Molecular evolution of rickettsia surface antigens: evidence of positive selection

The Rickettsia genus is a group of obligate intracellular parasitic alpha-proteobacteria that includes human pathogens responsible for the typhus disease and various types of spotted fevers. rOmpA and rOmpB are two members of the "surface cell antigen" (Sca) autotransporter (AT) protein family that may play key roles in the adhesion of the Rickettsia cells to the host tissue. These molecules are likely determinants for the pathogenicity of the Rickettsia and represent good candidates for vaccine development. We identified the 17 members of this family of outer-membrane proteins in nine fully sequenced Rickettsia genomes. The typical architecture of the Sca proteins is composed of an N-terminal signal peptide and a C-terminal AT domain that promote the export of the central passenger domain to the outside of the bacteria. A characteristic of this family is the frequent degradation of the genes, which results in different subsets of the sca genes being expressed among Rickettsia species. Here, we present a detailed analysis of their phylogenetic relationships and evolution. We provide strong evidence that rOmpA and rOmpB as well as three other members of the Sca protein family--Sca1, Sca2, and Sca4--have evolved under positive selection. The exclusive distribution of the predicted positively selected sites within the passenger domains of these proteins argues that these regions are involved in the interaction with the host and may be locked in "arms race" coevolutionary conflicts.     

Techniques of SNP genotyping and remote sensing applied for elucidation of the contribution of polygene and environmental factors to inter-individual variation in skin pigmentation phenotype

We present a conceptual framework for applying techniques of SNP genotyping as a molecular biological approach and remote sensing as an ecological approach to elucidation of the contribution of polygene and environmental factors to inter-individual variation in skin pigmentation phenotype. Additionally, we discuss the obstacles that frustrate our efforts to identify how the human genome encodes the complex phenotype and suggest the use of computational methods designed for knowledge discovery within hereditary database.     

New anatomical method of grain angles measurement using confocal microscopy and image cross-correlation

Some tropical trees with indistinct growth rings have a distinct interlocked grain that reveals their internal growth rhythm. To determine their growth rhythm, it is necessary to accurately measure the wood grain angle. The usual methods for grain angle measurement are radial splitting using wood disks, which occasionally provides inaccurate data, and serial tangential sectioning, which requires preparation and analysis of many sections. The present report proposes an easier but accurate method to measure grain angle using a single xylem transverse section. A confocal microscope was used to obtain two optical sections of different depths from a transverse section of a 7-year-old Hopea odorata Roxb. The tangential lag between the optical images was then calculated using image cross-correlation and transformed into grain angle. Radially consecutive sampling revealed distinct radial fluctuations in the grain angle. The fluctuation data were compared to data obtained by radial splitting and serial tangential sectioning. There was a strong correlation between grain angle using the three methods. In the region close to the cambium, however, the present method revealed an abrupt change in the grain angle, although radial splitting showed a smooth undulation throughout the radius. Using the present method, the analysis of a radial range of 5 cm required a single transverse section compared to 1,000 tangential sections 50-m thick. In conclusion, the present method using a single transverse section, confocal microscopy, and image cross-correlation analysis provides more accurate data than radial splitting, and is less time-consuming than serial tangential sectioning.     

Phylogenetic footprinting and genome scanning identify vertebrate BMP response elements and new target genes

The complex gene regulatory networks governed by growth factor signaling are still poorly understood. In order to accelerate the rate of progress in uncovering these networks, we explored the usefulness of interspecies sequence comparison (phylogenetic footprinting) to identify conserved growth factor response elements. The promoter regions of two direct target genes of Bone Morphogenetic Protein (BMP) signaling in Xenopus, Xvent2 and XId3, were compared with the corresponding human and/or mouse counterparts to identify conserved sequences. A comparison between the Xenopus and human Vent2 promoter sequences revealed a highly conserved 21 bp sequence that overlaps the previously reported Xvent2 BMP response element (BRE). Reporter gene assays using Xenopus animal pole ectodermal explants (animal caps) revealed that this conserved 21 bp BRE is both necessary and sufficient for BMP responsiveness. We combine the same phylogenetic footprinting approach with luciferase assays to identify a highly conserved 49 bp BMP responsive region in the Xenopus Id3 promoter. GFP reporters containing multimers of either the Xvent2 or XId3 BREs appear to recapitulate endogenous BMP signaling activity in transgenic Xenopus embryos. Comparison of the Xvent2 and the XId3 BRE revealed core sequence features that are both necessary and sufficient for BMP responsiveness: a Smad binding element (SBE) and a GC-rich element resembling an OAZ binding site. Based on these findings, we have implemented genome scanning to identify over 100 additional putative target genes containing 2 or more BRE-like sequences which are conserved between human and mouse. RT-PCR and in situ analyses revealed that this in silico approach can effectively be used to identify potential BMP target genes.     

