Rodriguez Mendoza, Victoria et al. (2022) MicroPubl Biol

Moravec, Sophie, Pilcher, Wendy, Choe, Keith Patrick, Harvey, Justin, Gibb, Gabrielle, Liu, Zhexin, Raju, Vikram, Choi, Thine, Rodriguez Mendoza, Victoria, Buddendorff, Lauren, Mihalik, Alva, Chandler, Luke, Al-Rajhi, Amal

[MicroPubl Biol, 2022]

Nematode cuticles are extracellular matrices (ECMs) that function as structural support and permeability barriers. Genetic disruption of specific cuticle collagen structures or secreted epidermal proteins in C. elegans activates stress response genes in epithelial cells suggesting the presence of an extracellular damage signaling mechanism. Cuticles are replaced during development via molting but investigations of extracellular signaling to stress responses have focused on adults. In our current study, we measured cuticle phenotypes and stress response gene expression in all post-embryonic stages of mutant strains for a collagen and two secreted epidermal proteins to gain insights into developmental patterns.

Rodriguez-Perez MA et al. Salud Publica Mex "[Problems in the investigation of the control of Onchocerca volvulus in Mexico]."

Rivas-Alcala AR, Rodriguez-Perez MA

[Salud Publica Mex]

The treatment and control of onchocerciasis in Mexico has been supported only on the administration of diethylcarbamazine and the removal of adult worms, which are in the onchocercomata. These actions seems to have diminished the prevalence and incidence of blindness in those individuals who are affected by this parasitosis. However, there has not been an important impact on onchocerciasis transmission. The objective of this paper is to critically analyze and discuss subjects related to diagnosis, treatment and control of onchocerciasis transmission in Mexico. Chemical vector control has been successfully achieved in other world regions; however, in Mexico, it has not been fully accepted as part of the integral onchocerciasis control due to several causes. Moreover, there has been few scientific research activities toward the search of new options for vector control. Recently, results of research on ivermectin (a microfilaricide agent) have indicated that this drug is effective and safe for the treatment of onchocerciasis. Additionally, it has been reported that ivermectin has an effect on the onchocerciasis transmission. However, there are several unanswered questions about the efficacy of ivermectin in stopping onchocerciasis transmission. In this report, the main efforts carried out in Mexico against onchocerciasis are analysed and problems related with diagnosis, treatment and control are also discussed. Some parameters for the correct evaluation of onchocerciasis control, with entomological emphasis, are proposed.

Rodriguez-Garcia MA et al. (2018) BMC Bioinformatics "Inferring ontology graph structures using OWL reasoning."

Hoehndorf R, Rodriguez-Garcia MA

[BMC Bioinformatics, 2018]

BACKGROUND: Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies' semantic content remains a challenge. RESULTS: We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph . CONCLUSIONS: Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

Rodriguez CR et al. (2019) Steroids "Synthesis and Biological Activity of Fluorinated Analogues of the DAF-12 Receptor Antagonist 24-Hydroxy-4-cholen-3-one."

Celeste Del Fueyo M, Rodriguez CR, Veleiro AS, Castro OA, Santillan VJ, Virginia Dansey M, Burton G

[Steroids, 2019]

The DAF-12 receptor is a ligand-activated transcription factor that in its ligand-bound form allows the expression of target genes needed to support the reproductive life cycle of the free-living nematode Caenorhabditis elegans, whereas unbound DAF-12 receptor leads to the developmentally arrested "dauer larvae", specialized for survival and dispersal. The endogenous ligands of the DAF-12 receptor are 3-keto-cholestenoic acids dubbed dafachronic acids. In a previous publication we reported that oxysterols with a shorter side chain (C₂₄) modulate the DAF-12 receptor activity either as partial agonists or, in the case of the C₂₄ alcohol 24-hydroxy-4-cholen-3-one, as an antagonist both in vitro and in vivo. Preliminary structure-activity relationships suggested that this activity profile could be improved with more lipophilic and less acidic functional groups at the end of the side chain. Thus, we have now synthesized two fluorine containing analogues in which the C-24 hydroxyl was replaced by a difluoromethyl group (regarded as a "lipophilic hydroxyl") or a difluoromethylidene group with similar lipophilicity but lacking the hydrogen bond donor capacity. Activity was evaluated in vitro using transactivation cell-based assays and in vivo by the effect on the development of wild-type C. elegans. The 24-difluoromethyl analogue retained the antagonist activity in vitro, being completely devoid of agonist activity and exhibited improved activity in vivo. The difluoromethylidene showed a slight antagonist tendency in vitro (statistically not significant), in the concentration range tested and was weakly active in vivo. None of the compounds were toxic, as treated worms recovered to normal development, when transferred to fresh media without added steroids.

