Role of CpG context and content in evolutionary signatures of brain DNA methylation

DNA methylation is essential in brain function and behavior; therefore, understanding the role of DNA methylation in brain-based disorders begins with the study of DNA methylation profiles in normal brain. Determining the patterns and scale of methylation conservation and alteration in an evolutionary context enables the design of focused but effective methylation studies of disease states. We applied an enzymatic-based approach, Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS), which utilizes second-generation sequencing technology to provide an unbiased representation of genome-wide DNA methylation profiles of human and mouse brains. In this large-scale study, we assayed CpG methylation in cerebral cortex of neurologically and psychiatrically normal human postmortem specimens, as well as mouse forebrain specimens. Cross-species human-mouse DNA methylation conservation analysis shows that DNA methylation is not correlated with sequence conservation. Instead, greater DNA methylation conservation is correlated with increasing CpG density. In addition to CpG density, these data show that genomic context is a critical factor in DNA methylation conservation and alteration signatures throughout mammalian brain evolution. We identify key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease.     

CONSERVATION IN THE MARINE ENVIRONMENT: SOME PROBLEMS WITH THE MANAGEMENT OF SHORE-ANGLING IN THE SOUTHWESTERN CAPE

Summary

Recreational shore angling is a very important sector of South Africa's diverse marine fisheries. The number of anglers participating in this sport is increasing at 6% per annum and currently stands at approximately 380 000. This number is expected to exceed one million within 20 years. The catch rates of many species caught from the shore have declined markedly for at least 50 years and the species composition of the catch has changed. This indicates that stocks of many species are overexploited and that effort increases cannot be sustained. Measures introduced to conserve these stocks appear to have been largely unsuccessful because they do not have the support of many anglers and they are ineffectively policed. It is concluded that, in order to sustain this fishery, current legislation needs to be improved and that a licensing system for anglers should be introduced through which an education campaign can be channelled.     

Wave energy alters biodiversity by shaping intraspecific traits of a habitat-forming species

The role of habitat-forming species in promoting biodiversity is widely acknowledged to vary across environmental gradients according to the extent to which they modify resources and environmental conditions. Population- and individual-level traits of habitat-forming species that influence species interactions may vary across gradients, but the importance of this indirect effect of environmental context is seldom considered. Here, we conducted surveys and field experiments to partition the effects of wave exposure on habitat-provisioning for invertebrates by oysters into direct and indirect effects, arising from morphological variation of the oysters. A survey of nine sites with varying degrees of wave exposure in Port Jackson, Australia revealed a decline in oyster densities and surface area as wave energy increased. Correlated to declining oyster surface area was a decrease in the richness and abundance of associated invertebrates. By contrast, taxon diversity increased with increasing wave energy. Experimental deployments of oysters at high and low wave energy sites confirmed that variations in oyster morphology was a phenotypically plastic response to environmental conditions. Oyster recruitment was also lower at high as compared to low wave energy sites, further contributing to the variation in oyster habitat among sites. A colonisation experiment in which exposed and sheltered morphologies of oysters were deployed under high and low wave energy conditions in a fully orthogonal design found that invertebrate communities were influenced by both the wave energy of sites and by habitat structure. Our study suggests that in some instances the indirect effects of environment on habitat availability, arising from changes in habitat-forming species density and morphology, may be as, or even more, important than the direct effects. Understanding how traits of habitat-forming species respond to environmental conditions, and how intraspecific trait-variation cascades to influence associated communities is critical to predicting when and where positive species interactions will be greatest.     

Trail following behaviour in relation to pedal mucus production in the intertidal gastropod Monodonta labio (Linnaeus)