Functional insights from the structure of the multifunctional C345C domain of C5 of complement

The complement protein C5 initiates assembly of the membrane attack complex. This remarkable process results in lysis of target cells and is fundamental to mammalian defense against infection. The 150-amino acid residue domain at the C terminus of C5 (C5-C345C) is pivotal to C5 function. It interacts with enzymes that convert C5 to C5b, the first step in the assembly of the membrane attack complex; it also binds to the membrane attack complex components C6 and C7 with high affinity. Here a recombinant version of this C5-C345C domain is shown to adopt the oligosaccharide/oligonucleotide binding fold, with two helices packed against a five-stranded beta-barrel. The structure is compared with those from the netrin-like module family that have a similar fold. Residues critical to the interaction with C5-convertase cluster on a mobile, hydrophobic inter-strand loop that protrudes from the open face of the beta-barrel. The opposite, helix-dominated face of C5-C345C carries a pair of exposed hydrophobic side chains adjacent to a striking negatively charged patch, consistent with affinity for positively charged factor I modules in C6 and C7. Modeling of homologous domains from complement proteins C3 and C4, which do not participate in membrane attack complex assembly, suggests that this provisionally identified C6/C7-interacting face is indeed specific to C5.     

Synthesis and some reactivity of amidinato(pyridine) complexes of molybdenum and tungsten formulated as [M(η-allyl)(amidinato)(CO)2(NC5H5)]

Bis(pyridine) complexes of molybdenum and tungsten, [M(η³-allyl)Cl(CO)₂(NC₅H₅)₂] (M=Mo; 3-Mo, M=W; 3-W), reacted with an equimolar amount of lithiated amidinate, Li[(PhN)₂CR] (R=H; 4a-Li, R = CH₃; 4b-Li), to yield corresponding amidinato(pyridine) complexes, [M(η³-allyl){(PhN)₂CR}(CO)₂(NC₅H₅)] (M=Mo, R=H; 5a-Mo, M=Mo, R=CH₃; 5b-Mo, M=W, R=H; 5a-W), as a yellow solid. The dissociation of pyridine ligand from the central metal in complexes 5a was observed in a polar solvent such as acetonitrile. In these cases, although the formation of amidinato(acetonitrile) complexes, [M(η³-allyl){(PhN)₂CH}(CO)₂(NCMe)] (M=Mo; 6a-Mo, M=W; 6a-W), was suggested spectroscopically, isolation of complexes 6a was not successful but the re-formation of pyridine complexes 5a was observed. In the reactions of complexes 5a with PEt₃ and with P(OMe)₃, the substitution reactions easily took place to give [M(η³-allyl){(PhN)₂CH}(CO)₂(PEt₃)] (M=Mo; 7a-Mo, M=W; 7a-W) and [M(η³-allyl){(PhN)₂CH}(CO)₂{P(OMe)₃}] (M=Mo; 8a-Mo, M=W; 8a-W), respectively. These complexes were characterized spectroscopically as well as, in some cases, by X-ray analyses.     

Complement components C5 and C7: recombinant factor I modules of C7 bind to the C345C domain of C5

Studies reported over 30 years ago revealed that latent, nonactivated C5 binds specifically and reversibly to C6 and C7. These reversible reactions are distinct from the essentially nonreversible associations with activated C5b that occur during assembly of the membrane attack complex, but they likely involve some, perhaps many, of the same molecular contacts. We recently reported that these reversible reactions are mediated by the C345C (NTR) domain at the C terminus of the C5 alpha-chain. Earlier work by others localized the complementary binding sites to a tryptic fragment of C6 composed entirely of two adjacent factor I modules (FIMs), and to a larger fragment of C7 composed of its homologous FIMs as well as two adjoining short consensus repeat modules. In this work, we expressed the tandem FIMs from C7 in bacteria. The mobility on SDS-polyacrylamide gels, lack of free sulfhydryl groups, and atypical circular dichroism spectrum of the recombinant product rC7-FIMs were all consistent with a native structure. Using surface plasmon resonance, we found that rC7-FIMs binds specifically to both C5 and the rC5-C345C domain with K(D) approximately 50 nM, and competes with C7 for binding to C5, as expected for an active domain. These results indicate that, like C6, the FIMs alone in C7 mediate reversible binding to C5. Based on available evidence, we suggest a model for an irreversible membrane attack complex assembly in which the C7 FIMs, but not those in C6, are bound to the C345C domain of C5 within the fully assembled complex.     

Survey on cellular phone usage on students in Thailand

The number of cellular phone subscribers is increasing every year and there have been reports of health disorders related to the high-frequency radio waves. This paper considers the dependence of Thai university and high school students on cellular phones. A survey form (cellular phone dependence questionnaire: CPDQ) was distributed to 181 female and 177 male Thai university students and to 240 female and 140 male Thai high school students. The surveys were collected, Cronbach alpha coefficient was calculated, and a factor analysis was performed using the principal factor method and varimax rotation. The total scores were 16.54 to 20.04 and the Cronbach's alpha coefficients were 0.808 to 0.930. According to a factor analysis of 20 scored items, 4 factors were extracted for both male and female high school students, and the cumulative correlation coefficients of the male and female groups were 64.85% and 62.70%, respectively. Five factors were extracted for male university students and 6 factors were extracted for female university students, and the cumulative correlation coefficients were 58.08% and 57.91%, respectively. The W value results of the Shapiro-Wilk W-test for male university students, female university students, male high school students and female high school students were 0.969, 0.984, 0.964, and 0.913 respectively, thus verifying the normality of the score distributions.The total scores for the Thai university students were higher than the scores for the Thai high school students. The factor analysis of female high school students confirmed a large difference compared to male university students, male high school students, and Japanese female university students. (The Japanese students were surveyed in an earlier study by Toda et al.). Also, the CPDQ total score was high, which indicated a strong tendency toward dependence.