Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream,the Tama River,Tokyo

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for?~?16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.     

Thermal tolerance of a thermally selected strain of rainbow trout <Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis> and the pedigrees of its F1 and F2 generations indicated by their critical thermal maxima

A thermally selected strain of rainbow trout has been established by selective breeding since 1966 in Miyazaki, Japan. In the present study, we compared the critical thermal maxima (CTMs), the temperatures at which organisms reach a predefined sublethal endpoint and lose their equilibrium, between a thermally selected and two normal (Donaldson) strains of rainbow trout. The CTM of one normal strain from Nikko (Nikko strain) acclimated to 20 °C (29.7 °C) was significantly lower than those of the thermally selected strain (30.0 °C) and the other Donaldson strain from Aomori (29.9 °C) (P?<?0.05). The F1 generations, F1T and F1N, were produced by crossing thermally selected strain females with Nikko strain males and Nikko strain females with thermally selected strain males, respectively. No significant difference was observed in the CTM between F1T [30.1?±?0.15 °C (n?=?30)] and F1N [30.1?±?0.16 °C (n?=?30)] (P?>?0.05) for fish acclimated to 20 °C, suggesting that the F1 offspring inherited the thermal tolerance trait from one thermally selected strain parent irrespective of whether it was the male or female. F2 offspring of F1T or F1N also showed the thermal tolerance trait. The coefficients of variation for CTM were also compared among all the datasets obtained in the present study and their values for F1 hybrids were lower than those of the parental generation of the Nikko strain (P?<?0.05). In contrast, the coefficients of variation of F2s were the same as those of their parental generation. Furthermore, the thermally selected strain and Nikko strain as a reference family provide a F2 generation for segregating phenotypes, which is required for in-depth genetic analysis of the thermally selected rainbow trout strain.     

A plant vacuolar protease, VPE, mediates virus-induced hypersensitive cell death

Programmed cell death (PCD) in animals depends on caspase protease activity. Plants also exhibit PCD, for example as a response to pathogens, although a plant caspase remains elusive. Here we show that vacuolar processing enzyme (VPE) is a protease essential for a virus-induced hypersensitive response that involves PCD. VPE deficiency prevented virus-induced hypersensitive cell death in tobacco plants. VPE is structurally unrelated to caspases, although VPE has a caspase-1 activity. Thus, plants have evolved a regulated cellular suicide strategy that, unlike PCD of animals, is mediated by VPE and the cellular vacuole.     

Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis

The mechanisms controlling axon guidance are of fundamental importance in understanding brain development. Growing corticospinal and somatosensory axons cross the midline in the medulla to reach their targets and thus form the basis of contralateral motor control and sensory input. The motor and sensory projections appeared uncrossed in patients with horizontal gaze palsy with progressive scoliosis (HGPPS). In patients affected with HGPPS, we identified mutations in the ROBO3 gene, which shares homology with roundabout genes important in axon guidance in developing Drosophila, zebrafish, and mouse. Like its murine homolog Rig1/Robo3, but unlike other Robo proteins, ROBO3 is required for hindbrain axon midline crossing.     

Polymerizing actin fibers position integrins primed to probe for adhesion sites

Migrating cells extend protrusions, probing the surrounding matrix in search of permissive sites to form adhesions. We found that actin fibers polymerizing along the leading edge directed local protrusions and drove synchronous sideways movement of beta1 integrin adhesion receptors. These movements lead to the clustering and positioning of conformationally activated, but unligated, beta1 integrins along the leading edge of fibroblast lamellae and growth cone filopodia. Thus, rapid actin-based movement of primed integrins along the leading edge suggests a "sticky fingers" mechanism to probe for new adhesion sites and to direct migration.     

