Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora).

Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable. Therefore, to design the new primer set, we sequenced the mitochondrial genomes of two pseudokeronopsids in the class Spirotrichea using next-generation sequencing technology (HiSeq™ 2000). Based on putative CO1 gene fragments of the pseudokeronopsids, we designed the new primer set and successfully sequenced the CO1 of 69 populations representing 47 species (five orders, 14 families, and 27 genera). We found that CO1 showed higher resolution for separating congeneric species than did nuclear SSU rRNA gene sequences, and we identified some putative cryptic species.

Monitor brightness changes under a wide range of surround conditions.

Display brightness data were collected under a wide range of surround conditions. A 24 in. (60.96 cm) LCD display was used to generate color stimuli, and a 107 in. (271.78 cm) two-dimensional illuminator was used to generate various surround conditions. The brightness values of the display under 89 monitor-surround-luminance combinations were collected from 10 or 24 observers. The surround ratio, SR, i.e., the luminance ratio between the surround and the monitor, varied from 0 to 90. Based on the collected brightness data, we propose a new c value as the log function of the surround ratio, SR, to improve the performance of the CIECAM02 brightness predictor Q.

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In this study, a new "non-oxytrichid Dorsomarginalia" ciliate, Urosomoida sejongensis n. sp. discovered from freshwater of the King George Island, Antarctica, was investigated using morphological, morphometrical, and molecular methods. Morphology of U. sejongensis is characterized as follows: body shape slender to elongated; cortical granules spherical and colorless, groups of granules formed patchy distribution; ring-shaped structures scattered in cytoplasm; 27-30 adoral membranelles with undulating membranes in Oxytricha pattern; usually 17 frontal-ventral-transverse (FVT) cirri composed of 3 frontal, 1 buccal, 4 frontoventral, 3 postoral ventral, 2 pretransverse ventral and 4 transverse cirri; 1 right and 1 left marginal rows; 3 dorsal kineties with 1 dorsomarginal row, 3 caudal cirri; 1 micronucleus between 2 macronuclear nodules. This new species mainly differs from other congeners by the combination of following morphological features: a micronucleus, cortical granules, and ciliatures (e.g., adoral membranelles, FVT cirri). Urosomoida sejongensis shows a nucleotide similarity of 97.3% with U. agilis, type of this genus, using the SSU rDNA sequence. Molecular phylogeny shows a non-monophyletic relationship among Urosomoida species and emphasizes the need for further morphogenetic studies of this genus and other related species to resolve morphological convergences.

Complete mitochondrial genome of the South Polar Skua Stercorarius maccormicki (Charadriiformes, Stercorariidae) in Antarctica.

The South Polar Skua, gull-like seabirds is the most fascinating Antarctic seabirds that lay two eggs at sites free of snow and ice and predominantly hunt pelagic fish and penguins. Blood samples of the South Polar Skua Stercorarius maccormicki was collected during the summer activity near King Sejong station in Antarctica. The complete mitochondrial DNA sequence of S. maccormicki was 16,669 bp, showing conserved genome structure and orientation found in other avian species. The control region of S. maccormicki was 93- and 80 bp shorter compared to those of Chroicocephalus saundersi and Synthliboramphus antiquus respectively. Interestingly, there is a (CAACAAACAA)6 repeat sequence in the control region. Our results of S. maccormicki mt genome including the repeat sequence, may provide useful genetic information for phylogenetic and phylogeographic histories of the southern skua complex.

Complete mitochondrial genome of the Antarctic barnacle Lepas australis (Crustacea, Maxillopoda, Cirripedia).

We present the complete mitochondrial genome of the Antarctic barnacle Lepas australis (Cirripedia, Thoracica, Lepadidae). The genome sequence is 15,502 bp in size. Except for CO1, 12 protein-coding genes (PCGs) start with an ATN initiation codon (ATA, ATG, ATC and ATT). Twelve PCGs were terminated with TAA or TAG stop codon, whereas ND1 possessed an incomplete termination codon (T- -). We compared the mitogenome structure of L. australis to those of other cirripeds and a typical arthropod Homarus americanus. The PCGs in the L. australis mtgenome showed a typical gene arrangement, identical to the arthropod pattern in other cirriped genomes. However, at least 8 tRNA genes were translocated and 2 tRNA genes were inverted in the coding polarity. Unique differences in L. australis mtgenome included translocation of trnS2, trnD and trnI. These results are useful for understanding the phylogenetic relationships among cirripedians, and additional mtgenome information of barnacles including the polar species would allow exploration of the thoracican relationships and mtgenome modifications in the barnacle evolution.

Visual appearance measurement of surfaces containing pearl flakes.

The color, gloss, and texture (i.e., pearliness) of 15 glossy samples containing pearl flakes were investigated. Psychophysical experimental data from 21 observers were compared with measurement data. Color measurement data obtained using the CIE D/0 and ASTM E2539-08 multiangle geometry did not predict the overall color appearance variation of pearly samples. Pearly samples have a lower perceived glossiness than non-pearly surfaces with the same level of gloss treatment, but a much higher measured gloss. Pearliness describes the texture of pearly samples well and can be predicted as a function of the pearl flakes' average size and area coverage measured from magnified surface images. These results suggest that an image statistics approach is required to properly describe the visual appearance of pearly surfaces.

Development of single-nucleotide polymorphism-based phylum-specific PCR amplification technique: application to the community analysis using ciliates as a reference organism.

Despite recent advance in mass sequencing technologies such as pyrosequencing, assessment of culture-independent microbial eukaryote community structures using universal primers remains very difficult due to the tremendous richness and complexity of organisms in these communities. Use of a specific PCR marker targeting a particular group would provide enhanced sensitivity and more in-depth evaluation of microbial eukaryote communities compared to what can be achieved with universal primers. We discovered that many phylum- or group-specific single-nucleotide polymorphisms (SNPs) exist in small subunit ribosomal RNA (SSU rRNA) genes from diverse eukaryote groups. By applying this discovery to a known simple allele-discriminating (SAP) PCR method, we developed a technique that enables the identification of organisms belonging to a specific higher taxonomic group (or phylum) among diverse types of eukaryotes. We performed an assay using two complementary methods, pyrosequencing and clone library screening. In doing this, specificities for the group (ciliates) targeted in this study in bulked environmental samples were 94.6% for the clone library and 99.2% for pyrosequencing, respectively. In particular, our novel technique showed high selectivity for rare species, a feature that may be more important than the ability to identify quantitatively predominant species in community structure analyses. Additionally, our data revealed that a target-specific library (or ciliate-specific one for the present study) can better explain the ecological features of a sampling locality than a universal library.