Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region

Background

In the Calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (FBP) and sedoheptulose-1, 7-bisphosphate (SBP) are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphosphatase/sedoheptulose-1, 7-bisphosphatase (F/SBPase), while in that of eukaryotic chloroplasts by two distinct enzymes: chloroplastic fructose-1, 6-bisphosphatase (FBPase) and sedoheptulose-1, 7-bisphosphatase (SBPase), respectively. It was proposed that these two eukaryotic enzymes arose from the divergence of a common ancestral eubacterial bifunctional F/SBPase of mitochondrial origin. However, no specific affinity between SBPase and eubacterial FBPase or F/SBPase can be observed in the previous phylogenetic analyses, and it is hard to explain why SBPase and/or F/SBPase are/is absent from most extant nonphotosynthetic eukaryotes according to this scenario.

Results

Domain analysis indicated that eubacterial F/SBPase of two different resources contain distinct domains: proteobacterial F/SBPases contain typical FBPase domain, while cyanobacterial F/SBPases possess FBPase_glpX domain. Therefore, like prokaryotic FBPase, eubacterial F/SBPase can also be divided into two evolutionarily distant classes (Class I and II). Phylogenetic analysis based on a much larger taxonomic sampling than previous work revealed that all eukaryotic SBPase cluster together and form a close sister group to the clade of epsilon-proteobacterial Class I FBPase which are gluconeogenesis-specific enzymes, while all eukaryotic chloroplast FBPase group together with eukaryotic cytosolic FBPase and form another distinct clade which then groups with the Class I FBPase of diverse eubacteria. Motif analysis of these enzymes also supports these phylogenetic correlations.

Conclusions

There are two evolutionarily distant classes of eubacterial bifunctional F/SBPase. Eukaryotic FBPase and SBPase do not diverge from either of them but have two independent origins: SBPase share a common ancestor with the gluconeogenesis-specific Class I FBPase of epsilon-proteobacteria (or probably originated from that of the ancestor of epsilon-proteobacteria), while FBPase arise from Class I FBPase of an unknown kind of eubacteria. During the evolution of SBPase from eubacterial Class I FBPase, the SBP-dephosphorylation activity was acquired through the transition ??from specialist to generalist??. The evolutionary substitution of the endosymbiotic-origin cyanobacterial bifunctional F/SBPase by the two light-regulated substrate-specific enzymes made the regulation of the Calvin cycle more delicate, which contributed to the evolution of eukaryotic photosynthesis and even the entire photosynthetic eukaryotes.     

Heparan Sulfate Phage Display Antibodies Identify Distinct Epitopes with Complex Binding Characteristics: INSIGHTS INTO PROTEIN BINDING SPECIFICITIES*

Heparan sulfate (HS) binds and modulates the transport and activity of a large repertoire of regulatory proteins. The HS phage display antibodies are powerful tools for the analysis of native HS structure in situ; however, their epitopes are not well defined. Analysis of the binding specificities of a set of HS antibodies by competitive binding assays with well defined chemically modified heparins demonstrates that O-sulfates are essential for binding; however, increasing sulfation does not necessarily correlate with increased antibody reactivity. IC₅₀ values for competition with double modified heparins were not predictable from IC₅₀ values with corresponding singly modified heparins. Binding assays and immunohistochemistry revealed that individual antibodies recognize distinct epitopes and that these are not single linear sequences but families of structurally similar motifs in which subtle variations in sulfation and conformation modify the affinity of interaction. Modeling of the antibodies demonstrates that they possess highly basic CDR3 and surrounding surfaces, presenting a number of possible orientations for HS binding. Unexpectedly, there are significant differences between the existence of epitopes in tissue sections and observed in vitro in dot blotted tissue extracts, demonstrating that in vitro specificity does not necessarily correlate with specificity in situ/vivo. The epitopes are therefore more complex than previously considered. Overall, these data have significance for structure-activity relationships of HS, because the model of one antibody recognizing multiple HS structures and the influence of other in situ HS-binding proteins on epitope availability are likely to reflect the selectivity of many HS-protein interactions in vivo.     

Antigen sharing of Salmonella typhi non-flagellar proteins with other salmonellae and some shigellae and Escherichia coli

Cathodal moving protein components were identified in agarose gel electrophoresis of the Veronal buffer extract of a non-motile strain of S. typhi (8393, Colindale). Rabbit antiserum was raised against these cationic proteins; it had both agglutinating and precipitating activity. A total of 80 salmonella strains belonging to serogroups A, B, C1, C2, D, E1 and E2 including 26 S. typhi and 10 S. paratyphi A were tested against this antiserum in a slide agglutination test; all strains were agglutinated. Among 94 other bacterial strains tested, the antiserum agglutinated all 16 strains of Shigella flexneri, 2 of 5 Shigella sonnei, 5 of 34 E. coli and 1 of 8 Citrobacter species. These results show that there is antigenic sharing of the non-flagellar proteins of S. typhi with many other salmonellae as well as with some shigellae and E. coli.     

