The Effects of Artificial Beach Nourishment on Marine Turtles: Differences between Loggerhead and Green Turtles

Marine turtle reproductive success is correlated with the stability and quality of the nesting environment. Female marine turtles show fidelity to nesting beaches, making artificial beach nourishment practices directly relevant to their recovery. We evaluated the impacts of artificial beach nourishment on Loggerhead ( Caretta caretta ) and Green turtles ( Chelonia mydas ) between artificially nourished and nonnourished beaches. We observed reduced nesting success (ratio of nesting emergences to emergences not resulting in nest deposition) for both species. This negative effect lasted for one season in Loggerheads and for at least one season in Green turtles. Physical attributes of the fill sand did not impede nesting attempts. We argue that the decrease in nesting success resulted from an altered beach profile not favorable for nest deposition, which subsequently improved in later seasons as the beach equilibrated to a more natural slope. We observed a 52.2% decrease in reproductive output (hatchlings km⁻¹ yr⁻¹) for Loggerheads one year postnourishment, with a 44.1% increase observed the two seasons postnourishment. In Green turtles, a 0.8% reduction was observed the first season postnourishment, despite a 13% increase in the nonnourished area. The reduction in reproductive output in both cases was primarily a consequence of decreased nesting success, lowering nest numbers. These results reveal stronger negative effects of beach nourishment on Loggerheads compared to Green turtles and the importance of minimizing excessive nonnesting emergences associated with artificial beach nourishment. Nourished areas also experienced more than 600% increase in the number of Loggerhead hatchlings disoriented by artificial lighting over two years postnourishment.     

Compaction properties of an intrinsically disordered protein: Sic1 and its kinase-inhibitor domain

IDPs in their unbound state can transiently acquire secondary and tertiary structure. Describing such intrinsic structure is important to understand the transition between free and bound state, leading to supramolecular complexes with physiological interactors. IDP structure is highly dynamic and, therefore, difficult to study by conventional techniques. This work focuses on conformational analysis of the KID fragment of the Sic1 protein, an IDP with a key regulatory role in the cell-cycle of Saccharomyces cerevisiae. FT-IR spectroscopy, ESI-MS, and IM measurements are used to capture dynamic and short-lived conformational states, probing both secondary and tertiary protein structure. The results indicate that the isolated Sic1 KID retains dynamic helical structure and populates collapsed states of different compactness. A metastable, highly compact species is detected. Comparison between the fragment and the full-length protein suggests that chain length is crucial to the stabilization of compact states of this IDP. The two proteins are compared by a length-independent compaction index.     

PRCl Marks the Difference in Plant PcG Repression

ABSTRACT From mammals to plants, the Polycomb Group （PcG） machinery plays a crucial role in maintaining the repres- sion of genes that are not required in a specific differentiation status. However, the mechanism by which PeG machinery mediates gene repression is still largely unknown in plants. Compared to animals, few PcG proteins have been identi- fied in plants, not only because just some of these proteins are clearly conserved to their animal counterparts, but also because some PcG functions are carried out by plant-specific proteins, most of them as yet uncharacterized. For a long time, the apparent lack of Polycomb Repressive Complex （PRC）I components in plants was interpreted according to the idea that plants, as sessile organisms, do not need a long-term repression, as they must be able to respond rapidly to environmental signals; however, some PRC1 components have been recently identified, indicating that this may not be the case. Furthermore, new data regarding the recruitment of PcG complexes and maintenance of PcG repression in plants have revealed important differences to what has been reported so far. This review highlights recent progress in plant PcG function, focusing on the role of the putative PRC1 components.     

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis

Background

In somatic cancer genomes, delineating genuine driver mutations against a background of multiple passenger events is a challenging task. The difficulty of determining function from sequence data and the low frequency of mutations are increasingly hindering the search for novel, less common cancer drivers. The accumulation of extensive amounts of data on somatic point and copy number alterations necessitates the development of systematic methods for driver mutation analysis.

