Analysis of the 16S-23S rDNA intergenic spacers (IGSs) of marine vibrios for species-specific signature DNA sequences

Vibrios are widespread in the marine environment and a few pathogenic species are known to be commonly associated with outbreaks of diarrheal diseases in humans due to the consumption of raw or improperly cooked seafood. However, there are also many Vibrio species which are potentially pathogenic to vertebrate and invertebrate aquatic animals, and of which little is known. In an attempt to develop rapid PCR detection methods for these latter class of vibrios, we have examined the 16S-23S intergenic spacers (IGSs) of 10 lesser-known Vibrio species and successfully developed species-specific primers for eight of them--Vibrio costicola, V. diazotrophicus, V. fluvialis, V. nigripulchritudo, V. proteolyticus, V. salmonicida, V. splendidus and V. tubiashii. The IGS amplicons were amplified using primers complementary to conserved regions of the 16S and 23S rRNA genes, and cloned into plasmid vectors and sequenced. Analysis of the IGS sequences showed that 37 ribosomal RNA (rrn) operons representing seven different IGS types have been cloned from the 10 vibrios. The three IGS types--IGS(0), IGS(IA) and IGS(Glu)--were the most prevalent forms detected. Multiple alignment of representative sequences of these three IGS types from different Vibrio species revealed several domains of high sequence variability, which were used to design species-specific primers for PCR. The specificity of the primers were evaluated using total DNA prepared from different Vibrio species and bacterial genera. The results showed that the PCR method can be used to reliably detect eight of the 10 Vibrio species in marine waters in this study.     

Small SiC grains and a nitride grain of circumstellar origin from the Murchison meteorite: implications for stellar evolution and nucleosynthesis

We report the results of SIMS isotopic analyses of carbon, nitrogen, oxygen, and silicon made on 849 small (approximately 1 micrometer) individual silicon carbide grains from the Murchison meteorite. The isotopic compositions of the major elements carbon and silicon of most grains (mainstream) are similar to those observed in larger grain studies suggesting an AGB star origin of these grains. In contrast, the trace element nitrogen shows a clear dependency on grain size. 14N/15N ratios increase with decreasing grain size, suggesting different stellar sources for grains of different size. Typically observed 14N/15N ratios in the small grains of this study are approximately 2700, clearly larger than the values expected from model calculations of AGB stars. In addition to the three dredge-up episodes characteristic for the evolution of AGB stars, extra-mixing of CNO-processed matter in low mass AGB stars appears to be a promising possibility in order to explain the high 14N/15N ratios of the small circumstellar SiC grains. A small fraction of grains shows a silicon isotopic signature not observed in larger circumstellar SiC grains from Murchison. Their stellar origin is still uncertain. The minor type A, B, Y, and X grains were found to be present at a level of a percent, which is similar to their abundance in the larger-grain SiC separates from Murchison. Oxygen isotopic compositions are normal within the experimental uncertainties of several 10%, indicating that oxygen of stellar origin is rare or even absent in the SiC grains. We conclude that most of the oxygen is a contaminant which was introduced into the SiC grains after their formation, e.g., during sample processing in the laboratory. We identified a nitride grain, most likely Si3N4 with little carbon, with highly anomalous isotopic compositions (12C/13C = 157 +/- 33, 14N/15N = 18 +/- 1, delta 29 Si = -43 +/- 56%, delta 30 Si = -271 +/- 50%). The isotopic patterns of carbon, nitrogen, and silicon resemble those of the rare SiC X grains suggesting that these two rare constituents of circumstellar matter formed in the same type of stellar source, namely, Type II supernovae.     

Induction, adaptation and recovery of biological responses: implications for environmental monitoring

A wide range of biological responses have been used to identify exposure to contaminants, monitor spatial and temporal changes in contamination levels, provide early warning of environmental deterioration and indicate occurrences of adverse ecological consequences. To be useful in environmental monitoring, a biological response must reflect the environmental stress over time in a quantitative way. We here argue that the time required for initial induction, maximum induction, adaptation and recovery of these stress responses must first be fully understood and considered before they can be used in environmental monitoring, or else erroneous conclusions (both false-negative and false-positive) may be drawn when interpreting results. In this study, data on initial induction, maximum induction, adaptation and recovery of stress responses at various biological hierarchies (i.e., molecular, biochemical, physiological, behavioral, cytological, population and community responses) upon exposure to environmentally relevant levels of contaminants (i.e., metals, oil, polycyclic aromatic hydrocarbons (PAHs), organochlorines, organophosphates, endocrine disruptors) were extracted from 922 papers in the biomarker literature and analyzed. Statistical analyses showed that: (a) many stress responses may decline with time after induction (i.e., adaptation), even if the level of stress remains constant; (b) times for maximum induction and recovery of biochemical responses are positively related; (c) there is no evidence to support the general belief that time for induction of responses at a lower biological hierarchy (i.e., molecular responses and biochemical responses) is shorter than that at higher hierarchy (i.e., physiological, cytological and behavioral responses), although longer recovery time is found for population and community responses; (d) there are significant differences in times required for induction and adaptation of biological responses caused by different types of contaminants; (e) times required for initial and maximum induction of physiological responses in fish are significantly longer than those in crustaceans; and (f) there is a paucity of data on adaptation and recovery of responses, especially those at population and community levels. The above analyses highlight: (1) the limitations and possible erroneous conclusions in the present use of biomarkers in biomonitoring programs, (2) the importance of understanding the details of temporal changes of biological responses before employing them in environmental management, and (3) the suitability of using specific animal groups as bioindicator species.     

