Kamila Sekiewicz et al. (2003) International Worm Meeting "Cross-species comparisons of signal transduction pathways."

Chi-hua Chiu, Garth Patterson, Kamila Sekiewicz

[International Worm Meeting, 2003]

C. elegans senses environmental cues such as pheromone, temperature and food, and develops accordingly into a reproductive adult or a dauer larva. The decision as to which developmental path is followed is controlled in part by a TGF signaling pathway.The components of the TGF signaling pathway in C. elegans include a ligand encoded by daf-7, two receptors encoded by daf-1 and daf-4 and transcription factors encoded by daf-8, daf-14 and daf-3. Another identified component of the pathway is DAF-5, which is antagonized by the TGF pathway and which was cloned in our lab (see abstract by Da Graca et al. this program).C. briggsae is a nematode worm morphologically and developmentally almost identical to C. elegans. The two species have diverged 20-100 MYA. When comparing the amino acid sequence of C. elegans DAF-5 and its C. briggsae ortholog, we have noticed a surprisingly low identity of only about 40%. To determine whether this low percent identity is a property of DAF-5 alone, or perhaps a group of TGF/dauer genes, we looked at the sequence conservation between C. elegans and C. briggsae in the following groups of genes: TGF dauer pathway, TGF body size pathway, insulin mediated pathway, other dauer genes, and a group of randomly selected genes.We have found that the weak sequence conservation between C. elegans and C. briggase genes was not specific to DAF-5 alone, and all the genes in the TGF dauer pathway share this property with the average of 41% identity. In contrast to this group, we have found that all of the genes in the TGF body size pathway are very highly conserved, with the exception of DAF-4, which acts in both the body size and the dauer TGF pathways. Excluding DAF-4 from the TGF body size group, the average percent identity is 84.6. The genes in the insulin mediated pathway and other dauer genes show a greater range of values, and their average percent identities are 72.2 and 79.2 respectively. The group of randomly selected genes gives an average of 77.5% identity. All possible pairwise comparisons of these groups show that only the genes in the TGF dauer pathway are significantly different from all the other groups.To further determine the signs of positive, negative, or neutral selection acting on individual genes in the TGF dauer pathway, we are taking a closer look at the conservation of individual functional domains of these genes.

Wu Y et al. (2003) Filaria J "Human immune responses to infective stage larval-specific chitinase of filarial parasite, Onchocerca volvulus, Ov-CHI-1."

Nutman TB, Bianco AE, McCarthy JS, Wu Y, Egerton G

[Filaria J, 2003]

BACKGROUND: Ov-CHI-1 is a chitinase specifically expressed in the infective stage larvae of the human filarial parasite Onchocerca volvulus. Evidence has show that it could be a vaccine candidate, however, there is no data available regarding the immunological status of people naturally exposed to infective stage larvae and thus provoked by this antigen. METHOD: We analysed the Ov-CHI-1-specific immune response present in four endemic foci of human onchocerciasis (Ecuador, Nigeria, Togo and Cameroon) by enzyme-linked immunosorbent assays and T-cell proliferation assays. RESULTS: In these foci of infection, antibodies to Ov-CHI-1 were found to be present in only 22% of individuals from Ecuador, but were detected in 42-62% of infected individuals in the three foci from West Africa (Nigeria, Togo and Cameroon). There was found to be no relationship between antibody level and age, gender, or infection intensity as indicated by microfilarial density and numbers of skin nodules. The isotype response to Ov-CHI-1 was dominated by the presence of IgG3, IgG1 was present to a lesser extent. Our results show a positive correlation between N- and C-termini of Ov-CHI-1 in their ability to provoke humoral and cellular immune responses in the human. Peripheral blood mononuclear cell (PBMC) proliferative responses to Ov-CHI-1 when assayed, were found to be significantly higher in the individuals from endemic areas and there was a statistically elevated response to Ov-CHI-1 in the infected individuals when compared to putative immune individuals. CONCLUSION: Ov-CHI-1 is an antigen that we have found strongly induces both humoral and cellular immune responses in humans.

Wu Y et al. (2001) J Biol Chem "Expression and secretion of a larval-specific chitinase (family 18 glycosyl hydrolase) by the infective stages of the parasitic nematode, Onchocerca volvulus."

