Computational study of depth completion consistent with human bi-stable perception for ambiguous figures

We propose a computational model that is consistent with human perception of depth in “ambiguous regions,” in which no binocular disparity exists. Results obtained from our model reveal a new characteristic of depth perception. Random dot stereograms (RDS) are often used as examples because RDS provides sufficient disparity for depth calculation. A simple question confronts us: “How can we estimate the depth of a no-texture image region, such as one on white paper?” In such ambiguous regions, mathematical solutions related to binocular disparities are not unique or indefinite. We examine a mathematical description of depth completion that is consistent with human perception of depth for ambiguous regions. Using computer simulation, we demonstrate that resultant depth-maps qualitatively reproduce human depth perception of two kinds. The resultant depth maps produced using our model depend on the initial depth in the ambiguous region. Considering this dependence from psychological viewpoints, we conjecture that humans perceive completed surfaces that are affected by prior-stimuli corresponding to the initial condition of depth. We conducted psychological experiments to verify the model prediction. An ambiguous stimulus was presented after a prior stimulus removed ambiguity. The inter-stimulus interval (ISI) was inserted between the prior stimulus and post-stimulus. Results show that correlation of perception between the prior stimulus and post-stimulus depends on the ISI duration. Correlation is positive, negative, and nearly zero in the respective cases of short (0–200 ms), medium (200–400 ms), and long ISI (>400 ms). Furthermore, based on our model, we propose a computational model that can explain the dependence

Multifunctional polyketide synthase genes identified by genomic survey of the symbiotic dinoflagellate, Symbiodinium minutum

Table S1. Predicted domains from transcriptome contigs Figure S1. Expression of KS domain-containing genes on scaffolds of S. minutum. Read coverages of RNAseq (gray line) on KS domain-containing genes (surrounded by green) show expression in our standard cultured conditions. In addition, the SL sequence containing reads (red line) from transcription start site (TSS) library suggest large multifunctional genes are expressed as a transcript that is not trans-spliced. Red arrows show trans-spliced sites, located internally in KS domain-containing genes. Figure S2. Molecular phylogenetic tree of Type I and Type II KS domains from prokaryotic and eukaryotic PKS and FAS, analyzed by maximum likelihood. Type II KS and acyl carrier protein synthases (ACPS) were used as outgroups. Bootstrap values ≥ 50 % are marked at appropriate nodes. Details regarding S. minutum sequences are provided in Table 1. (PDF 9386 kb

Embryonic expression of a hemichordate distal-less gene

Hemichordates occupy a critical phylogenetic position among deuterostomes because they exhibit echinoderm-like larval morphology and chordate-like adult morphology. Analyses of the expression and function of hemichordate developmental genes will therefore provide insight into the evolution of deuterostome body plans. The distal-less/dlx gene encodes a homeodomain transcription factor and plays roles in the development of appendages and the brain in a variety of animals. Here we have characterized a distal-less gene (Pf-dlx) of the hemichordate Ptychodera flava. During embryogenesis, Pf-dlx is expressed in the whole aboral ectoderm of the blastula and gastrula. Later, its expression appears in several cells in the boundary region between the oral and aboral ectoderm. The tornaria larvae express Pf-dlx in some specific cells of the ciliary band. The results are discussed in terms of an ancestral function of the distal-less/dlx gene in the formation of the nervous system

Expansion and Diversification of Fluorescent Protein Genes in Fifteen Acropora Species during the Evolution of Acroporid Corals

