Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records

Recent studies have shown that genotyping preserved plankton DNA in marine and lacustrine sediment records using ancient DNA methods is a promising approach for refining paleoenvironmental information. However, the extent to which the preservation of fossil plankton DNA differs between species is poorly understood. Using a continuous 2700 year sediment record from Watts Basin in Ellis Fjord (Antarctica), we compared the level of preservation of fossil DNA derived from important plankton members with varying cellular architecture. The amount of preserved small subunit ribosomal DNA (SSU rDNA; ca. 500 base pair fragments) of dinoflagellates (as extracellular DNA rather than as preserved cysts) that could be amplified by way of PCR declined up to five orders of magnitude with increasing sediment depth and age. In contrast, the amount of similar-sized, PCR-amplifiable, diatom SSU rDNA (predominantly from a cyst-forming Chaetoceros sp.) declined only up to tenfold over 2700 years of deposition. No obvious decline in copy numbers with increasing sediment age was observed for similar-sized SSU rDNA of past chemocline-associated photosynthetic green sulfur bacteria (GSB), which do not have a protective resting stage. In good agreement with the quantitative data, the extent of post-depositional natural degradation to fragments too small to serve as a template for the quantitative PCR assays was greatest for dinoflagellates and lowest for GSB. An increase in the ratio between GSB-derived DNA and intact carotenoids with sediment depth implies that short GSB DNA fragments were better preserved than intact carotenoids and provide a more accurate view into paleoproductivity and the sediment flux of GSB in Watts Basin. We discuss the possible causes behind the variation in the level of DNA preservation among the plankton groups investigated, as well as consequences for the use of using fossil DNA records in paleoecology studies.     

Population genetic diversity and structure of a dominant tropical seagrass,Cymodocea rotundata,in the Western Pacific region

Cymodocea rotundata is an ecologically important tropical pioneer seagrass species distributed in the Indo‐Pacific region. The population genetic diversity and structure of this species were analysed at 46 sites spanning the Philippines, Ryukyu Islands (northern limit) and Hainan Island, by using microsatellite simple sequence repeat (SSR) markers. Analyses revealed the persistence of C. rotundata likely relies on local population dynamics and fitness influenced by environmental gradients, with sexual reproduction prevalent in the Philippines while the Ryukyu and Hainan populations were predominantly established by clonal spread. Analysis of molecular variance showed significant genetic differentiation (P < 0.001) among three geographic regions: the Philippines, Ryukyu and Hainan. Furthermore, the mean fixation index value was very high (F_ST = 0.36), indicating poor dispersal potential or limited gene flow. Allelic richness and heterozygosity of C. rotundata was comparable in the Philippines and Ryukyu Islands populations. More private alleles were found in the Philippines and excess heterozygotes in the Ryukyu Islands. STRUCTURE analysis revealed that the Ryukyu and Hainan populations were mosaics of admixed alleles of individuals from the Philippines. An assignment test suggested that recruitment occurs from the Northeast Philippines to Ryukyu Islands. These results suggest that the Philippine populations are tropical seagrass hotspots and perhaps the origin of the populations in the Ryukyu and Hainan Islands. This scenario is most likely driven by the Kuroshio Current and island integration events during plate tectonic activities. The Philippine Archipelago is considered of high importance for conservation objectives and management plan of seagrasses. Likewise, the Ryukyu Islands are also important in terms of conserving regional diversity because locally adapted genotypes have important evolutionary potential in the face of environmental change.     

