Genomic imprinting: A missing piece of the Multiple Sclerosis puzzle?

Evidence for parent-of-origin effects in complex diseases such as Multiple Sclerosis (MS) strongly suggests a role for epigenetic mechanisms in their pathogenesis. In this review, we describe the importance of accounting for parent-of-origin when identifying new risk variants for complex diseases and discuss how genomic imprinting, one of the best-characterized epigenetic mechanisms causing parent-of-origin effects, may impact etiology of complex diseases. While the role of imprinted genes in growth and development is well established, the contribution and molecular mechanisms underlying the impact of genomic imprinting in immune functions and inflammatory diseases are still largely unknown. Here we discuss emerging roles of imprinted genes in the regulation of inflammatory responses with a particular focus on the Dlk1 cluster that has been implicated in etiology of experimental MS-like disease and Type 1 Diabetes. Moreover, we speculate on the potential wider impact of imprinting via the action of imprinted microRNAs, which are abundantly present in the Dlk1 locus and predicted to fine-tune important immune functions. Finally, we reflect on how unrelated imprinted genes or imprinted genes together with non-imprinted genes can interact in so-called imprinted gene networks (IGN) and suggest that IGNs could partly explain observed parent-of-origin effects in complex diseases. Unveiling the mechanisms of parent-of-origin effects is therefore likely to teach us not only about the etiology of complex diseases but also about the unknown roles of this fascinating phenomenon underlying uneven genetic contribution from our parents.This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.     

Wnt meets Warburg: another piece in the puzzle?

One of the most common abnormalities of cancer cells is their predilection to engage in a high rate of glycolysis despite the continued availability of oxygen. First described by Otto Warburg, this phenomenon of aerobic glycolysis (or the Warburg effect) has recently been proposed to result from cancer‐associated alterations in signal transduction pathways. In this issue of The EMBO Journal, Pate et al provide further support for this hypothesis by demonstrating that Wnt signaling plays an important role in establishing aerobic glycolysis as a mechanism to support in vivo cancer cell proliferation.     

Where are the missing pieces of the schizophrenia genetics puzzle?

On the basis of recent data from candidate region/gene and genome-wide association studies (GWAS) and their follow-up investigations, the number of genes potentially implicated in schizophrenia has been estimated to be over 1000. However, with regard to the identified odds ratio, it is likely that genetic variants with more definitive effect on schizophrenia phenotype are still missing. The hunt therefore remains open for the genetic variants that would explain the majority of the missing heritability of schizophrenia. This review aims at summarizing data from recent DNA microarray and target gene/region resequencing in order to propose new insights of where to look next. The review is divided into three sections: GWAS, copy-number variations and rare variant--candidate gene resequencing.     

Why Is the European Union Challenging Norway Over Snow Crab? Svalbard,Special Interests,and Arctic Governance

Abstract

Why is the European Union (EU) pursuing a relatively minor issue over the right to catch snow crab in the Barents Sea? The issue has highlighted an underlying disagreement between Norway and the EU over the status of the maritime zones around the archipelago of Svalbard, stemming from the 1920 Spitsbergen Treaty. Is the EU using the snow crab to challenge Norway’s Svalbard regime? The answer is that the EU is a multifaceted animal, where special interests can hijack the machinery and bring issues to the table, given the right circumstances. This article outlines these circumstances, as well as the evolution and the sources of the dispute over the snow crab, as it relates to not only economic interests, but international politics as well as law.     

The origin,composition and rates of organic nitrogen deposition: A missing piece of the nitrogen cycle?

