Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis

We present a computational method, TuMult, for reconstructing the sequence of copy number changes driving carcinogenesis, based on the analysis of several tumor samples from the same patient. We demonstrate the reliability of the method with simulated data, and describe applications to three different cancers, showing that TuMult is a valuable tool for the establishment of clonal relationships between tumor samples and the identification of chromosome aberrations occurring at crucial steps in cancer progression.     

Genetic mapping and QTL analysis in European hazelnut (<Emphasis Type="Italic">Corylus avellana</Emphasis> L.)

The European hazelnut (Corylus avellana L.) is the most economically important nut species in the Betulaceae family. Despite the need for new improved hazelnut cultivars, few breeding programs are carried out because of the large plant size, the long lifecycle of the plant, and the expense and time required. To date, there are no reports of maps with quantitative trait loci (QTL) in hazelnut. Our objective in the present study was to identify QTL associated with vegetative traits to allow marker-assisted selection (MAS). An F1 progeny (275 plants) of Tonda Gentile delle Langhe × Merveille de Bollwiller obtained in 2009 was used to develop a QTL linkage map for vigour, sucker habit, and time of bud burst, after three years of observations. A set of 163 plants were analysed with 152 microsatellite markers. A map of 11 linkage groups was obtained, covering 663.1 cM, and 15 QTLs were identified and mapped for the traits examined. Of them, 10 were ‘major’ QTL, including a stably expressed region on LG_02 for leaf bud burst. At least one major QTL for each year underlies the variation in each trait and a clustering of QTL for trunk circumference and suckers/trunk circumference ratio with high inter-trait correlations was observed on LG_05, suggesting a single pleiotropic locus. This research represents an initial step in the future identification of chromosomal regions carrying genes of interest, important for breeding programs and MAS.     

Roles of Poly(3-Hydroxybutyrate) Depolymerase and 3HB-Oligomer Hydrolase in Bacterial PHB Metabolism

Many poly-3-hydroxybutyrate (PHB)-degrading enzymes have been studied. But biological roles of 3HB-oligomer hydrolases (3HBOHs) and how PHB depolymerases (PHBDPs) and 3HBOHs cooperate in PHB metabolism are not fully elucidated. In this study, several PHBDPs and 3HBOHs from three types of bacteria were purified, and their substrate specificity, kinetic properties, and degradation products were investigated. From the results, PHBDP and 3HBOH seemed to play a role in PHB metabolism in three types of bacteria, as follows: (A) In Ralstonia pickettii T1, an extracellular PHBDP degrades extracellular PHB to various-sized 3HB-oligomers, which an extracellular 3HBOH hydrolyzes to 3HB-monomers. (B) In Acidovorax sp. SA1, an extracellular PHBDP hydrolyzes extracellular PHB to small 3HB-oligomers (dimer and trimer), which an intracellular 3HBOH efficiently degrades to 3HB in the cell. (C) In Ralstonia eutropha H16, an intracellular 3HBOH helps in the degradation of intracellular PHB inclusions by PHBDP.     

A multiple RSU collaborative scheduling scheme for data services in vehicular ad hoc networks

As studies on vehicular ad hoc networks have been conducted actively in recent years, convenient and reliable services can be provided to vehicles through traffic information, surrounding information, and file sharing. To provide services for multiple requests, road side units (RSUs) should receive requests from vehicles and provide a scheduling scheme for data transfer according to priority. In this paper, we propose a new scheduling scheme by which multiple RSUs are connected through wired networks and data is transferred through the collaboration of RSUs. The proposed scheme transfers safety and non-safety data by employing a collaborative strategy of multiple RSUs as well as reducing the deadline miss ratio and average response time. When safety data is generated, data is transferred from the previous RSU in advance, while priority is assigned considering the deadline and reception rate. Since non-safety data is an on-demand data processed by user requests, the proposed scheme provides a method that reduces the deadline miss ratio upon loads generated in RSUs. To prove the superiority of the proposed scheme, we perform a performance evaluation in which the number and velocities of vehicles were changed. It is shown through the performance evaluation that the proposed scheme has better deadline miss ratios and faster response time than the existing schemes.     

