Subgroup-specific structural variation across 1,000 medulloblastoma genomes

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4 alpha. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-beta signalling in Group 3, and NF-kappa B signalling in Group 4, suggest future avenues for rational, targeted therapy.

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

Genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. We conducted a meta-analysis of six ulcerative colitis genome-wide association study datasets, comprising 6,687 cases and 19,718 controls, and followed up the top association signals in 9,628 cases and 12,917 controls. We identified 29 additional risk loci (P < 5 × 10(-8)), increasing the number of ulcerative colitis-associated loci to 47. After annotating associated regions using GRAIL, expression quantitative trait loci data and correlations with non-synonymous SNPs, we identified many candidate genes that provide potentially important insights into disease pathogenesis, including IL1R2, IL8RA-IL8RB, IL7R, IL12B, DAP, PRDM1, JAK2, IRF5, GNA12 and LSP1. The total number of confirmed inflammatory bowel disease risk loci is now 99, including a minimum of 28 shared association signals between Crohn's disease and ulcerative colitis.

Paleomegnetic and geochemistry of sediments from the early Aptian Oceanic Anoxic Event

The early Aptian Oceanic Anoxic Event (OAE1a, 120 Ma) represents a geologically brief time interval in the mid-Cretaceous greenhouse world that is characterized by increased organic carbon accumulation in marine sediments, sudden biotic changes, and abrupt carbon-isotope excursions indicative of significant perturbations to global carbon cycling. The brevity of these drastic environmental changes (< 10**6 year) and the typically 10**6 year temporal resolution of the available chronologies, however, represent a critical gap in our knowledge of OAE1a. We have conducted a high-resolution investigation of three widely distributed sections, including the Cismon APTICORE in Italy, Santa Rosa Canyon in northeastern Mexico, and Deep Sea Drilling Project (DSDP) Site 398 off the Iberian margin in the North Atlantic Ocean, which represent a range of depositional environments where condensed and moderately expanded OAE1a intervals are recorded. The objectives of this study are to establish orbital chronologies for these sections and to construct a common, high-resolution timescale for OAE1a. Spectral analyses of the closely-spaced (corresponding to ~5 to 10 kyr) measurements of calcium carbonate content of the APTICORE, magnetic susceptibility (MS) and anhysteretic remanent magnetization (ARM) of the Santa Rosa samples, and MS, ARM and ARM/IRM, where IRM is isothermal remanent magnetization, of Site 398 samples reveal statistically significant cycles. These cycles exhibit periodicity ratios and modulation patterns similar to those of the mid-Cretaceous orbital cycles, suggesting that orbital variations may have modulated depositional processes. Orbital control allows us to estimate the duration of unique, globally identifiable stages of OAE1a. Although OAE1a had a duration of ~1.0 to 1.3 Myr, the initial perturbation represented by the negative carbon-isotope excursion was rapid, lasting for ~27-44 kyr. This estimate could serve as a basis for constraining triggering mechanisms for OAE1a.

Holocene sea-surface reconstructions for the Californian margin

Time series of alkenone unsaturation indices gathered along the California margin reveal large (4° to 8°C) glacial-interglacial changes in sea surface temperature (SST) over the past 550,000 years. Interglacial times with SSTs equal to or exceeding that of the Holocene contain peak abundances in the pollen of redwood, the distinctive component of the temperate rainforest of the northwest coast of California. In the region now dominated by the California Current, SSTs warmed 10,000 to 15,000 years in advance of deglaciation at each of the past five glacial maxima. SSTs did not rise in advance of deglaciation south of the modern California Current front. Glacial warming along the California margin therefore is a regional signal of the weakening of the California Current during times when large ice sheets reorganized wind systems over the North Pacific. Both the timing and magnitude of the SST estimates suggest that the Devils Hole (Nevada) calcite record represents regional but not global paleotemperatures, and hence does not pose a fundamental challenge to the orbital ("Milankovitch") theory of the Ice Ages.

Bryoliths constructed by bryozoans in symbiotic associations with hermit crabs, Golfe d'Arguin, Mauritania

The Golfe d'Arguin offshore of northern Mauritania hosts a rare modern analogue for heterozoan carbonate production in a tropical marine setting. Dominated by ocean upwelling and with additional fertilisation by iron-rich aeolian dust, this naturally eutrophic marine environment lacks typical photozoan communities. A highly productive, tropical cosmopolitan biota dominated by molluscs and suspension-feeders such as bryozoans and balanids characterises the carbonate-rich surface sediments. Overall biodiversity is relatively low and the species present are tolerant against the eutrophic and low-light conditions, the strong hydrodynamic regime governed by ocean upwelling, and the unstable, soft-bottom seafloor with few hard substrata. Here, we describe an ectosymbiosis between the hermit crab Pseudopagurus granulimanus (Miers, 1881) and monospecific assemblages of the encrusting cheilostome bryozoan Acanthodesia commensale (Kirkpatrick and Metzelaar, 1922) that cohabits vacant gastropod shells. Nucleating on an empty gastropod shell, the bryozoan colonies form multilamellar skeletal crusts that produce spherical encrustations and extend the living chamber of the hermit crab through helicospiral tubular growth. This non-obligate mutualistic symbiosis illustrates the adaptive capabilities and benefits from a close partnership in a complex marine environment, driven by trophic conditions, high water energies and instable substratum. Sectioned bryoliths show that between 49 and 97 % of the solid volume of the specimens consists of bryozoan skeleton.

