Synthesis and conformational characterization of the epidermal growth factor-like domain of blood coagulation factor IX carrying xylosyl-glucose

Solid-phase synthesis of glycopeptide generally requires the protection of both peptide side chains and hydroxyl groups of the carbohydrate portion. However, if the mild coupling conditions are used, the protection of the carbohydrate portion can be omitted. In this paper, we demonstrated it by the synthesis of Fmoc-serine carrying unmasked xylosyl glucose followed by the solid-phase synthesis of epidermal growth factor (EGF)-like domain of factor IX (45-87) using the unit. The product was well characterized by enzymatic digestion, amino acid analysis and mass spectrometry. The secondary structure of the product as well as glucosylated and non-glycosylated EGF-like domain was characterized by circular dichroism (CD) spectroscopy.     

Pleiotropic effects on mandibular morphology II: differential epistasis and genetic variation in morphological integration

The evolution of morphological modularity through the sequestration of pleiotropy to sets of functionally and developmentally related traits requires genetic variation in the relationships between traits. Genetic variation in relationships between traits can result from differential epistasis, where epistatic relationships for pairs of loci are different for different traits. This study maps relationship quantitative trait loci (QTLs), specifically QTLs that affect the relationship between individual mandibular traits and mandible length, across the genome in an F2 intercross of the LG/J and SM/J inbred mouse strains (N = 1045). We discovered 23 relationship QTLs scattered throughout the genome. All mandibular traits were involved in one or more relationship QTL. When multiple traits were affected at a relationship QTL, the traits tended to come from a developmentally restricted region of the mandible, either the muscular processes or the alveolus. About one-third of the relationship QTLs correspond to previously located trait QTLs affecting the same traits. These results comprise examples of genetic variation necessary for an evolutionary response to selection on the range of pleiotropic effects.     

Free oxygen radicals are generated at the time of aspiration of oocytes from ovaries that have been stored for a long time

In ischaemic tissues, reperfusion induces acute injury and functional changes. In this work, ovaries were stored for various times, and superoxide dismutase (SOD) and dimethylthiourea (DTMU) were used at the time of oocyte aspiration. We then attempted to determine whether free oxygen radicals are generated at oocyte aspiration and whether they impair the developmental competence of oocytes. Over 2 mM of DMTU and 1000 U/ml of SOD significantly improved the rate of blastulation 8 days after insemination. For ovaries that were preserved for 3 and 7 h, using antioxidants also significantly improved the rate of blastulation 8 days after insemination. However, no effect was observed on oocytes from ovaries preserved for 1 h. We examined how the antioxidants affected the presence of germinal vesicles, chromatin configuration, and polar body extrusion 6 or 21 h after culture. Chromatin configuration was classified into three groups according to the amount of chromatin condensation (group 1, strong condensation; group 2, moderate; group 3, slight). Storing ovaries for a long time decreased the frequency of occurrence of group 2, but increased groups 1 and 3. However, using antioxidants at oocyte aspiration decreased the frequency of group 3 and increased group 1. Moreover, there was no difference in the rate of germinal vesicle breakdown and polar body extrusion. Our results show that preserving ovaries for a long time induces the generation of free oxygen radicals and that these chemicals impair oocyte viability. Using antioxidants at oocyte aspiration was beneficial for embryo production.     

MotX and MotY,specific components of the sodium-driven flagellar motor,colocalize to the outer membrane in Vibrio alginolyticus

Rotation of the sodium-driven polar flagella of Vibrio alginolyticus requires four motor proteins: PomA, PomB, MotX and MotY. MotX and MotY, which are unique components of the sodium-driven motor of Vibrio, have been believed to be localized in the inner (cytoplasmic) membrane via their N-terminal hydrophobic segments. Here we show that MotX and MotY colocalize to the outer membrane. Both proteins, when expressed together, were detected in the outer membrane fraction separated by sucrose density gradient centrifugation. As mature MotX and MotY proteins do not have N-terminal hydrophobic segments, the N-termini of the primary translation products must have signal sequences that are removed upon translocation across the inner membrane. Moreover, MotX and MotY require each other for efficient localization to the outer membrane. Based on these lines of evidence, we propose that MotX and MotY form a complex in the outer membrane. This is the first case that describes motor proteins function in the outer membrane for flagellar rotation.     

Interactions of MotX with MotY and with the PomA/PomB sodium ion channel complex of the Vibrio alginolyticus polar flagellum

Rotation of the sodium ion-driven polar flagellum of Vibrio alginolyticus requires the inner membrane sodium ion channel complex PomA/PomB and the outer membrane components MotX and MotY. None of the detergents used in this study were able to solubilize MotX when it was expressed alone. However, when co-expressed with MotY, MotX was solubilized by some detergents. The change in the solubility of MotX suggests that MotY interacts with MotX. In agreement with this, a pull-down assay showed the association of MotY with MotX. Solubilized MotX and MotY eluted in the void volume from a gel-filtration column, suggesting that MotX and MotY form a large oligomeric structure(s). In the absence of MotY, MotX affected membrane localization of the PomA/PomB complex and of PomB alone but not of PomA alone, suggesting an interaction between MotX and PomB. We propose that MotX exhibits multiple interactions with the other motor components, first with MotY for its localization to the outer membrane and then with the PomA/PomB complex through PomB for the motor rotation.     

