Sensitivity of the phylogenetic analysis to rate heterogeneity and compositional heterogeneity among lineages.

<p>Bootstrap support values for the monophyly of Cnidaria inclusive Myxozoa (upper values) and of Myxozoa+Medusozoa (lower values in italic).</p

Results of the approximately unbiased test.

a<p>Δ Likelihood: differences between the likelihood of a constrained tree and the maximum likelihood tree.</p>b<p>AU: approximately unbiased test (<i>p</i>-values). Values for topologies significantly rejected at the 0.05 level are indicated by an asterisk.</p

Agent of Whirling Disease Meets Orphan Worm: Phylogenomic Analyses Firmly Place Myxozoa in Cnidaria

<div><p>Myxozoa are microscopic obligate endoparasites with complex live cycles. Representatives are <em>Myxobolus cerebralis</em>, the causative agent of whirling disease in salmonids, and the enigmatic “orphan worm” <em>Buddenbrockia plumatellae</em> parasitizing in Bryozoa. Originally, Myxozoa were classified as protists, but later several metazoan characteristics were reported. However, their phylogenetic relationships remained doubtful. Some molecular phylogenetic analyses placed them as sister group to or even within Bilateria, whereas the possession of polar capsules that are similar to nematocysts of Cnidaria and of minicollagen genes suggest a close relationship between Myxozoa and Cnidaria. EST data of <em>Buddenbrockia</em> also indicated a cnidarian origin of Myxozoa, but were not sufficient to reject a closer relationship to bilaterians. Phylogenomic analyses of new genomic sequences of <em>Myxobolus cerebralis</em> firmly place Myxozoa as sister group to Medusozoa within Cnidaria. Based on the new dataset, the alternative hypothesis that Myxozoa form a clade with Bilateria can be rejected using topology tests. Sensitivity analyses indicate that this result is not affected by long branch attraction artifacts or compositional bias.</p> </div

Maximum likelihood tree calculated with the LG+G+F model based on 32,933 amino acid positions derived from 128 proteins of 57 taxa.

<p>Bootstrap values larger than 50% are shown to the right of the nodes; 100% bootstrap values are indicated by black circles.</p

Additional file 1: Figure S1. of A comparative study of the localization and membrane topology of members of the RIFIN, STEVOR and PfMC-2TM protein families in Plasmodium falciparum-infected erythrocytes

Characterization of α-VSA sera. In order to specify the exact target sequence of the polyclonal antisera, the semi-conserved and the variable domain of the RIFIN variants RIF40 and RIF50 and of the STEVOR proteins PFL2610w and MAL13P1.7 were separately expressed as recombinant proteins. The RIFIN antisera α-RIF40.2, α-RIF44 and α-RIF50 (A) as well as the STEVOR α-PFL2610w, α-MAL13P1.7, α-PFC0025c and α-PFA0750w (B), which were generated by immunization with a protein spanning the semi-conserved and the variable domain, were subsequently used for Western blot analysis. Furthermore, the α-PfMC-2TM-SC serum generated solely against the semi-conserved region of PFF1525c was included in the analysis to check the specificity for its protein family (C). Approximately 20 ng of each recombinant protein or lysate from 1x107 cell membranes were loaded in each lane as indicated. All four antisera, α-RIF40.2, α-RIF50, α-PFL2610w and α-MAL13P1.7, are specific to the semi-conserved region of their own antigen. Furthermore, all antisera used in this study were shown to recognize the semi-conserved region of their own protein family, but are not cross-reactive with other VSA families. Unspecific cross-reactions of the small VSA antisera with the His-tag were excluded using an unrelated Entamoeba histolytica His-tagged protein recombinantly expressed under the same conditions (His-tag control) and lysate from uninfected red blood cells (RBC lysate). The recombinant proteins of all three small VSA families tend to form multimer complexes; accordingly bands corresponding in size to monomers are labelled with a single *, dimers with ** and trimers with *** as calculated by the size of the recombinant His-tagged protein

Expression of peptidase genes of the isolate HM-1:IMSS as determined by microarrays

<p><b>Copyright information:</b></p><p>Taken from "The genome: primary structure and expression of proteolytic enzymes"</p><p>http://www.biomedcentral.com/1471-2164/8/170</p><p>BMC Genomics 2007;8():170-170.</p><p>Published online 14 Jun 2007</p><p>PMCID:PMC1913524.</p><p></p> Error bars represent the standard error of the mean of nine hybridizations (biological replicates)

Additional file 1: Figure S1. of A comparative study of the localization and membrane topology of members of the RIFIN, STEVOR and PfMC-2TM protein families in Plasmodium falciparum-infected erythrocytes