Results

We introduce a framework for detecting driver mutations via functional network analysis, which is applied to individual genomes and does not require pooling multiple samples. It probabilistically evaluates 1) functional network links between different mutations in the same genome and 2) links between individual mutations and known cancer pathways. In addition, it can employ correlations of mutation patterns in pairs of genes. The method was used to analyze genomic alterations in two TCGA datasets, one for glioblastoma multiforme and another for ovarian carcinoma, which were generated using different approaches to mutation profiling. The proportions of drivers among the reported de novo point mutations in these cancers were estimated to be 57.8% and 16.8%, respectively. The both sets also included extended chromosomal regions with synchronous duplications or losses of multiple genes. We identified putative copy number driver events within many such segments. Finally, we summarized seemingly disparate mutations and discovered a functional network of collagen modifications in the glioblastoma. In order to select the most efficient network for use with this method, we used a novel, ROC curve-based procedure for benchmarking different network versions by their ability to recover pathway membership.

Conclusions

The results of our network-based procedure were in good agreement with published gold standard sets of cancer genes and were shown to complement and expand frequency-based driver analyses. On the other hand, three sequence-based methods applied to the same data yielded poor agreement with each other and with our results. We review the difference in driver proportions discovered by different sequencing approaches and discuss the functional roles of novel driver mutations. The software used in this work and the global network of functional couplings are publicly available at http://research.scilifelab.se/andrej_alexeyenko/downloads.html.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-308) contains supplementary material, which is available to authorized users.     

小鼠胚胎致密化起始的调控机制

植入前小鼠胚胎的发育事件包括第一次卵裂、胚胎基因组激活、桑椹胚致密、囊胚形成。小鼠受精卵胚胎的致密化发生在8-细胞阶段晚期, 致密过程中, 胚胎卵裂球本身以及卵裂球之间发生了一系列的变化。这些变化包括卵裂球微绒毛以及胞质成分的极性化分布, 卵裂球之间形成特殊的胞间连接。致密化是哺乳动物胚胎发育过程中的第一个细胞分化事件, 即导致了内细胞团以及滋养外胚层的产生。植入后, 内细胞团将发育成为胚体, 滋养外胚层将发育成为胎盘等胚外组织。细胞粘附分子E-cadherin介导的胞间粘附起始了致密化。卵裂球发生粘附所需的组分在致密前已经存在, 但是直至8-细胞阶段晚期连接复合体才表现出明显的粘附活性。敲除E-cadherin基因, 发现母源性的E-cadherin足以介导致密。E-cadherin介导的胞间粘附是细胞粘附的第一步。文章综述了E-cadherin介导胞间粘附的具体过程以及蛋白激酶C(Protein kinase C, PKC)调控该过程的相关 机制。     

Responses of Woody Plants To Human-Induced Environmental Stresses: Issues,Problems, and Strategies for Alleviating Stress

Forest ecosystems are enormously important to mankind.They not only supply wood,foods,medicines,waxes,oils,gums,resins and tannins,but they also regulate climate, hydrology,mineral cycling,soil erosion,and cleansing of air and water.A variety of natural and human-induced environmental stresses have both beneficial and harmful effects on forest ecosystems.However,human-induced stresses are much more harmful than naturally induced disturbances.Human-induced stresses,which often are catastrophic although avoidable,include defor estation,fire,pollution,flooding,and soil compaction.Such stresses variously injure woody plants,impede vegetative and reproductive growth,and induce mortality,largely by causing physiological dysfunction in plants.Human-induced environmental stresses have led to decimation of forest ecosystems,loss of biodiversity,forest declines,and potential global warming. Short-rotation plantations,especially in the tropics,are increasing rapidly,largely to produce wood quickly.Plantations also stabilize soil,prevent water runoff,provide shelter from wind and heat,and relieve pressure for exploiting natural forests.However,plantations alone are unlikely to satisfy society 's growing needs for the products and services that can be provided by woody plant ecosystems.Hence,several multiple concurrent strategies are urgently needed to lessen the many destructive effects of human-induced environmental stresses on woody plants.These include not only the expansion of plantations but also of agroferestry systems and forest reserves as well as the development of innovative silvicultural techniques with a focus on the preservation of natural forests.Conserving sustainability of natural forests will require a land ethic as prelude to understanding the functioning of forest ecosystems,ecological and physiological impacts of disturbances on ecosystems,and the processes involved in recovery of disturbed ecosystems. Many of the harmful effects of pollution,fire,flooding,and soil compaction can be abated by judicious planning to create and perpetuate the critical components of forest stand structure and species composition.Strategies for continuous production of the products and services that can be supplied by woody plants will need to be reinforced by expanded long-term research and close cooperation among forest biologists,social scientists,economists,and regulatory government agencies.     

