NADH:ubiquinone oxidoreductase) from C. elegans, grown on agar plates. We demonstrate that considerably lower amounts of mitochondrial protein are sufficient to isolate complex I and to display clear in-gel activity results. Moreover, we present the first complex I assembly profile for C. elegans, obtained by two-dimensional BN/SDS-PAGE.

van den Ecker, Daniela et al. (2010) C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany "Blue native electrophoresis to study mitochondrial complex I in C. elegans."

van den Brand, Mariel A M, Bossinger, Olaf, Distelmaier, Felix, Mayatepek, Ertan, van den Ecker, Daniela, Nijtmans, Leo G J

[C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany, 2010]

Isolation of mitochondrial proteins and subsequent analysis with blue native / SDS gel electrophoresis (BN-PAGE) is an essential tool to investigate defects of the mitochondrial respiratory chain. During the last years, Caenor habditis elegans ( C. elegans ) has become an important model system to study human disease associated with mitochondrial dysfunction. However, with current BN-PAGE protocols for C. elegans , high quantities of mitochondrial protein are required to yield clear results. To obtain these protein amounts, liquid culture was used so far. However, growth in axenic medium alters metabolism and might have adverse effects on oxidative phosphorylation, which is potentially disadvantageous in view of studies about mitochondrial function . On the other hand, mitochondrial dysfunction in C. elegans is often associated with slow growth and larval arrest. Therefore, it might be difficult to culture sufficient worm quantities on agar plates. Here, we present an optimized approach to isolate mitochondria and respiratory chain complex I from C. elegans grown on solid NGM culture plates. We demonstrate that considerably lower amounts of mitochondrial protein are sufficient to isolate complex I and to display clear in-gel activity results. Moreover, we present the first complex I assembly profiles for C. elegans , obtained by two dimensional BN-PAGE.

Sinha R et al. (2009) Nucleic Acids Res "Accurate prediction of NAGNAG alternative splicing."

Platzer M, Jahn N, Sinha R, Backofen R, Nikolajewa S, Szafranski K, Huse K, Hiller M

[Nucleic Acids Res, 2009]

Alternative splicing (AS) involving NAGNAG tandem acceptors is an evolutionarily widespread class of AS. Recent predictions of alternative acceptor usage reported better results for acceptors separated by larger distances, than for NAGNAGs. To improve the latter, we aimed at the use of Bayesian networks (BN), and extensive experimental validation of the predictions. Using carefully constructed training and test datasets, a balanced sensitivity and specificity of >or=92% was achieved. A BN trained on the combined dataset was then used to make predictions, and 81% (38/47) of the experimentally tested predictions were verified. Using a BN learned on human data on six other genomes, we show that while the performance for the vertebrate genomes matches that achieved on human data, there is a slight drop for Drosophila and worm. Lastly, using the prediction accuracy according to experimental validation, we estimate the number of yet undiscovered alternative NAGNAGs. State of the art classifiers can produce highly accurate prediction of AS at NAGNAGs, indicating that we have identified the major features of the ''NAGNAG-splicing code'' within the splice site and its immediate neighborhood. Our results suggest that the mechanism behind NAGNAG AS is simple, stochastic, and conserved among vertebrates and beyond.

Piecyk K et al. (2015) Biochem Biophys Res Commun "Effect of different N7 substitution of dinucleotide cap analogs on the hydrolytic susceptibility towards scavenger decapping enzymes (DcpS)."

Stepinski J, Darzynkiewicz E, Darzynkiewicz ZM, Piecyk K, Ferenc-Mrozek A, Jankowska-Anyszka M, Bojarska E

[Biochem Biophys Res Commun, 2015]

Scavenger decapping enzymes (DcpS) are involved in eukaryotic mRNA degradation process. They catalyze the cleavage of residual cap structure m(7)GpppN and/or short capped oligonucleotides resulting from exosom-mediated the 3' to 5' digestion. For the specific cap recognition and efficient degradation by DcpS, the positive charge at N7 position of guanine moiety is required. Here we examine the role the N7 substitution within the cap structure on the interactions with DcpS (human, Caenorhabditis elegans and Ascaris suum) comparing the hydrolysis rates of dinucleotide cap analogs (m(7)GpppG, et(7)GpppG, but(7)GpppG, bn(7)GpppG) and the binding affinities of hydrolysis products (m(7)GMP, et(7)GMP, but(7)GMP, bn(7)GMP). Our results show the conformational flexibility of the region within DcpS cap-binding pocket involved in the interaction with N7 substituted guanine, which enables accommodation of substrates with differently sized N7 substituents.