Juvenile hormone metabolism in the plasma,integument, midgut,fat body,and brain during the last instar of the tobacco hornworm,Manduca sexta (L.)

Juvenile hormone (JH) III esterase and JH III epoxide hydrolase activity was found in the integument, midgut, fat body, and brain during last instar development of the tobacco hornworm, Manduca sexta. JH esterase activity was primarily located in the cytosol in these tissues while the majority of the JH epoxide hydrolase activity was found in the microsomes. A prewandering (on day 3) and postwandering (on day 8) peak in plasma JH III esterase activity occurs in the last instar of gate I M. sexta. The JH esterase activity profile in integument, midgut, fat body, and brain followed a similar pattern to that of the plasma. The only exception to this was the absence of the postwandering, prepupal (on day 8) JH esterase peak in the fat body. The topical application of the juvenoid, (RS)-methoprene, failed to induce fat body JH esterase activity but increased activity in the plasma, integument, midgut, and brain in M. sexta prepupae. These results indicate that the source of plasma JH esterase activity is not always the fat body as previously hypothesized. The developmental profile of tissue JH epoxide hydrolase activity was also similar to that of JH esterase suggesting that both enzymes may be regulated partly by the same factors and that JH epoxide hydrolase may also have an important, previously unrecognized functional role in JH regulation and insect metamorphosis. Multiple isoelectric forms of tissue-specific JH esterases and JH epoxide hydrolases were found in integument, midgut, fat body, and brain. The JH esterases in these tissues had isoelectric points more acidic than that for plasma. Tissue α-naphthyl acetate esterase, developmental profiles, and inhibitor sensitivity to 3-(octylthio)-1,1,1-trifluoropropan-2-one differed significantly from that for JH esterase, suggesting that they represent different enzymes. ©1992 Wiley-Liss, Inc.     

Incorporation of microbiologically treated spent brewery grains into broiler rations

The cellulolytic fungus Trichoderma reesei QM9414 was cultivated on spent brewery grains to partially hydrolyse the grains into soluble sugars and to alter the amino acid profile of the substrate. Aflatoxins were not detected in either the treated or the untreated spent grains. Amino acid profiles indicated that both the untreated and partially hydrolysed spent grains possess the entire range of essential amino acids required by poultry. Treated grains contained higher levels of lysine, histidine, glycine, methionine, phenylalanine, proline and alanine compared to those in untreated grains. The incorporation of treated grains at 8% and 12% into starter rations for broiler chickens in the first 4 weeks resulted in significant improvement in their growth and feed conversion ratio. There was no significant difference in feed conversion after 6 and 8 weeks of growth.     

Anticipating endoplasmic reticulum stress. A novel early response before pathogenesis-related gene induction

When it is attacked by a pathogen, a plant produces a range of defense-related proteins. Many of these are synthesized by the rough endoplasmic reticulum (RER) to be secreted from the cell or deposited in vacuoles. Genes encoding endoplasmic reticulum (ER)-resident chaperones, such as the lumenal binding protein (BiP), are also induced under these conditions. Here, we show that BiP induction occurs systemically throughout the plant. Furthermore, this induction occurs rapidly and precedes expression of genes encoding pathogenesis-related (PR) proteins. The underlying signal transduction pathway was shown to be independent of the signaling molecule salicylic acid and the unfolded protein response pathway. In addition, BiP induction was independent of PR gene induction. Overproduction of BiP alone was not sufficient to cause induction of PR gene expression; however, limiting the amount of BiP in the ER lumen via superimposed ER stress inhibited the induction of PR gene expression. We propose that the induction of BiP expression during plant-pathogen interactions is required as an early response to support PR protein synthesis on the RER and that a novel signal transduction pathway exists to trigger this rapid response.     

Cloud computing and validation of expandable in silico livers

Background  

In Silico Livers (ISLs) are works in progress. They are used to challenge multilevel, multi-attribute, mechanistic hypotheses about the hepatic disposition of xenobiotics coupled with hepatic responses. To enhance ISL-to-liver mappings, we added discrete time metabolism, biliary elimination, and bolus dosing features to a previously validated ISL and initiated re-validated experiments that required scaling experiments to use more simulated lobules than previously, more than could be achieved using the local cluster technology. Rather than dramatically increasing the size of our local cluster we undertook the re-validation experiments using the Amazon EC2 cloud platform. So doing required demonstrating the efficacy of scaling a simulation to use more cluster nodes and assessing the scientific equivalence of local cluster validation experiments with those executed using the cloud platform.