Stable RNA hairpins in 88 coding regions of human mRNA

RNA hairpins containing UNCG, GNRA, CUUG (N = A, U, C or G, R = G or A) loops are unusually thermodynamic stable and conserved structures. The structural features of these hairpin loops are very special, and they play very important roles in vivo. They are prevalent in rRNA, catalytic RNA and non-coding mRNA. However, the 5' C(UUCG)G 3' hairpin is not found in the folding structure of 88 human mRNA coding regions. It is also different from rRNA in that there is no preference for certain sequences among tetraloops in these 88 mRNA folding structures.

The identification and quantification of highly stable 'common hairpin' in the dynamic process of co-transcriptional mRNA folding

In our studies, 88 human mRNA samples were collected from the Integrated Sequence-Structure database and then the dynamic process in co-transcriptional mRNA folding was simulated using the RNAstructure version 4.1 program. Through statistical analyses of the frequencies of occurrence of hairpins, a group of special folding structures-the 'common hairpins'-were identified. These 'common hairpins' have lower energies and occur in all the subsequent folding units that formed in the dynamic folding process. By applying the formulas (1)-(4) of the 'common hairpins' statistical model, 163 'common hairpins' were found, to make up about 7% of the total of 2286 hairpins. Classified studies further show that the 'common hairpins' that were studied may oscillate in the dynamic folding process. However, the hairpin loops of the 'common hairpins' and stems proximal to those 'common hairpins' loops maintain topologically stable structures, while other loops and stems distal to the 'common hairpins' loops are shown to be alterable structures. Strikingly, further studies indicate that the stable structures of these 'common hairpins' may have unbeknown effects on controlling the formation of protein structures in the translation process (unpublished results). (c) 2005 Elsevier B.V. All rights reserved.

Seasonal variations in stable isotope ratios of two biomanipulation fishes and seston in a large pen culture in hypereutrophic Meiliang Bay, Lake Taihu

This paper reports on seasonal changes in stable carbon and nitrogen isotope ratios of seston and muscle tissue of silver carp and bighead carp during 2004 and 2005, focusing primarily on the carbon sources and trophic relationships among phytoplankton, zooplankton and silver carp and bighead carp in a large fish pen of Meiliang Bay (Lake Taihu, China). delta C-13 showed a minimal value in March 2005 and a maximal value in August 2005 in seston both inside and outside the pen, whereas delta N-15 of seston showed the minimum in winter and the maximum during algal blooms. A positive correlation between delta C-13 of silver carp and that of seston suggested that temporal variation Of delta C-13 in seston was preserved in fish via the food chain. The differences of delta C-13 among seston, zooplankton and muscle tissue of silver carp and bighead carp ranged only 0.2-1.7%, indicating that plankton production was the primary food source of filter-feeding fishes. According to a mass balance model, we estimated that the contributions of zooplankton to the diets of silver carp and bighead carp were 45.7% and 54.3%, respectively, based on the delta N-15 values of zooplankton and planktivorous fishes. (C) 2007 Elsevier B.V. All rights reserved

Growth and food availability of silver and bighead carps: evidence from stable isotope and gut content analysis

A 2-year investigation of growth and food availability of silver carp and bighead was carried out using stable isotope and gut content analysis in a large pen in Meiliang Bay of Lake Taihu, China. Both silver carp and bighead exhibited significantly higher delta 13C in 2005 than in 2004, which can probably be attributed to two factors: (i) the difference between isotopic compositions at the base of the pelagic food web and (ii) the difference between the compositions of prey items and stable isotopes. The significantly positive correlations between body length, body weight and stable isotope ratios indicated that isotopic changes in silver carp and bighead resulted from the accumulation of biomass concomitant with rapid growth. Because of the drastic decrease in zooplankton in the diet in 2005, silver carp and bighead grew faster in 2004 than in 2005. Bighead carp showed a lower trophic level than silver carp in 2005 as indicated by stable nitrogen isotope ratios, which was possibly explained by the interspecific difference between the prey species and the food quality of silver carp and bighead.

Contributions of Pelagic and Benthic Dietary Sources to Freshwater Mussels: Evidence from Stable Carbon Isotope Analysis

In Gonghu Bay of Lake Taihu, tissue of five mussel species showed delta C-13 values similar to or slightly below that of pelagic suspended particulate organic matter (SPOM). This indicated that mussels in this area either fed non-selectively and so reflected available carbon in the pelagic habitat or selected for phytoplankton. The situation was the same for Anodonta woodiana woodiana and Cristaria plicata in Meiliang Bay; however, for the remaining three species, Hyriopsis cumingii, Arconaia lanceolata, and Lamprotula rochechouarti, tissue had intermediate delta C-13 values, falling between those for pelagic SPOM and benthic sediment organic matter (SOM), suggesting a possible preferential selection of phytoplankton from the pelagic SPOM but more likely reflecting local differences in pelagic SPOM and benthic SOM composition and available organic carbon sources. The mixing model showed that pelagic SPOM accounted for over 98% of carbon incorporated by all mussels in Gonghu Bay and two mussels in Meiliang Bay, suggesting the dietary importance of pelagic food sources for mussels. Less than 50% of the assimilation in H. cumingii, A. lanceolata, and L. rochechouarti came from the pelagic carbon sources in Meiliang Bay, which suggested that these species consumed a mix of benthic and pelagic derived carbon sources.