Rodriguez-Palero MJ et al. (2018) Sci Rep "An automated method for the analysis of food intake behaviour in Caenorhabditis elegans."

Marsac R, Rodriguez-Palero MJ, Olmedo M, Gomes JE, Artal-Sanz M, Lopez-Diaz A

[Sci Rep, 2018]

The study of mechanisms that govern feeding behaviour and its related disorders is a matter of global health interest. The roundworm Caenorhabditis elegans is becoming a model organism of choice to study these conserved pathways. C. elegans feeding depends on the contraction of the pharynx (pumping). Thanks to the worm transparency, pumping can be directly observed under a stereoscope. Therefore, C. elegans feeding has been historically investigated by counting pharyngeal pumping or by other indirect approaches. However, those methods are short-term, time-consuming and unsuitable for independent measurements of sizable numbers of individuals. Although some particular devices and long-term methods have been lately reported, they fail in the automated, scalable and/or continuous aspects. Here we present an automated bioluminescence-based method for the analysis and continuous monitoring of worm feeding in a multi-well format. We validate the method using genetic, environmental and pharmacological modulators of pharyngeal pumping. This flexible methodology allows studying food intake at specific time-points or during longer periods of time, in single worms or in populations at any developmental stage. Additionally, changes in feeding rates in response to differential metabolic status or external environmental cues can be monitored in real time, allowing accurate kinetic measurements.

Rodriguez M et al. (2012) Exp Gerontol "Genetic variation for stress-response hormesis in C. elegans lifespan."

Riksen JA, Rodriguez M, Kammenga JE, Snoek LB, Bevers RP

[Exp Gerontol, 2012]

Increased lifespan can be associated with greater resistance to many different stressors, most notably thermal stress. Such hormetic effects have also been found in C. elegans where short-term exposure to heat lengthens the lifespan. Genetic investigations have been carried out using mutation perturbations in a single genotype, the wild type Bristol N2. Yet, induced mutations do not yield insight regarding the natural genetic variation of thermal tolerance and lifespan. We investigated the genetic variation of heat-shock recovery, i.e. hormetic effects on lifespan and associated quantitative trait loci (QTL) in C. elegans. Heat-shock resulted in an 18% lifespan increase in wild type CB4856 whereas N2 did not show a lifespan elongation. Using recombinant inbred lines (RILs) derived from a cross between wild types N2 and CB4856 we found natural variation in stress-response hormesis in lifespan. Approx. 28% of the RILs displayed a hormesis effect in lifespan. We did not find any hormesis effects for total offspring. Across the RILs there was no relation between lifespan and offspring. The ability to recover from heat-shock mapped to a significant QTL on chromosome II which overlapped with a QTL for offspring under heat-shock conditions. The QTL was confirmed by introgressing relatively small CB4856 regions into chromosome II of N2. Our observations show that there is natural variation in hormetic effects on C. elegans lifespan for heat-shock and that this variation is genetically determined.

Rodriguez A et al. (2014) J Neurosci Res "Analysis of differential gene expression profiles in Caenorhabditis elegans knockouts for the v-SNARE master protein 1."

McKay K, Graham M, Rodriguez A, Dittrich J, Holgado AM

[J Neurosci Res, 2014]

At chemical synapses, neurons communicate information to other cells by secreting neurotransmitters or neuropeptides into the synaptic cleft, which then bind to receptors on the target cell. Preliminary work performed in our laboratory has shown that mutant nematodes lacking a protein called VSM-1 have increased synaptic density compared with the wild type. Consequently, we hypothesized that genes expressed in vsm-1 mutants mediate enhanced synaptogenesis. To identify these genes of interest, we utilized microarray technology and quantitative PCR. To this end, first we isolated the total RNA from young-adult wild-type and vsm-1 mutant Caenorhabditis elegans. Next, we synthesized cDNA from reverse transcription of the isolated RNA. Hybridization of the cDNA to a microarray was performed to facilitate gene expression profiling. Finally, fluorescently labeled microarrays were analyzed, and the identities of induced and repressed genes were uncovered in the open-source software Magic Tool. Analyses of microarray experiments performed using three independent biological samples per strain and three technical replicas and dye swaps showed induction of genes coding for major sperm proteins and repression of SPP-2 in vsm-1 mutants. Microarray results were also validated and quantified by using quantitative PCR.

Rodriguez-Perez MA et al. (2008) Am J Trop Med Hyg "Evidence for suppression of Onchocerca volvulus transmission in the Oaxaca focus in Mexico."