Trail following behaviour and pedal mucus production were investigated in the mid-shore topshell, Monodonta labio (Linnaeus) in Hong Kong. On the shore, individuals exhibited both conspecific and self trail following while awash on ebb and flood tides, although fidelity to resting sites during emersion on successive days was low. In the laboratory, animals that encountered trails that had been aged on the shore for different periods showed similar patterns of movement (distance moved, speed and tortuosity) suggesting that degradation of cues in the mucus that animals responded to did not occur until > 3 days post-deposition. Animals moved faster, with a lower rate of radular rasping, on freshly laid mucus trails than on a biofilm-covered substratum and did not change their speed when moving over aged (biofilm-covered) mucus compared to fresh mucus. Mucus production rates were similar when animals were crawling on vertical or horizontal surfaces, but significantly more mucus was produced when animals were emersed than when submerged. Mucus trail profiles were of variable thickness, but ‘double’ mucus trails (marker + tracker trails) did not contain significantly more mucus than ‘single’ trails (marker mucus only) and were considerably thinner than single trails suggesting tracker snails utilized mucus laid by marker snails, reducing their own deposition of mucus. Thus, while M. labio do not appear to utilize trails for orientation or refuge location, snails that follow trails have the potential to save energy through reducing mucus production or to gain energy through mucus ingestion. Given the role of pedal mucus production in the overall energy balance of gastropods, such energetic benefits are considerable and may have implications for the life history of the snail.     

Shore‐based observations of seasonality,movements, and group behavior of southern right whales in a nonnursery area on the South African west coast

The southern right whale's (Eubalaena australis) demography, occurrence, habitat use, and behavior off South Africa are known predominantly from an ongoing aerial survey data set that started in 1971. The fixed timeframes of these surveys and their geographical bias towards south coast nursery areas have constrained our knowledge about the right whale's seasonal distribution elsewhere. We present shore‐based observations and tracking of right whales at Saldanha Bay on the west coast (2001–2003) that reveal a near year‐round presence and strongly nearshore distribution. With seasonal progression from winter to summer we observed a gradual increase in sighting rate, reduction in swimming speed, less directionality of movement, an increase in group size, and more surface active groups. The area appears to be important for feeding and socializing but not as a calving or nursery area. Individual transits between the south and west coasts, bidirectional alongshore movements, and extended seasonal presence may all be indicative of reoccupation of their former range along the west coast. This is important given the increasing ship traffic at Saldanha Bay, the rapid expansion of the region's oil and gas industry, and the known vulnerability of the closely related North Atlantic right whale (E. glacialis) to ship strikes.     

The prevalence and species richness of spiders associated with marine strandlines on different shore types around Banks Peninsula,New Zealand

ABSTRACT

Marine strandlines provide habitat for a variety of littoral and terrestrial invertebrates, including arachnids. In this study we recorded spiders in strandlines at 35 sites on Banks Peninsula, New Zealand. On average, only 1.5 named species were recorded per thirty-minute hand search, and many sample visits (30%) recorded no spiders. Species accumulation curves suggested further species could be recorded with further sampling, but these may be tourist species rather than strandline residents. Thirty-eight species were recorded in total, with the introduced theridiid Steatoda capensis being the most common (30 records) and widespread (17 locations). The New Zealand endemic species Otagoa nova (25 records) (Toxopidae), Anoteropsis litoralis (15) and Anoteropsis hilaris (15) (Lycosidae), and the introduced Tenuiphantes tenuis (24) (Linyphiidae), were also common. Spiders were more frequent in strandlines on boulder beaches compared with shingle beaches, although there was no statistical differences in the numbers of species recorded on the different beach types.     

陀螺旋转式立体定向放射治疗联合NP 方案治疗局部晚期非小细胞肺癌 的临床疗效观察

目的:观察陀螺旋转式立体定向放射治疗系统(陀螺刀)联合长春瑞滨、顺铂(NP)方案治疗局部晚期非小细胞肺癌(NSCLC)的临床疗效观察及毒副反应。方法:94例局部晚期NSCLC患者,先给予陀螺刀治疗,单次治疗剂量3.2-5.0 Gy,等剂量曲线50%-70%,计划靶体积(PTV)覆盖95%以上,总剂量35-50 Gy,治疗后进行NP方案化疗4-6个周期。与同期144例单纯陀螺刀治疗局部晚期NSCLC患者治疗结果相比较。结果:联合治疗的94例患者,近期有效率为86.17%(81/94),6、12和24个月生存率分别为86.17%(81/94)、60.64%(57/94)和36.17%(34/94),毒性反应较轻。同期单纯陀螺刀治疗患者,近期有效率为88.19%(127/144),6、12和24个月生存率分别为87.50%(126/144)、44.44%(64/144)和23.68%(33/144)。结论:陀螺刀联合NP方案是一种对局部晚期NSCLC比较有效的治疗方法,毒副反应较轻。     

