The Bacillus subtilis gene pgsA, which codes for the phosphatidylglycerophosphate synthase that catalyzes the committed step for the synthesis of phosphatidylglycerol (PG), is essential since Pspac-pgsA cells require IPTG for growth. Removal of the inducer caused a dramatic decrease of PG content in the membranes of cells and retarded growth. At 60 min and 120 min after removal, it was reduced to 14.1% and 8.9% of total lipid, respectively, from an initial content of 28.1%. We conjectured that the activity of some extracytoplasmic function (ECF) sigma factors, most of which are caught and regulated directly by cognate transmembrane anti-sigma factors, are affected by altered lipid composition of the membranes. Induction of the activities of ECF sigma factors (σ^M and σ^V) was observed after removal of IPTG, though that of σ^V was small. But other ECF sigma factors (σ^W, σ^X, σ^Y, σ^YlaC and σ^Z) and the general stress sigmas σ^B and σ^I were not induced. Especially σ^M was activated strongly with the reduction of PG content and sustained a high level of activity, in contrast to the transient activation in PG normal cells after exposure to high salinity. This study demonstrates a new relationship between the alterations of lipid composition in the membranes and the activation of ECF sigma factors.

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Phylogenetic relationships and genome affinities were investigated by utilizing all the biological Avena species consisting of 11 diploid species (15 accessions), 8 tetraploid species (9 accessions) and 4 hexaploid species (5 accessions). Genomic DNA regions of As120a, avenin, and globulin were amplified by PCR. A total of 130 polymorphic fragments were detected out of 156 fragments generated by digesting the PCR-amplified fragments with 11 restriction enzymes. The number of fragments generated by PCR-amplification followed by digestion with restriction enzymes was almost the same as those among the three repeated DNA sequences. A high level of genetic distance was detected between A. damascena (Ad) and A. canariensis (Ac) genomes, which reflected their different morphology and reproductive isolation. The A. longiglumis (Al) and A. prostrata (Ap) genomes were closely related to the As genome group. The AB genome species formed a cluster with the AsAs genome artificial autotetraploid and the As genome diploids indicating near-autotetraploid origin. The A. macrostachya is an outbreeding autotetraploid closely related with the C genome diploid and the AC genome tetraploid species. The differences of genetic distances estimated from the repeated DNA sequence divergence among the Avena species were consistent with genome divergences and it was possible to compare the genetic intra- and inter-ploidy relationships produced by RFLPs. These results suggested that the PCR-mediated analysis of repeated DNA polymorphism can be used as a tool to examine genomic relationships of polyploidy species.

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Dwarfism is a common type of mutation in many plant species. The pathways and factors regulating biosynthesis and signaling of several plant growth regulators have been clarified through analyses of dwarf mutants in rice, Arabidopsis, pea, and maize. However, the genetic mechanisms controlling dwarfism are not well characterized, and the causal genes underlying most dwarf mutants are still uncovered. Here, we report a dominant mutant, Twisted dwarf 1-1 (Tid1-1), showing dwarfism and twisted growth in rice. Tid1-1 exhibit right helical growth of the leaves and stem and shortening of the roots. They also show an increased number of cells in the shoot apical meristem. Cells in the leaves of Tid1-1 are often ill-shapen, possibly owing to irregular cell division. Cell elongation in roots is suppressed in the elongation zone, and cells in the root apical meristem are enlarged. Map-based cloning of TID1 revealed that it encodes an α-tubulin protein comprising microtubules and is an ortholog of Arabidopsis LEFTY genes. Our analysis of the Tid1-1 mutant revealed that the dynamics of microtubules affects not only anisotropic growth in both dicots and monocots, but also meristematic activity and gross plant morphology.

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The hallmark of age-related (presbycusis) and noise-induced hearing loss is high-frequency (> 20 kHz) hearing loss. Through a collaborative study with TMGC (Tennessee Mouse Genome Consortium), seventeen ENU-induced mouse mutation strains with high-frequency hearing loss have been identified, but affected genes are yet identified. As a first step in identifying the gene/s underlying the ENU mutations, we created a F2 population between a representative mutation strain, 118 TNE and a wild type strain, CAST/EJ (CAST). Phenotypic analysis showed that there is a 3:1 ratio of segregation between normal and hearing loss in the F2 population, suggestion a single locus regulation. However, the linkage mapping identified 2 QTLs, each on chromosomes 15 and 16. Further statistical analysis of marker segregation patterns revealed that the locus on Chr 16 was ENU induced while the one on Chr 15 was derived from the parental strain, CAST.