Carbon nanotubes with temperature-invariant viscoelasticity from -196 degrees to 1000 degrees C

Viscoelasticity describes the ability of a material to possess both elasticity and viscosity. Viscoelastic materials, such as rubbers, possess a limited operational temperature range (for example, for silicone rubber it is -55° to 300°C), above which the material breaks down and below which the material undergoes a glass transition and hardens. We created a viscoelastic material composed from a random network of long interconnected carbon nanotubes that exhibited an operational temperature range from -196° to 1000°C. The storage and loss moduli, frequency stability, reversible deformation level, and fatigue resistance were invariant from -140° to 600°C. We interpret that the thermal stability stems from energy dissipation through the zipping and unzipping of carbon nanotubes at contacts.     

Imaging doped holes in a cuprate superconductor with high-resolution Compton scattering

The high-temperature superconducting cuprate La(2-x)Sr(x)CuO(4) (LSCO) shows several phases ranging from antiferromagnetic insulator to metal with increasing hole doping. To understand how the nature of the hole state evolves with doping, we have carried out high-resolution Compton scattering measurements at room temperature together with first-principles electronic structure computations on a series of LSCO single crystals in which the hole doping level varies from the underdoped (UD) to the overdoped (OD) regime. Holes in the UD system are found to primarily populate the O 2p(x)/p(y) orbitals. In contrast, the character of holes in the OD system is very different in that these holes mostly enter Cu d orbitals. High-resolution Compton scattering provides a bulk-sensitive method for imaging the orbital character of dopants in complex materials.     

Relative contributions from exposed inshore and estuarine nursery grounds to the recruitment of stone flounder, Platichthys bicoloratus, estimated using otolith Sr:Ca ratios

In Sendai Bay, stone flounder larvae settle and spend their juvenile period in either shallow exposed inshore nursery grounds or estuarine nursery grounds. The purpose of this study is to examine the relative contributions of these two kinds of nursery grounds to the flounder population using otolith strontium:calcium ratios. Stone flounder juveniles were collected from both nursery grounds, and one- and two-year-old flounder were caught deeper in Sendai Bay. Sr and Ca content in the otoliths were measured by electron probe micro analysis. The Sr:Ca ratios in the otolith section corresponding to the early postsettlement period ranged from 3.06 to 3.85 for the exposed inshore areas with stable low temperature and high salinity conditions, and from 3.81 to 5.32 in brackish estuaries with high temperature and low salinity conditions but with large diel and tidal cyclical fluctuations. Values from an estuarine site with stable salinity ranged from 3.58 to 4.15 overlapping with both the above ranges. Rearing experiments supported our inference that the high otolith Sr:Ca ratios of juveniles inhabiting estuarine nursery grounds are attributable to higher temperature and physiological stress caused by the large diel temperature and salinity fluctuations within the estuaries. Estimation of the Sr:Ca ratio of recruited fish using the otolith section formed while in the nursery area showed that at least 20 out of 42 individuals examined originated from estuarine nursery grounds. The present study indicates that estuaries play an important role as nursery grounds for stone flounder, producing about half of the stock in spite of the small and restricted area compared with the wide expanse of the exposed inshore area.     

Species diversity of the marine diatom genus Skeletonema in Japanese brackish water areas

The genus Skeletonema includes phytoplankton species that are important primary producers in marine food chains. Brackish waters have been reported to be one of the important habitats of some species of Skeletonema. To elucidate the species diversity of Skeletonema in brackish waters, we investigated three Japanese brackish bodies of water: the coastal waters of Toyama Bay, a tidal area of the Chikugo River, and a constructed reservoir in Isahaya Bay. We used molecular analysis based on large subunit rDNA and fine morphological structure to identify species. Skeletonema costatum s.s. (sensu stricto) was isolated at salinities as low as 0.6, but Skeletonema dohrnii, Skeletonema subsalsum, and Skeletonema tropicum were not found at salinities below 11.0. S. costatum s.s. could survive transfer from a medium with a salinity of 15 to a salinity of 2, but S. dohrnii did not survive in the same experiment. Only S. costatum s.s. germinated from the sediment of a reservoir in which the salinity was 0.1–1.4; incubation conditions included temperatures of 10, 15, 20, 25, and 30 °C and salinities of 5 and 30. Skeletonema costatum s.s. was identified as the species most adaptable to low-level salinity variations throughout its lifecycle.