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- Wortman, J. R., et al.
(author)
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The 2008 update of the Aspergillus nidulans genome annotation: A community effort
- 2009
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In: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46, s. S2-S13
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Journal article (peer-reviewed)abstract
- The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. (C) 2009 Elsevier Inc. All rights reserved.
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- Heard, J. M., et al.
(author)
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Availability, accessibility and delivery to patients of the 28 orphan medicines approved by the European Medicine Agency for hereditary metabolic diseases in the MetabERN network
- 2020
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In: Orphanet Journal of Rare Diseases. - : Springer Science and Business Media LLC. - 1750-1172. ; 15:1
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Journal article (peer-reviewed)abstract
- Background The European Medicine Agency granted marketing approval to 164 orphan medicinal products for rare diseases, among which 28 products intended for the treatment of hereditary metabolic diseases. Taking advantage of its privileged connection with 69 healthcare centres of excellence in this field, MetabERN, the European Reference Network for hereditary metabolic diseases, performed a survey asking health care providers from 18 European countries whether these products are available on the market, reimbursed and therefore accessible for prescription, and actually delivered in their centre. Results Responses received from 52 centres (75%) concerned the design of treatment plans, the access to marketed products, and the barriers to delivery. Treatment options are always discussed with patients, who are often involved in their treatment plan. Most products (26/28) are available in most countries (15/18). Among the 15 broadly accessible products (88.5% of the centres), 9 are delivered to most patients (mean 70.1%), and the others to only few (16.5%). Among the 10 less accessible products (40.2% of the centres), 6 are delivered to many patients (66.7%), and 4 are rarely used (6.3%). Information was missing for 3 products. Delay between prescription and delivery is on average one month. Beside the lack of availability or accessibility, the most frequent reasons for not prescribing a treatment are patients' clinical status, characteristic, and personal choice. Conclusions Data collected from health care providers in the MetabERN network indicate that two-third of the orphan medicines approved by EMA for the treatment of hereditary metabolic diseases are accessible to treating patients, although often less than one-half of the patients with the relevant conditions actually received the approved product to treat their disease. Thus, in spite of the remarkable achievement of many products, patients concerned by EMA-approved orphan medicinal products have persistent unmet needs, which deserve consideration. The enormous investments made by the companies to develop products, and the high financial burden for the Member States to purchase these products emphasize the importance of a scrupulous appreciation of treatment value involving all stakeholders at early stage of development, before marketing authorization, and during follow up.
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| 4. |
- Barker, Abigail, et al.
(author)
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Disequilibrium in historic volcanic rocks from Fogo, Cape Verde traces carbonatite metasomatism of recycled ocean crust
- 2023
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In: Lithos. - : Elsevier. - 0024-4937 .- 1872-6143. ; , s. 107328-107328
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Journal article (peer-reviewed)abstract
- Fogo, Cape Verde, located upon thick oceanic lithosphere, provides a window into processes occurring in the mantle where recycled ocean crust in an upwelling mantle plume interacts with ambient mantle. Our objective is to investigate the nature of the lithologies of the mantle sources involved in the petrogenesis of historic volcanic rocks from Fogo. We observe enclaves and mingling textures in the lavas combined with oxygen isotope disequilibrium between olivine and clinopyroxene phenocrysts. Olivine δ18O values display positive correlations with Zr/Hf and Zr/Y and a negative correlation with U/Th, whereas clinopyroxene δ 18O values correlate positively with Ba/Nb. Heterogeneity between crystal populations and within the groundmass indicates that multiple magma batches are mixed beneath Fogo. In terms of mantle endmembers and source lithologies, a HIMU endmember was generated by melting of carbonated eclogite as indicated by low δ 18O values, Zr/Hf, Ba/Nb and high U/Th ratios. In contrast, we show the EM1 endmember has high δ 18O, Zr/Hf, Ba/Nb and low U/Th ratios, derived from melting of variably carbonated peridotite. Additionally, Ba/Th ratio are high, indicating that carbonatite melts have contributed to alkaline magma compositions at Fogo.
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| 6. |
- Deegan, Frances M., et al.
