Preferential nucleosome occupancy at high values of DNA helical rise

Nucleosomes are the basic structural units of eukaryotic chromatin and play a key role in the regulation of gene expression. Nucleosome formation depends on several factors, including properties of the sequence itself, but also physical constraints and epigenetic factors such as chromatin-remodelling enzymes. In this view, a sequence-dependent approach is able to capture a general tendency of a region to bind a histone octamer. A reference data set of positioned nucleosomes of Saccharomyces cerevisiae was used to study the role of DNA helical rise in histone-DNA interaction. Genomic sequences were transformed into arrays of helical rise values by a tetranucleotide code and then turned into profiles of mean helical rise values. These profiles resemble maps of nucleosome occupancy, suggesting that intrinsic histone-DNA interactions are linked to helical rise. The obtained results show that preferential nucleosome occupancy occurs where the mean helical rise reaches its largest values. Mean helical rise profiles obtained by using maps of positioned nucleosomes of the Drosophila melanogaster and Plasmodium falciparum genomes, as well as Homo sapiens chromosome 20 confirm that nucleosomes are mainly located where the mean helical rise reaches its largest values.     

Restoring Ecological Function to a Submerged Salt Marsh

Impacts of global climate change, such as sea level rise and severe drought, have altered the hydrology of coastal salt marshes resulting in submergence and subsequent degradation of ecosystem function. A potential method of rehabilitating these systems is the addition of sediment‐slurries to increase marsh surface elevation, thus ameliorating effects of excessive inundation. Although this technique is growing in popularity, the restoration of ecological function after sediment addition has received little attention. To determine if sediment subsidized salt marshes are functionally equivalent to natural marshes, we examined above‐ and belowground primary production in replicated restored marshes receiving four levels of sediment addition (29–42 cm North American Vertical Datum of 1988 [NAVD 88]) and in degraded and natural ambient marshes (4–22 cm NAVD 88). Moderate intensities of sediment‐slurry addition, resulting in elevations at the mid to high intertidal zone (29–36 cm NAVD 88), restored ecological function to degraded salt marshes. Sediment additions significantly decreased flood duration and frequency and increased bulk density, resulting in greater soil drainage and redox potential and significantly lower phytotoxic sulfide concentrations. However, ecological function in the restored salt marsh showed a sediment addition threshold that was characterized by a decline in primary productivity in areas of excessive sediment addition and high elevation (>36 cm NAVD 88). Hence, the addition of intermediate levels of sediment to submerging salt marshes increased marsh surface elevation, ameliorated impacts of prolonged inundation, and increased primary productivity. However, too much sediment resulted in diminished ecological function that was equivalent to the submerged or degraded system.     

干旱叠加海平面上升、氮负荷增加对河口潮汐沼泽生态系统净CO2交换的影响

河口潮汐沼泽湿地是全球重要的蓝碳生态系统之一。海平面上升和氮负荷增加是入海河流河口湿地面临的两个主要环境问题。近年来,干旱事件频发,干旱及其与海平面上升、氮负荷增加的叠加将如何影响河口潮汐沼泽湿地生态系统净CO₂交换,目前还未见报道。2020年夏秋,福建沿海经历了数月严重的气象干旱,这为揭示干旱对河口潮汐沼泽湿地生态系统净CO₂交换量(NEE)和生态系统呼吸(ER)的影响提供了一个契机。分别于2019年8—10月(正常天气)和2020年8—10月(干旱天气),在闽江河口微咸水短叶茳芏沼泽湿地运用光合作用测定仪+箱法测定不同处理(对照、模拟海平面上升、模拟氮负荷增加、模拟海平面上升+模拟氮负荷增加)短叶茳芏湿地生态系统NEE和ER,以期揭示气象干旱与海平面上升、氮负荷增加的叠加对河口沼泽湿地生态系统净CO₂交换的影响。与正常天气相比,干旱天气下各处理(包含对照)的NEE均显著降低(P<0.05);对照、海平面上升以及氮负荷增加处理样地的ER显著减少(P<0.05),海平面上升+氮负荷增加处理ER显著增加(P&l...     