Organic forms of nitrogen are widespread in the atmosphere and their deposition may constitute a substantive input of atmospheric N to terrestrial and aquatic ecosystems. Recent studies have expanded the pool of available measurements and our awareness of their potential significance. Here, we use these measurements to provide a coherent picture of the processes that produce both oxidized and reduced forms of organic nitrogen in the atmosphere, examine how those processes are linked to human activity and how they may contribute to the N load from the atmosphere to ecosystems. We summarize and synthesize data from 41 measurements of the concentrations and fluxes of atmospheric organic nitrogen (AON). In addition, we examine the contribution of reduced organic nitrogen compounds such as amino acids, bacterial/particulate N, and oxidized compounds such as organic nitrates to deposition fluxes of AON. The percentage contribution of organic N to total N loading varies from site to site and with measurement methodology but is consistently around a third of the total N load with a median value of 30% (Standard Deviation of 16%). There are no indications that AON is a proportionally greater contributor to N deposition in unpolluted environments and there are not strong correlations between fluxes of nitrate and AON or ammonium and AON. Possible sources for AON include byproducts of reactions between NO_x and hydrocarbons, marine and terrestrial sources of reduced (amino acid) N and the long-range transport of organic matter (dust, pollen etc.) and bacteria. Both dust and organic nitrates such as PAN appear to play an important role in the overall flux of AON to the surface of the earth. For estimates of organic nitrate deposition, we also use an atmospheric chemical transport model to evaluate the spatial distribution of fluxes and the globally integrated deposition values. Our preliminary estimate of the magnitude of global AON fluxes places the flux between 10 and 50 Tg of N per year with substantial unresolved uncertainties but clear indications that AON deposition is an important aspect of local and global atmospheric N budgets and deserves further consideration.     

Insular and disjunct distribution of the Arctic wolf in Greenland, 1978�C1998

Little research has been conducted on the spatial and temporal distribution of wolves in the High Arctic, and the processes that influence distributional patterns are not well understood. The present study addressed this information void in north and east Greenland by determining bi-seasonal distribution patterns and core areas based upon 303 sightings of wolves or their tracks during 1978–1998. The data suggested that this wolf population were predominantly distributed in semi-isolated patches in an insular and disjunct distribution. Evidence of wolf occurrence in some areas was so irregular that wolves should be considered absent in most years. Where such areas were clustered over several hundreds of kilometers, they collectively constituted areas of general wolf absence that could be considered gaps in distribution. There was no evidence that this population functioned in a mosaic of closely, interlocking pack territories similar to those reported in lower latitudes. The observed distributional pattern likely reflected the exceptionally impoverished and fragmented polar desert and semi-desert habitat that compelled wolves to adopt differing spatial distribution patterns relative to wolves in temperate areas. The broader scientific significance of this study is that, even in the most remote, vast, and uninhabited regions, it is possible to produce meaningful results on distributional patterns of rare, terrestrial carnivores that can serve as foundation for the next generation of testable hypotheses.     

The size of lipid depots-a factor contributing to the control of food intake in Arctic charr,Salvelinus alpinus?

Food intake of Arctic charr was greatest in the fish with reduced lipid depots. It is suggested that appetite declines as lipid accumulates and energy reserves become repleted, such that energy reserves are then maintained close to some set-point.     

Diversity and distribution of cultured endolichenic fungi in the Ny-Ålesund Region,Svalbard (High Arctic)

Endolichenic fungi within 17 lichen species in the area near Ny-Ålesund (Svalbard, High Arctic) were studied by a culture-based method. The 247 fungal isolates were obtained from 2712 lichen thallus segments. The colonization rate of endolichenic fungi ranged from 1.6 to 26.5 %, respectively. These isolates were identified to 40 fungal taxa, including 35 Ascomycota (10 orders), 4 Basidiomycota (3 orders), and 1 unidentified fungus. Thelebolales was the most abundant order, while Sordariales were the most diverse order. The common fungal taxa shared by more than 3 lichen species were Thelebolus microsporus (93 isolates), Coniochaeta hoffmannii (7 isolates), Sarocladium kiliense (33 isolates), Coniochaeta sp. 1 (5 isolates), Coniochaeta sp. 4 (28 isolates), and Coniochaeta sp. 2 (5 isolates). Low Sorenson’s similarity coefficients were observed among different lichen species, indicating that host-related factor may shape the endolichenic fungal communities in this region. In addition, no endolichenic fungal taxa were previously found in the Antarctica and Austrian Alps, suggesting endolichenic fungal communities in this region might be also shaped by the Arctic climate. The results demonstrate the existence of specific cultured endolichenic fungal species, which may be suitable objects for further study of their possible functional roles in the lichen thalli.     