(author)
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Crustal versus source processes recorded in dykes from the Northeast volcanic rift zone of Tenerife, Canary Islands
- 2012
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In: Chemical Geology. - : Elsevier BV. - 0009-2541 .- 1872-6836. ; 334, s. 324-344
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Journal article (peer-reviewed)abstract
- The Miocene–Pliocene Northeast Rift Zone (NERZ) on Tenerife is a well exposed example of a feeder system to a major ocean island volcanic rift. We present elemental and O–Sr–Nd–Pb isotope data for dykes of the NERZ with the aim of unravelling the petrological evolution of the rift and ultimately defining the mantle source contributions. Fractional crystallisation is found to be the principal control on major and trace element variability in the dykes. Differing degrees of low temperature alteration and assimilation of hydrothermally altered island edifice and pre-island siliciclastic sediment elevated the δ18O and the 87Sr/86Sr ratio of many of the dykes, but had little to no discernible effect on Nd and Pb isotopes. Once the data are screened for alteration and shallow level contamination, the underlying source variations of the NERZ essentially reflect derivation from a young High-μ (HIMU, where μ = 238U/204Pb)-type mantle component mixed with depleted mid-ocean ridge-type mantle (DMM). The Pb isotope data of the NERZ rocks (206Pb/204Pb and 207Pb/204Pb range from 19.591 to 19.838 and 15.603 to 15.635, respectively) support a model of initiation and growth of the rift from the Central Shield volcano (Roque del Conde), consistent with latest geochronology results. The similar isotope signature of the NERZ to both the Miocene Central Shield and the Pliocene Las Cañadas central volcano suggests that the central part of Tenerife Island was supplied from a mantle source that remained of similar composition through the Miocene to the Pliocene. This can be explained by the presence of a discrete column of young HIMU-like plume material, ≤ 100 km in vertical extent, occupying the melting zone beneath central Tenerife throughout this period. The most recent central magmatism on Tenerife appears to reflect greater entrainment of DMM material, perhaps due to waning of the HIMU-like “blob” with time.
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| 7. |
- Deegan, Frances, et al.
(author)
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Magma-carbonate interaction processes and associated CO2 release at Merapi volcano, Indonesia: insights from experimental petrology
- 2010
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In: Journal of Petrology. - : Oxford University Press (OUP). - 0022-3530 .- 1460-2415. ; 51:5, s. 1027-1051
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Journal article (peer-reviewed)abstract
- There is considerable evidence for continuing, late-stage interaction between the magmatic system at Merapi volcano, Indonesia, and local crustal carbonate (limestone). Calc-silicate xenoliths within Merapi basaltic-andesite eruptive rocks display textures indicative of intense interaction between magma and crustal carbonate, and Merapi feldspar phenocrysts frequently contain crustally contaminated cores and zones. To resolve the interaction processes between magma and limestone in detail we have performed a series of time-variable decarbonation experiments in silicate melt, at magmatic pressure and temperature, using a Merapi basaltic-andesite and local Javanese limestone as starting materials. We have used in situ analytical methods to determine the elemental and strontium isotope composition of the experimental products and to trace the textural, chemical, and isotopic evolution of carbonate assimilation. The major processes of magma-carbonate interaction identified are: (1) rapid decomposition and degassing of carbonate; (2) generation of a Ca-enriched, highly radiogenic strontium contaminant melt, distinct from the starting material composition; (3) intense CO2 vesiculation, particularly within the contaminated zones; (4) physical mingling between the contaminated and unaffected melt domains; (5) chemical mixing between melts. The experiments reproduce many of the features of magma-carbonate interaction observed in the natural Merapi xenoliths and feldspar phenocrysts. The Ca-rich, high 87Sr/86Sr contaminant melt produced in the experiments is considered as a precursor to the Ca-rich (often 'hyper-calcic') phases found in the xenoliths and the contaminated zones in Merapi feldspars.The xenoliths also exhibit micro-vesicular textures that can be linked to the CO2 liberation process seen in the experiments.This study, therefore, provides well-constrained petrological insights into the problem of crustal interaction at Merapi and points toward the substantial impact of such interaction on the volatile budget of the volcano.
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| 8. |
- Delcamp, A., et al.
