Echinococcus granulosus antigen B structure: subunit composition and oligomeric states

Background

Antigen B (AgB) is the major protein secreted by the Echinococcus granulosus metacestode and is involved in key host-parasite interactions during infection. The full comprehension of AgB functions depends on the elucidation of several structural aspects that remain unknown, such as its subunit composition and oligomeric states.

Methodology/Principal Findings

The subunit composition of E. granulosus AgB oligomers from individual bovine and human cysts was assessed by mass spectrometry associated with electrophoretic analysis. AgB8/1, AgB8/2, AgB8/3 and AgB8/4 subunits were identified in all samples analyzed, and an AgB8/2 variant (AgB8/2v8) was found in one bovine sample. The exponentially modified protein abundance index (emPAI) was used to estimate the relative abundance of the AgB subunits, revealing that AgB8/1 subunit was relatively overrepresented in all samples. The abundance of AgB8/3 subunit varied between bovine and human cysts. The oligomeric states formed by E. granulosus AgB and recombinant subunits available, rAgB8/1, rAgB8/2 and rAgB8/3, were characterized by native PAGE, light scattering and microscopy. Recombinant subunits showed markedly distinct oligomerization behaviors, forming oligomers with a maximum size relation of rAgB8/3>rAgB8/2>rAgB8/1. Moreover, the oligomeric states formed by rAgB8/3 subunit were more similar to those observed for AgB purified from hydatid fluid. Pressure-induced dissociation experiments demonstrated that the molecular assemblies formed by the more aggregative subunits, rAgB8/2 and rAgB8/3, also display higher structural stability.

Conclusions/Significance

For the first time, AgB subunit composition was analyzed in samples from single hydatid cysts, revealing qualitative and quantitative differences between samples. We showed that AgB oligomers are formed by different subunits, which have distinct abundances and oligomerization properties. Overall, our findings have significantly contributed to increase the current knowledge on AgB expression and structure, highlighting issues that may help to understand the parasite adaptive response during chronic infection.     

Longitudinal differentiation among pelagic populations in a planktic foraminifer

Evolutionary processes in marine plankton have been assumed to be dependent on the oceanic circulation system, which transports plankton between populations in marine surface waters. Gene flow facilitated by oceanic currents along longitudinal gradients may efficiently impede genetic differentiation of pelagic populations in the absence of confounding marine environmental effects. However, how responsible oceanic currents are for the geographic distribution and dispersal of plankton is poorly understood. We examined the phylogeography of the planktic foraminifer Pulleniatina obliquiloculata in the Indo-Pacific Warm Pool (IPWP) by using partial small subunit ribosomal DNA (SSU rDNA) sequences. We found longitudinal clines in the frequencies of three distinct genetic types in the IPWP area. These frequencies were correlated with environmental factors that are characteristic of three water masses in the IPWP. Noteworthy, populations inhabiting longitudinally distant water masses at the Pacific and Indian sides of the IPWP were genetically different, despite transportation of individuals via oceanic currents. These results demonstrate that populations of pelagic plankton have diverged genetically among different water masses within a single climate zone. Changes of the oceanic circulation system could have impacted the geographic patterns of dispersal and divergence of pelagic plankton.     

Genetic diversity of mountain plants: two migration episodes of Mediterranean Erodium (Geraniaceae)

This paper examines the phylogeny of Erodium subsect. Petraea, a group of six morphologically and genetically very similar species from the mountains of the western Mediterranean. Combined trnL-F-ITS analysis was unable to determine the phylogenetic relationships of these species owing to sequence similarity. AFLP fragment analysis showed different populations to cluster in six closely related phylogroups that partially coincided with morphological species. In the Iberian Peninsula, high temperatures during interstadial periods probably impeded the survival of these species at low altitudes, and their populations may have been forced to migrate northward within Iberia or remain isolated on high mountains. AFLP variation suggests that this might have led to their differentiation into groups and speciation during interglacials, but it probably also provided the basis for recurrent recolonisations and the mixing of neighbouring populations at the last glacial maxima. The genetic diversity of the two Erodium lineages suggests two migration episodes took place from southern Iberia towards the north, with one lineage migrating via western Iberia and the other via eastern Iberia. The patterns of genetic diversity observed in populations of 56 European species (27 genera) leads to the hypothesis that disparate proportions of unique polymorphic fragments are the result of the evolutionary histories of their mountain populations irrespective of the currently recognised species.     