Can phosphorus limitation inhibit dissolved organic carbon consumption in aquatic microbial food webs? A study of three food web structures in microcosms

Microcosms with three different food web structures and phosphorus (P) limited growth medium were used to study the interactions between P and organic carbon (C) fractions in pelagic food webs. The cultures were run with low dilution to allow the biological processes to determine the outcome. A double isotope technique was used to follow the C and P compartments. In all systems the primary production was P limited. The measured P:C ratios and the observed accumulation of degradable dissolved organic carbon (DOC) indicated that the growth of heterotrophic bacteria was also P limited. The presence of neither algal grazers nor flagellates feeding on bacteria altered the limitation pattern. A net loss of P from the bacterial fraction was observed after the bloom. Different strategies for nutrient aquisition and growth are proposed as mechanisms enabling simultaneous P limitation of algae and bacteria, and a concomitant accumulation of degradable DOC. The ability of the algae to grow with low P:C ratio keeps the regeneration of P through grazers low enough to cause sustained P limitation of both algae and bacteria. The grazers were important producers of DOC when present. This implies that the usual assumption of carbon limited bacterial growth may lead to wrong conclusions regarding the dynamics of plankton communities and the DOC pool.     

Growth and population parameters of the world’s northernmost harbour seals Phoca vitulina residing in Svalbard, Norway

The harbour seals (Phoca vitulina) in Svalbard are the northernmost population of this species. The population size is thought to be less than 1,000 individuals; these animals reside principally within a national park on Prins Karls Forland on the west coast of Spitsbergen, Svalbard, at about 78°20N. The material presented in this study was collected from 367 live-captured animals, aged based on growth layers read from stained, decalcified incisor sections (except for pups of the year). Standard length (F_1,246=45.70, P<0.0001) and body mass (F_1,258=25.28; P<0.0001) were both significantly influenced by sex when age was taken into account. Adult males are both longer [152.9±4.8 (SE) vs 140.1±2.0 cm, standard length] and heavier (104.0±5.0 vs 83.2±2.7 kg, body mass) than adult females in this population. Age at sexual maturity was assessed based on analyses of sex hormones. Testosterone levels in males showed an abrupt increase at 6 years of age, while estradiol levels in females increased from age 4. The reproductive rate of adult females was 0.93. The longevity of Svalbard harbour seals was short compared to harbour-seal populations from other areas. However, these seals are not exposed to terrestrial predation; there is no known mortality due to fisheries or hunting and their pollution burdens are low. Extreme seasonality and perhaps other harsh environmental conditions at the northern edge of this species distribution may exert long-term low levels of stress that result in short life span, or there are currently unknown acute sources of mortality in this population. To our knowledge, this is the first study of population parameters on a pinniped species using cross-sectional, non-terminal sampling.     

