Identification of Differentially Expressed Genes Between Cloned and Zygote-Developing Zebrafish (Danio rerio) Embryos at the Dome Stage Using Suppression Subtractive Hybridization

Comparative analyses of differentially expressed genes between somatic cell nuclear transfer (SCNT) embryos and zygote-developing (ZD) embryos are important for understanding the molecular mechanism underlying the reprogramming processes. Herein, we used the suppression subtractive hybridization approach and from more than 2900 clones identified 96 differentially expressed genes between the SCNT and ZD embryos at the dome stage in zebrafish. We report the first database of differentially expressed genes in zebrafish SCNT embryos. Collectively, our findings demonstrate that zebrafish SCNT embryos undergo significant reprogramming processes during the dome stage. However, most differentially expressed genes are down-regulated in SCNT embryos, indicating failure of reprogramming. Based on Ensembl description and Gene Ontology Consortium annotation, the problems of reprogramming at the dome stage may occur during nuclear remodeling, translation initiation, and regulation of the cell cycle. The importance of regulation from recipient oocytes in cloning should not be underestimated in zebrafish.

Evolution of height distribution of Ge islands on Si(1 0 0)

Evolution of the height distribution of Ge islands during in situ annealing of Ge films on Si(1 0 0) has been studied. Island height is found to have a bimodal distribution. The standard deviation of the island height divided by the mean island height, for the mode of larger island size is more than that for the other mode. We suggest that the presence of Ehrlich-Schwoebel barriers, combined with the misfit strain, can lead to the bimodal distribution of island size, the mode of larger island size having narrower base size distribution, but wider height distribution for Ge islands on Si(1 0 0). The bimodal distribution of island size could be stable due to kinetics without necessarily regarding it as minimum-energy configuration. (C) 1999 Elsevier Science B.V. All rights reserved.

A study of the scaling height of the tropospheric aerosol and its extinction coefficient profile

IEECAS SKLLQG

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion.Including the configurational dependence will challenge the transition state theory of protein folding.

Sea surface height and transport stream function of the South China Sea from a variable-grid global ocean circulation model

A fine-grid model (1/6degrees) covering the South China Sea (SCS), East China Sea and Japan/East Sea, which is embedded into a coarse-grid (3degrees) global model, was established to study the SCS circulation. In the present paper, we report the model-produced monthly and annual mean transport stream functions and sea surface heights(SSH) and their anomalies of the SCS. Comparison to the TOPEX/Poseidon data shows that the model-produced monthly sea surface height anomalies (SSHA) are in good agreement with altimeter measurements. Based on the results, the circulation of the SCS, especially the upper layer circulation, is discussed. In the surface layer, the western Philippine Sea water intrudes into the SCS through the Luzon Strait in autumn, winter and spring, but not in summer. However, as far as the whole water column is concerned, the water intrudes into the SCS through the Luzon Strait all the year round. This indicates that in summer the water still intrudes into the SCS in the subsurface and intermediate layers. The area near the northern continental slope of the SCS is dominated by a cyclonic circulation all the year round. The SCS Southern Anticyclonic Gyre, SE Vietnam Off-Shore Current in summertime and SCS Southern Cyclonic Gyre in wintertime are reproduced reasonably. The difference between the monthly averaged SSH and SSHA is significant, indicating the importance of the mean SSH in the SCS circulation.

Comparison of nonlinear and linear PCA on surface wind, surface height, and SST in the South China Sea

We compared nonlinear principal component analysis (NLPCA) with linear principal component analysis (LPCA) with the data of sea surface wind anomalies (SWA), surface height anomalies (SSHA), and sea surface temperature anomalies (SSTA), taken in the South China Sea (SCS) between 1993 and 2003. The SCS monthly data for SWA, SSHA and SSTA (i.e., the anomalies with climatological seasonal cycle removed) were pre-filtered by LPCA, with only three leading modes retained. The first three modes of SWA, SSHA, and SSTA of LPCA explained 86%, 71%, and 94% of the total variance in the original data, respectively. Thus, the three associated time coefficient functions (TCFs) were used as the input data for NLPCA network. The NLPCA was made based on feed-forward neural network models. Compared with classical linear PCA, the first NLPCA mode could explain more variance than linear PCA for the above data. The nonlinearity of SWA and SSHA were stronger in most areas of the SCS. The first mode of the NLPCA on the SWA and SSHA accounted for 67.26% of the variance versus 54.7%, and 60.24% versus 50.43%, respectively for the first LPCA mode. Conversely, the nonlinear SSTA, localized in the northern SCS and southern continental shelf region, resulted in little improvement in the explanation of the variance for the first NLPCA.