Characterization of rocking shallow foundations using centrifuge model tests

This paper presents new results of centrifuge model tests exploring the behavior of rocking shallow foundations embedded in dry sand, which provides a variety of factors of safety for vertical bearing. The results of slow (quasi‐static) cyclic tests of rocking shear walls and dynamic shaking tests of single‐column rocking bridge models are presented. The moment–rotation and settlement–rotation relationships of rocking footings are investigated. Concrete pads were placed in the ground soil to support some models with the objective of reducing the settlement induced by rocking. The behavior of rocking foundation was shown to be sensitive to the geometric factor of safety with respect to bearing failure, L_f/L_c, where L_f was the footing length, and the L_c was the critical soil‐footing contact length that would be required to support pure axial loading. Settlements were shown to be small if L_f/L_c was reasonably large. Placement of concrete pads under the edges of the footing was shown to be a promising approach to reduce settlements resulting from rocking, if settlements were deemed to be excessive and also had impacts on the energy dissipation and rocking moment capacity. A general discussion of the tradeoffs between energy dissipation and re‐centering of rocking foundations and other devices is included. Copyright © 2011 John Wiley & Sons, Ltd.     

Bender Elements在测试土样剪切波速中的应用

本文以作者在香港理工大学土木与结构工程系设计制作的一套BenderElements为例,介绍了BenderElements的原理、发展历史、应用范围、使用方法和注意事项等。BenderElements是由压电陶瓷材料制成的,在拉伸、压缩作用下,会产生正、负电荷,反过来,给它施加正、负电荷后,它又可产生弯曲振动,正是利用它的这一特性,将其作成接收和发射装置,来测试土样的剪切波速Vs。BenderElements在安装使用时,防水和静电屏蔽十分关键。Vs可在场地地震反应、液化判别、动力基础设计、检测地基改良效果等方面获得应用。震相识别的原则是接收信号的第一个峰值为到时。     

The constancy of galactic cosmic rays as recorded by cosmogenic nuclides in iron meteorites

We measured the He, Ne, and Ar isotopic concentrations and the ¹⁰Be, ²⁶Al, ³⁶Cl, and ⁴¹Ca concentrations in 56 iron meteorites of groups IIIAB, IIAB, IVA, IC, IIA, IIB, and one ungrouped. From ⁴¹Ca and ³⁶Cl data, we calculated terrestrial ages indistinguishable from zero for six samples, indicating recent falls, up to 562 ± 86 ka. Three of the studied meteorites are falls. The data for the other 47 irons confirm that terrestrial ages for iron meteorites can be as long as a few hundred thousand years even in relatively humid conditions. The ³⁶Cl‐³⁶Ar cosmic ray exposure (CRE) ages range from 4.3 ± 0.4 Ma to 652 ± 99 Ma. By including literature data, we established a consistent and reliable CRE age database for 67 iron meteorites. The high quality of the CRE ages enables us to study structures in the CRE age histogram more reliably. At first sight, the CRE age histogram shows peaks at about 400 and 630 Ma. After correction for pairing, the updated CRE age histogram comprises 41 individual samples and shows no indications of temporal periodicity, especially not if one considers each iron meteorite group separately. Our study contradicts the hypothesis of periodic GCR intensity variations (Shaviv 2002, 2003), confirming other studies indicating that there are no periodic structures in the CRE age histogram (e.g., Rahmstorf et al. 2004; Jahnke 2005). The data contradict the hypothesis that periodic GCR intensity variations might have triggered periodic Earth climate changes. The ³⁶Cl‐³⁶Ar CRE ages are on average 40% lower than the ⁴¹K‐K CRE ages (e.g., Voshage 1967). This offset can either be due to an offset in the ⁴¹K‐K dating system or due to a significantly lower GCR intensity in the time interval 195–656 Ma compared to the recent past. A 40% lower GCR intensity, however, would have increased the Earth temperature by up to 2 °C, which seems unrealistic and leaves an ill‐defined ⁴¹K‐K CRE age system the most likely explanation. Finally, we present new ²⁶Al/²¹Ne and ¹⁰Be/²¹Ne production rate ratios of 0.32 ± 0.01 and 0.44 ± 0.03, respectively.     

