Mobilization of a transposon in the rice genome

Rice (Oryza sativa L.) is an important crop worldwide and, with the availability of the draft sequence, a useful model for analysing the genome structure of grasses. To practice efficient rice breeding through genetic engineering techniques, it is important to identify the economically important genes in this crop. The use of mobile transposons as gene tags in intact plants is a powerful tool for functional analysis because transposon insertions often inactivate genes. Here we identify an active rice transposon named miniature Ping (mPing) through analysis of the mutability of a slender mutation of the glume-the seed structure that encloses and determines the shape of the grain. The mPing transposon is inserted in the slender glume (slg) mutant allele but not in the wild-type allele. Search of the O. sativa variety Nipponbare genome identified 34 sequences with high nucleotide similarity to mPing, indicating that mPing constitutes a family of transposon elements. Excision of mPing from slg plants results in reversion to a wild-type phenotype. The mobility of the transposon mPing in intact rice plants represents a useful alternative tool for the functional analysis of rice genes.     

Shadow free texture acquisition of a large scale scene for city modeling

Texture acquisition of a large scale scene is one of the critical research areas in computer vision and can be used in other application areas such as computer graphics (CG), the intelligent transportation system (ITS) and the 3D geographic information system (GIS). Moreover, to acquire texture without noise (e. g. , a shadow, an obstacle body) is vital for such work. Although obstacles can be removed by using 3D geometric data, shadow elimination is still a difficult problem and strongly required for the CG and ITS community, especially for city modeling and simulation purposes. In this paper, we propose an automatic multiple image fusion technique and an efficient and simple shadow removing technique to retrieve high quality texture images of an urban area. The image fusion can be efficiently achieved by epipolar plane image (EPI) analysis, and the shadow elimination can be successfully carried out by an illumination-independent color clustering technique. The strength of this algorithm is that we can successfully fuse multiple images and eliminate shadows from the fused single image, especially in low dynamic range images, which have proven difficult using previous techniques.     

Nearest neighbor search algorithm for GBD tree spatial data structure

This paper describes the nearest neighbor (NN) search algorithm on the GBD(generalized BD) tree. The GBD tree is a spatial data structure suitable for two-or three-dimensional data and has good performance characteristics with respect to the dynamic data environment. On GIS and CAD systems, the R-tree and its successors have been used. In addition, the NN search algorithm is also proposed in an attempt to obtain good performance from the R-tree. On the other hand, the GBD tree is superior to the R-tree with respect to exact match retrieval, because the GBD tree has auxiliary data that uniquely determines the position of the object in the structure. The proposed NN search algorithm depends on the property of the GBD tree described above. The NN search algorithm on the GBD tree was studied and the performance thereof was evaluated through experiments.     

Nearest neighbor search algorithm forGBD tree spatial data structure

： This paper describes the nearest neighbor （NN） search algorithm on the GBD（generalized BD） tree. The GBD tree is a spatial data structure suitable for two- or three-dimensional data and has good performance characteristics with respect to the dynamic data environment. On GIS and CAD systems, the R-tree and its-successors have been used. In addition, the NN search algorithm is also proposed in an attempt to obtain good performance from the R-tree. On the other hand, the GBD tree is superior to the R-tree with respect to exact match retrieval, because the GBD tree has auxiliary data that uniquely determines the position of the object in the structure. The proposed NN search algorithm depends on the property of the GBD tree described above. The NN search algorithm on the GBD tree was studied and the performance thereof was evaluated through experiments.     

Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D

Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support the lives of photosynthetic eukaryotes, including higher plants. Here we report the 16,520,305-base-pair sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome. We identified 5,331 genes in total, of which at least 86.3% were expressed. Unique characteristics of this genomic structure include: a lack of introns in all but 26 genes; only three copies of ribosomal DNA units that maintain the nucleolus; and two dynamin genes that are involved only in the division of mitochondria and plastids. The conserved mosaic origin of Calvin cycle enzymes in this red alga and in green plants supports the hypothesis of the existence of single primary plastid endosymbiosis. The lack of a myosin gene, in addition to the unexpressed actin gene, suggests a simpler system of cytokinesis. These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.     

How cancer cells dictate their microenvironment: present roles of extracellular vesicles

Intercellular communication plays an important role in cancer initiation and progression through secretory molecules, including growth factors and cytokines. Recent advances have revealed that small membrane vesicles, termed extracellular vesicles (EVs), served as a regulatory agent in the intercellular communication of cancer. EVs enable the transfer of functional molecules, including proteins, mRNA and microRNAs (miRNAs), into recipient cells. Cancer cells utilize EVs to dictate the unique phenotype of surrounding cells, thereby promoting cancer progression. Against such “education” by cancer cells, non-tumoral cells suppress cancer initiation and progression via EVs. Therefore, researchers consider EVs to be important cues to clarify the molecular mechanisms of cancer biology. Understanding the functions of EVs in cancer progression is an important aspect of cancer biology that has not been previously elucidated. In this review, we summarize experimental data that indicate the pivotal roles of EVs in cancer progression.