轮耕对关中一年两熟区土壤物理性状和冬小麦根系生长的影响

针对关中地区土壤连续单一耕作存在的主要问题,进行了土壤轮耕效应研究。2009年至2012年在关中一年两熟区采用连续4a旋耕(RT)、翻耕-免耕-翻耕-免耕(PNT)和深松-免耕-深松-免耕(SNT)3种耕作处理,对土壤容重、紧实度及小麦根系生长进行了研究。结果表明,与试验前相比,夏玉米收获后(2013年10月)两种轮耕处理显著(P0.05)降低了0—10、10—20 cm土壤容重,旋耕处理在0—10 cm处差异不显著,而10—20 cm土壤容重显著增大;与旋耕处理相比,两种轮耕处理0—10、10—20 cm土壤容重在第4季冬小麦整个生育期内变异系数较小,土壤紧实度较低,且改善效果在冬小麦生育中后期10—20 cm土层体现更为显著;旋耕处理0—10、10—20 cm土壤紧实度与含水量均呈显著负相关,相关系数分别为-0.89、-0.85,两种轮耕处理相关性不显著;0—40 cm土层根重密度和根系活力表现为:两种轮耕处理连年旋耕。可见,长期旋耕后进行轮耕(免耕与翻耕、深松)有利于改善土壤物理状况,促进作物根系生长。     

Effects of Soil Structure on Pea (Pisum sativum L.) Root Development According to Sowing Date and Cultivar

Spring peas are known to be very sensitive to compaction, particularly when sowing takes place soon after winter. Winter peas, which are sown in autumn, should present an opportunity to sow the crop in better soil structural conditions than for spring peas, because of more favourable moisture conditions at that time. As environmental conditions have a big influence on root systems, it is important to determine the effects of soil structure on pea root systems for different cultivars and sowing dates. A spring pea cultivar and a winter pea cultivar were both sown at two dates (one in autumn and one in spring) on soils with different plough-layer structures (compacted and uncompacted) at two sites in 2002 and one site in 2003. Soil structure was characterised by bulk density and the percentage of highly compacted zones in the ploughed layer. Root distribution maps were produced every month, from February to maturity. Root development was described in terms of general root dynamics, root elongation rate (RER) in the subsoil, final maximum root depth (Dmax) and root distribution at maturity. Root depth dynamics depended on compaction and its interaction with climatic conditions. The effects of compaction on RER in the subsoil depended on the experimental conditions. Dmax was reduced by 0.10 m by compaction. Compaction also reduced root distribution between 10 and 40% in the ploughed layer only. Pea cultivars differed in sensitivity to soil compaction, with a direct effect on the final depth explored by roots. These results are discussed in terms of their relevance to water and nutrient uptake.     

Phosphorus availability to maize from partially acidulated phosphate rocks and phosphate rocks compacted with triple superphosphate

Two phosphate rocks (PR), moderately reactive Hila PR from Colombia and slightly reactive Capinota PR from Bolivia, were compacted with triple superphosphate (TSP) such that 50% of total P in the mixture was in water-soluble form. The effectiveness of these materials as phosphorus sources was compared with that of partially acidulated phosphate rocks (PAPR) at 50% acidulation with sulfuric acid and TSP in Hartsells silt loam (pH 4.5) with maize as the test crop. Huila PAPR and Huila PR compacted with TSP were as effective as TSP as phosphorus sources. Huila PR was only half as effective. The slightly reactive Capinota PR with 8.8% Al₂O₃ + Fe₂O₃ content was not suited for direct application, and Capinota PAPR was only half as effective as TSP. Capinota PR compacted with TSP, however, was as effective as TSP. PR compacted with TSP, urea, and KCl was no more effective as phosphorus source than PR compacted with TSP alone.