In addition to a purple, non-fluorescent chromoprotein (ChrP), fluorescent proteins (FPs) account for the vivid colors of corals, which occur in green (GFP), cyan (CFP), and red (RFP) FPs. To understand the evolution of the coral FP gene family, we examined the genomes of 15 Acropora species and three confamilial taxa. This genome-wide survey identified 219 FP genes. Molecular phylogeny revealed that the 15 Acropora species each have 9-18 FP genes, whereas the other acroporids examined have only two, suggesting a pronounced expansion of the FP genes in the genus Acropora. The data estimates of FP gene duplication suggest that the last common ancestor of the Acropora species that survived in the period of high sea surface temperature (Paleogene period) has already gained 16 FP genes. Different evolutionary histories of lineage-specific duplication and loss were discovered among GFP/CFPs, RFPs, and ChrPs. Synteny analysis revealed core GFP/CFP, RFP, and ChrP gene clusters, in which a tandem duplication of the FP genes was evident. The expansion and diversification of Acropora FPs may have contributed to the present-day richness of this genus

Establishing Sustainable Cell Lines of a Coral, Acropora tenuis

Planula larvae of the scleractinian coral, Acropora tenuis, consist of elongated ectodermal cells and developing inner endodermal cells. To establish in vitro cell lines for future studies of cellular and developmental potential of coral cells, larvae were successfully dissociated into single cells by treating them with a tissue dissociation solution consisting of trypsin, EDTA, and collagenase. Brown-colored cells, translucent cells, and pale blue cells were the major components of dissociated larvae. Brown-colored cells began to proliferate transiently in the culture medium that was devised for the coral, while translucent cells and pale blue cells decreased in number about 1 week after cell dissociation. In addition, when a modular protease, plasmin, was added to the cell culture medium, brown-colored cells extended pseudopodia and assumed amorphous shapes. They then continued to proliferate in clumps for more than 6 months with a doubling time of approximately 4-5 days. From 3 weeks of cell culture onward, brown-colored cells often aggregated and exhibited morphogenesis-like behavior to form flat sheets, and blastula-like clusters or gastrula-like spheres. Single cells or cell-clusters of the cell lines were analyzed by RNA-seq. This analysis showed that genes expressed in these cells in vitro were A. tenuis genes. Furthermore, each cell line expressed a specific set of genes, suggesting that their properties include gastroderm, secretory cells, undifferentiated cells, neuronal cells, and epidermis. All cell properties were maintained stably throughout successive cell cultures. These results confirm the successful establishment of a coral in vitro cell line

Differential gene expression in fronds and stolons of the siphonous macroalga, Caulerpa lentillifera

The green alga, Caulerpa lentillifera, is composed of a single cell with multiple nuclei, but it possesses structures analogous to leaves or fronds, stems or stolons, and roots or rhizoids. To understand molecular mechanisms involved in formation and function of these structures, we carried out RNA-seq analysis of fronds and stolons (including rhizoids). Taking advantage of the decoded genome of C. lentillifera, the present RNA-seq analysis addressed transcripts corresponding to 9,311 genes identified in the genome. RNA-seq data suggested that 8,734 genes are expressed in sporophytes. Despite the siphonous body of the alga, differential gene expression was evident in the two structures. 1,027 (11.8%) and 1,129 (12.9%) genes were preferentially expressed in fronds and stolons, respectively, while the remaining 6,578 (75.3%) genes were expressed at the same level in both. Most genes preferentially expressed in fronds are associated with photosynthesis and plant hormone pathways, including abscisic acid signaling. In contrast, those preferentially expressed in stolons are associated with translation and DNA replication. These results indicate that gene expression is regulated differently between fronds and stolons, which probably governs the function of each structure. Together with genomic information, the present transcriptomic data provide genic information about development and physiology of this unique, siphonous organism

Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera

In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates

Spontaneous remission of a non-small cell lung cancer possibly caused by anti-NY-ESO-1 immunity.

Spontaneous remission of malignant tumors is rare and the biological mechanism of such remission has not been addressed. We report the case of a 71-year-old Japanese patient with non-small cell lung cancer with a right hilar tumor and pleural dissemination that spontaneously regressed. NY-ESO-1 is a cancer/testis antigen that can elicit specific immune responses in patients with cancer. Strong anti-NY-ESO-1 immunity was detected in this patient. His tumor cells expressed NY-ESO-1 and MHC class I molecules. Anti-NY-ESO-1 immunity might have contributed to spontaneous remission in this patient