Kim SK et al. (2001) Science "A gene expression map for Caenorhabditis elegans."

Davidson GS, Stuart JM, Kiraly M, Wylie BN, Duke K, Jiang M, Lund J, Eizinger A, Kim SK

[Science, 2001]

We have assembled data from Caenorhabditis elegans DNA microarray experiments involving many growth conditions, developmental stages, and varieties of mutants. Co-regulated genes were grouped together and visualized in a three-dimensional expression map that displays correlations of gene expression profiles as distances in two dimensions and gene density in the third dimension. The gene expression map can be used as a gene discovery toot to identify genes that are co-regulated with known sets of genes (such as heat shock, growth control genes, germ line genes, and so forth) or to uncover previously unknown genetic functions (such as genomic instability in mates and sperm caused by specific transposons).

Shemer G et al. (2002) Genes Dev "LIN-39/Hox triggers cell division and represses EFF-1/fusogen-dependent vulval cell fusion."

Podbilewicz B, Shemer G

[Genes Dev, 2002]

General mechanisms by which Hox genes establish cell fates are known. However, a few Hox effectors mediating cell behaviors have been identified. Here we found the first effector of LIN-39/HoxD4/Dfd in Caenorhabditis elegans. In specific vulval precursor cells (VPCs), LIN-39 represses early and late expression of EFF-1, a membrane protein essential for cell fusion. Repression of eff-1 is also achieved by the activity of CEH-20/Exd/Pbx, a known cofactor of Hox proteins. Unfused VPCs in lin-39(-),eff-1(-) double mutants fail to divide but migrate, executing vulval fates. Thus, Bn-39 is essential for inhibition of EFF-1-dependent cell fusion and stimulation of cell proliferation during vulva formation.

Jeong J et al. (2019) Nanotoxicology "Developing adverse outcome pathways on silver nanoparticle-induced reproductive toxicity via oxidative stress in the nematode Caenorhabditis elegans using a Bayesian network model."

Choi I, Song T, Choi J, Chatterjee N, Jeong J, Cha YK

[Nanotoxicology, 2019]

An adverse outcome pathway (AOP) is a framework that organizes the mechanistic or predictive relationships between molecular initiating events (MIEs), key events (KEs), and adverse outcomes (AOs). Previously, we intensively investigated the molecular mechanism that underlies toxicity caused by AgNPs in the nematode Caenorhabditis elegans. Using transcriptomics, functional genetics, and various molecular/biochemical tools, we identified oxidative stress as the major mechanism underlying toxicity and reproduction failure as the outcome. With this information, here we conducted a case study of building an AOP to link oxidative stress with reproductive toxicity. To validate this AOP, we filled the gaps by conducting further experiments on its elements, such as NADPH oxidase, ROS formation, PMK-1 P38 MAPK activation, HIF-1 activation, mitochondrial damage, DNA damage, and apoptosis. The establishment of a causal link between the MIE and AO is critical for the construction of an AOP. Therefore, causal relationships between each KE and AO were verified by using functional genetic mutants of each KE. By combining these experimental data with our previously published results, we established causal relationships between the MIE, KEs, and AO using a Bayesian network (BN) model, culminating in an AOP entitled 'NADPH oxidase and P38 MAPK activation leading to reproductive failure in C. elegans ( https://aopwiki.org/aops/207)' . Overall, our approach shows that an AOP can be developed using existing data and further experiments can be conducted to fill the gaps between the MIE, KEs, and the AO. This study also shows that BN modeling has the potential to identify causal relationships in an AOP.

