Parasitism related KEGG categories.

<p>* “hit” is the number of genes mapping to a KO of that category which is a) overexpressed in the Adult (parasitic) stage of <i>N</i>. <i>americanus</i> as compared to its iL3 stage and b) underexpressed in the Adult stage of <i>C</i>. <i>elegans</i> as compared to its Dauer stage.</p><p>+ “background” is the number of genes mapping to a KO of that category which is present in both genomes.</p><p>Parasitism related KEGG categories.</p

Enzyme annotation, module completion and phylogenetic distribution of metabolic potential.

<p>A. Number of complete modules and distinct KOs mapped to them. B. Clustering based on module presence correlation. A version of the figure that includes the module names is presented as <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003788#pntd.0003788.s005" target="_blank">S5 Fig</a>.</p

Enzyme diversification between host and parasite.

<p>A. Enzyme diversification between human and human hookworm <i>Necator americanus</i>. Reactions R01518 (2-Phospho-D-glycerate 2,3-phosphomutase) and R00200 (pyruvate kinase) are indispensable steps for the completion of M00001 (Glycolysis Embden-Meyerhof pathway). <i>N</i>. <i>americanus</i>, a human hookworm parasite, uses KO K15633 for R01518, which the human proteome lacks. Human proteome has genes mapping to K01837 and K01834 instead, which completes the same reaction. For R00200, both Human and <i>N</i>. <i>americanus</i> have K00873 available for completion, but only human have K12406 as an alternative for reaction completion. B. Enzyme diversification between plants and plant –parasitic nematodes. Plants have many more examples of exclusive KO usage between hosts and parasites. Module M00087 (beta-oxidation) is an interesting case where the last 2 reactions—R04727 and R03991—use different KOs for completion in all the 3 plants vs the 3 plant parasite nematodes. Different KOs are likely to be mapped to genes that are not orthologous to each other, providing an opportunity to target the parasite-specific activity.</p

Combined analysis of differentially abundant enzymes in <i>Caenorhabditis elegans</i> and <i>Necator americanus</i>.

<p>Infective L3 stage in <i>N</i>. <i>americanus</i> is developmentally analogous to the Dauer stage of <i>C</i>. <i>elegans</i>. KOs that are overabundant in the parasitic Adult stage in the hookworm, as compared to the infective L3 stage are likely to be enriched from parasitism related enzymes, but this result is confounded by the development related KOs needed in the adult stage. We obtain a highly enriched subset of parasitism related KOs by only compiling those KOs that are underabundant in the Adult stage of <i>C</i>. <i>elegans</i>, hence, less likely to be important for the worms’ adult stage for any non-parasitism related function. The shaded region represents KOs that are among the top 25 percentile in abundance rank differential between the Dauer stage and the adult stage in <i>C</i>. <i>elegans</i> and among the bottom 25 percentile in abundance rank differential between the infective L3 stage and the adult stage in <i>N</i>. <i>americanus</i>. A total of 133 KOs lie in this region, and hence are putative parasitism-relevant KOs.</p

Developmental stage based metabolic profiles for <i>Caenorhabditis elegans</i> and <i>Brugia malayi</i>.

<p>The clusters are based on similarity between abundance profiles across developmental stages (<i>see</i><a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003788#pntd.0003788.s012" target="_blank">S12 Fig</a>). The black line (green bounds) represents the mean (standard deviation) of the Z-score of abundances for that developmental stage of all modules in the cluster. The Z-score is a measure of relative over- of under-abundance of the module in that developmental stage compared to its mean over all stages. EE: Early Embryo; LE: Late Embryo; IM: Immature Microfilariae; MM: Mature Microfilariae; YA: Young Adult; AM: Adult Male; AF: Adult Female.</p

Examples of exclusive enzyme usage by parasite and host.

<p>* R01518 is the only reaction that uses mutually exclusive KOs in the 2 animal-parasite pairs studied.</p><p>+ The plants have a lot more such cases and we list only the cases involved in the modules that are complete in all 3 plant parasites and all 3 plants in the dataset. The details of these comparisons can be obtained from <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003788#pntd.0003788.s018" target="_blank">S4 Table</a>.</p><p>Examples of exclusive enzyme usage by parasite and host.</p

Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine

<p>The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of <i>Ascaris suum</i>, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among 3 contiguous regions of the adult <i>A. suum</i> intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. <i>A. suum</i> intestinal miRNAs were identified that are conserved with intestinal miRNAs from <i>C. elegans</i> (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, <i>Heligmosomoides polygyrus</i> (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.</p

Investigations of Host–Guest Interactions with Shape-Persistent Nonionic Dendritic Micelles

The interaction of self-assembled dendritic amphiphiles with drugs and dyes in aqueous solutions is of great significance for designing and optimizing shape-persistent delivery systems. Here we present deeper insight for two examples of low molecular weight (LMW) nonionic dendritic amphiphiles as host molecules and a series of selected aromatic guest model molecules (benzene, naphthalene, biphenyl, terphenyl, anthracene, and pyrene). Aromatic guest molecules were incorporated into the self-assemblies of dendritic nanocarriers, and the resultant complexes were studied by a combination of UV, NMR, computational simulation, and small-angle X-ray-scattering (SAXS) techniques in order to determine the loading capacity, localization, and specific interactions in dendritic amphiphiles with guest molecules. Our findings revealed that the localization of guest molecules in the hydrophobic region and the loading capacity of guest molecules are dependent on their size and the arrangement of aromatic rings instead of the loading amount. Furthermore, the shape of self-assembled host molecules was found to be ellipsoidal and highly persistent even after loading the guest molecules. To the best of our knowledge, this is the first systematic host–guest study, particularly with low molecular weight nonionic dendritic amphiphilies and aromatic guest molecules. Thus, this study opens new possibilities and ways to explore the transport behavior of aromatic drugs with such nanocarriers

Additional file 1: Figure S1. of Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini

Quality metrics for RNA samples used in the RNA-Seq experiment. Electrophoresis results and RIN graphs are included for (A) P. westermani and (B) P. skrjabini. (TIF 372 kb

Additional file 4: Table S3. of Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini

KEGG module representation and completeness for P. westermani and P. skrjabini. (XLSX 49 kb