Sakuda S, Egerton G, Bianco AE, Underwood AP, Wu Y

[J Biol Chem, 2001]

A recently reported chitinase gene, expressed in the infective, third-stage (L3) larvae of the human filarial parasite Onchocerca volvulus, belongs to the family 18 glycosyl hydrolases and has been designated Ov-chi-1. The gene product of Ov-chi-1 is chitinolytic. Allosamidin ablates activity of the native enzyme in a dose-dependent manner but did not significantly inhibit the moulting of L3 larvae. Mono-specific antibodies were used to characterize Ov-CHI-1 as a 60-kDa protein expressed almost exclusively in L3 stages. Immunoelectron microscopy showed that Ov-CHI-1 expression is initiated in late L2 larvae and increases markedly in infective, L3 larvae. It is synthesized exclusively in the glandular esophagus and stored within discrete secretory granules. Secretion occurs through de-granulation during post-infective development, and the primary route of transport appears to be via the pseudo-coelom. An orthologue of Ov-chi-1 was detected in Caenorhabditis elegans by BLAST analysis. It is constitutively expressed at a low level and is overexpressed in dauer larvae and embryonated eggs. It is chitinolytic. We conclude that Ov-CHI-1 is a highly stage-specific enzyme that may have a role in infectivity of the parasite, aiding escape from the vector or participating in early post-infective migration and/or development. The identification of an orthologue in C. elegans opens the way for further studies into the biological function(s) of this intriguing parasite product.

Shi C et al. (2016) Genes Dev "Feeding the germline."

Murphy CT, Shi C

[Genes Dev, 2016]

Nucleotides are required in order to replicate DNA in the developing germline. Here, Chi and colleagues (pp. 307-320) have used Caernohabditis elegans to identify a GLP-1-dependent checkpoint that senses food (bacterially)-supplied nucleotide levels, arresting reproductive development in the absence of sufficient nucleotide supplies.

Robertson FM (2010) IDrugs "High-Content Analysis--CHI's Seventh Annual Conference--Developments in HCA and Pathway Analysis."

Robertson FM

[IDrugs, 2010]

CHI''s Seventh Annual Conference on High-Content Analysis (HCA), held in San Francisco, incorporated topics covering new developments in the field of HCA, including hardware and software updates, new biological models for HCA and pathway analysis. This conference report highlights selected presentations on the use of HCA for the characterization of stem cells, cell-colony analysis, the validation of disease models and the identification of antiparasitic compounds.

Catherine Chiu et al. (2002) West Coast Worm Meeting "Three miscellaneous axon guidance genes"

Ray Squires, Scott G Clark, Catherine Chiu

[West Coast Worm Meeting, 2002]

To understand further the molecular mechanisms involved in growth cone guidance, we performed several screens to identify new genes involved in axon extension and pathfinding. Mutants with a variety of axon outgrowth, branching and pathfinding defects as well as mutants with either axonal degeneration, cell fate, cell migration, cell position or programmed cell death defects were recovered. Over 160 mutants were isolated that define over 40 genes (see abstract by Chiu, Sabater, Squires & Clark). We cloned five of these genes: zag-1, tba-1, klp-7, mig-11 and wly-1.

Norice-Tra CT et al. (2017) J Infect Dis "Insights Into Onchocerca volvulus Population Biology Through Multilocus Immunophenotyping."

Mitreva M, Nutman TB, Norice-Tra CT, Bennuru S, Tyagi R, Ribeiro J, Fay MP

[J Infect Dis, 2017]

We have developed a serologically based immunophenotyping approach to study Onchocerca volvulus (Ov) population diversity. Using genomic sequence data and polymerase chain reaction-based genotyping, we identified nonsynonymous single-nucleotide polymorphisms (SNPs) in the genes of 16 major immunogenic Ov proteins: Ov-CHI-1/Ov-CHI-2, Ov16, Ov-FAR-1, Ov-CPI-1, Ov-B20, Ov-ASP-1, Ov-TMY-1, OvSOD1, OvGST1, Ov-CAL-1, M3/M4, Ov-RAL-1, Ov-RAL-2, Ov-ALT-1, Ov-FBA-1, and Ov-B8. We assessed the immunoreactivity of onchocerciasis patient sera (n = 152) from the Americas, West Africa, Central Africa, and East Africa against peptides derived from 10 of these proteins containing SNPs. Statistically significant variation in immunoreactivity among the regions was seen in SNP-containing peptides derived from 8 of 10 proteins tested: OVOC1192(1-15), OVOC9988(28-42), OVOC9225(320-334), OVOC7453(22-36), OVOC11517(14-28), OVOC3177(283-297), OVOC7911(594-608), and OVOC12628(174-188). Our data show that differences in immunoreactivity to variant antigenic peptides may be used to characterize Ov populations, thereby elucidating features of Ov population biology previously inaccessible because of the limited availability of parasite material.