Schmidt, Minna Y. et al. MicroPubl Biol

Lithgow, Gordon J., Chamoli, Manish, Andersen, Julie K., Schmidt, Minna Y.

[MicroPubl Biol, 2021]

Parkinson's disease (PD) patients have been shown to benefit greatly from intense physical activity (Schenkman et al. 2018). Recent studies have demonstrated that exercise causes changes in the levels of alpha-synuclein aggregate species, a hallmark of PD, in different mammalian animal models (Koo and Cho 2017; Shin et al. 2017; Zhou et al. 2017; Minakaki et al. 2019). However, questions still remain about how exercise affects specifically native alpha-synuclein protein species directly after the cessation of exercise and the longer-term downstream effects which exercise may have on organismal health. It was recently discovered that periods of thrashing in liquid solution, otherwise called swimming exercise, in C. elegans worms, induces many mechanisms invoked during mammalian exercise (Laranjeiro et al. 2017). This has provided an avenue for studying exercise conditions in various C. elegans models of neurodegeneration (Laranjeiro et al. 2019). In order to study the effect of exercise on native human alpha-synuclein protein species, we utilized the NL5901- pkIs2386 worm model of Parkinson's which contains human alpha-synuclein tagged to a yellow fluorescent protein (YFP) in the muscle cells (van Ham et al. 2008). We performed tissue analysis via Blue Native (BN) page westerns and confocal microscopy. In addition, because pharyngeal pumping is decreased while worms are swimming, we controlled for this effect by exposing worms in parallel to a period of food restriction (FR) conditions (Vidal-Gadea et al. 2012). We also performed thrashing assays to assess longer term downstream behavioral effects on the animals after either exercise or food restriction conditions.

Zhang Y et al. (2024) Cell Commun Signal "Pediococcus acidilactici reduces tau pathology and ameliorates behavioral deficits in models of neurodegenerative disorders."

Li J, Ma Y, Long Y, Zhang Y, Wan X, Qian J, Wei X, Qian W

[Cell Commun Signal, 2024]

BACKGROUND: Alzheimer's disease (AD), affecting many elders worldwide, is characterized by A-beta and tau-related cognitive decline. Accumulating evidence suggests that brain iron accumulation is an important characteristic of AD. However, the function and mechanism of the iron-mediated gut-brain axis on AD is still unclear. METHODS: A Caenorhabditis elegans model with tau-overexpression and a high-Fe diet mouse model of cognitive impairment was used for probiotic function evaluation. With the use of qPCR, and immunoblotting, the probiotic regulated differential expression of AD markers and iron related transporting genes was determined. Colorimetric kits, IHC staining, and immunofluorescence have been performed to explore the probiotic mechanism on the development of gut-brain links and brain iron accumulation. RESULTS: In the present study, a high-Fe diet mouse model was used for evaluation in which cognitive impairment, higher A-beta, tau and phosphorylated (p)-tau expression, and dysfunctional phosphate distribution were observed. Considering the close crosstalk between intestine and brain, probiotics were then employed to delay the process of cognitive impairment in the HFe mouse model. Pediococcus acidilactici (PA), but not Bacillus subtilis (BN) administration in HFe-fed mice reduced brain iron accumulation, enhanced global alkaline phosphatase (AP) activity, accelerated dephosphorylation, lowered phosphate levels and increased brain urate production. In addition, because PA regulated cognitive behavior in HFe fed mice, we used the transgenic Caenorhabditis elegans with over-expressed human p-tau for model, and then PA fed worms became more active and longer lived than E.coli fed worms, as well as p-tau was down-regulated. These results suggest that brain iron accumulation influences AD risk proteins and various metabolites. Furthermore, PA was shown to reverse tau-induced pathogenesis via iron transporters and AP-urate interaction. CONCLUSIONS: PA administration studies demonstrate that PA is an important mediator of tau protein reduction, p-tau expression and neurodegenerative behavior both in Caenorhabditis elegans and iron-overload mice. Finally, our results provide candidates for AP modulation strategies as preventive tools for promoting brain health. Video Abstract.