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Sequences from ten species of Mus (Rodentia, Muridae) of the melanocortin-1 receptor (Mc1r) gene (945 bp), which plays a key role in coat color determination, were compared with an existing Mc1r dataset (ca. 498 bp) from 12 species of Mustela and Martes (Carnivora, Mustelidae). The dN/dS ratio (ω) was estimated at 0.19 for Mus and 0.35 for the mustelids, using a likelihood-based one-ratio model with empirical codon frequencies. Running the model with equal codon frequencies gave a dramatic increase in ω for the mustelids (1.02) but not for Mus (0.31), indicating stronger codon usage bias in Mc1r among mustelids. When ω was estimated with the free-ratio model, significantly accelerated rates of amino acid replacement (nearly 1 in ω) were seen in several regions of the Mus phylogeny, such as in the ancestral subgeneric lineages, possibly associated with ecological niche shifting. Our results suggest that both functional constraints on coat color variation and selective constraints on codon usage bias have participated in structuring Mc1r gene sequences. Furthermore, they suggest that these contrasting influences have acted differentially in Mus and the mustelid lineages, and also differentially during the course of evolution within the genus Mus.

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The Q locus located on the long arm of chromosome 5A is a key factor in evolution and widespread cultivation of domesticated wheat. The Q locus pleiotropically affects many agronomically important traits including threshability, glume shape and tenacity, rachis fragility and others. Genotyping of the Q locus based on the complex traits is ambiguous due to their multi-genetic control through interactions with the Q locus. To determine the Q locus genotype of wheat accessions possessing A genome, we developed a method based on polymerase chain reaction – restriction fragment length polymorphism (PCR-RFLP) analysis. The Q and q alleles were clearly distinguished by PCR-RFLP analysis at six conserved single nucleotide polymorphisms in common wheat and wild and cultivated einkorn, emmer and timopheevi wheat. The Q locus genotype of Triticum sinskajae, which is one of the einkorn wheat species and exhibits free-threshing trait, was determined to be qq as expected. This simple PCR-RLFP-based genotyping method should serve as a useful tool in studying the origin of Q and thus wheat evolution after domestication and the following widespread cultivation.

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In eukaryotic cells, intracellular transport is mediated by coated vesicular carriers. Coat proteins I (COPI) vesicles are involved in the retrograde transport from Golgi apparatus to the endoplasmic reticulum. The COPI complex is composed of ADP-ribosylation factor 1 and coatomer comprising seven subunits, termed α–ζ. We isolated and characterised a cDNA sequence from rainbow trout homolog to δ-subunit of COPI complex (δ-COP). Trout δ-COP gene encodes a protein of 509 aa including a characteristic Mu homology domain. Searches at the Ensemble Genome browser identified three additional teleostean δ-COP-like sequences from pufferfish, rice fish, and stickleback. Sequence identity of piscine δ-COP protein sequences is greater than 84%. Moreover, a phylogenetic analysis indicates that δ-COP protein sequences are strongly conserved among vertebrate species. δ-COP homologue is ubiquitously expressed in trout tissues. Quantitative Real-Time RT-PCR revealed that δ-COP is differentially expressed in liver and gill tissue of two rainbow trout strains, the freshwater strain STEELHEAD and the brackish water-adapted strain BORN.

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To investigate the population structure of five dog breeds in South Korea and to validate polymorphic microsatellite markers for the parentage test, microsatellite loci analyses were conducted for two Korean native dog breeds, Poongsan and Jindo, and three imported dog breeds, German Shepherd, Beagle and Greyhound. Overall genetic diversity was high across all dog breeds (expected heterozygosity range: 0.71 to 0.85), although breeds differed in deviations from Hardy-Weinberg equilibrium (HWE). Significant reduction of heterozygosity in the Poongsan and Greyhound breeds was caused by non-random mating and population substructure within these breeds (the Wahlund effects). The close relationship and high degree of genetic diversity for two Korean native dog breeds were substantial. The mean polymorphism information content value was highest in Jindos (0.82) and Poongsans (0.81), followed by Beagles (0.74), Greyhounds (0.72), and German Shepherds (0.66). Accumulated exclusion power values, as an indication of marker validity for parentage tests, were varied but very high across breeds, 0.9999 for Jindos, Poongsans, and Beagles, 0.9997 for Greyhounds, and 0.9995 for German Shepherds. Taken together, the microsatellite loci investigated in this study can serve as suitable markers for the parentage test and as individual identification to establish a reliable pedigree verification system of dog breeds in South Korea. This study also stresses that the population subdivision within breeds can become an important cause of deviation from HWE in dog breeds.

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