Characterization of α-VSA sera. In order to specify the exact target sequence of the polyclonal antisera, the semi-conserved and the variable domain of the RIFIN variants RIF40 and RIF50 and of the STEVOR proteins PFL2610w and MAL13P1.7 were separately expressed as recombinant proteins. The RIFIN antisera α-RIF40.2, α-RIF44 and α-RIF50 (A) as well as the STEVOR α-PFL2610w, α-MAL13P1.7, α-PFC0025c and α-PFA0750w (B), which were generated by immunization with a protein spanning the semi-conserved and the variable domain, were subsequently used for Western blot analysis. Furthermore, the α-PfMC-2TM-SC serum generated solely against the semi-conserved region of PFF1525c was included in the analysis to check the specificity for its protein family (C). Approximately 20 ng of each recombinant protein or lysate from 1x107 cell membranes were loaded in each lane as indicated. All four antisera, α-RIF40.2, α-RIF50, α-PFL2610w and α-MAL13P1.7, are specific to the semi-conserved region of their own antigen. Furthermore, all antisera used in this study were shown to recognize the semi-conserved region of their own protein family, but are not cross-reactive with other VSA families. Unspecific cross-reactions of the small VSA antisera with the His-tag were excluded using an unrelated Entamoeba histolytica His-tagged protein recombinantly expressed under the same conditions (His-tag control) and lysate from uninfected red blood cells (RBC lysate). The recombinant proteins of all three small VSA families tend to form multimer complexes; accordingly bands corresponding in size to monomers are labelled with a single *, dimers with ** and trimers with *** as calculated by the size of the recombinant His-tagged protein

Transcriptional Regionalization of the Fruit Fly’s Airway Epithelium

<div><p>Although airway epithelia are primarily devoted to gas exchange, they have to fulfil a number of different tasks including organ maintenance and the epithelial immune response to fight airborne pathogens. These different tasks are at least partially accomplished by specialized cell types in the epithelium. In addition, a proximal to distal gradient mirroring the transition from airflow conduction to real gas exchange, is also operative. We analysed the airway system of larval <i>Drosophila melanogaster</i> with respect to region-specific expression in the proximal to distal axis. The larval airway system is made of epithelial cells only. We found differential expression between major trunks of the airways and more distal ones comprising primary, secondary and terminal ones. A more detailed analysis was performed using DNA-microarray analysis to identify cohorts of genes that are either predominantly expressed in the dorsal trunks or in the primary/secondary/terminal branches of the airways. Among these differentially expressed genes are especially those involved in signal transduction. <i>Wnt</i>-signalling associated genes for example are predominantly found in secondary/terminal airways. In addition, some G-protein coupled receptors are differentially expressed between both regions of the airways, exemplified by those activated by octopamine or tyramine, the invertebrate counterparts of epinephrine and norepinephrine. Whereas the OAMB is predominantly found in terminal airway regions, the oct3βR has higher expression levels in dorsal trunks. In addition, we observed a significant association of both, genes predominantly expressed in dorsal trunks or in primary to terminal branches branches with those regulated by hypoxia. Taken together, this observed differential expression is indicative for a proximal to distal transcriptional regionalization presumably reflecting functional differences in these parts of the fly’s airway system.</p></div

Expression pattern of selected G-protein coupled receptors in the airway system of <i>Drosophila</i> larvae.

<p>Promotor-Gal4 lines of different G-protein coupled receptors were used to study their expression pattern in the airway system. The promoter of the OAMB receptor drives expression to terminal branches or cells (A overview, B intestine with terminal cell). The <i>TyrR</i> show higher expression in primary branches (C), the <i>frizzled</i> receptor is also predominantly found in these structures (D) octopamine/tyramine receptors drive expression in different parts of the airway system. The Oct2βR-Gal4 is primarily present in the dorsal trunks (A). The OAMB receptor can be observed in the primary airways (B). Especially the terminal cells located directly adjacent to different organ systems show a strong expression of this receptor (C). The OA2 receptor is also found predominantly in the primary airways (D). In contrast, the TyrRII (E), the DopR2 (F) and the OAR2 (G) show a broader expression pattern. Scale bars in A, C, D, E is 50 µm, in B, F 20 µm and in G 10 µm.</p

Proportion of infected erythrocytes with VSAs exported to host cell compartments in clinical isolates and 3D7 at different developmental stages.

1<p>Time point not determined for isolate #1.</p>2<p>Time point of 44 h for isolate #4.</p><p>hpi, hours post-infection.</p