Socioeconomic and nutritional factors account for the association of gastric cancer with amerindian ancestry in a latin american admixed population

Gastric cancer is one of the most lethal types of cancer and its incidence varies worldwide, with the Andean region of South America showing high incidence rates. We evaluated the genetic structure of the population from Lima (Peru) and performed a case-control genetic association study to test the contribution of African, European, or Native American ancestry to risk for gastric cancer, controlling for the effect of non-genetic factors. A wide set of socioeconomic, dietary, and clinic information was collected for each participant in the study and ancestry was estimated based on 103 ancestry informative markers. Although the urban population from Lima is usually considered as mestizo (i.e., admixed from Africans, Europeans, and Native Americans), we observed a high fraction of Native American ancestry (78.4% for the cases and 74.6% for the controls) and a very low African ancestry (<5%). We determined that higher Native American individual ancestry is associated with gastric cancer, but socioeconomic factors associated both with gastric cancer and Native American ethnicity account for this association. Therefore, the high incidence of gastric cancer in Peru does not seem to be related to susceptibility alleles common in this population. Instead, our result suggests a predominant role for ethnic-associated socioeconomic factors and disparities in access to health services. Since Native Americans are a neglected group in genomic studies, we suggest that the population from Lima and other large cities from Western South America with high Native American ancestry background may be convenient targets for epidemiological studies focused on this ethnic group.     

Barcoding sponges: an overview based on comprehensive sampling

Background

Phylum Porifera includes ∼8,500 valid species distributed world-wide in aquatic ecosystems ranging from ephemeral fresh-water bodies to coastal environments and the deep-sea. The taxonomy and systematics of sponges is complicated, and morphological identification can be both time consuming and erroneous due to phenotypic convergence and secondary losses, etc. DNA barcoding can provide sponge biologists with a simple and rapid method for the identification of samples of unknown taxonomic membership. The Sponge Barcoding Project (www.spongebarcoding.org), the first initiative to barcode a non-bilaterian metazoan phylum, aims to provide a comprehensive DNA barcode database for Phylum Porifera.

Methodology/Principal Findings

∼7,400 sponge specimens have been extracted, and amplification of the standard COI barcoding fragment has been attempted for approximately 3,300 museum samples with ∼25% mean amplification success. Based on this comprehensive sampling, we present the first report on the workflow and progress of the sponge barcoding project, and discuss some common pitfalls inherent to the barcoding of sponges.

Conclusion

A DNA-barcoding workflow capable of processing potentially large sponge collections has been developed and is routinely used for the Sponge Barcoding Project with success. Sponge specific problems such as the frequent co-amplification of non-target organisms have been detected and potential solutions are currently under development. The initial success of this innovative project have already demonstrated considerable refinement of sponge systematics, evaluating morphometric character importance, geographic phenotypic variability, and the utility of the standard barcoding fragment for Porifera (despite its conserved evolution within this basal metazoan phylum).     

The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data

Halichondrid sponges play a pivotal role in the classification of demosponges as changes in their classification has had direct consequences for the classification of Demospongiae. Historically, the systematics of halichondrids has been unstable. During the 1950s, the order was divided into two subclasses, which were based on empirical and assumed reproductive data. Subsequent morphological and biochemical analyses postulated the re-merging of halichondrid families, but recent molecular data indicate their polyphyly. Here we review the classification history of halichondrid taxa, compare it with the current and predominantly ribosomal molecular data, and support the new phylogenetic hypotheses with mitochondrial data from DNA barcoding.     

Identification of positive selection in disease response genes within members of the Poaceae

Millions of years of coevolution between plants and pathogens can leave footprints on their genomes and genes involved on this interaction are expected to show patterns of positive selection in which novel, beneficial alleles are rapidly fixed within the population. Using information about upregulated genes in maize during Colletotrichum graminicola infection and resources available in the Phytozome database, we looked for evidence of positive selection in the Poaceae lineage, acting on protein coding sequences related with plant defense. We found six genes with evidence of positive selection and another eight with sites showing episodic selection. Some of them have already been described as evolving under positive selection, but others are reported here for the first time including genes encoding isocitrate lyase, dehydrogenases, a multidrug transporter, a protein containing a putative leucine-rich repeat and other proteins with unknown functions. Mapping positively selected residues onto the predicted 3-D structure of proteins showed that most of them are located on the surface, where proteins are in contact with other molecules. We present here a set of Poaceae genes that are likely to be involved in plant defense mechanisms and have evidence of positive selection. These genes are excellent candidates for future functional validation.     