Cd/Ca ratios and element analyses of ODP Hole 115-709C

During three to four d18O cycles (determined on Globigerinoides ruber), more positive d18O (= higher global ice volume) values correlated with higher Globorotalia menardii percentages, total numbers of benthic foraminifers, number of benthic foraminifer species, and the percent of total foraminifers composed of benthic foraminifers. During the same intervals, barite and insoluble residues also generally recorded higher values; however, there was no clear evidence of systematic variation in cadmium/calcium ratios (in benthic foraminifers). Maximum percentages of Globigerinoides sacculifer and Globigerinoides ruber correlate with more negative d18O (= lower global ice volume) values, although they sometimes appear to lead the d18O changes by < =4,000 yr. The increase in percentage of the tropical "divergence" planktonic foraminifer species G. menardii and the reduction of the "nondivergence" tropical species G. ruber and G. sacculifer at times of inferred ice growth is attributed to periodic intensification of divergence associated with the Equatorial Counter Current. Barite and insoluble residue sedi- mentation at the site also generally show a relative increase at those times.

Seawater carbonate chemistry and MgCO3 concentration in bryozoan Myriapora truncata branches during experiments, 2011

There are serious concerns that ocean acidification will combine with the effects of global warming to cause major shifts in marine ecosystems, but there is a lack of field data on the combined ecological effects of these changes due to the difficulty of creating large-scale, long-term exposures to elevated CO2 and temperature. Here we report the first coastal transplant experiment designed to investigate the effects of naturally acidified seawater on the rates of net calcification and dissolution of the branched calcitic bryozoan Myriapora truncata (Pallas, 1766). Colonies were transplanted to normal (pH 8.1), high (mean pH 7.66, minimum value 7.33) and extremely high CO2 conditions (mean pH 7.43, minimum value 6.83) at gas vents off Ischia Island (Tyrrhenian Sea, Italy). The net calcification rates of live colonies and the dissolution rates of dead colonies were estimated by weighing after 45 days (May-June 2008) and after 128 days (July-October) to examine the hypothesis that high CO2 levels affect bryozoan growth and survival differently during moderate and warm water conditions. In the first observation period, seawater temperatures ranged from 19 to 24 °C; dead M. truncata colonies dissolved at high CO2 levels (pH 7.66), whereas live specimens maintained the same net calcification rate as those growing at normal pH. In extremely high CO2 conditions (mean pH 7.43), the live bryozoans calcified significantly less than those at normal pH. Therefore, established colonies of M. truncata seem well able to withstand the levels of ocean acidification predicted in the next 200 years, possibly because the soft tissues protect the skeleton from an external decrease in pH. However, during the second period of observation a prolonged period of high seawater temperatures (25-28 °C) halted calcification both in controls and at high CO2, and all transplants died when high temperatures were combined with extremely high CO2 levels. Clearly, attempts to predict the future response of organisms to ocean acidification need to consider the effects of concurrent changes such as the Mediterranean trend for increased summer temperatures in surface waters. Although M. truncata was resilient to short-term exposure to high levels of ocean acidification at normal temperatures, our field transplants showed that its ability to calcify at higher temperatures was compromised, adding it to the growing list of species now potentially threatened by global warming.

Pliocene-Pleistocene stack of globally distributed benthic stable oxygen isotope records

We present a 5.3-Myr stack (the ''LR04'' stack) of benthic d18O records from 57 globally distributed sites aligned by an automated graphic correlation algorithm. This is the first benthic delta18O stack composed of more than three records to extend beyond 850 ka, and we use its improved signal quality to identify 24 new marine isotope stages in the early Pliocene. We also present a new LR04 age model for the Pliocene-Pleistocene derived from tuning the delta18O stack to a simple ice model based on 21 June insolation at 65 N. Stacked sedimentation rates provide additional age model constraints to prevent overtuning. Despite a conservative tuning strategy, the LR04 benthic stack exhibits significant coherency with insolation in the obliquity band throughout the entire 5.3 Myr and in the precession band for more than half of the record. The LR04 stack contains significantly more variance in benthic delta18O than previously published stacks of the late Pleistocene as the result of higher resolution records, a better alignment technique, and a greater percentage of records from the Atlantic. Finally, the relative phases of the stack's 41- and 23-kyr components suggest that the precession component of delta18O from 2.7-1.6 Ma is primarily a deep-water temperature signal and that the phase of d18O precession response changed suddenly at 1.6 Ma.

(Table 1) Sea surface temperature reconstruction for eastern equatorial Pacific surface sediment samples

Significant uncertainties persist in the reconstruction of past sea surface temperatures in the eastern equatorial Pacific, especially regarding the amplitude of the glacial cooling and the details of the post-glacial warming. Here we present the first regional calibration of alkenone unsaturation in surface sediments versus mean annual sea surface temperatures (maSST). Based on 81 new and 48 previously published data points, it is shown that open ocean samples conform to established global regressions of Uk'37 versus maSST and that there is no systematic bias from seasonality in the production or export of alkenones, or from surface ocean nutrient concentrations or salinity. The flattening of the regression at the highest maSSTs is found to be statistically insignificant. For the near-coastal Peru upwelling zone between 11-15°S and 76-79°W, however, we corroborate earlier observations that Uk'37 SST estimates significantly over-estimate maSSTs at many sites. We posit that this is caused either by uncertainties in the determination of maSSTs in this highly dynamic environment, or by biasing of the alkenone paleothermometer toward El Niño events as postulated by Rein et al. (2005).