Carta LK et al. (2000) Nematology "Nematode specific gravity profiles and applications to flotation extraction and taxonomy."

Carta DG, Carta LK

[Nematology, 2000]

A technique is described that refines the standard sugar flotation procedure used to isolate nematodes from their surroundings. By centrifuging nematodes in a number of increasing specific gravity solutions and plotting the fraction floating, the cumulative probability distribution of the population's specific gravity is generated. By assuming normality, the population mean, mu, and standard deviation, sigma, are found by a nonlinear least squares procedure. These density parameters along with their error covariance matrix may be used as a taxonomic physical character. A chi-squared test is derived for comparing populations. Mean and standard deviation pairs (mu, sigma) were found for the specific gravities of the adult stage of the plant parasites Pratylenchus agilis (1.068, 0.017), P. scribneri (1.073, 0.028), P. penetrans (1.058, 0.008) and the bacterial-feeder Caenorhabditis elegans (1.091, 0.016).

Nguyen C et al. (2008) J Bioinform Comput Biol "ClusFCM: an algorithm for predicting protein functions using homologies and protein interactions."

Gardiner K, Cios KJ, Mannino M, Nguyen C

[J Bioinform Comput Biol, 2008]

We introduce a new algorithm, called ClusFCM, which combines techniques of clustering and fuzzy cognitive maps (FCM) for prediction of protein functions. ClusFCM takes advantage of protein homologies and protein interaction network topology to improve low recall predictions associated with existing prediction methods. ClusFCM exploits the fact that proteins of known function tend to cluster together and deduce functions not only through their direct interaction with other proteins, but also from other proteins in the network. We use ClusFCM to annotate protein functions for Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), and Drosophila melanogaster (fly) using protein-protein interaction data from the General Repository for Interaction Datasets (GRID) database and functional labels from Gene Ontology (GO) terms. The algorithm''s performance is compared with four state-of-the-art methods for function prediction - Majority, chi(2) statistics, Markov random field (MRF), and FunctionalFlow - using measures of Matthews correlation coefficient, harmonic mean, and area under the receiver operating characteristic (ROC) curves. The results indicate that ClusFCM predicts protein functions with high recall while not lowering precision. Supplementary information is available at http://www.egr.vcu.edu/cs/dmb/ClusFCM/.

Lagatie O et al. (2018) Parasite Immunol "Linear epitopes in Onchocerca volvulus vaccine candidate proteins and excretory-secretory proteins."

Stuyver LJ, Van Dorst B, Batsa Debrah L, Verheyen A, Debrah A, Lagatie O

[Parasite Immunol, 2018]

In our previous study, a proteome-wide screen was conducted to identify linear epitopes in this parasite's proteome, resulting in the discovery of three immunodominant motifs. Here we investigated whether such antigenic peptides were found in proteins that were already known as vaccine candidates and excretome/secretome proteins for O. volvulus. This approach led to the identification of 71 immunoreactive stretches in 46 proteins. A deep-dive into the immunoreactivity profiles of eight vaccine candidates that were chosen as most promising candidates for further development (Ov-CPI-2,Ov-ALT-1,Ov-RAL-2,Ov-ASP-1,Ov-103,Ov-RBP-1,Ov-CHI-1, andOv-B20), resulted in the identification of a poly-glutamine stretch in Ov-RAL-2 that has properties for use as a serodiagnostic marker for O. volvulus infection. A peptide ELISA was developed, and the performance of this assay was evaluated. Based on this assessment, it was found that this assay has a sensitivity of 75.0% [95% CI: 64.9%-83.5%] and a specificity of 98.5% [95% CI: 94.6%-99.8%]. Furthermore, 8.7% reactivity in Asian parasite-infected individuals (8 out of 92) was observed. Besides this identification of a linear epitope marker, the information on the presence of linear epitopes in vaccine candidate proteins might be useful in the study of vaccines for river blindness. This article is protected by copyright. All rights reserved.