Young IM et al. (1998) European Journal of Soil Science "Nematode (Caenorhabditis elegans) movement in sand as affected by particle size, moisture and the presence of bacteria (Escherichia coli)."

Griffiths BS, Robertson WM, McNicol JW, Young IM

[European Journal of Soil Science, 1998]

The movement of bacterial-feeding nematodes (Caenorhabditis elegans) through sand was investigated using a range of sand sizes, equilibrated at a range of matric potentials, in the presence or absence of an attractant source (Escherichia coli) at the distal end of a column. In the presence of E. coli there was significantly greater movement of the nematode population towards the E. coli population, and the extent of the movement depended on the matric potential of the sand. Over time, an increasing proportion of the C. elegans population responded to the presence of the E. coli. The processes controlling these effects are discussed with respect to taxis and kinesis mechanisms of the nematode population, and with regard to the diffusive characteristics of the physical structure of the sand.

Zhao YG et al. (2017) Mol Cell "The ER-Localized Transmembrane Protein EPG-3/VMP1 Regulates SERCA Activity to Control ER-Isolation Membrane Contacts for Autophagosome Formation."

Li D, Zhao H, Zhao YG, Feng D, Chen S, Chen Y, Liu N, Miao G, Li L, Zhang H, Wang Z, Qu W, Liu P

[Mol Cell, 2017]

During autophagosome formation in mammalian cells, isolation membranes (IMs; autophagosome precursors) dynamically contact the ER. Here, we demonstrated that the ER-localized metazoan-specific autophagy protein EPG-3/VMP1 controls ER-IM contacts. Loss of VMP1 causes stable association of IMs with the ER, thus blocking autophagosome formation. Interaction of WIPI2 with the ULK1/FIP200 complex and PI(3)P contributes to the formation of ER-IM contacts, and these interactions are enhanced by VMP1 depletion. VMP1 controls contact formation by promoting SERCA (sarco[endo]plasmic reticulum calcium ATPase) activity. VMP1 interacts with SERCA and prevents formation of the SERCA/PLN/SLN inhibitory complex. VMP1 also modulates ER contacts with lipid droplets, mitochondria, and endosomes. These ER contacts are greatly elevated by the SERCA inhibitor thapsigargin. Calmodulin acts as a sensor/effector to modulate the ER contacts mediated by VMP1/SERCA. Our study provides mechanistic insights into the establishment and disassociation of ER-IM contacts and reveals that VMP1 modulates SERCA activity to control ER contacts.

Li BW et al. (2004) Filaria J "Antibody responses to Brugia malayi antigens induced by DNA vaccination."

Rush A, Zhang SR, Weil GJ, Curtis KC, Li BW

[Filaria J, 2004]

BACKGROUND: DNA vaccination is a convenient means of immunizing animals with recombinant parasite antigens. DNA delivery methods are believed to affect the qualitative nature of immune responses to DNA vaccines in ways that may affect their protective activity. However, relatively few studies have directly compared immune responses to plasmids encoding the same antigens after injection by different routes. Therefore, the purpose of this study was to explore the influence of the route of administration on antibody responses to plasmids encoding antigens from the filarial nematode parasite Brugia malayi. METHODS: Four B. malayi genes and partial genes encoding paramyosin (BM5), heat shock protein (BMHSP-70), intermediate filament (BMIF) and a serodiagnostic antigen (BM14) were inserted in eukaryotic expression vectors (pJW4303 and pCR trade mark 3.1). BALB/c mice were immunized with individual recombinant plasmids or with a cocktail of all four plasmids by intramuscular injection (IM) or by gene gun-intradermal inoculation (GG). Antibody responses to recombinant antigens were measured by ELISA. Mean IgG1 to IgG2a antibody ratios were used as an indicator of Th1 or Th2 bias in immune responses induced with particular antigens by IM or GG immunization. The statistical significance of group differences in antibody responses was assessed by the non-parametric Kruskal-Wallis test. RESULTS: Mice produced antibody responses to all four filarial antigens after DNA vaccination by either the IM or GG route. Antibody responses to BM5 paramyosin were strongly biased toward IgG1 with lower levels of IgG2a after GG vaccination, while IM vaccination produced dominant IgG2a antibody responses. Antibody responses were biased toward IgG1 after both IM and GG immunization with BMIF, but antibodies were biased toward IgG2a after IM and GG vaccination with BMHSP-70 and BM14. Animals injected with a mixture of four recombinant plasmid DNAs produced antibodies to all four antigens. CONCLUSIONS: Our results show that monovalent and polyvalent DNA vaccination successfully induced antibody responses to a variety of filarial antigens. However, antibody responses to different antigens varied in magnitude and with respect to isotype bias. The isotype bias of antibody responses following DNA vaccination can be affected by route of administration and by intrinsic characteristics of individual antigens.

