Sequence analysis and quantitative detection of Norwalk-like viruses in cultured oysters of China

We isolated 4 Norwalk-like viruses (NLVs) contaminated oysters from 33 Chinese oysters collected from local commer-cial sources of Shandong Province. After amplification of the RNA-dependent RNA polymerase (RdRp) region of NLVs genomes with RT-PCR, the open reading frame 1 (ORF1) of the RdRp was sequenced and subjected to multiple-sequence alignment. The re-suits showed that NLVs in the four isolates belong to genogroup Ⅱ. The sequence comparison showed that the similarity between four Chinese oyster isolates were higher than 99.0%, which indicated that NLVs prevalent in close areas have high homogeneity in genome sequences. In addition, the most conserved sequences between diverse NLVs were used to design primers and TaqMan probes, then the real-time quantitative PCR assay was performed. According to the standard curve of GII NLVs, the original amounts (copies) of NLVs in positive patient's fecal isolate, positive Japanese oyster isolate, and the Chinese oyster isolate were 8.9×108, 1.25×108 and 4.7×101 respectively. The detecting limit of NLVs was 1×101 copies. This study will be helpful for routine diagnosis of NLVs pathogens in foods and thus for avoiding food poisoning in the future.     

Method for evaluating the degrees of land use sustainability of mountainous county and its application in Yunnan Province,China

The evaluation of sustainable land use is the key issue in the field of studying the sustainable land utilization. In general analysis, the sustainable land use is evaluated respectively from its ecological sustainability, economic sustainability and social sustainability in China and other countries in recent years. Although this evaluation is an important work, it seems insufficient and hard to comprehensively reflect the whole degree of land use sustainability. Thus, to make up this deficiency, this paper brings forward the evaluation indexes, which make it possible to quantitatively reflect the whole degree of land use sustainability, namely, the concept of ＂degrees of overall land use sustainability＂ （Dos）, and research and measurement development of the method of and calculation in Dos. Taking the evaluation of the degree of land use sustainability in county regions of Yunnan Province as the actual example for analysis, results are basically as follows：
1） The degree of land use sustainability （Dos） is the ration index to organically and systematically integrate the degree of ecological friendliness （DeF）, the degree of economic viability （Dev） and the degree of social acceptability （Dsa）, able to comprehensively reflect the whole sustainability degree of regional land use
2） Based on the value of Dos, the grading system and standard for the sustainability of land use may be established and totally divided into five grades, namely, the high-degree sustainability, middle-degree sustainability, low-degree sustainability, conditional sustainability and non-sustainability. Meanwhile, the standard for distinguishing sustainability grades has also been confirmed so as to determine the nature of sustainability degrees in different grades. This makes the possibility for the combination of nature determination with ration in research result and provides with the scientific guideline and decision-making gist for better implementation of sustainable land use strategy.
3） The pract     

Population ecology of the endangered Himalayan Yew in Khokhan Wildlife Sanctuary of North Western Himalaya for conservation management

The Himalayan Yew （Taxus baccata subsp, wallichiana） is an endangered native high value medicinal plant of the Himalayan Region. The several medicinal properties of the bark and leaves of this species have increased its risk of extinction due to pressures for utilization. It is also subjected to harvest for fuelwood. The species does not regenerate well from seed and that is another risk factor. The objective of this research was to investigate the population ecology of the species as a foundation for its conservation. Six forest communities in the Khokhan Wildlife Sanctuary where the species is present were sampled. The abundance of the species, impacts of harvesting and its current regeneration patterns indicate that it may soon be extirpated from the Sanctuary. A plan for conserving the remaining sub-populations is presented. It could provide a template for conservation in other locations where the species is at risk.     