A trophic cascade in a macrophyte-based food web at the land–water ecotone

Trophic cascades may purportedly be more common in aquatic than terrestrial food webs, but herbivory on freshwater vascular plants has historically been considered low. Water lilies are an exception, suffering severe grazing damage by leaf beetles. To test whether a central prediction of cascade models—that predator effects propagate downwards to plants—operates in a macrophyte-based food web, we experimentally manipulated predation pressure on a key herbivore of water lilies in the littoral zone of a lake in Michigan, USA. Field experiments comprised combinations of caging treatments to alter the number of predators (larvae of the ladybird beetle Coleomegilla maculata) that hunt the grazers of the macrophytes (larvae of the leaf beetles Galerucella nymphaeae) on the leaves of the water lily Nuphar advena. Predatory larvae of the ladybird beetles significantly reduced grazing damage to water-lily leaves by 35–43%. The predators reduced plant damage chiefly via density-mediated effects, when lower densities of grazers translated to significant declines in plant damage. Plant damage caused by the surviving herbivores was less than predicted from individual grazing rates under predator-free conditions. This suggests that trait-mediated effects may possibly also operate in this cascade. The observed strong effect of predators on a non-adjacent trophic level concurs with an essential component of the trophic cascade model, and the cascade occurred at the ecotone between aquatic and terrestrial habitats: Nuphar is an aquatic macrophyte with emergent and floating leaves, whereas both beetle species are semi-terrestrial and use the dry, emergent and floating leaves of the water lily as habitat. Also, the cascade is underpinned by freshwater macrophytes—a group for which trophic processes have often been underappreciated in the past.     

Which sharks attract research? Analyses of the distribution of research effort in sharks reveal significant non-random knowledge biases

Reviews in Fish Biology and Fisheries - Research effort is unevenly distributed across species, which can cause important biases in our understanding of evolutionary and ecological processes and...     

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, “Candidatus Nitrosopumilus sediminis” AR2, from Svalbard in the Arctic Circle

Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments. We herein present the draft genome sequence of an ammonia-oxidizing archaeon, “Candidatus Nitrosopumilus sediminis” AR2, which was enriched in culture from a marine sediment obtained off Svalbard, within the Arctic Circle. The typical genes involved in archaeal ammonia oxidation and carbon fixation necessary for chemolithoautotrophic growth were observed. Interestingly, the AR2 genome sequence was revealed to possess, uniquely among cultivated AOA from marine environments, a capability for urea utilization.     

Ecogeochemistry of the subsurface food web at pH 0–2.5 in Iron Mountain,California, U.S.A.

Pyrite oxidation in the underground mining environment of Iron Mountain, California, has created the most acidic pH values ever reported in aquatic systems. Sulfate values as high as 120000 mg l^–1 and iron as high as 27600 mg l^–1 have been measured in the mine water, which also carries abundant other dissolved metals including Al, Zn, Cu, Cd, Mn, Sb and Pb. Extreme acidity and high metal concentrations apparently do not preclude the presence of an underground acidophilic food web, which has developed with bacterial biomass at the base and heliozoans as top predators. Slimes, oil-like films, flexible and inflexible stalactites, sediments, water and precipitates were found to have distinctive communities. A variety of filamentous and non-filamentous bacteria grew in slimes in water having pH values <1.0. Fungal hyphae colonize stalactites dripping pH 1.0 water; they may help to form these drip structures. Motile hypotrichous ciliates and bdelloid rotifers are particularly abundant in slimes having a pH of 1.5. Holdfasts of the iron bacterium Leptothrix discophora attach to biofilms covering pools of standing water having a pH of 2.5 in the mine. The mine is not a closed environment – people, forced air flow and massive flushing during high intensity rainfall provide intermittent contact between the surface and underground habitats, so the mine ecosystem probably is not a restricted one.     

Is the scaling of swim speed in sharks driven by metabolism?

The movement rates of sharks are intrinsically linked to foraging ecology, predator–prey dynamics and wider ecosystem functioning in marine systems. During ram ventilation, however, shark movement rates are linked not only to ecological parameters, but also to physiology, as minimum speeds are required to provide sufficient water flow across the gills to maintain metabolism. We develop a geometric model predicting a positive scaling relationship between swim speeds in relation to body size and ultimately shark metabolism, taking into account estimates for the scaling of gill dimensions. Empirical data from 64 studies (26 species) were compiled to test our model while controlling for the influence of phylogenetic similarity between related species. Our model predictions were found to closely resemble the observed relationships from tracked sharks, providing a means to infer mobility in particularly intractable species.