We compared two haploid genotypes of one Ciona savignyi individual and identified codons at which these genotypes differ by two nonsynonymous substitutions. Using the C. intestinalis genome as an outgroup, we showed that both substitutions tend to occur in the same genotype. Only in 53 (34.4%) of 154 codons, one substitution occurred in each of the two genotypes, although 77 (50%) of such codon...

We engage the experimental and computational challenges of de novo regulatory module discovery in a complex and largely unstudied metazoan genome. Our analysis is based on the comprehensive characterization of regulatory elements of 20 muscle genes in the chordate, Ciona savignyi. Three independent types of data we generate contribute to the characterization of a muscle-specific regulatory modu...

The possibility of distinguishing between two higgs production mechanisms, W fusion and gluon fusion, due to rapidity gap existence is investigated using the Monte Carlo event generator PYTHIA. It is shown that, considering the designed CM energy and luminosity for the LHC, it is not possible to distinguish between the two higgs production processes as, for a given integrated luminosity, they l...

Tunicates are lower chordates that include among others the two ascidians Ciona intestinalis and Ciona savignyi. This subphylum is particularly interesting because it shares many developmental and physiological characteristics, as well as basic gene repertoires, with vertebrates [1,2]. A fertilized ascidian egg develops within a day in a transparent tadpole-like larva having a body plan similar...

The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25-70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of po...

Evidence for the tickborne nature of Alkhurma hemorrhagic fever virus (AHFV) is indirect because AHFV has not been detected in arthropods. One Ornithodoros savignyi tick from Saudi Arabia contained AHFV RNA. This is the first direct evidence that AHFV is a tickborne flavivirus and confirms the association between human AHFV cases and tickbite history.

A long-spined sea urchin Diadema-sp reported from Japanese waters was genetically distinct from all known Diadema species, but it remained undescribed. Extensive field surveys in Japan with molecular identification performed in the present study determined five phenotypes (I to V) in Diadema-sp according to the presence and/or shape of a white streak and blue iridophore lines in the naked space...

The origins of tick toxicoses remain a subject of controversy because no molecular data are yet available to study the evolution of tick-derived toxins. In this study we describe the molecular structure of toxins from the soft tick, Ornithodoros savignyi. The tick salivary gland proteins (TSGPs) are four highly abundant proteins proposed to play a role in salivary gland granule biogenesis of th...

The rhomboid fossa of clavicle is used to determine the age and sex in anthropology and forensic sciences. The variant types of rhomboid fossa on inferior surface have been reported in many races except in Thais. This study therefore was aimed at classifying the types of the rhomboid fossa in Northeastern Thais. The identified 476 Northeastern Thais dried clavicles (270 males and 206 females) w...