Adakites and adakitic melts: Compositions of rocks,quenched glasses,and inclusions in minerals

Data set of rocks and glasses whose compositions correspond to the term “adakite” (SiO₂ > 56 wt %, Sr > 400 ppm, Sr/Y > 18) was compiled from two large geochemical data bases. It was revealed that the adakitic melts are characterized by extremely low abundance as compared to adakitic rocks. Only 50 adakitic compositions (~0.5%) were identified in the data base that includes the major and trace element compositions of over 9700 quenched and melt inclusion glasses. It was established that only 22 of selected analyses characterize melt inclusion glasses, while other analyses represent residual glass or “pocket melts” in ultramafic mantle xenoliths. The question of a genetic relationship between adakitic rocks, adakitic melts, and melting of subsiding plate remains open. Original data on the Shiveluch volcanic center (Kamchatka) were used to demonstrate the formation of adakitic signatures through mineral accumulation.     

AnnGIS: Integration of GIS and a Continuous Simulation Model for Non-Point Source Pollution Assessment

Non-Point Source (NPS) models and monitoring data are often used to evaluate management practices and develop NPS pollution control plans. Application of a dynamic NPS model requires efficient input data acquisition, storage, organization, reduction, and analysis accompanied by manipulation, interpretation, reporting, and display of model outputs. A Geographic Information System (GIS) helps extract, store, and organize input data as well as manipulate and display model outputs. This paper illustrates the development of an integrated GIS system for a continuous simulation, pollutant-loading model, AnnAGNPS ( Ann ualized AG ricultural N on- P oint S ource Pollution). The integrated system, called AnnGIS, was developed using the ArcView GIS and related program extensions. Using AnnGIS, modeling studies and management plans can be efficiently and easily developed. AnnGIS helps store, organize, and manipulate spatial and tabular data, extract spatial input parameters, develop analysis scenarios, and visualize input and output data in spatial, tabular, and graphical forms. AnnGIS is generic in nature (not limited to a particular geographic location) and can be successfully used in regions for which AnnAGNPS is designed. AnnGIS's powerful graphical user interface and reference data sets facilitate efficient and informed decision-making concerning agricultural non-point pollution control and management.     

Groundwater-level response to land-use change and the implications for salinity management in the West Moorabool River catchment, Victoria, Australia

The connection between the removal of native vegetation, rising water tables and increasing stream salinity has been established for many catchments across Australia. However, the West Moorabool River in south west Victoria is an example of a catchment where there has been little discernable effect on groundwater levels following land clearing. Over the past 150 years, a significant portion of the catchment has been cleared of dense forest for agricultural development. Historic standing water-level records from 1870–1871 and 1881 are compared with contemporary measurements (1970s to 2007) recorded in the government bore databases. The data show that the earliest recorded groundwater levels are well within the seasonal range of values observed today. By integrating geology and hydrogeology with historical observations of groundwater levels, climate data and land use, the contemporary field observations of stream salinity are linked to the changed water use and shift in rainfall. In contrast to the normally accepted axiom, reafforestation as a management strategy to mitigate the rising salinity in the West Moorabool River catchment would seem inappropriate.     

青藏高原东缘龙门山晚新生代剥蚀厚度与弹性挠曲模拟

龙门山是青藏高原东缘边界山脉,具有青藏高原地貌、龙门山高山地貌和山前冲积平原三个一级地貌单元。利用数字高程模式图像和裂变径迹年代测定方法研究和计算龙门山晚新生代剥蚀厚度与剥蚀速率,结果表明:3.6 Ma以来龙门山的剥蚀厚度介于1.91-2.16 km之间,剥蚀速率介于0.53-0.60 mm/a之间。在此基础上,开展了该地区岩石圈的弹性挠曲模拟,结果表明龙门山的隆升机制具有以构造缩短隆升和剥蚀卸载隆升相叠合的特点。3.6 Ma之前,龙门山的隆升与逆冲推覆构造负载有关,以构造缩短驱动的构造隆升为特色;3.6 Ma之后,龙门山的隆升与剥蚀卸载驱动的抬升有关,并以剥蚀卸载隆升为特色,进而提出了龙门山晚新生代以来的隆升机制以剥蚀成山作用为主的认识。