Sorptive interaction between goethite and strongly reducing organic substances from anaerobic decomposition of green manures

Strongly reducing organic substances (SROS) and iron oxides exist widely in soils and sediments and have been implicated in many soil and sediment processes. In the present work, the sorptive interaction between goethite and SROS derived from anaerobic decomposition of green manures was investigated by differential pulse voltammetry (DPV). Both green manures, Astragaltus sinicus (Astragalus) and Vicia varia (Vicia) were chosen to be anaerobically decomposed by the mixed microorganisms isolated from paddy soils for 30 d to prepare different SROS. Goethite used in experiments was synthesized in laboratory. The anaerobic incubation solutions from green manures at different incubation time were arranged to react with goethite, in which SROS concentration and Fe(II) species were analyzed. The anaerobic decomposition of Astragalus generally produced SROS more in amount but weaker in reducibility than that of Vicia in the same incubation time. The available SROS from Astragalus that could interact with goethite was 0.69 +/- 0.04, 0.84 +/- 0.04 and 1.09 +/- 0.03 cmol kg(-1) as incubated for 10, 15 and 30 d, respectively, for Vicia, it was 0.12 +/- 0.03, 0.46 +/- 0.02 and 0.70 +/- 0.02 cmol kg(-1). One of the fates of SROS as they interacted with goethite was oxidation. The amounts of oxidizable SROS from Astragalus decreased over increasing incubation time from 0.51 +/- 0.05 cmol kg(-1) at day 10 to 0.39 +/- 0.04 cmol kg(-1) at day 30, but for Vicia, it increased with the highest reaching to 0.58 +/- 0.04 cmol kg(-1) at day 30. Another fate of these substances was sorption by goethite. The SROS from Astragalus were sorbed more readily than those from Vicia, and closely depended upon the incubation time, whereas for those from Vicia, the corresponding values were remarkably less and apparently unchangeable with incubation time. The extent of goethite dissolution induced by the anaerobic solution from Vicia was greater than that from Astragalus, showing its higher reactivity. (c) 2008 Published by Elsevier Ltd.

Stable isotope changes in freshwater shrimps (Exopalaemon modestus and Macrobrachium nipponensis): trophic pattern implications

Trophic patterns of omnivorous freshwater shrimps, Exopalaemon modestus and Macrobrachium nipponensis, were investigated in two shallow eutrophic lakes by using stable isotope analysis. delta N-15 and delta C-13 of M. nipponensis and E. modestus increased with increasing body weight, which might be attributed to larger individuals ingesting organisms that feed higher up the food chain and/or increased assimilation of benthic food items with enriched isotopic signatures. Of the freshwater shrimps occurring in the studied lakes, those from Lake Taihu had significantly elevated delta N-15 and delta C-13 values (4.3% and 1.8%, respectively) compared with those from the less eutrophic Lake Chaohu, indicating that the isotopic signature might partially reflect the trophic states of their habitats. Mixing model results suggested that the benthic food web provides the primary carbon source for both shrimp species, and that E. modestus assimilated relatively more pelagic food sources than M. nipponensis in these lakes.

Stable carbon isotope variations in surface bloom scum and subsurface seston among shallow eutrophic lakes

Carbon stable isotope analysis of surface bloom scum and subsurface seston samples was conducted in shallow eutrophic lakes in China during warm seasons from 2003 to 2004. delta C-13 values of bloom scum were always higher (averaged 5 parts per thousand) than those of seston in this study, and the possible reasons were attributed to (i) direct use of atmospheric CO2 at the air-water interface, (ii) decrease in C-13 fractionation due to higher carbon fixation, (iii) active CO2 transport, and/or (iv) HCO3 accumulation. Negative correlation between delta C-13(scum) - delta C-13(seston) and pH in the test lakes indicated that phytoplankton at the subsurface water column increased isotopic enrichment under the-carbon limitation along with the increase of pH, which might in turn decreased the differences in 313 C between the subsurface seston and the surface scums. Significant positive correlations of seston 8 13C with total concentrations of nitrogen and phosphorus in water column suggested that the increase in delta C-13 of seston with trophic state was depending on nutrient (N or P, or both) supply. Our study showed that delta C-13 of phytoplankton was indicative of carbon utilization, primary productivity, and nutrient supply among the eutrophic lakes. (C) 2007 Elsevier B.V All rights reserved.