Molecular expression of Ly6k, a putative glycosylphosphatidyl-inositol-anchored membrane protein on the mouse testicular germ cells

Claudin 1 is one of the tight junctional proteins involved in the tight sealing of the cellular sheets and plays a crucial role in the maintenance of cell polarity. Although its structure and physiological function in intercellular adhesion is relatively well understood, we have little information about its possible involvement in early development of vertebrates. We found Xclaudin 1 is expressed maternally in the oocyte of Xenopus laevis and the zygotic expression initiates stage 9 in the animal hemisphere but not in the vegetal hemisphere, limited on the ectoderm and mesoderm until the end of gastrulation. We have investigated a potential role for claudin 1 at gastrulation by gain and loss-of-function studies. Over-expression of Xclaudin 1 resulted in gastrulation defect in a dose-dependent manner. Knockdown of Xclaudin 1 by antisense morpholino oligonucleotides (MOs) blocked convergent extension, whereas ectopic expression of Xclaudin 1-myc mRNA rescued these defects. However, altered expression of Xclaudin 1 did not inhibit mesodermal gene expression. Taken together, our results suggest that Xclaudin 1 is required for proper convergent extension movement during Xenopus gastrulation.     

The Effect of Ostracism and Optional Participation on the Evolution of Cooperation in the Voluntary Public Goods Game

Not only animals, plants and microbes but also humans cooperate in groups. The evolution of cooperation in a group is an evolutionary puzzle, because defectors always obtain a higher benefit than cooperators. When people participate in a group, they evaluate group member’s reputations and then decide whether to participate in it. In some groups, membership is open to all who are willing to participate in the group. In other groups, a candidate is excluded from membership if group members regard the candidate’s reputation as bad. We developed an evolutionary game model and investigated how participation in groups and ostracism influence the evolution of cooperation in groups when group members play the voluntary public goods game, by means of computer simulation. When group membership is open to all candidates and those candidates can decide whether to participate in a group, cooperation cannot be sustainable. However, cooperation is sustainable when a candidate cannot be a member unless all group members admit them to membership. Therefore, it is not participation in a group but rather ostracism, which functions as costless punishment on defectors, that is essential to sustain cooperation in the voluntary public goods game.     

Isolation of mitochondrial and plastid ftsZ genes and analysis of the organelle targeting sequence in the diatom Chaetoceros neogracile (Diatoms,Bacillariophyceae)

Mitochondria and plastids multiply by division in eukaryotic cells. Recently, the eukaryotic homolog of the bacterial cell division protein FtsZ was identified and shown to play an important role in the organelle division process inside the inner membrane. To explore the evolution of FtsZ proteins, and to accumulate data on the protein import system in mitochondria and plastids of the red algal lineage, one mitochondrial and three plastid ftsZ genes were isolated from the diatom Chaetoceros neogracile, whose plastids were acquired by secondary endosymbiotic uptake of a red alga. Protein import into organelles depends on the N‐terminal organelle targeting sequences. N‐terminal bipartite presequences consisting of an endoplasmic reticulum signal peptide and a plastid transit peptide are required for protein import into diatom plastids. To characterize the organelle targeting peptides of C. neogracile, we observed the localization of each green fluorescent protein‐tagged predicted organelle targeting peptide in cultured tobacco cells and diatom cells. Our data suggested that each targeting sequences functioned both in tobacco cultured cells and diatom cells.     

No chromosomal clustering of housekeeping genes in the marine chordate Ciona intestinalis

Housekeeping genes, widely expressed genes that are required for the basal function of most cell types, are clustered in the human and worm genomes. This arrangement suggests coordinate control of housekeeping gene expression at the chromosomal level. Here we examined whether this notion is applicable to a marine chordate, Ciona intestinalis. Using microarrays, we analyzed genes that were expressed in 11 organs of the adult, including the neural complex, branchial sac, esophagus, stomach, endostyle, intestine, body-wall muscle, heart, blood cells, ovary and testis. This analysis identified 158 genes that are expressed ubiquitously in these organs. These housekeeping genes could be classified into a range of Gene Ontology categories, in particular, ribosomal protein components. Of these 158 genes, we were able to map 141 genes onto the 14 pairs of the C. intestinalis chromosomes. They were distributed rather evenly over all the chromosomes, except for small clusters containing two or three genes. Therefore, the notion of chromosomal clustering of housekeeping genes is not applicable in this chordate.     

Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues

In CAPRI Rounds 1 and 2, we assumed that because there are many ionic charges that weaken electrostatic interaction forces in living cells, the hydrophobic interaction force might be important entropically. As a result of Rounds 1 and 2, the predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor, because only the largest benzene cluster was used for generating the initial docking structures. These were generated by fitting of benzene clusters formed on the surface of receptor and ligand. In CAPRI Rounds 3-5, the grid-scoring sum on the protein-protein interaction surface and the pairwise potential of the amino acid residues, which were indicated as coming easily into the protein-protein interaction regions, were used as the calculation methods, along with the smaller benzene clusters that participated in benzene cluster fitting. Good predicted models were obtained for Targets 11 and 12. When the modeled receptor proteins were superimposed on the experimental structures, the smallest ligand root-mean-square deviation (RMSD) values corresponding to the RMSD between the model and experimental structures were 6.2 A and 7.3 A, respectively.