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

Flagellated heterotrophic microeukaryotes have key roles for the functioning of marine ecosystems as they channel large amounts of organic carbon to the upper trophic levels and control the population sizes of bacteria and archaea. Still, we know very little on the diversity patterns of most groups constituting this evolutionary heterogeneous assemblage. Here, we investigate 11 groups of uncultured flagellates known as MArine STramenopiles (MASTs). MASTs are ecologically very important and branch at the base of stramenopiles. We explored the diversity patterns of MASTs using pyrosequencing (18S rDNA) in coastal European waters. We found that MAST groups range from highly to lowly diversified. Pyrosequencing (hereafter ‘454'') allowed us to approach to the limits of taxonomic diversity for all MAST groups, which varied in one order of magnitude (tens to hundreds) in terms of operational taxonomic units (98% similarity). We did not evidence large differences in activity, as indicated by ratios of DNA:RNA-reads. Most groups were strictly planktonic, although we found some groups that were active in sediments and even in anoxic waters. The proportion of reads per size fraction indicated that most groups were composed of very small cells (∼2–5 μm). In addition, phylogenetically different assemblages appeared to be present in different size fractions, depths and geographic zones. Thus, MAST diversity seems to be highly partitioned in spatial scales. Altogether, our results shed light on these ecologically very important but poorly known groups of uncultured marine flagellates.     

Evaluation of SPLAT with spinosad and methyl eugenol or cue-lure for "attract-and-kill" of oriental and melon fruit flies (Diptera: Tephritidae) in Hawaii

Specialized Pheromone and Lure Application Technology (SPLAT) methyl eugenol (ME) and cue-lure (C-L) "attract-and-kill" sprayable formulations containing spinosad were compared with other formulations under Hawaiian weather conditions against oriental fruit fly, Bactrocera dorsalis (Hendel), and melon fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae), respectively. Field tests were conducted with three different dispensers (Min-U-Gel, Acti-Gel, and SPLAT) and two different insecticides (naled and spinosad). SPLAT ME with spinosad was equal in performance to the standard Min-U-Gel ME with naled formulation up to 12 wk. SPLAT C-L with spinosad was equal in performance to the standard Min-U-Gel C-L with naled formulation during weeks 7 to12, but not during weeks 1-6. In subsequent comparative trials, SPLAT ME + spinosad compared favorably with the current standard of Min-U-Gel ME + naled for up to 6 wk, and it was superior from weeks 7 to 12 in two separate tests conducted in a papaya (Carica papaya L.) orchard and a guava (Psidium guajava L.) orchard, respectively. In outdoor paired weathering tests (fresh versus weathered), C-L dispensers (SPLAT + spinosad, SPLAT + naled, and Min-U-Gel + naled) were effective up to 70 d. Weathered ME dispensers with SPLAT + spinosad compared favorably with SPLAT + naled and Min-U-Gel + naled, and they were equal to fresh dispensers for 21-28 d, depending on location. Our current studies indicate that SPLAT ME and SPLAT C-L sprayable attract-and-kill dispensers containing spinosad are a promising substitute for current liquid organophosphate insecticide formulations used for areawide suppression of B. dorsalis and B. cucurbitae in Hawaii.     

Mutagenic activity of airborne particulate matter in a petrochemical industrial area

Exposure to airborne particulate matter has adverse effects on human health and ecosystem. Mutagenic activity of airborne particulate organic matter extracts in three time periods from total suspended particles (TSP) and particles less than 10 microm (PM10) was evaluated in an area under the influence of a petrochemical industry located in the town of Triunfo, Brazil. The extracts were investigated using the Salmonella/microsome assay, with the microsuspension method. The extracts were obtained by sonication extracted using dichloromethane (DCM) solvent. The fractions were tested for mutagenicity with the Salmonella typhimurium strains TA98 (with and without metabolic activation), TA98NR and TA98/1,8DNP(6); or YG1021 and YG1024. A positive frameshift mutagenic response was observed for the environmental samples during the different periods. The responses according to percentage of extractable organic matter (EOM%), EOM/m(3), revertants/microg (rev/microg) and revertants/m(3) (rev/m(3)) were lower for TSP than for PM10 extracts. The highest rev/m(3) values were observed in PM10 extract samples collected in winter, July 2005, in the presence (13.79 rev/m(3)) or absence (6.87 rev/m(3)) of S9 fraction. Similarly in the first (1995) or second period (2000) the highest values for TSP were observed in winter, but with lower activity (3.00 and 0.89 rev/m(3) respectively). The responses observed for the nitrosensitive strains suggest the contribution of nitro, amino and/or hydroxylamino derivatives of PAHs to the total mutagenicity of matter extracted from airborne particles. The Salmonella/microsome assay was a sensitive method to define areas contaminated by genotoxic compounds, even in samples with TSP or PM10 values that are acceptable according to legal environmental quality standards, favoring environmental control measures with an effective response seen in the population's improved quality of life.