Grazing effects in macroalgal communities depend on timing of patch colonization

Rocky macroalgal assemblages are typically composed of patches differing in age and species composition and grazing is generally a very important modifier of such assemblages. We hypothesized that patch colonization time determines its algal community and that grazing effects depend on the colonization time and vary with depth. We created patches by placing empty substrates at two sublittoral depths over five consecutive months, manipulated grazer entry and determined the algal species composition in each patch in the next growing season. Distinct algal colonization periods resulted in different algal assemblages. Although algal communities in our study area consist mainly of opportunistic species, thus being highly dynamic, the resulting macroalgal assemblages differed in species richness, diversity, composition, and total biomass even a year after first colonization. Substrates close to the water-surface supported a higher species richness and diversity than those in the deeper littoral. The community characteristics, total density, total biomass and species richness were only slightly, if at all affected by grazing. However, individual algal species or taxa showed varying and even contrasting responses to grazing, often differently between depths and depending on colonization time. In the deeper littoral, but not close to the water surface, grazing increased the density of filamentous brown algae while reducing the green alga Cladophora glomerata. In these taxa, grazing effects were strongest in patches colonized during the early growing season. Grazing at the colonization stage had lasting consequences for the density of several individual species.     

Biocontrol of the shore fly Scatella tenuicosta with Hypoaspis miles and H. aculeifer in peat pots

Hypoaspis miles Berlese and H. aculeiferCanestrini (Acari: Laelapidae) were usedagainst Scatella tenuicosta Collin(Diptera: Ephydridae) at the rates of 7, 14and 36 mites per 0.3-l peat pot (1000, 2000 and5000 per net-m² of peat) with mint (Mentha piperita L.) as the crop. The predatorswere applied either one day (preventivecontrol) or nine days after (curative control)exposing the pots to the flies in thegreenhouse. Based on the number of flies thatemerged from the pots, the control efficacy of preventive H. aculeifer treatments at therate of 36 mites per pot was 84–100% and 92–97% (range over four replicate blocks)after two and three weeks, respectively, fromthe application. The control efficacy ofcurative treatments was 93–100% and 83–94% after two and three weeks, respectively,from the application. Preventive treatmentswith H. miles applied at the rate of 36per pot controlled the flies by 92–100% and 68–97% two and three weeks, respectively, afterthe application. Curative treatments with 36H. miles per pot were less effective (–53–68% and –16–65%, respectively). All treatments with lower mite rates with eitherspecies were ineffective. Due to moreconsistent reduction of fly numbers by Hypoaspis aculeifer, the species was concluded to be a better biocontrol agent ofshore flies in short-term greenhouse cropsgrown in peat pots, probably due to its higherpredation capacity in comparison to H. miles.     

Indirect effects shape macroalgal epifaunal communities

We tested the response of algal epifauna to the direct effects of predation and the indirect consequences of habitat change due to grazing and nutrient supply through upwelling using an abundant intertidal rhodophyte, Gelidium pristoides. We ran a mid‐shore field experiment at four sites (two upwelling sites interspersed with two non‐upwelling sites) along 450 km of the south coast of South Africa. The experiment was started in June 2014 and ran until June 2015. Four treatments (predator exclusion, grazer exclusion, control, and procedural control) set out in a block design (n = 5) were monitored monthly for algal cover for the first 6 months and every 2 months for the last 6 months. Epifaunal abundance, species composition, algal cover, and algal architectural complexity (measured using fractal geometry) were assessed after 12 months. Predation had no significant effect on epifaunal abundances, while upwelling interacted with treatment. Grazing reduced the architectural complexity of algae, with increased fractal dimensions in the absence of grazers, and also reduced algal cover at all sites, though the latter effect was only significant for upwelling sites. Epifaunal community composition was not significantly affected by the presence of herbivores or predators but differed among sites independently of upwelling; sites were more similar to nearby sites than those farther away. In contrast, total epifaunal abundance was significantly affected by grazing, when normalized to algal cover. Grazing reduced the cover of algae; thus, epifaunal abundances were not affected by the direct top‐down effects of predation but did respond to the indirect effects of grazing on habitat availability and quality. Our results indicate that epifaunal communities can be strongly influenced by the indirect consequences of biotic interactions.