Esperanza Paniagua

Generalized lattice graphs for 2D-visualization of biological information

Abstract Several graph representations have been introduced for different data in theoretical biology. For instance, complex networks based on Graph theory are used to represent the structure and/or dynamics of different large biological systems such as protein–protein interaction networks. In addition, Randic, Liao, Nandy, Basak, and many others developed some special types of graph-based representations. This special type of graph includes geometrical constrains to node positioning in space and adopts final geometrical shapes that resemble lattice-like patterns. Lattice networks have been used to visually depict DNA and protein sequences but they are very flexible. However, despite the proved efficacy of new lattice-like graph/networks to represent diverse systems, most works focus on only one specific type of biological data. This work proposes a generalized type of lattice and illustrates how to use it in order to represent and compare biological data from different sources. We exemplify the following cases: protein sequence; mass spectra (MS) of protein peptide mass fingerprints (PMF); molecular dynamic trajectory (MDTs) from structural studies; mRNA microarray data; single nucleotide polymorphisms (SNPs); 1D or 2D-Electrophoresis study of protein polymorphisms and protein-research patent and/or copyright information. We used data available from public sources for some examples but for other, we used experimental results reported herein for the first time. This work may break new ground for the application of Graph theory in theoretical biology and other areas of biomedical sciences.

Genetic variability of natural populations of trematodes of the genus Lecithochirium parasites of eels.

Allozyme variation within and among populations of 3 species of the genus Lecithochirium (Trematoda: Hemiuridae) was studied by starch gel electrophoresis. In total, 19 loci were analysed in 7 populations. The level of genetic variability was relatively high in all populations. The percentage of polymorphic loci (0.95 criterion) observed per population varied from 21.0% to 55.5%, and expected heterozygosity levels varied from 0.082 to 0.197. All populations showed significant heterozygote deficiencies. In Lecithochirium fusiforme most of the deviations from Hardy-Weinberg proportions were within the populations and this species showed moderate population structuring (F(IS)=0.486, F(ST)=0.142, Nm= 1.51) and accordingly low intraspecific genetic distances (D=0.003 to 0.027). A significant lack of heterozygotes for several polymorphic loci was revealed in Lecithochirium rufoviride and Lecithochirium musculus. The most probable cause of the population genetic subdivision in L. rufoviride is the presence of at least 1 cryptic species in the populations studied. Although the lowest percentage of fixed genetic differences was that between L. fusiforme and L. musculus, two different algorithms for the construction of evolutionary trees on a matrix of genetic distances confirmed that L. fusiforme and L. rufoviride are phenetically the most closely related species.

More than meets the eye: detecting cryptic microgeographic population structure in a parasite with a complex life cycle

Nonrandom recruitment of parasites among hosts can lead to genetic differentiation among hosts and mating dynamics that promote inbreeding. It has been hypothesized that strictly aquatic parasites with intermediate hosts will behave as panmictic populations among hosts because ample opportunity exists for random mixing of unrelated individuals during transmission to the definitive host. A previous allozyme study on the marine trematode Lecithochirium fusiforme did not support this hypothesis; in that, there was genetic differentiation among, and significant heterozygote deficiencies within, definitive hosts. We revisit this system and use microsatellites to obtain multilocus genotypes. Our goal was to determine whether cryptic subgroups and/or the presence of clones could account for the apparent deviation from ‘panmixia’. We find strong evidence for cryptic subdivision (three genetic clusters) that causes the Wahlund effect and differentiation among definitive hosts. After accounting for these cryptic groups, we see panmictic genetic structure among definitive hosts that is consistent with the ‘high mixing in aquatic habitats’ hypothesis. We see evidence for cotransmission of clones in all three clusters, but this level of clonal structure did not have a major impact in causing deviations from Hardy–Weinberg equilibrium, and only affected genetic differentiation among hosts in one cluster. A cursory examination of the data may have led to incorrect conclusions about nonrandom transmission. However, it is obvious in this system that there is more than meets the eye in relation to the actual make‐up of parasite populations. In general, the methods we employ will be useful for elucidating hidden patterns in other organisms where cryptic structure may be common (e.g. those with limited morphology or complex life histories).