Anderson ARA et al. (1997) Fundamental and Applied Nematology "Nematode movement along a chemical gradient in a structurally heterogeneous environment. 2. Theory."

Griffiths BS, Anderson ARA, Sleeman BD, Young IM

[Fundamental and Applied Nematology, 1997]

The effects of structural heterogeneity on both chemical diffusion and nematode movement are examined with the development of a theoretical model. The model considers three factors affecting nematode movement: soil structure, nematode foraging strategy and chemotaxis. Using a continuous model, we develop a discrete system which allows nematode trails to be simulated in any of the four experimental conditions given by Anderson et al (1997). We show that structural heterogeneity causes mixed levels of attractant concentration over small areas as well as "fingering" of the attractant. Soil structural heterogeneity also restricts the foraging strategy of the nematode which then becomes a strategy to avoid structural "traps". The effect of localised increases in structural density is shown to increase significantly "fingering" of the attractant.

Anderson ARA et al. (1997) Fundamental and Applied Nematology "Nematode movement along a chemical gradient in a structurally heterogeneous environment. 1. Experiment."

Griffiths BS, Anderson ARA, Young IM, Robertson WM, Sleeman BD

[Fundamental and Applied Nematology, 1997]

The interaction between soil structural heterogeneity and chemical gradients, and their effect on the movement of free-living nematodes was investigated. Four experimental treatments were used. These consisted of a nematode (Caenorhabditis elegans) on a homogeneous layer of nutrient agar in a Petri dish, with or without a localised bacterial food source (Escherichia coli) acting as an attractant. Structural heterogeneity was then introduced by adding a monolayer of sand grains onto both of the homogeneous treatments. AU trails were recorded using time-lapse video, and subsequently digitised prior to analysis. Turning angle distributions and the fractal dimension of the trails were calculated for each treatment. There was a statistically significant effect (P less than or equal to 0.01) of all treatments on the movement of the nematode. In the presence of the attractant, nematode movement was more linear and directed towards the bacterial source. Structural heterogeneity caused the nematode to have more linear movement compared to a homogeneous environment. The fractal dimension of the nematode trails was significantly higher (P less than or equal to 0.01) for the treatment without structure or bacteria, than for the other treatments. The results, for the first time, quantify the degree to which nematodes carry out random foraging type behaviour in a homogeneous environment and produce more directed non-random movement in the presence of attractant. Finally, when structure is present the foraging strategy becomes more of an avoidance strategy, allowing the nematode to escape structural traps, such as ''dead-end'' pores, and then continue to react to attractant gradients.

Asef CK et al. (2023) Anal Chem "Unknown Metabolite Identification Using Machine Learning Collision Cross-Section Prediction and Tandem Mass Spectrometry."

Gouveia GJ, Asef CK, Edison AS, Fernandez FM, Garcia BM, McIntyre LM, Rainey MA, Shaver AO, Morse AM, Leach FE

[Anal Chem, 2023]

Ion mobility (IM) spectrometry provides semiorthogonal data to mass spectrometry (MS), showing promise for identifying unknown metabolites in complex non-targeted metabolomics data sets. While current literature has showcased IM-MS for identifying unknowns under near ideal circumstances, less work has been conducted to evaluate the performance of this approach in metabolomics studies involving highly complex samples with difficult matrices. Here, we present a workflow incorporating de novo molecular formula annotation and MS/MS structure elucidation using SIRIUS 4 with experimental IM collision cross-section (CCS) measurements and machine learning CCS predictions to identify differential unknown metabolites in mutant strains of Caenorhabditis elegans. For many of those ion features, this workflow enabled the successful filtering of candidate structures generated by in silico MS/MS predictions, though in some cases, annotations were challenged by significant hurdles in instrumentation performance and data analysis. While for 37% of differential features we were able to successfully collect both MS/MS and CCS data, fewer than half of these features benefited from a reduction in the number of possible candidate structures using CCS filtering due to poor matching of the machine learning training sets, limited accuracy of experimental and predicted CCS values, and lack of candidate structures resulting from the MS/MS data. When using a CCS error cutoff of +/-3%, on average, 28% of candidate structures could be successfully filtered. Herein, we identify and describe the bottlenecks and limitations associated with the identification of unknowns in non-targeted metabolomics using IM-MS to focus and provide insights into areas requiring further improvement.