Interaction between inorganic nutrients and organic matter in controlling coral reef communities in Glovers Reef Belize

We studied the responses of algae, corals, and small fish to elevated inorganic fertilizer, organic matter, and their combination over a 49-day summer period in cages that simulated the coral reef in the remote Glovers reef atoll, Belize. The addition of organic matter reduced while fertilization had no effect on the numbers of herbivorous damsel and parrotfishes. All measures of algal biomass were influenced by fertilization. The combined inorganic and organic enrichment produced the highest algal biomass, which is most likely due to the combined effect of higher nutrients and lower herbivory. The cover of turf and total algae were influenced by all treatments and their interactions and most strongly and positively influenced by fertilization followed by organic matter and the combination of organic matter and inorganic fertilizer. The inorganic and combined treatments were both dominated by two turf algae, Enteromorpha prolifera and Digenia simplex, while the nonfertilized treatments were dominated by brown frondose algae Lobophora variegata, Padina sanctae, and Dictyota cervicornis. The organic matter treatment had greater cover of P. sanctae and D. cervicornis than the untreated control, which was dominated by Lobophora variegata, also the dominant algae on the nearby patch reefs. Crustose corallines grew slowly ( approximately 2.5 mm/49 days) and were not influenced by the treatments when grown on vertical surfaces but decreased on horizontal coral plates in the combined organic matter and fertilization treatment. No mortality occurred for the two coral species that were added to the cages. Porites furcata darkened in the fertilized cages while there was a mix of paling and darkening for a small amount of the coral tissue of Diploria labyrinthiformes. Inorganic fertilization stimulates small filamentous turf algae and Symbiodinium living in coral but inhibits brown frondose algae. Organic matter inhibits small herbivorous fish, L. variegata, and encrusting coralline algae when growing on horizontal surfaces.     

Tectonic Evolution and Hydrocarbon Potential in Northern Area of the South Yellow Sea

The northern area of the South Yellow Sea, located in the offshore region of China, resulted from the continental-continental collision orogeny during the Mesozoic and can be divided into four stages in terms of tectonic evolution: (1) pre-orogenic passive continental margin stage (Z-T2); (2) foreland basin stage corresponding with the late phase of the Sulu (苏鲁) orogeny (J3-K); (3) post-orogenic intracontinental rifted basin stage (K2t-E); and (4) regional subsidence and coverage stage (N-Q). Based on deta...     

龙门山地区的P波速度结构与汶川地震的深部构造特征

利用四川地震台网2000年1月～2008年4月的地震数据,使用地震层析成像方法反演了龙门山及其邻近地区的地壳P波速度结构,以此为依据分析了龙门山断裂带和汶川Ms8.0地震的深部构造特征.研究结果表明,龙门山的地壳速度结构和深部动力学性质与汶川Ms8.0地震的破裂起始点、震源深度以及破裂传播方向密切相关.龙门山西侧的彭灌杂岩体是地壳内部应变强度较大、易于应力长期积累的主要载体,汶川Ms8.0地震即位于彭灌杂岩体的南端,毗邻四川盆地的西部边缘,该块体与四川盆地地壳的碰撞是引发汶川Ms8.0地震的直接原因.在汶川以北,沿着龙门山断裂的高速异常有利于破裂的发生和传递,而汶川以南地壳强度相对较弱,不易产生脆性破裂而引发地震,这可能是地震破裂自汶川向东北方向延伸、汶川以南缺少地震活动的重要原因.汶川Ms8.0地震的深部动力成因与龙门山断裂两侧的构造差异有关,松潘-甘孜造山带中下地壳强度较弱,青藏高原的向东运动受到四川盆地刚性岩石层阻碍,迫使龙门山发生垂向变形,中下地壳厚度增加,莫霍面弯曲下沉,基底则褶皱抬升向山前盆地逆冲,地壳形变所产生的应力积累为汶川地震的发生提供了深部动力来源.     

南海前新生代残留盆地分布综合地球物理研究

为了对南海海域的前新生代残留盆地分布有个整体而全面的认识,本文开展了南海残留盆地宏观分布的综合地球物理研究.通过岩石物性分析,综合重、磁、震等地球物理方法,利用正演与反演方法,分区计算并求取了南海的重力基底和磁性基底埋深,得到了中生界及前中生界残余厚度,给出了整个南海前新生代残留盆地的宏观格架与残余厚度分布特征并讨论了...     

南海西南次海盆北缘海底地震仪测线深部地壳结构研究

基于2009年和2011年采集的海底地震仪数据,辅以多道地震数据,对南海西南次海盆北缘的地壳结构进行了探索.利用二维射线追踪的反演方法建立测线上的模型.利用声学基底面的反射波,下地壳顶界面的反射波和莫霍面的反射波走时的反演勾绘了地层中的不连续界面,利用自声学基底面下的折射波和来自上地幔的首波来反演整条测线的P波速度结构...