Hassan HK, Richards F, Lizarazo-Ortega C, Rodriguez-Perez MA, Sauerbrey M, Dominguez-Vasquez A, Unnasch TR, Mendez-Galvan J, Lugo-Moreno P

[Am J Trop Med Hyg, 2008]

Entomologic and serologic surveys were performed in four sentinel communities in the Oaxaca focus in southern Mexico to assess the level of transmission and exposure incidence to Onchocerca volvulus. All communities have been receiving ivermectin mass treatment twice per year since 1997. In one community, parasite DNA was detected by polymerase chain reaction-enzyme-linked immunosorbent assay in 2004 in one pool of 50 vector heads of 170 such pools (8,500 flies) examined, which indicated an estimated transmission potential of 6.7 third-stage larvae/person/year. No evidence for transmission was found in the three other communities in 13,650 flies examined. All persons in a cohort consisting of 117 children in the four communities remained serologically negative for antibodies recognizing a cocktail of recombinant antigens over a four-year period from 2001 to 2004, which indicated an exposure incidence of 0%. Taken together, these data suggest that transmission has been suppressed in the four communities.

Rodriguez-Perez MA et al. (2010) Am J Trop Med Hyg "Interruption of transmission of Onchocerca volvulus in the Oaxaca focus, Mexico."

Orozco-Algarra ME, Rodriguez-Perez MA, Morales-Castro AL, Dominguez-Vazquez A, Rendon VG, Pena-Flores GP, Arredondo-Jimenez JI, Vasquez-Rodriguez MA, Unnasch TR, Richards F

[Am J Trop Med Hyg, 2010]

All endemic communities of the Oaxaca focus of onchocerciasis in southern Mexico have been treated annually or semi-annually with ivermectin since 1994. In-depth epidemiologic assessments were performed in communities during 2007 and 2008. None of the 52,632 Simulium ochraceum s.l. collected in four sentinel communities was found to contain parasite DNA when tested by polymerase chain reaction-enzyme-linked immunosorbent assay (PCR-ELISA), resulting in an upper bound of the infection rate in the vectors of 0.07/2,000. The prevalence of microfilariae (mf) in the cornea and/or anterior chamber of the eye was also zero (0 of 1,039 residents examined; 95%-UL = 0.35%). Similarly, all 1,164 individuals examined by skin biopsy were mf negative (95%-UL = 0.31%), and sera collected from 3,569 children from 25 communities did not harbor Ov16 IgG4-antibodies (95%-UL = 0.09%). These meet the criteria for absence of morbidity and parasite transmission in the Oaxaca focus. As a result mass treatments with ivermectin were halted in 2009.

Rodriguez de la Vega M et al. (2007) FASEB J "Nna1-like proteins are active metallocarboxypeptidases of a new and diverse M14 subfamily."

Tanco S, Diez A, Rodriguez de la Vega M, Sevilla RG, Aviles FX, Fricker LD, Hermoso A, Bautista JM, Lorenzo J

[FASEB J, 2007]

Nna1 has some sequence similarity to metallocarboxypeptidases, but the biochemical characterization of Nna1 has not previously been reported. In this work we performed a detailed genomic scan and found >100 Nna1 homologues in bacteria, Protista, and Animalia, including several paralogs in most eukaryotic species. Phylogenetic analysis of the Nna1-like sequences demonstrates a major divergence between Nna1-like peptidases and the previously known metallocarboxypeptidases subfamilies: M14A, M14B, and M14C. Conformational modeling of representative Nna1-like proteins from a variety of species indicates an unusually open active site, a property that might facilitate its action on a wide variety of peptide and protein substrates. To test this, we expressed a recombinant form of one of the Nna1-like peptidases from Caenorhabditis elegans and demonstrated that this protein is a fully functional metallocarboxypeptidase that cleaves a range of C-terminal amino acids from synthetic peptides. The enzymatic activity is activated by ATP/ADP and salt-inactivated, and is preferentially inhibited by Z-Glu-Tyr dipeptide, which is without precedent in metallocarboxypeptidases and resembles tubulin carboxypeptidase functioning; this hypothesis is strongly reinforced by the results depicted in Kalinina et al. published as accompanying paper in this journal (1). Our findings demonstrate that the M14 family of metallocarboxypeptidases is more complex and diverse than expected, and that Nna1-like peptidases are functional variants of such enzymes, representing a novel subfamily (we propose the name M14D) that contributes substantially to such diversity.--Rodriguez de la Vega, M., Sevilla, R. G., Hermoso, A., Lorenzo, J., Tanco, S., Diez, A., Fricker, L. D., Bautista, J. M., Aviles, F. X. Nna1-like proteins are active metallocarboxypeptidases of a new and diverse M14 subfamily.