GOPred: GO Molecular Function Prediction by Combined Classifiers

Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred)

Origin and ascent history of unusually crystal-rich alkaline basaltic magmas from the western Pannonian Basin

The last eruptions of the monogenetic Bakony-Balaton Highland Volcanic Field (western Pannonian Basin, Hungary) produced unusually crystal- and xenolith-rich alkaline basalts which are unique among the alkaline basalts of the Carpathian- Pannonian Region. Similar alkaline basalts are only rarely known in other volcanic fields of the world. These special basaltic magmas fed the eruptions of two closely located volcanic centres: the Bondoró-hegy and the Füzes-tó scoria cone. Their uncommon enrichment in diverse crystals produced unique rock textures and modified original magma compositions (13.1-14.2 wt.% MgO, 459-657 ppm Cr, 455-564 ppm Ni contents). Detailed mineral-scale textural and chemical analyses revealed that the Bondoró-hegy and Füzes-tó alkaline basaltic magmas have a complex ascent history, and that most of their minerals (~30 vol.% of the rocks) represent foreign crystals derived from different levels of the underlying lithosphere. The most abundant xenocrysts, olivine, orthopyroxene, clinopyroxene and spinel, were incorporated from different regions and rock types of the subcontinental lithospheric mantle. Megacrysts of clinopyroxene and spinel could have originated from pegmatitic veins / sills which probably represent magmas crystallized near the crust-mantle boundary. Green clinopyroxene xenocrysts could have been derived from lower crustal mafic granulites. Minerals that crystallized in situ from the alkaline basaltic melts (olivine with Cr-spinel inclusions, clinopyroxene, plagioclase, Fe-Ti oxides) are only represented by microphenocrysts and overgrowths on the foreign crystals. The vast amount of peridotitic (most common) and mafic granulitic materials indicates a highly effective interaction between the ascending magmas and wall rocks at lithospheric mantle and lower crustal levels. However, fragments from the middle and upper crust are absent from the studied basalts, suggesting a change in the style (and possibly rate) of magma ascent in the crust. These xenocryst- and xenolith-rich basalts yield divers tools for estimating magma ascent rate that is important for hazard forecasting in monogenetic volcanic fields. According to the estimated ascent rates, the Bondoró-hegy and Füzes-tó alkaline basaltic magmas could have reached the surface within hours to few days, similarly to the estimates for other eruptive centres in the Pannonian Basin which were fed by "normal" (crystal- and xenolith-poor) alkaline basalts

Mantle metasomatism

Mantle metasomatism is a relatively recent concept introduced in the early 1970s when detailed studies of lithospheric mantle rock fragments (xenoliths), brought to the surface of in basaltic to kimberlitic magmas, became widespread. Two main types of metasomatism were defined: modal (or patent) metasomatism describes the introduction of new minerals; cryptic metasomatism describes changes in composition of pre-existing minerals without formation of new phases. A new type of metasomatism is introduced here, stealth metasomatism; this process involves the addition of new phases (e.g. garnet and/or clinopyroxene), but is a “deceptive” metasomatic process that adds phases indistinguishable mineralogically from common mantle peridotite phases. The recognition of stealth metasomatism reflects the increasing awareness of the importance of refertilisation by metasomatic fluid fronts in determining the composition of mantle domains. Tectonically exposed peridotite massifs provide an opportunity to study spatial relationships of metasomatic processes on a metre to kilometre scale. The nature of mantle fluids can be determined from the nature of fluid inclusions in mantle minerals and indirectly from changes in the chemical (especially trace-element) compositions of mantle minerals. Metasomatic fluids in off-craton regions cover a vast spectrum from silicate to carbonate magmas containing varying types and abundances of dissolved fluids and solutes including brines, C-O-H species and sulfur-bearing components. Fluid inclusions in diamond and deep xenoliths reveal the presence of high-density fluids with carbonatitic and hydro-silicic and/or saline-brine end-members. The deep cratonic xenolith data also reinforce the importance of highly mobile melts spanning the kimberlite-carbonatite spectrum and that may become immiscible with changing conditions. A critical conceptual advance in understanding Earth’s geodynamic behaviour is emerging from understanding the linkage between mantle metasomatism and the physical properties of mantle domains recorded by geophysical data. For example, metasomatic refertilisation of cratonic lithospheric mantle increases its density, lowers its seismic velocity and strongly affects its rheology. Introduction of heat-producing elements (U, Th, K) increases heat production, and the key to understanding electromagnetic signals from mantle domains may be closely related to fluid distribution and type (e.g. carbonatitic) and its residence in or between grains. The lithospheric mantle is a palimpsest recording the multiple fluid events that have affected each domain since it formed. These events, involving different fluids and compositions, have repeatedly overprinted variably depleted original mantle wall-rocks. This produces a complex, essentially ubiquitously metasomatised lithospheric mantle, heterogeneous on scales of microns to terranes and perhaps leaving little or no “primary” mantle wall-rock. Decoding this complex record by identifying significant episodes and processes is a key to reconstructing lithosphere evolution and the nature and origin of the volatile flux from the deep Earth through time.63 page(s