Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing

Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.     

Omissions and Byproducts across Moral Domains

Research indicates that moral violations are judged less wrong when the violation results from omission as opposed to commission, and when the violation is a byproduct as opposed to a means to an end. Previous work examined these effects mainly for violent offenses such as killing. Here we investigate the generality of these effects across a range of moral violations including sexuality, food, property, and group loyalty. In Experiment 1, we observed omission effects in wrongness ratings for all of the twelve offenses investigated. In Experiments 2 and 3, we observed byproduct effects in wrongness ratings for seven and eight offenses (out of twelve), respectively, and we observed byproduct effects in forced-choice responses for all twelve offenses. Our results address an ongoing debate about whether different cognitive systems compute moral wrongness for different types of behaviors (surrounding violence, sexuality, food, etc.), or, alternatively, a common cognitive architecture computes wrongness for a variety of behaviors.     

Evolutionary conservation, developmental expression, and genomic mapping of mammalian Twisted gastrulation

The twisted gastrulation gene (tsg) encodes a secreted protein required for the correct specification of dorsal midline cell fate during gastrulation in Drosophila. We report that tsg homologs from human, mouse, zebrafish, and Xenopus share 72–98% identity at the amino acid level and retain all 24 cysteine residues from Drosophila. In contrast to Drosophila where tsg expression is limited to early embryos, expression is found throughout mouse and human development. In Drosophila, tsg acts in synergy with decapentaplegic (dpp), a member of the TGF-β family of secreted proteins. The vertebrate orthologs of dpp, BMP-2 and -4, are crucial for gastrulation and neural induction, and aberrant signaling by BMPs and other TGF-β family members results in developmental defects including holoprosencephaly (HPE). Interestingly, human TSG maps to the HPE4 locus on Chromosome 18p11.3, and our analysis places the gene within 5 Mbp of TG-interacting factor (TGIF). Received: 21 August 2000 / Accepted: 9 March 2001     

Amino acid alterations essential for increasing the catalytic activity of the nylon-oligomer-degradation enzyme of Flavobacterium sp

The structural genes of two homologous enzymes, 6-aminohexanoate-dimer hydrolase (EII; nylB) and its evolutionally related protein EII' (nylB') of Flavobacterium sp. KI72 have an open reading frame encoding a peptide of 392 amino acids, of which 47 are different, and conserved restriction sites. The specific activity of EII towards 6-aminohexanoate dimer is about 1000-fold that of EII'. Construction of various hybrid genes obtained by exchanging fragments flanked by conserved restriction sites of the two genes demonstrated that two amino acid replacements in the EII' enzyme, i.e. Gly181----Asp (EII type) and His266----Asn (EII type), enhanced the activity toward 6-aminohexanoate dimer 1000-fold.     

Posttranslational modification of ras proteins: detection of a modification prior to fatty acid acylation and cloning of a gene responsible for the modification

Products of ras genes are synthesized as precursors in the cytosol and transported to the plasma membrane by a process which involves posttraslational modification by fatty acid. In this paper, we present evidence for the occurrence in the cytosol of an intermediate modification of ras proteins prior to the fatty acid acylation. The modification is detected by a slight shift in the mobility of the protein on SDS polyacrylamide gel. The fatty acid acylation does not contribute to this mobility shift. This modification is affected by the dprl mutation which has recently been shown to affect the processing of yeast RAS proteins. To further characterize the nature of the modification event, we have cloned DPR1 gene from the DNA of Saccharomyces cerevisiae. The gene is actively transcribed in yeast cells producing mRNA of approximately 1.6 kb. Genes related to the DRP1 appear to be present in a distantly related yeast, Schizosaccharomyces pombe as well as in guinea pig and human cells.     

The usefulness of anti-fucosylated antigen antibody YB-2 for diagnosis of hepatocellular carcinoma

Levels of fucosylated antigens in sera from patients with liver diseases were examined by a newly developed sandwich-type enzyme immuno assay with the aid of anti-fucosylated antigen antibody, YB-2 which reacts simultaneously with Y, Leb and H type 2 antigens. When the cut-off value was set arbitrarily at mean [3 SD values of normal, 30 (69.8%) of the 43 patients with HCC, 14 (53.8%) of the 26 patients with liver cirrhosis (LC) and 24 (45.3%) of the 53 patients with chronic hepatitis (CH) were found to be positive, whereas all of the 30 samples from healthy controls were negative. The levels of -fetoprotein (AFP) and protein induced by vitamin K absence or antagonist-II (PIVKA-II) in HCC were not correlated with those of YB-2 antigens. The positive rates of the combination YB-2 and AFP assay and YB-2 and PIVKA-II assay in HCC were significantly higher (83.7 and 86.0%, respectively) than that of the AFP and PIVKA-II combination (65.1%) which had been reported to be the best combination up to this time.     

Frontal cortical oxygenation changes during gravity-induced loss of consciousness in humans: a near-infrared spatially resolved spectroscopic study.

Gravity (G)-induced loss of consciousness (G-LOC), which is presumably caused by a reduction of cerebral blood flow resulting in a decreased oxygen supply to the brain, is a major threat to pilots of high-performance fighter aircraft. The application of cerebral near-infrared spectroscopy (NIRS) to monitor gravity-induced cerebral oxygenation debt has generated concern over potential sources of extracranial contamination. The recently developed NIR spatially resolved spectroscopy (SRS-NIRS) has been confirmed to provide frontal cortical tissue hemoglobin saturation [tissue oxygenation index (TOI)]. In this study, we monitored the TOI and the standard NIRS measured chromophore concentration changes of oxygenated hemoglobin and deoxygenated hemoglobin in 141 healthy male pilots during various levels of +G(z) (head-to-foot inertial forces) exposure to identify the differences between subjects who lose consciousness and those who do not during high +G(z) exposure. Subjects were exposed to seven centrifuge profiles, with +G(z) levels from 4 to 8 G(z) and an onset rate from 0.1 to 6.0 G(z)/s. The SRS-NIRS revealed an approximately 15% decrease in the TOI in G-LOC. The present study also demonstrated the TOI to be a useful variable to evaluate the effect of the anti-G protection system. However, there was no significant difference found between conditions with and without G-LOC in subjects with terminated G exposure. Further studies that elucidate the mechanism(s) behind the wide variety of individual differences may be needed for a method of G-LOC prediction to be effectively realized.     

Production of mouse monoclonal antibody with galactose-extended sugar chain by suspension cultured tobacco BY2 cells expressing human beta(1,4)-galactosyltransferase

Previously, we developed a transgenic tobacco BY2 cell line (GT6) in which glycosylation was modified by expressing human beta(1,4)-galactosyltransferase (betaGalT). In this study, we produced a mouse monoclonal antibody in GT6 cells, and determined the sugar chain structures of plant-produced antibodies. Galactose-extended N-linked glycans comprised 16.7%, and high-mannose-type and complex-type glycans comprised 38.5% and 35.0% of the total number of glycans, respectively. N-linked glycans with the plant-specific sugars beta(1,2)-xylose and alpha(1,3)-fucose comprised 9.8%. The introduction of human betaGalT into suspension cultured tobacco cells resulted in the production of recombinant proteins with galactose-extended glycans and decreased contents of beta(1,2)-xylose and alpha(1,3)-fucose.