Stable isotope variations in particulate organic matter and a planktivorous fish in the Yangtze River

Temporal and spatial changes in delta(13) C and delta 15 N of particulate organic matter (POM) and Hemiculter leucisculus were studied in the Yangtze River of China. Isotopic signatures of POM showed seasonal variations, which was assumed to be associated with allochthonous organic input and autochthonous phytoplankton growth. delta C-13 of H. leucisculus was 1.1 % higher than that of POM, which suggested that the food source of H. leucisculus was mostly from the POM. A mass balance model indicated the trophic position of H. leucisculus in the food web of Yangtze River was estimated to be 2.0 - 2.1, indicating that this fish mainly feeds on planktonic organic matter, which agreed with previous gut content analysis.

Trophic relationship between the parasitic isopod ichthyoxenus japonensis and the fish carassius auratus auratus as revealed by stable isotopes

Stable carbon and nitrogen isotope analysis was used to investigate the host-parasite trophic relationship between the parasitic isopod Ichthyoxenus japonensis and one of its freshwater fish host Carassius auratus auratus from Lake Fuxian, China. No significant differences in delta C-13 and delta N-15 were observed between the heterosexual pairs of I. japonensis in the same host. delta C-13 and delta N-15 of I. japonensis were significantly lower than those of its host fish, and the isotopic ratios of the isopod increased with the increase of host fish isotopic signatures. Unlike isotopic fractionation patterns generally observed among consumers and their diets, isopod parasite was delta C-13 and N-15 depleted relative to the muscle tissue of this host fish. Differential isotopic fractionation patterns in the isopod parasite and the fish may be attributed to differences in parasite and host metabolism.

Mutations stabilize small subunit ribosomal RNA in desiccation-tolerant cyanobacteria Nostoc

The ribosomal RNA molecule is an ideal model for evaluating the stability of a gene product under desiccation stress. We isolated 8 Nostoc strains that had the capacity to withstand desiccation in habitats and sequenced their 16S rRNA genes. The stabilities of 16S rRNAs secondary structures, indicated by free energy change of folding, were compared among Nostoc and other related species. The results suggested that 163 rRNA secondary structures of the desiccation-tolerant Nostoc strains were more stable than that of planktonic Nostocaceae species. The stabilizing mutations were divided into two categories: (1) those causing GC to replace other types of base pairs in stems and (2) those causing extension of stems. By mapping stabilizing mutations onto the Nostoc phylogenetic tree based on 16S rRNA gene, it was shown that most of stabilizing mutations had evolved during adaptive radiation among Nostoc spp. The evolution of 16S rRNA along the Nostoc lineage is suggested to be selectively advantageous under desiccation stress.

Variation in stable isotope signatures of seston and a zooplanktivorous fish in a eutrophic Chinese lake

Temporal and spatial changes in delta(13)C and delta(15)N of seston (mainly phytoplankton) and isotopic relationship between seston and the lake anchovy (Coilia ectenes) were studied in the large eutrophic freshwater Lake Chaohu in China. Much of the spatial and temporal variation in delta(13)C of lake anchovies was explained by variation in seston, indicating a strong link between pelagic primary production and higher order consumers. Because the lake is shallow, there were no significant differences in delta(13)C and delta(15)N of seston between surface and overlying waters. Spatially, the relatively high delta(13)C and delta(15)N of seston in the western part of the lake might be due to high levels of anthropogenically derived N and C introduced from the surrounding cities through sewage drainage systems. The trophic position of the lake anchovy in the food web of Lake Chaohu was estimated to be 2.9-4.1 (3.5 +/- 0.4), which agrees well with the previous stomach content analysis suggesting that the lake anchovy fed both on zooplankton and small planktivorous fishes.

Studies on the food web structure of Lake Donghu using stable carbon and nitrogen isotope ratios

Food web structure was studied by using carbon and nitrogen isotope ratios in a hypereutrophic subtropical Chinese lake, Lake Donghu. High external nutrient loading and the presence of abundant detritus from submersed macrophytes were responsible for the high sediment delta(15)N and delta(13)C, respectively. C-13 was significantly higher in submersed macrophytes than in other macrophytes. The similar delta(13)C values in phytoplankton, zooplankton, zoobenthos, and planktivorous fish indicate that phytoplankton was the major food source for the consumers. By using a delta(15)N mass balance model, we estimate that the contributions of zooplankton to the diet of silver carp and bighead carp were 54% and 74%, respectively, which is in agreement with previous microscopic observations on intestinal contents of these fishes.

Polarization dependence of absorption in strongly vertically coupled InAs/GaAs quantum dots for two-color far-infrared photodetector

Strongly vertically coupled InAs/GaAs quantum dots (QDs) with modulation doping are investigated, and polarization dependence of two-color absorptions was observed. Analysis of photoluminescence (PL) and absorption spectra shows that s-polarized absorptions at. 10.0 and 13.4 mu m, stem from the first excited state E-1 and the second excited state E-2 in the QDs to the bound state E-InGaAs in the InGaAs spacer, respectively, whereas p-polarized absorptions at 10.0 and 8.2 mu m stem from the first excited state E-1 and the ground E-g in the QDs to the bound state E-InGaAs in the InGaAs spacer, respectively. These measurements illustrate that transitions from excited states are more sensitive to normal incidence, which are very important in designing QD infrared detector. (C) 2007 Elsevier B.V. All rights reserved.