Genetic variation within and among infrapopulations of the marine digenetic trematode Lecithochirium fusiforme.

Allozyme markers were used to study genetic variation in Lecithochirium fusiforme within a natural population of Conger conger. Six of 16 enzyme-coding loci studied were found to be polymorphic. These loci were surveyed in 12 infrapopulations of adult flukes. High levels of genetic variation were detected (P = 0.375); Ho = 0.048; He = 0.085). However, the population did not conform to Hardy-Weinberg expectations, as it showed a significant deficit of heterozygotes. L. fusiforme also exhibited low differentiation between infrapopulations (FST = 0.064). Despite significant linkage disequilibrium at Pgm-1 and Pgm-2 (P < 0.05), mating system does not appear to be the principal reason for the deficit of heterozygotes detected, because some polymorphic loci were in Hardy-Weinberg equilibrium. Association between FIS and FST statistics suggests the existence of the Wahlund effect. However, all infrapopulations showed a strong deficit of heterozygotes for most polymorphic loci (FIS = 0.409). Detection of significant genetic differentiation among temporal samples and the existence of paratenic hosts in the life-cycle suggests the Wahlund effect, caused by the mixture of genetically distinct temporal samples in the infrapopulations. Occasional temporal gene flow also might explain the high estimated genetic polymorphism.

Contrasting patterns of population genetic structure of Fasciola hepatica from cattle and sheep: Implications for the evolution of anthelmintic resistance

Twelve polymorphic genetic markers, eight allozymic loci and four microsatellites, were used to characterize 20 infrapopulations of Fasciola hepatica (all flukes from 10 individual cattle and 10 sheep) from 11 farms in Northwest Spain. Results suggest different patterns of population genetic structure depending on the host species. Individuals identified as clones were much more frequent in sheep. The common presence of clones and its nonrandom occurrence among individual hosts suggests clumped transmission of liver flukes in sheep. After reducing significant repeated multilocus genotypes to one unique copy within infrapopulations, results show relatively high levels of gene diversity within infrapopulations from cattle and sheep (0.411 and 0.360 on average, respectively). However, parasites of sheep appear to show significantly more structured variation at the infrapopulation level (Standardized F(ST)=0.087 and 0.170 for parasites of cattle and sheep, respectively). Compared to the parasites from cattle, results suggest that populations from sheep show lower levels of gene flow, higher degree of aggregate transmission, higher probability of mating within clones, and lower parasitic load. These differences have implications for the evolution of anthelmintic resistance because they affect the effective population size and the degree of inbreeding. The development and rapid spread of resistance seems likely in the parasites of cattle because populations from the study area are characterized by high gene flow. However, results also suggest that the efficient selection of a new recessive advantageous mutation would be favored in parasites of sheep due to a greater potential for inbreeding.

Allozyme markers suitable for population genetic analysis of Fasciola hepatica.

Protein electrophoresis was used to study allozyme variation in Fasciola hepatica collected from three locations in Galicia (NW Spain), an area where fascioliasis is endemic. Eleven of 16 loci showed variation in at least one population and 7 loci were polymorphic in all populations studied. Five of these markers showed expected heterozygosities ranging from 0.137 to 0.569. The Neis unbiased genetic diversity within populations ranged from 0.146 to 0.168. Genotypic frequencies were consistent with panmixia in 25 of 28 cases. Only 2 loci showed a significant deficit of heterozygotes. Genetic distances between populations were small (D(a)=0.003-0.010). These results suggest high levels of genetic variability and low population structure. This study shows that several of the markers developed are useful for study the population genetic structure of the parasite, which is essential to investigate the evolution of drug resistance that has recently emerged in populations of the study area.

