Systematic cross-validation of 454 sequencing and pyrosequencing for the exact quantification of DNA methylation patterns with single CpG resolution

Background  

New high-throughput sequencing technologies promise a very sensitive and high-resolution analysis of DNA methylation patterns in quantitative terms. However, a detailed and comprehensive comparison with existing validated DNA methylation analysis methods is not yet available. Therefore, a systematic cross-validation of 454 sequencing and conventional pyrosequencing, both of which offer exact quantification of methylation levels with a single CpG dinucleotide resolution, was performed.     

Oxidation of HRas cysteine thiols by metabolic stress prevents palmitoylation in vivo and contributes to endothelial cell apoptosis

Here we demonstrate a new paradigm in redox signaling, whereby oxidants resulting from metabolic stress directly alter protein palmitoylation by oxidizing reactive cysteine thiolates. In mice fed a high-fat, high-sucrose diet and in cultured endothelial cells (ECs) treated with high palmitate and high glucose (HPHG), there was decreased HRas palmitoylation on Cys181/184 (61±24% decrease for cardiac tissue and 38±7.0% in ECs). This was due to oxidation of Cys181/184, detected using matrix-assisted laser desorption/ionization time of flight (MALDI TOF)-TOF. Decrease in HRas palmitoylation affected its compartmentalization and Ras binding domain binding activity, with a shift from plasma membrane tethering to Golgi localization. Loss of plasma membrane-bound HRas decreased growth factor-stimulated ERK phosphorylation (84±8.6% decrease) and increased apoptotic signaling (24±6.5-fold increase) after HPHG treatment that was prevented by overexpressing wild-type but not C181/184S HRas. The essential role of HRas in metabolic stress was made evident by the similar effects of expressing an inactive dominant negative N17-HRas or a MEK inhibitor. Furthermore, the relevance of thiol oxidation was demonstrated by overexpressing manganese superoxide dismutase, which improved HRas palmitoylation and ERK phosphorylation, while lessening apoptosis in HPHG treated ECs.     

Random mating with respect to mating status in the simultaneously hermaphroditic land snail Arianta arbustorum

In promiscuous species with sperm storage, males are expected to show a preference for mating with virgin and young females to reduce the risk of sperm competition. In the simultaneous hermaphrodite land snail Arianta arbustorum, sperm production precedes egg production by 2–4 weeks, resulting in a short period of protandric hermaphroditism before shell growth is completed. In natural populations, copulating pairs involving individuals which have not yet completed shell growth (virgins) have been observed. We ran a series of mate-choice experiments to examine whether virgin and nonvirgin (experienced) individuals of A. arbustorum discriminate between virgin and nonvirgin mating partners. We also assessed the number of sperm delivered to partners with different mating status. Neither virgin nor nonvirgin snails showed any preference for mating with a virgin partner. In all test situations mating was random and the number of sperm delivered was not adjusted to the mating status of the partner. Mating success was mainly determined by the activity of the individual. The random mating pattern does not imply random fertilization of eggs because the presence of a sperm-digesting organ and the morphology of the sperm storage organ allow a selective storage and use of sperm in A. arbustorum.     

Morphological and metrical comparison of San and Central Sotho dentitions from southern Africa

Comparative morphological and metrical study of San and Central Sotho dentitions indicates that the teeth of the two samples are significantly different from one another. The San dental complex contains traits that add mass to the occlusal surface of microdontic dentitions: moderate low-grade UI1 (13.5%) and UI2 shoveling (24.7%), high Bushman canine (43.1%), fairly low UM2 hypocone reduction (23.3%), high UM2 cusp 5 (55.6%), high LM1 cusp 7 (35.2%), LM1 distal trigonid crest (7.1%), and LM2 deflecting wrinkle (5.3%), lack of reduction of LM1 and LM2 cusp number, in the presence of very low UM1 Carabelli's trait (6.7%) and high LM2 Y-groove (86.3%). Culturally, males occasionally exhibit filed UI1 and females are missing LI1. Conversely, mesodontic Central Sotho dentitions display a more simplified morphology, with the exception of moderately high incidence of UM1 Carabelli's trait (41.0%) and very high LM1 cusp 7 (71.3%). Discriminant analysis of mesiodistal and buccolingual diameters and tooth crown surface area data for the left maxillary teeth supports classification of San dentitions as microdont and Central Sotho dentitions as mesodont. Additionally, metrical analysis indicates that San teeth are more sexually dimorphic than are those of Central Sotho.     

Comparison of the stability of glutathione and related synthetic tetrapeptides by HPLC and capillary electrophoresis.

Glutathione and related peptides are interesting targets as protectors of biological systems against an oxidative injury. Two novel glutathione analogues, UPF1 and UPF15, have been designed and synthesised. As a result of different reactions taking place, the thiol-containing compounds oxidise to disulfides. In this study, the stability of UPF1, UPF15 and glutathione in various solutions was investigated by using HPLC and CE. The results showed that UPF1 and UPF15 are powerful hydroxyl radical scavengers and their dimerisation process velocity is higher than that of glutathione.     

Comparison of the expression of medaka (Oryzias latipes) pitx genes with other vertebrates shows high conservation and a case of functional shuffling in the pituitary

With the availability of an increasing number of whole genome sequences in chordates, exhaustive comparisons of multigene families become feasible. Relationships of orthology/paralogy can not only be inferred from sequence similarity but also by comparing synteny conservation on chromosomes. More accurate scenarios for gene and expression domain gain or loss can now be proposed. Here, we take benefit from the recent release of the medaka (Oryzias latipes) genome to analyse the orthology relationships and expression patterns of the three different sub-families of the pitx homeobox genes belonging to the paired class. They are involved in a wide variety of developmental processes and have pleiotropic expression patterns, especially in the case of the pitx2 sub-family. The emerging picture is a strong conservation of expression domains, suggesting that most functions have been present in the common ancestor of actinopterygians and sarcopterygians. Almost all pitx genes are expressed in anterior placodes in all species studied so far, including medaka. It has previously been shown that in mammals, pitx1 and 2 are expressed in the pituitary. Interestingly we demonstrate here that only pitx3 is expressed in medaka pituitary. It will be interesting to analyze what are the corresponding changes in the regulatory elements of pitx genes.