Statistical distribution of nonlinear random wave height

A statistical model of random wave is developed using Stokes wave theory of water wave dynamics. A new nonlinear probability distribution function of wave height is presented. The results indicate that wave steepness not only could be a parameter of the distribution function of wave height but also could reflect the degree of wave height distribution deviation from the Rayleigh distribution. The new wave height distribution overcomes the problem of Rayleigh distribution that the prediction of big wave is overestimated and the general wave is underestimated. The prediction of small probability wave height value of new distribution is also smaller than that of Rayleigh distribution. Wave height data taken from East China Normal University are used to verify the new distribution. The results indicate that the new distribution fits the measurements much better than the Rayleigh distribution.

东南极格罗夫山地区的土壤特征及其环境研究

The Grove Mountains, including 64 nunataks, is situated on an area about 3200km2 in the inland ice cap of east Antarctica in Princess Elizabeth land (72o20'-73°101S, 73°50'-75o40'E), between Zhongshan station and Dome A, about 450km away from Zhongshan station (69°22'S, 76°22'E). Many workers thought there was no pedogenesis in the areas because of the less precipitation and extreme lower temperature. However, during the austral summer in 1999-2000, the Chinaer 16 Antarctic expedition teams entered the inland East Antarctica and found three soil spots in the Southern Mount Harding, Grove Mountains, East Antarctica. It is the first case that soils are discovered in the inland in East Antarctica. Interestingly, the soils in this area show clay fraction migration, which is different from other cold desert soils. In addition, several moraine banks are discovered around the Mount Harding. The soil properties are discussed as below. Desert pavement commonly occurs on the three soil site surfaces, which is composed of pebbles and fragments formed slowly in typical desert zone. Many pebbles are subround and variegated. These pebbles are formed by abrasion caused by not only wind and wind selective transportation, but also salt weathering and thaw-freezing action on rocks. The wind blows the boulders and bedrocks with snow grains and small sands. This results in rock disintegration, paved on the soil surface, forming desert pavement, which protects the underground soil from wind-blow. The desert pavement is the typical feature in ice free zone in Antarctica. There developed desert varnish and ventifacts in this area. Rubification is a dominant process in cold desert Antarctic soils. In cold desert soils, rubification results in relatively high concentrations of Fed in soil profile. Stained depth increases progressively with time. The content of Fed is increasing up to surface in each profile. The reddish thin film is observed around the margin of mafic minerals such as biotite, hornblende, and magnetite in parent materials with the microscope analyzing on some soil profiles. So the Fed originates from the weathering of mafic minerals in soils. Accumulations of water-soluble salts, either as discrete horizons or dispersed within the soil, occur in the soil profiles, and the salt encrustations accumulate just beneath surface stones in this area. The results of X-ray diffraction analyses show that the crystalline salts consist of pentahydrite (MgSO4-5H2O), hexahydrite (MgSO4-6H2O), hurlbutite (CaBe2(PO4)2), bloedite (Na2Mg(S04)2-4H2O), et al., being mainly sulfate. The dominant cations in 1:5 soil-water extracts are Mg2+ and Na+, as well as Ca2+ and K+, while the dominant anion is SO42-, then NO3-, Cl- and HCO3-. There are white and yellowish sponge materials covered the stone underside surface, of which the main compounds are quartz (SiO2, 40.75%), rozenite (FeSOKkO, 37.39%), guyanaite (Cr2O3-1.5H2O, 9.30%), and starkeyite (MgSO4-4H2O, 12.56%). 4) The distribution of the clay fraction is related to the maximum content of moisture and salts. Clay fraction migration occurs in the soils, which is different from that of other cold desert soils. X-ray diffraction analyses show that the main clay minerals are illite, smectite, then illite-smectite, little kaolinite and veirniculite. Mica was changed to illite, even to vermiculite by hydration. Illite formed in the initial stage of weathering. The appearance of smectite suggests that it enriched in magnesium, but no strong eluviation, which belongs to cold and arid acid environment. 5) Three soil sites have different moisture. The effect moisture is in the form of little ice in site 1. There is no ice in site 2, and ice-cement horizon is 12 cm below the soil surface in site 3. Salt horizon is 5-10 cm up to the surface in Site 1 and Site 2, while about 26cm in site 3. The differentiation of the active layer and the permafrost are not distinct because of arid climate. The depth of active layer is about 10 cm in this area. Soils and Environment: On the basis of the characteristics of surface rocks, soil colors, horizon differentiation, salt in soils and soil depth, the soils age of the Grove Mountains is 0.5-3.5Ma. No remnants of glaciations are found on the soil sites of Mount Harding, which suggests that the Antarctic glaciations have not reached the soil sites since at least 0.5Ma, and the ice cap was not much higher than present, even during the Last Glacial Maximum. The average altitude of the contact line of level of blue ice and outcrop is 2050m, and the altitude of soil area is 2160m. The relative height deviation is about 110m, so the soils have developed and preserved until today. The parental material of the soils originated from alluvial sedimentary of baserocks nearby. Sporepollen were extracted from the soils, arbor pollen grains are dominant by Pinus and Betula, as well as a small amount Quercus, Juglans, Tilia and Artemisia etc. Judging from the shape and colour, the sporepollen group is likely attributed to Neogene or Pliocene in age. This indicates that there had been a warm period during the Neogene in the Grove Mountains, East Antarctica.