Coastal upwelling along the north coast of Papua New Guinea and SST cooling over the pacific warm pool: A case study for the 2002/03 El Niño event

We investigate an overlooked mechanism—coastal upwelling—for sea surface temperature (SST) cooling in the western side of the mean location of the Pacific warm pool (WSWP: 5°S–5°N, 140°E–150°E) prior to El Niño onset. We analyze various observed data such as the TRIangle Trans-Ocean buoy Network (TRITON) moored buoy data, Conductivity-Temperature-Depth (CTD) data, satellite data and a hindcast experiment output by a high-resolution ocean general circulation model (OGCM). We focus on the precondition of the 2002/03 El Niño event, for which many datasets are available. Relatively cool water upwelled along the north coast of Papua New Guinea (PNG) during December 2001, prior to the onset of the 2002/03 El Niño event, and then spread out over a wider area to the northeast. Simultaneously, strong west-northerly surface winds occur along the north coast. Heat budget analysis of TRITON buoy data in the WSWP reveals that negative zonal heat advection due to eastward current is the main factor for cooling the mixed layer in the WSWP in contrast to the warming effect of the surface heat flux during the period. This cooling requires a source of colder water to the west. Similar analysis of OGCM outputs also suggests that the upwelled relatively cool water along the PNG north coast, and its northeastward extension to the equatorial region, contributes to cooling of the surface water over the WSWP mainly via negative zonal heat advection. Similar mechanisms are confirmed also for the 1982/83 and 1997/98 El Niño events by analyses of OGCM outputs and historical SST data. The low SST in the WSWP generated a positive zonal SST gradient together with high SST east of the WSWP. It may contribute to enhancement of the westerly surface wind in this region, leading to the onset of the 2002/03 El Niño event.     

Bathymetry enhancement by altimetry-derived gravity anomalies in the East Sea (Sea of Japan)

The gravity-geologic method (GGM) was used to enhance the bathymetry of the East Sea (Sea of Japan) with satellite altimetry-derived free-air gravity anomalies and shipborne depth measurements. By comparison with the bathymetry model of Smith and Sandwell’s (SAS) approach (1994), GGM was found to have an advantage with short wavelength (≤12 km) components, while SAS better predicts longer wavelength (≥25 km) components, despite its dependency on density contrast. To mitigate this limitation, a tuning density contrast of 10.25 g/cm³ between seawater and the seafloor was primarily estimated by the downward continuation method and then validated by the check points method with GGM. Similarly, SAS is limited by the “A” value in low-pass part of the Wiener filter, which defines the effective range of the wavelength components on bathymetry. As a final result, we present an enhanced GGM bathymetry model by integrating all available data.     

Effects of cold eddy on phytoplankton production and assemblages in Luzon strait bordering the South China Sea

The biochemical effects of a cold-core eddy that was shed from the Kuroshio Current at the Luzon Strait bordering the South China Sea (SCS) were studied in late spring, a relatively unproductive season in the SCS. The extent of the eddy was determined by time-series images of SeaWiFS ocean color, AVHRR sea surface temperature, and TOPEX/Jason-1 sea surface height anomaly. Nutrient budgets, nitrate-based new production, primary production, and phytoplankton assemblages were compared between the eddy and its surrounding Kuroshio and SCS waters. The enhanced productivity in the eddy was comparable to wintertime productivity in the SCS basin, which is supported by upwelled subsurface nitrate under the prevailing Northeastern Monsoon. There were more Synechococcus, pico-eucaryotes, and diatoms, but less Trichodesmium in the surface water inside the eddy than outside. Prochlorococcus and Richelia intracellularis showed no spatial differences. Water column-integrated primary production (IPP) inside the eddy was 2–3 times that outside the eddy in the SCS (1.09 vs. 0.59 g C m⁻²d⁻¹), as was nitrate-based new production (INP) (0.67 vs. 0.25 g C m⁻²d⁻¹). INP in the eddy was 6 times that in the Kuroshio (0.12 g C m⁻²d⁻¹). IPP and INP in the eddy were higher than the maximum production values ever measured in the SCS basin. Surface chlorophyll a concentration (0.40 mg m⁻³) in the eddy equaled the maximum concentration registered for the SCS basin and was higher than the wintertime average (0.29 ± 0.04 mg m⁻³). INP was 3.5 times as great and IPP was doubled in the eddy compared to the wintertime SCS basin. As cold core eddies form intermittently all year round as the Kuroshio invades the SCS, their effects on phytoplankton productivity and assemblages are likely to have important influences on the biogeochemical cycle of the region.     

