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J Vis Exp,
2022]
The nematode Caenorhabditis elegans is a model system for host-microbe and host-microbiome interactions. Many studies to date use batch digests rather than individual worm samples to quantify bacterial load in this organism. Here it is argued that the large inter-individual variability seen in bacterial colonization of the C. elegans intestine is informative, and that batch digest methods discard information that is important for accurate comparison across conditions. As describing the variation inherent to these samples requires large numbers of individuals, a convenient 96-well plate protocol for disruption and colony plating of individual worms is established.
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Tropenmed Parasitol,
1975]
Preliminary enzyme-linked immunosorbent assay (ELISA) with serum from a patient with onchoceriasis revealed extensive cross-reactions with various nematode antigens. Further tests on a batch of sera from people with proven O. volvulus infections using O. gutturosa antigen, showed that almost all the sera gave higher ELISA values than did control African sera.
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Andersen EC, McIntyre LM, Shaver AO, Leach FE, Borges RM, Gouveia GJ, Morse AM, Garcia BM, Ferná\;ndez FM, Liu Z, Edison AS, Amster IJ, Asef CK
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Front Mol Biosci,
2022]
Untargeted metabolomics studies are unbiased but identifying the same feature across studies is complicated by environmental variation, batch effects, and instrument variability. Ideally, several studies that assay the same set of metabolic features would be used to select recurring features to pursue for identification. Here, we developed an anchored experimental design. This generalizable approach enabled us to integrate three genetic studies consisting of 14 test strains of Caenorhabditis elegans prior to the compound identification process. An anchor strain, PD1074, was included in every sample collection, resulting in a large set of biological replicates of a genetically identical strain that anchored each study. This enables us to estimate treatment effects within each batch and apply straightforward meta-analytic approaches to combine treatment effects across batches without the need for estimation of batch effects and complex normalization strategies. We collected 104 test samples for three genetic studies across six batches to produce five analytical datasets from two complementary technologies commonly used in untargeted metabolomics. Here, we use the model system C. elegans to demonstrate that an augmented design combined with experimental blocks and other metabolomic QC approaches can be used to anchor studies and enable comparisons of stable spectral features across time without the need for compound identification. This approach is generalizable to systems where the same genotype can be assayed in multiple environments and provides biologically relevant features for downstream compound identification efforts. All methods are included in the newest release of the publicly available SECIMTools based on the open-source Galaxy platform.
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Exp Gerontol,
2023]
Aging is a ubiquitous biological process that limits the maximal lifespan of most organisms. Significant efforts by many groups have identified mechanisms that, when triggered by natural or artificial stimuli, are sufficient to either enhance or decrease maximal lifespan. Previous aging studies using the nematode Caenorhabditis elegans (C. elegans) generated a wealth of publicly available transcriptomics datasets linking changes in gene expression to lifespan regulation. However, a comprehensive comparison of these datasets across studies in the context of aging biology is missing. Here, we carry out a systematic meta-analysis of over 1200 bulk RNA sequencing (RNASeq) samples obtained from 74 peer-reviewed publications on aging-related transcriptomic changes in C. elegans. Using both differential expression analyses and machine learning approaches, we mine the pooled data for novel pro-longevity genes. We find that both approaches identify known and propose novel pro-longevity genes. Further, we find that inter-lab experimental variance complicates the application of machine learning algorithms, a limitation that was not solved using bulk RNA-Seq batch correction and normalization techniques. Taken as a whole, our results indicate that machine learning approaches may hold promise for the identification of genes that regulate aging but will require more sophisticated batch correction strategies or standardized input data to reliably identify novel pro-longevity genes.
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Environ Sci Pollut Res Int,
2015]
Elevated levels of adsorbable organic bromine compounds (AOBr) have been detected in German lakes, and cyanobacteria like Microcystis, which are known for the synthesis of microcystins, are one of the main producers of natural organobromines. However, very little is known about how environmental realistic concentrations of organobromines impact invertebrates. Here, the nematode Caenorhabditis elegans was exposed to AOBr-containing surface water samples and to a Microcystis aeruginosa-enriched batch culture (MC-BA) and compared to single organobromines and microcystin-LR exposures. Stimulatory effects were observed in certain life trait variables, which were particularly pronounced in nematodes exposed to MC-BA. A whole genome DNA-microarray revealed that MC-BA led to the differential expression of more than 2000 genes, many of which are known to be involved in metabolic, neurologic, and morphologic processes. Moreover, the upregulation of cyp- and the downregulation of abu-genes suggested the presence of chronic stress. However, the nematodes were not marked by negative phenotypic responses. The observed difference in MC-BA and microcystin-LR (which impacted lifespan, growth, and reproduction) exposed nematodes was hypothesized to be likely due to other compounds within the batch culture. Most likely, the exposure to low concentrations of organobromines appears to buffer the effects of toxic substances, like microcystin-LR.