A culture system for the live analysis of successive developmental processes and the morphological control of mammalian vertebral cartilage

The mesoderm-derived segmental somite differentiates into dermomyotome and sclerotome, the latter of which undergoes vertebrogenesis to spinal cartilage and ultimately to vertebral bones. However, analysis and manipulation of the developing mammalian vertebrae in the same embryo has been infeasible because of their placental-dependent embryogenesis. Here, we report a novel culture system of the mouse embryonic tailbud, by which the developmental processes of mammalian vertebral cartilage are traceable and manipulatable in the same sample. The anaplastic segmental somites/sclerotomes in the tailbud of 13 gestational day (g.d.) embryo that are structurally continuous to the vertebral column underwent progressive vertebrogenesis when (1) the ectoderm-derived nascent epidermis was microsurgically removed prior to cultivation, and (2) the sample was incubated at the air-medium interface. After cultivation for 5 days, the size and shape of the instructed vertebral cartilage showed features comparable to well-differentiated body vertebra along with the expression of the cartilage marker collagen type II, suggesting that aggressive differentiation of the sclerotomal cell lineage was achieved. In the presence of recombinant bone morphogenic protein (BMP) and Noggin, or adenoviral particles for extracellular epimorphin, dramatic alteration of the vertebral morphology ensued in the explants. Thus, this model system provides an approach to study the detailed molecular mechanisms of mammalian vertebrogenesis and enables pretreatment strategies of precartilagious fragments for improving the efficacy of subsequent transplantation.     

Cell source,differentiation, functional stimulation,and potential application of human thermogenic adipocytes in vitro

Recent investigations have showed that the functional thermogenic adipocytes are present in both infants and adult humans. Accumulating evidence suggests that the coexistence of classical and inducible brown (brite) adipocytes in humans at adulthood and these adipocytes function to generate heat from energy resulting in reducing body fat and improving glucose metabolism. Human thermogenic adipocytes can be differentiated in vitro from stem cells, cell lines, or adipose stromal vascular fraction. Pre-activated human brite adipocytes in vitro can maintain their thermogenic function in normal or obese immunodeficient mice; therefore, they improve glucose homeostasis and reduce fat mass in obese animals. These key findings have opened a new door to use in vitro thermogenic adipocytes as a cell therapy to prevent obesity and related disorders. Thus, this paper intends to highlight our knowledge in aspects of in vitro human brite/brown adipocytes for the further studies.     

Early ontogeny of a South Pacific gonostomatid fish <Emphasis Type="Italic">Sigmops longipinnis</Emphasis>

 During the R/V Hakuho-maru Cruise KH-95-2, Ocean Research Institute, University of Tokyo, from Tokyo, Japan to the South Pacific east of Australia (22° N–30° S; 126° E–176° E) from June to September, 1995, 77 unidentified gonostomatid larvae (5.5–20.0 mm SL) were collected south of 20° S with an IKMT net. They subsequently were identified as Sigmops longipinnis (Mukhacheva), and its ontogeny during the latter part of the larval stage (body form and proportions, photophores, pigmentation, and meristics) is described here. The larvae develop a species-specific row of melanophores along the midlateral line anterior to the caudal peduncle and another along the middorsal line from before the dorsal fin to just before the caudal fin. Received: June 24, 2002 / Revised: November 2, 2002 / Accepted: January 31, 2003     

Floristic diversity patterns in the White Carpathians biosphere reserve,Czech Republic

The flora of the White Carpathians, a mountain range in the south-east of the Czech Republic, is documented by about 485,000 records of vascular plant occurrences collected since the mid-19^th century. A total of 1299 species recorded in 93 grid cells of 2.8 × 3.1 km were used for an analysis of spatial patterns of floristic diversity in the White Carpathians. Multivariate statistical techniques such as ordination and classification were used to reveal the main gradients in floristic composition and species richness, and measured environmental data and Ellenberg indicator values were used to assess underlying environmental factors. There is a striking floristic contrast between the western and eastern part of the study area, which is associated with differences in climate, mean altitude, topographic heterogeneity measured as altitudinal range, and land use. The western part is characterised by thermophilous, continental and calcicolous species of open habitats. In contrast, the more forested eastern part along the state border with Slovakia and the north-eastern part of the area are characterised by acidophilous species with higher moisture requirements. This pattern is consistent with the established phytogeographical division of the Czech Republic into the phytogeographical regions of Thermophyticum and Mesophyticum. The further division of the area into four regions, based on classified grid data, is also similar to the current division into phytogeographical districts, except for the Javorníky district. There are two distinct hot spots of species richness, in the western and the extreme north-eastern part. A poorer flora was found in landscapes with intensive agriculture. Species richness is associated with different environmental factors than species composition, namely with soil types and land-use categories. Alien species are more common in areas with a higher incidence of arable land and built-up areas, and less common in areas dominated by grasslands and forests.