Time-domain simulation of berthing problem between FPSO and shuttle tanker in waves

A time-domain simulation method based on potential flow model has been developed to investigate the berthing problem between two floating bodies in wave. The boundary value problem is formulated with respect to an earth-fixed coordinate system because the relative positions of the two vessels continuously change during the berthing operation. The classical finite element method is used to solve the Laplace equation in the fluid domain with moving boundary. The linearized free-surface boundary conditions are integrated in time by applying 4th-order Adams–Bashforth–Moulton method. A simple re-mesh algorithm with local and global mesh systems is introduced to update mesh by considering large horizontal movement of the berthing vessel. The developed numerical method is used to investigate the berthing problem between a FPSO and shuttle tanker in waves. The focus is on the wave-induced motion response during the berthing process. The characteristics of the motion responses in berthing operation are examined with various wave frequencies, berthing speeds and wave headings.     

青蛤(Cyclina sinensis) TRAF6基因克隆及其在Poly I:C胁迫下的免疫应答

对青蛤(Cyclina sinensis)转录组文库筛选并克隆得到青蛤TRAF6(Cs TRAF6)基因的c DNA序列,其开放阅读框为2337bp,编码778个氨基酸,分子量为86.59k Da。Cs TRAF6蛋白包含RING型锌指结构,两个TRAF型锌指结构,coiled-coil结构域以及MATH结构域。经生物信息学及分子系统学分析表明Cs TRAF6属于TRAF6家族的一员。利用实时荧光定量PCR方法检测了Cs TRAF6基因在青蛤各个组织以及在Poly I:C侵染下在血淋巴中的时序性表达情况。结果表明,Cs TRAF6基因在青蛤血淋巴、闭壳肌、鳃、性腺、外套膜和肝脏中普遍表达,其中在血淋巴中的表达水平最高。在Poly I:C刺激后的3h,青蛤血淋巴中Cs TRAF6的表达量迅速升高,在6h达到最大值,说明青蛤的Cs TRAF6基因参与了病毒类似物侵染下的免疫应答反应。     

Incremental elastoplastic FEM for simulating the deformation process of suction caissons subjected to cyclic loads in soft clays

This paper presents an incremental elastoplastic finite element method (FEM) to simulate the undrained deformation process of suction caisson foundations subjected to cyclic loads in soft clays. The method is developed by encoding the total-stress-based bounding surface model proposed by the authors in the ABAQUS software package. According to the model characteristics, elastoplastic stress states associated with the incremental strains of each iteration are determined using the sub-incremental explicit Euler algorithm, and the state parameters describing the cyclic accumulative rates of strains are updated by setting state variables during the calculations. The radial fallback method is also proposed to modify the stress states outside the bounding surface to the surface during determination of the elastoplastic stress states. The stress reversals of soil elements are judged by the angle between the incremental deviatoric stress and the exterior normal vector at the image stress point on the bounding surface to update the mapping centre and state variables during cyclic loading. To assess the general validity of the method, the reduced scale model tests and centrifuge tests of suction caissons subjected to cyclic loads are simulated using the method. Predictions are in relative good agreement with test results. Compared with the limit equilibrium and quasi-static methods, the method can not only determine the cyclic bearing capacity, but can also analyse the deformation process and the failure mechanisms of suction caisson under cyclic loads in soft clays.     

Sexual reproduction and early life‐history traits of the Mediterranean soft coral Alcyonium acaule