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[
Trans R Soc Trop Med Hyg
]
The viability and drug responses of cryopreserved adult Onchocerca have been examined in vitro. Male worms were cryopreserved in liquid nitrogen (-196 degrees C) using ethanediol as a cryoprotectant in a 2-step incubation procedure. After thawing, 85-90% of O. gutturosa males were normally motile. These motile worms were evaluated for viability using 4 measurements (long-term motility/survival in culture; [U-14C]adenine uptake and leakage; glucose utilization; MTT-formazan colorimetry) and were no different from unfrozen controls. Subsequent experiments demonstrated that the motility responses of cryopreserved worms exposed to the antifilarial drugs ivermectin, CGP 6140 and levamisole were virtually identical to unfrozen controls. Some success was also obtained with this technique in cryopreserving O. volvulus males, with 2 thawed specimens surviving in culture for 93 and 106 d respectively. Following collagenase isolation, female worms were cryopreserved in medium +10% serum without protectant at -79 degrees C. A batch of 8 female O. gutturosa were all motile when thawed 14 d later, with a mean survival time (based on 5 specimens) of 71 d (range 60-90). However, a batch of worms transferred from -79 degrees C to -196 degrees C were badly damaged when thawed. Female O. volvulus were cryopreserved at -79 degrees C in Guatemala and sent by air freight on solid CO2 to the UK. Most specimens were active when thawed. Survival of motile specimens ranged from 7 to 272 d in culture. It is concluded that these techniques are of practical value for the storage and transportation of adult Onchocerca.
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Biotechniques,
2019]
<i>Caenorhabditis elegans</i> is an invertebrate model organism used in many areas of biology including developmental biology and the identification of molecular mechanisms and pathways. However, several experimental approaches require large quantities of worms, which is limiting and time-consuming. We present a protocol that uses modern fermentation methodology to effectively produce large numbers of <i>C. elegans</i> using a 7-l bioreactor in a fed-batch cultivation procedure. The production is modular and flexible as well as being a self-controlled system, thus not much labor is required until harvesting <i>C. elegans</i>. The high-yield worm cultivation is flexible and simple to amend, and now allows for the extended application of <i>C. elegans</i> as a model organism and expression system, including large-scale protein production.
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J Transl Autoimmun,
2020]
Studies in humans and animals have demonstrated that infection with helminths (parasitic worms) is protective against a range of hyperinflammatory diseases. A number of factors limit translation into clinical use, including: potential contamination of helminths obtained from infected humans or animals, lack of batch to batch stability, and potential pathological risks derived from live worm infections. To overcome these limitations we tested whether an antigen homogenate of the non-pathogenic nematode <i>Caenorhabditis elegans</i> confers protection against type 1 diabetes mellitus (T1D) using the Non Obese Diabetic (NOD) mouse model. Our study demonstrates that twice weekly intraperitoneal injections of axenically cultured <i>C.elegans</i> antigen (aCeAg) confers substantial protection against type 1 diabetes in NOD mice. Whereas 80% of control mice (PBS-injected) developed clinical disease, only 10% of aCeAg-treated mice became diabetic. Additionally, aCeAg treated mice had significantly greater numbers of insulin-producing pancreatic islets and greater numbers of islets negative for lymphocyte infiltration. Immunological changes observed in aCeAg treated mice included increases in total IgE and total IgG1, consistent with induction of a type 2 immune response similar to that typically seen in parasitic worm infection. Although evidence suggests that helminth infections induce strong immunoregulatory signals, we did not observe significant changes in regulatory T cell numbers or in production of the regulatory cytokines TGF and IL-10. The lack of a regulatory response may be due to our time point of observation, or perhaps the mechanism of aCeAg efficacy may differ from that of helminth infection. Discovery that antigens obtained from a non-parasitic environmental nematode replicate the protective phenotype induced by parasitic worm infections may accelerate our ability to develop nematode-derived therapies for allergy and autoimmune diseases.
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Proc. Society for Experimental Biology & Medicine,
1970]
Cultivation of metazoa under bacteria-free conditions is valuable for biochemical and nutritional studies and avoids the complexity introduced by associated organisms. For such studies the nematode has particular advantages. Investigation of the nutritional requirements of the free-living nematode Caenorhabditis briggsae led to the development of a chemically defined medium which required addition of a low level of an organic supplement to obtain continued reproduction. One very effective supplement is a partially purified protein designated growth factor (GF). This has been used in the culture of free-living nematodes and parasitic helminths. GF was originally prepared by a slow, laborious, stepwise elution from hydroxylapatite columns. In the present paper a rapid, efficient "batch" technique is described. Using this new method, batches yielding more than 2 g of GF have been prepared easily in a day.
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J Ind Microbiol Biotechnol,
2010]
Abundant larval transcript (ALT), a novel filarial protein, has been shown to have great potential as a vaccine in the prevention of human lymphatic filariasis. In this study, we report a method for the production of recombinant ALT-2 protein, expressed in the cytoplasm of bacterium Escherichia coli in soluble form and purification in a single step using hydrophobic interaction chromatography (HIC). Fermentation was done by continuous fed-batch methodology with dissolved oxygen (DO)-controlled feed addition. The culture was induced with 1mM isopropyl--D: -thiogalactopyranoside (IPTG). Up to 9g/l dry cell weight (DCW) of biomass was obtained from 1.6l of Luria-Bertani (LB) broth in a bench-scale reactor. Around 200mg/l of purified ALT-2 with a yield of about 60% was obtained. This is almost a 2.5-fold increase in final protein yield compared to purification using immobilized metal affinity chromatography (IMAC).