Arctic sea-ice motion and its relation to pressure field

Daily Arctic sea-ice motion maps during the winter seasons (December–March) from December 1988 to March 2003 derived from NSCAT, QuikSCAT, SSM/I, and AMSRE data by a wavelet analysis method have been merged with those derived from buoy data. These merged sea-ice motion data have been used to study the circulation regimes and winter-to-winter variability of Arctic sea-ice motion. The relation between sea-ice motion and the pressure field in the Arctic Ocean was also studied by applying Principal Component Analysis (PCA) to the monthly merged sea-ice motion data and the monthly pressure field data from IABP. The mean Arctic sea-ice motion map of the 15 winter seasons has two distinct features: the Beaufort Gyre and a cyclonic circulation system in the Eurasian Basin, which moves ice from the Laptev Sea to Fram Strait. The strengths and sizes of the two features change from one winter season to another. Seasons with a strong or normal Beaufort Gyre alternate with seasons with a weak or no Beaufort Gyre every one to three seasons. The principal components of the first two modes of PCA of the monthly sea-ice motion are closely correlated with their counterparts of the monthly pressure field in the Arctic Ocean. The mode-one components of these two anomalies alternate between anticyclonic and cyclonic circulation systems. The correlation between Arctic Oscillation indexes and the principal components of the first mode of PCA of the monthly Arctic sea-ice motion is low but statistically significant.     

Trend and dynamic cause of sediment particle size on the adjacent continental shelf of the Yangtze Estuary

Based on the measured data in recent 20 years, the variation trends of the median grain size of the surface sediment, the sand-silt boundary and the mud area on the adjacent continental shelf of the Yangtze Estuary were analyzed in depth, and the effects of natural mechanism and human activities were discussed. The results show that:(1) In recent years(2006-2013), the median grain size of sediment and the distribution pattern of grouped sediments in the adjacent continental shelf area to the Yangtze Estuary have presented no obvious change compared with those before 2006;(2) The median diameter of the surface sediment in the continental shelf area displayed a coarsening trend with the decrease of sediment discharge from the basin and the drop in suspended sediment concentration in the shore area;(3) In 2004-2007, the sand-silt boundary in the north part(31°30′N) of the continental shelf area presented no significant changes, while that in the south part(31°30′S) moved inwards; In 2008-2013, both the sand-silt boundaries in the north and south parts of the continental shelf area moved inwards, mainly due to the fact that in the dry season, a relatively enhanced hydrodynamic force of the tides was generated in the Yangtze River, as well as a decreased suspended sediment concentration and a flow along the banks in North Jiangsu;(4) The mud area where the maximum deposition rate is found in the Yangtze Estuary, tends to shrink due to the drop in sediment discharge from the basin, and the decrease in suspended sediment concentration in the shore area and erosion in the delta. Moreover, it tended to shift to the south at the same time because the implement of the training works on the deep-water channel of the North Passage changed the split ratio between the North and South Passages with an increase in the power of the discharged runoff in the South Passage.     

Conversion of kinetic energy from synoptic scale disturbance to low-frequency fluctuation over the Yangtze River valley in the summers of 1997 and 1999

In order to investigate the conversion of kinetic energy from a synoptic scale disturbance （SSD; period≤seven days） to a low-frequency fluctuation （LFF; period〉seven days）, the budget equation of the LFF kinetic energy is derived. The energy conversion is then calculated and analyzed for the summers of 1997 and 1999. The results show that the energy conversion from the SSD to the LFF is obviously enhanced in the middle and lower troposphere during the heavy rainfall, suggesting this to be one of mechanisms inducing the heavy rainfall, although the local LFF kinetic energy may not be enhanced.