Nutrient enrichment effects on mangrove sediments from differing tree height zones in Bocas del Toro, Panama

Red mangrove (Rhizophora mangle L.) forests have distinct tree-height zones, with tall trees fringing the ocean and shorter trees in interior stands. A long-term nitrogen (N) and phosphorus (P) fertilization experiment in Almirante Bay, Bocas del Toro Province, Panama has shown that tree-height zonation is primarily related to nutrient limitation. This experiment was used to test the effects of in-situ nutrient additions and tree zonation on mangrove sediments. The sediments underlying the experimental R. mangle trees were sampled and N₂ fixation, ¹⁵N, chlorophyll a, percent N and P, and percent organic biomass were quantified. Both N and P additions significantly affected almost every parameter measured in both zones within this experiment. These results are likely to have implications for management since N and P inputs are predicted to increase throughout the tropics and subtropics worldwide.

Bivariate distribution modeling with tree diameter and height data

The Logit-Logistic (LL), Johnson's SB, and the Beta (GBD) are flexible four-parameter probability distribution models in terms of the (skewness-kurtosis) region covered, and each has been used for modeling tree diameter distributions in forest stands. This article compares bivariate forms of these models in terms of their adequacy in representing empirical diameter-height distributions from 102 sample plots. Four bivariate models are compared: SBB, the natural, well-known, and much-used bivariate generalization of SB; the bivariate distributions with LL, SB, and Beta as marginals, constructed using Plackett's method (LL-2P, etc.). All models are fitted using maximum likelihood, and their goodness-of-fits are compared using minus log-likelihood (equivalent to Akaike's Information Criterion, the AIC). The performance ranking in this case study was SBB, LL-2P, GBD-2P, and SB-2P

Relating sardine recruitment in the Northern Benguela to satellite-derived sea surface height using a neural network pattern recognition approach