Understanding processes that contribute to a better comprehension of the population dynamics of long‐lived species is critical for the maintenance and potential recovery of such species. Despite the abundance of soft corals in Mediterranean rocky reefs, little information exists on their life histories and reproductive patterns. In this study, we assessed the main reproductive characteristics and early life‐history traits of the long‐lived soft coral Alcyonium acaule. The sex ratio was 1:1; the smallest fertile colonies were one finger in size (2.1 ± 0.6 cm in height), and both colony and polyp fertility increased with colony size. Likewise, the number of eggs and spermary sacs per polyp increased significantly with colony size, whereas the diameter of the female and male sexual products did not. Over 6 years of observations (2007–2012), spawning occurred primarily in July, after the seawater reached 20 °C, in a single spawning episode per year. Approximately 80% of female colonies released eggs, which were retained on the surface of the mother colony by mucous strings for up to a few days. High fertilization rates were observed during spawning in 2008 and 2009 (94.9% and 87.0%, respectively). The timing of development was ~24 h for the blastulae, ~48–72 h for the planulae and 8–22 days for metamorphosis into primary polyps. Survivorship of planulae was relatively high (~50% at 45 days after release), but only 24% of larvae metamorphosed into primary polyps, and their survivorship was moderate after 2 months (65% in 2008 and 74% in 2009). Asexual reproduction was negligible, indicating that sexual reproduction is the main mechanism supporting the maintenance and recovery of populations.     

Spatial distribution of crustaceans associated with shallow soft‐bottom habitats in a coral reef lagoon

The ecology and diversity of the shallow soft‐bottom areas adjacent to coral reefs are still poorly known. To date, the few studies conducted in these habitats dealing with macroinvertebrate fauna have focused on their abundance spatial patterns at high taxonomic levels. Thus, some aspects important to evaluate the importance and vulnerability of these habitats, such as species diversity or the degree of habitat specialization, have often been overlooked. In this study we compared the crustacean assemblages present in four different habitats at Magoodhoo Island coral reef lagoon (Maldives): coral rubble, sandy areas and two different seagrass species (Thalassia hemprichii and Cymodocea sp.). Forty‐two different crustacean species belonging to 30 families and four orders were found. ‘Site’ was a significant factor in all of the statistical analyses, indicating that tropical soft‐bottom habitats can be highly heterogeneous, even at a spatial scale between tens and hundreds of meters. Although traditionally it has been considered that seagrass beds host greater species diversity and abundance of organisms than adjacent unvegetated habitats, no differences in the univariate measures of fauna (abundance of organisms, number of species and Shannon diversity) were observed among habitats. However, sandy areas, coral rubble and seagrass beds exhibited different species composition of crustacean communities. The percentage of taxa considered as potential habitat specialists was 27% and the number of species exclusively occurring in one habitat was especially high in seagrass beds. Thus, degradation of this vegetated habitat would result in a great loss of biodiversity in tropical shallow soft‐bottom habitats.     

Enhalus acoroides responses to experimental shoot density reductions in Haad Chao Mai National Park,Trang Province,Thailand

The effect of self‐shading and competition for light in the seagrass Enhalus acoroides were investigated with a density reduction experiment in Haad Chao Mai National Park, Trang Province, Thailand. The study was carried out in a monospecific meadow with a natural density of 141.0 ± 8.7 shoots·m^?2. The intent was to determine the response of E. acoroides beds to loss of shoots and thinning, which often occur during typhoons and severe storm activity. Permanent quadrats were manipulated by clipping the seagrass shoots to 140, 72, 36 and 16 shoots·m^?2, to yield natural, 50%, 25% and 10% densities, respectively. Reducing shoot density in E. acoroides increased underwater light intensity below the canopy, generating increased leaf surface area and shoot weight. Seagrass leaf width, growth rate, and number of leaves per shoot also increased with greater light. The extent of flowering varied among treatments with no consistent trend. Our results demonstrate that increasing the available light to E. acoroides produces an increasing leaf size response as self‐shading in the bed is reduced.     

Differentiation in reproductive traits of geminate mangrove crabs of the genus Aratus (Decapoda: Brachyura) across the Central American Isthmus