Hogger CH et al. (1977) Nematologica "Surface scanning observations of changes in C. briggsae during aging."

Hogger CH, Zuckerman BM, Estey RH, Kisiel MJ

[Nematologica, 1977]

SEM observations of adult Caenorhabditis briggsae females showed differences between young and old nematodes. In young nematodes the cuticle was generally smooth, whereas in old ones it was wrinkled. Deirids were located at the level of the excretory pore in the lateral field. They were distinct in young nematodes but indistinct in old ones. The oral opening was formed by six lips, which were closed in old nematodes and open in young ones. The vulva possessed two semi-circular lips and was bordered by two lateral flaps. These lips were smooth in young specimens and wrinkled in old ones. Cryofractures of old nematodes showed cavities in the intestinal epithelium corresponding to areas in which age pigment granules normally occur. No such cavities were seen in young nematodes.

Li H et al. (2022) Sci Total Environ "Direct toxicity of environmentally persistent free radicals to nematode Caenorhabditis elegans after excluding the concomitant chemicals."

Xing B, Lang D, Zuo N, Pan B, Liu Y, Li H, Steinberg C

[Sci Total Environ, 2022]

Environmentally persistent free radicals (EPFRs) have attracted extensive attention due to their potential toxicity. However, EPFRs-containing particles always coexist with their parent organic contaminants and intermediate degradation products (IM), which may have hindered the toxicity assessment of EPFRs. In this study, the toxicity of EFFRs was specifically verified after comparing the systems without EPFRs, such as the immediate mixture of catechol (CT) and particles, solutions of CT only, IM extracted from the particles, as well as particles after EPFRs quenching. Caenorhabditis elegans (C. elegans) were used as model organisms. Our results showed that EPFRs-containing particles (Si-Al-CT) exhibited significant toxicity to C. elegans, but not for the parent chemical CT and IM on the particles. Higher levels of reactive oxygen species (ROS) and malondialdehyde (MDA) in the Si-Al-CT system were attributed to the mediated generation of -O₂^- and -OH via EPFRs. EPFRs could increase gene expressions related not only to oxidative stress and biotransformation in C. elegans, but also to indications of disturbances in energy homeostasis, survival, proliferation, cell and embryonic development. Overall, these results confirmed the direct toxicity of EPFRs and highlighted the key role of EPFRs which may be neglected in assessing the environmental risks of organic contaminants.

Rodger S et al. (2004) Microb Ecol "The impact of bacterial diet on the migration and navigation of Caenorhabditis elegans."

Rodger S, Griffiths BS, Young IM, McNicol JW, Wheatley RW

[Microb Ecol, 2004]

Can diet have a significant impact on the ability of organisms to sense and locate food? Focusing on the bacterial feeder Caenorhabditis elegans, we investigated what effect preconditioning on a range of bacterial substrates had on the subsequent chemotaxis process involved in the nematode locating other bacterial populations. Remarkably, we found that C. elegans, initially fed on a diet of Escherichia coli OP50, was significantly impaired in finding E. coli OP50 populations, compared to other available bacterial populations (P < 0.001). We found similar results for another bacterial feeding nematode species, suggesting that a general "substrate legacy" may operate across a wide range of organisms. We discuss this important finding with respect to the variation in response exhibited within a given nematode population, and the impact nematode migration has on bacterial dispersal in the environment.

Sutphin GL (2019) Elife "A new defense in the battle of the sexes."

Sutphin GL

[Elife, 2019]

Young <i>Caenorhabditis elegans</i> hermaphrodites use their own sperm to protect against the negative consequences of mating.