Processes of enrichment, concentration and retention are thought to be important for the successful recruitment of small pelagic fish in upwelling areas, but are difficult to measure. In this study, a novel approach is used to examine the role of spatio-temporal oceanographic variability on recruitment success of the Northern Benguela sardine Sardinops sagax. This approach applies a neural network pattern recognition technique, called a self-organising map (SOM), to a seven-year time series of satellite-derived sea level data. The Northern Benguela is characterised by quasi-perennial upwelling of cold, nutrient-rich water and is influenced by intrusions of warm, nutrient-poor Angola Current water from the north. In this paper, these processes are categorised in terms of their influence on recruitment success through the key ocean triad mechanisms of enrichment, concentration and retention. Moderate upwelling is seen as favourable for recruitment, whereas strong upwelling, weak upwelling and Angola Current intrusion appear detrimental to recruitment success. The SOM was used to identify characteristic patterns from sea level difference data and these were interpreted with the aid of sea surface temperature data. We found that the major oceanographic processes of upwelling and Angola Current intrusion dominated these patterns, allowing them to be partitioned into those representing recruitment favourable conditions and those representing adverse conditions for recruitment. A marginally significant relationship was found between the index of sardine recruitment and the frequency of recruitment favourable conditions (r super(2) = 0.61, p = 0.068, n = 6). Because larvae are vulnerable to environmental influences for a period of at least 50 days after spawning, the SOM was then used to identify windows of persistent favourable conditions lasting longer than 50 days, termed recruitment favourable periods (RFPs). The occurrence of RFPs was compared with back-calculated spawning dates for each cohort. Finally, a comparison of RFPs with the time of spawning and the index of recruitment showed that in years where there were 50 or more days of favourable conditions following spawning, good recruitment followed (Mann-Whitney U-test: p = 0.064, n = 6). These results show the value of the SOM technique for describing spatio-temporal variability in oceanographic processes. Variability in these processes appears to be an important factor influencing recruitment in the Northern Benguela sardine, although the available data time series is currently too short to be conclusive. Nonetheless, the analysis of satellite data, using a neural network pattern-recognition approach, provides a useful framework for investigating fisheries recruitment problems.

Ocean structure and climate (Eastern North Atlantic): in situ measurement and remote sensing

Structure and climate of the east North Atlantic are appraised within a framework of in situ measurement and altimeter remote sensing from 0 degree - 60 degree N. Long zonal expendable bathythermograph /conductivity-temperature-depth probe sections show repeating internal structure in the North Atlantic Ocean. Drogued buoys and subsurface floats give westward speeds for eddies and wavelike structure. Records from longterm current meter deployments give the periodicity of the repeating structure. Eddy and wave characteristics of period, size or wavelength, westward propagation speed, and mean currents are derived at 20 degree N, 26 degree N, 32.5 degree N, 36 degree N and 48 degree N from in situ measurements in the Atlantic Ocean. It is shown that ocean wave and eddy-like features measured in situ correlate with altimeter structure. Interior ocean wave crests or cold dome-like temperature structures are cyclonic and have negative surface altimeter anomalies; mesoscale internal wave troughs or warm structures are anticyclonic and have positive surface height anomalies. Along the Eastern Boundary, flows and temperature climate are examined in terms of sla and North Atlantic Oscillation (NAO) Index. Longterm changes in ocean climate and circulation are derived from sla data. It is shown that longterm changes from 1992 to 2002 in the North Atlantic Current and the Subtropical Gyre transport determined from sla data correlate with winter NAO Index such that maximum flow conditions occurred in 1995 and 2000. Minimum circulation conditions occurred between 1996-1998. Years of extreme negative winter NAO Index result in enhanced poleward flow along the Eastern Boundary and anomalous winter warming along the West European Continental Slope as was measured in 1990, 1996, 1998 and 2001.

Shore height and differentials between macrobenthic assemblages in vegetated and unvegetated areas of an intertidal sandflat

Intertidal macrobenthic faunal assemblages of a dual seagrass/callianassid-structured sandflat system were investigated in subtropical Moreton Bay, Queensland. Consistently across all 20 stations, the gastropod-dominated seagrass supported greater abundance (2.5×) and species richness (2×) than the amphipod-dominated sandflat. There was no evidence of along-shore or up-shore variation in the overall assemblage properties such as total abundance, species richness or diversity within either habitat type, except for variation in sandflat abundance between sites. But seagrass and sandflat assemblages both varied significantly in composition from site to site, and seagrass assemblage composition also varied with shore height. Shore height and site, however, only accounted for ≤41% of total variation. The two faunal assemblages showed a Bray–Curtis dissimilarity of 97.7% and within-habitat similarities of <20%. There was no consistency in distribution of greater diversity, dominance or evenness. No differential between any assemblage features in adjacent sandflat and seagrass samples changed with shore height, supporting hypotheses that such differentials are not maintained by predation. Macrofaunal species richness and diversity were closely coupled within sandflat stations but were uncoupled within seagrass ones, questioning the value of diversity as a comparative measure.