(author)
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Dykes and structures of the NE rift of Tenerife, Canary Islands : a record of stabilisation and destabilisation of ocean island rift zones
- 2012
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In: Bulletin of Volcanology. - : Springer. - 0258-8900 .- 1432-0819. ; 74:5, s. 963-980
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Journal article (peer-reviewed)abstract
- Many oceanic island rift zones are associated with lateral sector collapses, and several models have been proposed to explain this link. The North–East Rift Zone (NERZ) of Tenerife Island, Spain offers an opportunity to explore this relationship, as three successive collapses are located on both sides of the rift. We have carried out a systematic and detailed mapping campaign on the rift zone, including analysis of about 400 dykes. We recorded dyke morphology, thickness, composition, internal textural features and orientation to provide a catalogue of the characteristics of rift zone dykes. Dykes were intruded along the rift, but also radiate from several nodes along the rift and form en échelon sets along the walls of collapse scars. A striking characteristic of the dykes along the collapse scars is that they dip away from rift or embayment axes and are oblique to the collapse walls. This dyke pattern is consistent with the lateral spreading of the sectors long before the collapse events. The slump sides would create the necessary strike-slip movement to promote en échelon dyke patterns. The spreading flank would probably involve a basal decollement. Lateral flank spreading could have been generated by the intense intrusive activity along the rift but sectorial spreading in turn focused intrusive activity and allowed the development of deep intra-volcanic intrusive complexes. With continued magma supply, spreading caused temporary stabilisation of the rift by reducing slopes and relaxing stress. However, as magmatic intrusion persisted, a critical point was reached, beyond which further intrusion led to large-scale flank failure and sector collapse. During the early stages of growth, the rift could have been influenced by regional stress/strain fields and by pre-existing oceanic structures, but its later and mature development probably depended largely on the local volcanic and magmatic stress/strain fields that are effectively controlled by the rift zone growth, the intrusive complex development, the flank creep, the speed of flank deformation and the associated changes in topography. Using different approaches, a similar rift evolution has been proposed in volcanic oceanic islands elsewhere, showing that this model likely reflects a general and widespread process. This study, however, shows that the idea that dykes orient simply parallel to the rift or to the collapse scar walls is too simple; instead, a dynamic interplay between external factors (e.g. collapse, erosion) and internal forces (e.g. intrusions) is envisaged. This model thus provides a geological framework to understand the evolution of the NERZ and may help to predict developments in similar oceanic volcanoes elsewhere.
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| 9. |
- Berg, Sylvia, et al.
(author)
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Making Earth’s earliest continental crust : an analogue from voluminous Neogene silicic volcanism in NE-Iceland
- 2014
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Conference paper (peer-reviewed)abstract
- Borgarfjörður Eystri in NE-Iceland represents the second-most voluminous exposure of silicic eruptive rocksin Iceland and is a superb example of bimodal volcanism (Bunsen-Daly gap), which represents a long-standingcontroversy that touches on the problem of crustal growth in early Earth. The silicic rocks in NE-Iceland approach25 % of the exposed rock mass in the region (Gústafsson et al., 1989), thus they significantly exceed the usual≤ 12 % in Iceland as a whole (e.g. Walker, 1966; Jonasson, 2007). The origin, significance, and duration of thevoluminous (> 300 km3) and dominantly explosive silicic activity in Borgarfjörður Eystri is not yet constrained(c.f. Gústafsson, 1992), leaving us unclear as to what causes silicic volcanism in otherwise basaltic provinces.Here we report SIMS zircon U-Pb ages and δ18O values from the region, which record the commencement ofsilicic igneous activity with rhyolite lavas at 13.5 to 12.8 Ma, closely followed by large caldera-forming ignimbriteeruptions from the Breiðavik and Dyrfjöll central volcanoes (12.4 Ma). Silicic activity ended abruptly with dacitelava at 12.1 Ma, defining a ≤ 1 Myr long window of silicic volcanism. Magma δ18O values estimated fromzircon range from 3.1 to 5.5 (± 0.3; n = 170) and indicate up to 45 % assimilation of a low-δ18O component (e.g.typically δ18O = 0 h Bindeman et al., 2012). A Neogene rift relocation (Martin et al., 2011) or the birth of anoff-rift zone to the east of the mature rift associated with a thermal/chemical pulse in the Iceland plume (Óskarsson& Riishuus, 2013), likely brought mantle-derived magma into contact with fertile hydrothermally-altered basalticcrust. The resulting interaction triggered large-scale crustal melting and generated mixed-origin silicic melts. Suchrapid formation of silicic magmas from sustained basaltic volcanism may serve as an analogue for generatingcontinental crust in a subduction–free early Earth (e.g. ≥ 3 Ga, Kamber et al., 2005).REFERENCES:Bindeman, I.N., et al., 2012. Terra Nova 24, 227–232.Gústafsson, L.E., et al., 1989. Jökull, v. 39, 75–89.Gústafsson, L.E., 1992. PhD dissertation, Freie Universität Berlin.Jonasson, K., 2007. Journal of Geodynamics, 43, 101–117.Kamber, B.S., et al., 2005. Earth Planet. Sci. Lett., Vol. 240 (2), 276-290.Martin, E., et al., 2011. Earth Planet. Sc. Lett., 311, 28–38.Óskarsson, B.V., & Riishuus, M.S., 2013. J. Volcanol. Geoth.Res., 267, 92–118.Walker, G.P.L., 1966. Bull. Volcanol., 29 (1), 375-402.
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