The mangrove crab Aratus pisonii was considered to have an amphi‐American distribution; however, a recent study revealed that the Eastern Tropical Pacific populations were genetically distinct, thus representing a new species: Aratus pacificus. These species separated by the Isthmus of Panama have diverged under different environmental conditions that may have influenced their reproductive biology. As the available information about this genus concerns almost exclusively the Caribbean species, the aim of the present study was to analyse and compare reproductive aspects of A. pacificus and A. pisonii obtained from both the Pacific and Caribbean coasts of Costa Rica. Females were collected from April 2011 to April 2012, and reproductive features such as breeding season, size distribution of ovigerous females, fecundity, reproductive output, embryo volume and embryo water content were assessed. Both species produced embryos during the entire sampled period. Most females of A. pacificus carrying embryos close to hatching were found during the rainy season. Ovigerous females of A. pisonii were substantially larger and reached sexual maturity at a larger size than females of A. pacificus. Embryo production started in A. pacificus at a smaller female size than in A. pisonii. As fecundity increased with female size, the average fecundity was lower in A. pacificus. Females of A. pisonii produced larger embryos, which might be related to lower food availability: higher energy content in the embryo enhances the chances of larval survival. These data regarding reproductive features of the Pacific and Caribbean species support the conclusion to separate A. pacificus from A. pisonii.     

高阶边界元方法求解规则波在三维局部渗透海床上的传播

基于线性势流理论,利用高阶边界元法研究了规则波在三维局部渗透海床上的传播。根据Darcy渗透定律推导出渗透海床的控制方程,利用渗透海床顶部和海底处法向速度和压强连续条件得到渗透海床顶部满足的边界条件。根据绕射理论,利用满足自由水面条件的格林函数建立了求解渗透海床绕射势的边界积分方程,采用高阶边界元方法求解边界积分方程进而得到自由水面的绕射势和波浪在局部渗透海床上传播过程中幅值的变化情况。通过与已发表的波浪对圆柱形暗礁的时域全绕射结果对比,证明了本文建立的频域方法计算波幅的正确性和有效性。利用这一模型研究了三维矩形渗透海床区域上波浪的传播特性,并分析了入射波波长、海床渗透特性系数等参数对波浪传播的影响。     

Ontogenic variation and effect of collection procedure on leaf biomechanical properties of Mediterranean seagrass Posidonia oceanica (L.) Delile

Leaf mechanical traits are important to understand how aquatic plants fracture and deform when subjected to abiotic (currents or waves) or biotic (herbivory attack) mechanical forces. The likely occurrence of variation during leaf ontogeny in these traits may thus have implications for hydrodynamic performance and vulnerability to herbivory damage, and may be associated with changes in morphologic and chemical traits. Seagrasses, marine flowering plants, consist of shoot bundles holding several leaves with different developmental stages, in which outer older leaves protect inner younger leaves. In this study we examined the long‐lived seagrass Posidonia oceanica to determine ontogenic variation in mechanical traits across leaf position within a shoot, representing different developmental stages. Moreover, we investigated whether or not the collection procedure (classical uprooted shoot versus non‐destructive shoot method: cutting the shoot without a portion of rhizome) and time span after collection influence mechanical measurements. Neither collection procedure nor time elapsed within 48 h of collection affected measurements of leaf biomechanical traits when seagrass shoots were kept moist in dark cool conditions. Ontogenic variation in mechanical traits in P. oceanica leaves over intermediate and adult developmental stages was observed: leaves weakened and lost stiffness with aging, while mid‐aged leaves (the longest and thickest ones) were able to withstand higher breaking forces. In addition, younger leaves had higher nitrogen content and lower fiber content than older leaves. The observed patterns may explain fine‐scale within‐shoot ecological processes of leaves at different developmental stages, such as leaf shedding and herbivory consumption in P. oceanica.     

Closely related thyasirid bivalves associate with multiple symbiont phylotypes

Species of thyasirid bivalves are considered to be representative of early stages of chemosymbiosis, given that bacterial symbionts occur outside gill epithelial cells, vary among species in their abundance and nutritional importance, and are environmentally acquired. For these reasons, assessing the extent of host–symbiont specificity in thyasirids could provide valuable information on the evolution of chemosymbiosis. We show that individuals of two closely related and sympatric Thyasira cf. gouldi operational taxonomic units collected from three sites in a fjord in Newfoundland, Canada, associate with one of three distinct, closely related symbiont phylotypes. While associations show some site‐specificity, there is flexibility in host–symbiont pairings within the fjord, further supporting an early and relatively unspecific stage of chemosymbiosis in this family. Morphologic differences observed both within and among symbiont phylotypes suggest physiologic variation, possibly induced by small‐scale differences in sedimentary conditions.