Sexual reproduction is light-limited as marsh grasses colonize maritime forest

Climate change is driving abiotic shifts that can threaten the conservation of foundation species and the habitats they support. Directional range shifting is one mechanism of escape, but requires the successful colonization of habitats where interspecific interactions may differ from those to which a species has adapted. For plants with multiple reproductive strategies, these range-edge interactions may alter the investment or allocation toward a given reproductive strategy. In this study, we quantified sexual reproduction of the clonal marsh grass Spartina patens across an inland colonization front into maritime forest being driven by sea-level rise. We find that flowering is variable across S. patens meadows, but consistently reduced in low light conditions like those of the forest understory. Observational surveys of S. patens flowering at four sites in the Delmarva Peninsula agreed with the results of two experimental manipulations of light availability (shading experiment in S. patens-dominated marsh and a forest dieback manipulation). These three approaches pinpointed light limitation as a principal control on S. patens flowering capacity, suggesting that light competition with taller upland species can suppress S. patens flowering along its upland migration front. Consequently, all propagation in shaded conditions must occur clonally or via seeds from the marsh, a reproductive restriction that could limit the potential for local adaptation and reduce genetic diversity. Future research is needed to determine whether the lack of flowering is the result of a trade-off between sexual and clonal reproduction or results from insufficient photosynthetic products needed to achieve either reproductive method.     

The effect of a 94 GHz electromagnetic field on neuronal microtubules

Hardware that generates electromagnetic waves with wavelengths from 1 to 10 mm (millimeter waves, “MMW”) is being used in a variety of applications, including high‐speed data communication and medical devices. This raises both practical and fundamental issues concerning the interaction of MMW electromagnetic fields (EMF) with biological tissues. A 94 GHz EMF is of particular interest because a number of applications, such as active denial systems, rely on this specific frequency. Most of the energy associated with MMW radiation is absorbed in the skin and, for a 94 GHz field, the power penetration depth is shallow (≈0.4 mm). At sufficiently high energies, skin heating is expected to activate thermal pain receptors, leading to the perception of pain. In addition to this “thermal” mechanism of action, a number of “non‐thermal” effects of MMW fields have been previously reported. Here, we investigated the influence of a 94 GHz EMF on the assembly/disassembly of neuronal microtubules in Xenopus spinal cord neurons. We reasoned that since microtubule array is regulated by a large number of intracellular signaling cascades, it may serve as an exquisitely sensitive reporter for the biochemical status of neuronal cytoplasm. We found that exposure to 94 GHz radiation increases the rate of microtubule assembly and that this effect can be entirely accounted for by the rapid EMF‐elicited temperature jump. Our data are consistent with the notion that the cellular effects of a 94 GHz EMF are mediated entirely by cell heating. Bioelectromagnetics 34:133–144, 2013. © 2012 Wiley Periodicals, Inc.     

Coastal retreat and improved water quality mitigate losses of seagrass from sea level rise

The distribution and abundance of seagrass ecosystems could change significantly over the coming century due to sea level rise (SLR). Coastal managers require mechanistic understanding of the processes affecting seagrass response to SLR to maximize their conservation and associated provision of ecosystem services. In Moreton Bay, Queensland, Australia, vast seagrass meadows supporting populations of sea turtles and dugongs are juxtaposed with the multiple stressors associated with a large and rapidly expanding human population. Here, the interactive effects of predicted SLR, changes in water clarity, and land use on future distributions of seagrass in Moreton Bay were quantified. A habitat distribution model of present day seagrass in relation to benthic irradiance and wave height was developed which correctly classified habitats in 83% of cases. Spatial predictions of seagrass and presence derived from the model and bathymetric data were used to initiate a SLR inundation model. Bathymetry was iteratively modified based on SLR and sedimentary accretion in seagrass to simulate potential seagrass habitat at 10 year time steps until 2100. The area of seagrass habitat was predicted to decline by 17% by 2100 under a scenario of SLR of 1.1 m. A scenario including the removal of impervious surfaces, such as roads and houses, from newly inundated regions, demonstrated that managed retreat of the shoreline could potentially reduce the overall decline in seagrass habitat to just 5%. The predicted reduction in area of seagrass habitat could be offset by an improvement in water clarity of 30%. Greater improvements in water clarity would be necessary for larger magnitudes of SLR. Management to improve water quality will provide present and future benefits to seagrasses under climate change and should be a priority for managers seeking to compensate for the effects of global change on these valuable habitats.     