Free and bound biotin molecules in helminths: a source of artifacts for avidin biotin-based immunoassays

Abstract The avidin-biotin molecular recognition system is widely used in parasite immunology. However, the presence of biotin and/or biotin-containing molecules (BCMs) in samples may lead to erroneous results. In the work reported herein we investigated the extent to which biotin and BCMs present in helminth extracts may interfere in avidin/biotin-based immunoassays and developed an enzyme-linked immunosorbent assay (ELISA) for quantification of these components. In avidin-based ELISA using antinematode monoclonal antibodies, an extract of the nematode Anisakis simplex showed very high background reactivity due to biotin/BCMs, whereas the background reactivity in an extract of the nematode Trichinella spiralis was negligible. To investigate interspecies differences further, we performed Western-blot analyses (with avidin as the detector) of extracts from seven nematodes (A. simplex, Ascaris suum, Toxocara canis, Hysterothylacium aduncum, T. spiralis, and Trichuris muris) and the cestode Bothriocephalus scorpii. Even within superfamilies there was considerable variation in the banding patterns obtained. The above-mentioned results confirm that biotin and BCMs may be a significant source of interference in ELISA and immunoblotting, two of the techniques most widely used in parasitological immunodiagnosis. A competition ELISA designed to allow accurate quantification of biotin and BCMs in helminth extracts likewise indicated very considerable interspecies variation. Both A. simplex and H. aduncum had very high biotin/BCM contents. Microdialysis of extracts in the presence of dimethylsulfoxide to remove free biotin prior to ELISA indicated that the high biotin/BCM content of the H. aduncum extract (but not the A. simplex extract) was very largely due to free biotin. Taken together, these results indicate that extreme caution should be exercised in the use of avidin/biotin-based immunoassays for the detection of helminth antigens and that in many cases it may be better to use an alternative recognition system.

Allozyme analysis of two polymorphic enzymes in a natural population of Lecithochirium musculus.

Abstract Genetic variability among 112 individuals of Lecithochirium musculus from Anguilla anguilla from northwestern Spain was examined using allozyme analysis. Starch-gel electrophoresis was used to investigate the genetic variation in two polymorphic enzymes, glucose phosphate isomerase (GPI) and phosphoglucomutase (PGM). The banding patterns obtained for GPI were consistent with a dimeric structure for this enzyme and with single-locus control. The inferred genotype frequencies did not significantly differ as compared with those predicted by the Hardy–Weinberg equation. Two PGM loci were detected (Pgm-1 and Pgm-2). Pgm-1 was polymorphic and showed a striking departure from Hardy-Weinberg predictions (total absence of heterozygotes for alleles in high frequencies), raising the possibility of the existence of two reproductively isolated populations. However, other reasons for this observation are discussed.

Analysis of the antigenicity in mice of biotinyl enzymes from Anisakis simplex and other nematodes.

Abstract We analyzed the antigenicity of biotinyl enzymes contained in somatic extracts from Anisakis simplex and other parasite nematodes and show in this report that these molecules are an important source of cross-reactivity problems among these nematodes. Cross-reactivity was most pronounced among members of the superfamily Ascaridoidea. These results suggest that the presence of biotinyl enzymes in whole somatic extracts of A. simplex and other parasites may make serodiagnostic assays based on this kind of antigenic preparation unreliable.

Electrophoretic and morphological differentiation of three sympatric species of the genus Lecithochirium (Trematoda: Hemiuridae), parasites of marine fishes

Abstract. Three sympatric species of the genus Lecithochirium, Lecithochirium fusiforme, Lecithochirium rufoviride and Lecithochirium musculus, parasites of Conger conger and Anguilla anguilla, were compared morphologically and electrophoretically. The three species can be discriminated by enzyme analysis, and differentiation can also be made by the analysis of several morphometric features, in particular body size and sucker ratio. Fourteen enzyme systems representing 15 loci were examined by starch gel electrophoresis. Two of the enzyme systems studied (ALD and GOT) were totally diagnostic among Lecithochirium species. Fixed allelic differences between L. fusiforme and L. musculus were observed at five loci, between L. fusiforme and L. rufoviride at nine loci, and between L. musculus and L. rufoviride at ten loci. The percentage of fixed differences among the species under study ranged from 33 to 77%. The results show that the three taxa can be clearly differentiated, and that L. fusiforme is genetically more similar to L. musculus than to L. rufoviride.