Taxonomy,distribution, and natural history of flying foxes (Chiroptera,Pteropodidae) in the Mortlock Islands and Chuuk State,Caroline Islands

The taxonomy, biology, and population status of flying foxes (Pteropus spp.) remain little investigated in the Caroline Islands, Micronesia, where multiple endemic taxa occur. Our study evaluated the taxonomic relationships between the flying foxes of the Mortlock Islands (a subgroup of the Carolines) and two closely related taxa from elsewhere in the region, and involved the first ever field study of the Mortlock population. Through a review of historical literature, the name Pteropus pelagicus Kittlitz, 1836 is resurrected to replace the prevailing but younger name Pteropus phaeocephalus Thomas, 1882 for the flying fox of the Mortlocks. On the basis of cranial and external morphological comparisons, Pteropus pelagicus is united taxonomically with Pteropus insularis “Hombron and Jacquinot, 1842” (with authority herein emended to Jacquinot and Pucheran 1853), and the two formerly monotypic species are now treated as subspecies — Pteropus pelagicus pelagicus in the Mortlocks, and Pteropus phaeocephalus insularis on the islands of Chuuk Lagoon and Namonuito Atoll. The closest relative of Pteropus pelagicus is Pteropus tokudae Tate, 1934, of Guam, which is best regarded as a distinct species. Pteropus pelagicus pelagicus is the only known resident bat in the Mortlock Islands, a chain of more than 100 atoll islands with a total land area of <12 km². Based on field observations in 2004, we estimated a population size of 925–1,200 bats, most of which occurred on Satawan and Lukunor Atolls, the two largest and southernmost atolls in the chain. Bats were absent on Nama Island and possibly extirpated from Losap Atoll in the northern Mortlocks. Resident Mortlockese indicated bats were more common in the past, but that the population generally has remained stable in recent years. Most Pteropus phaeocephalus pelagicus roosted alone or in groups of 5–10 bats; a roost of 27 was the largest noted. Diet is comprised of at least eight plant species, with breadfruit (Artocarpus spp.) being a preferred food. Records of females with young (April, July) and pregnant females (July) suggest an extended breeding season. Pteropus pelagicus pelagicus appears most threatened by the prospect of sea level rise associated with global climate change, which has the potential to submerge or reduce the size of atolls in the Mortlocks. Occasional severe typhoons probably temporarily reduce populations on heavily damaged atolls, but hunting and ongoing habitat loss are not current problems for the subspecies.     

Survival costs of reproduction are mediated by parasite infection in wild Soay sheep

A trade‐off between current and future fitness potentially explains variation in life‐history strategies. A proposed mechanism behind this is parasite‐mediated reproductive costs: individuals that allocate more resources to reproduction have fewer to allocate to defence against parasites, reducing future fitness. We examined how reproduction influenced faecal egg counts (FEC) of strongyle nematodes using data collected between 1989 and 2008 from a wild population of Soay sheep in the St. Kilda archipelago, Scotland (741 individuals). Increased reproduction was associated with increased FEC during the lambing season: females that gave birth, and particularly those that weaned a lamb, had higher FEC than females that failed to reproduce. Structural equation modelling revealed future reproductive costs: a positive effect of reproduction on spring FEC and a negative effect on summer body weight were negatively associated with overwinter survival. Overall, we provide evidence that parasite resistance and body weight are important mediators of survival costs of reproduction.     

Assessing climate change associated sea‐level rise impacts on sea turtle nesting beaches using drones,photogrammetry and a novel GPS system

Climate change associated sea‐level rise (SLR) is expected to have profound impacts on coastal areas, affecting many species, including sea turtles which depend on these habitats for egg incubation. Being able to accurately model beach topography using digital terrain models (DTMs) is therefore crucial to project SLR impacts and develop effective conservation strategies. Traditional survey methods are typically low‐cost with low accuracy or high‐cost with high accuracy. We present a novel combination of drone‐based photogrammetry and a low‐cost and portable real‐time kinematic (RTK) GPS to create DTMs which are highly accurate (<10 cm error) and visually realistic. This methodology is ideal for surveying coastal sites, can be broadly applied to other species and habitats, and is a relevant tool in supporting the development of Specially Protected Areas. Here, we applied this method as a case‐study to project three SLR scenarios (0.48, 0.63 and 1.20 m) and assess the future vulnerability and viability of a key nesting habitat for sympatric loggerhead (Caretta caretta) and green turtle (Chelonia mydas) at a key rookery in the Mediterranean. We combined the DTM with 5 years of nest survey data describing location and clutch depth, to identify (a) regions with highest nest densities, (b) nest elevation by species and beach, and (c) estimated proportion of nests inundated under each SLR scenario. On average, green turtles nested at higher elevations than loggerheads (1.8 m vs. 1.32 m, respectively). However, because green turtles dig deeper nests than loggerheads (0.76 m vs. 0.50 m, respectively), these were at similar risk of inundation. For a SLR of 1.2 m, we estimated a loss of 67.3% for loggerhead turtle nests and 59.1% for green turtle nests. Existing natural and artificial barriers may affect the ability of these nesting habitats to remain suitable for nesting through beach migration.