Analysis of eruptive and seismic sequences to improve the short-and long-term eruption forecasting

Forecasting the time, location, nature, and scale of volcanic eruptions is one of the most urgent aspects of modern applied volcanology. The reliability of probabilistic forecasting procedures is strongly related to the reliability of the input information provided, implying objective criteria for interpreting the historical and monitoring data. For this reason both, detailed analysis of past data and more basic research into the processes of volcanism, are fundamental tasks of a continuous information-gain process; in this way the precursor events of eruptions can be better interpreted in terms of their physical meanings with correlated uncertainties. This should lead to better predictions of the nature of eruptive events. In this work we have studied different problems associated with the long- and short-term eruption forecasting assessment. First, we discuss different approaches for the analysis of the eruptive history of a volcano, most of them generally applied for long-term eruption forecasting purposes; furthermore, we present a model based on the characteristics of a Brownian passage-time process to describe recurrent eruptive activity, and apply it for long-term, time-dependent, eruption forecasting (Chapter 1). Conversely, in an effort to define further monitoring parameters as input data for short-term eruption forecasting in probabilistic models (as for example, the Bayesian Event Tree for eruption forecasting -BET_EF-), we analyze some characteristics of typical seismic activity recorded in active volcanoes; in particular, we use some methodologies that may be applied to analyze long-period (LP) events (Chapter 2) and volcano-tectonic (VT) seismic swarms (Chapter 3); our analysis in general are oriented toward the tracking of phenomena that can provide information about magmatic processes. Finally, we discuss some possible ways to integrate the results presented in Chapters 1 (for long-term EF), 2 and 3 (for short-term EF) in the BET_EF model (Chapter 4).

Seismic sequences analysis for estimation of earthquake source parameters: corner frequency, stress drop, and seismic moment observations

The present study has been carried out with the following objectives: i) To investigate the attributes of source parameters of local and regional earthquakes; ii) To estimate, as accurately as possible, M0, fc, Δσ and their standard errors to infer their relationship with source size; iii) To quantify high-frequency earthquake ground motion and to study the source scaling. This work is based on observational data of micro, small and moderate -earthquakes for three selected seismic sequences, namely Parkfield (CA, USA), Maule (Chile) and Ferrara (Italy). For the Parkfield seismic sequence (CA), a data set of 757 (42 clusters) repeating micro-earthquakes (0 ≤ MW ≤ 2), collected using borehole High Resolution Seismic Network (HRSN), have been analyzed and interpreted. We used the coda methodology to compute spectral ratios to obtain accurate values of fc , Δσ, and M0 for three target clusters (San Francisco, Los Angeles, and Hawaii) of our data. We also performed a general regression on peak ground velocities to obtain reliable seismic spectra of all earthquakes. For the Maule seismic sequence, a data set of 172 aftershocks of the 2010 MW 8.8 earthquake (3.7 ≤ MW ≤ 6.2), recorded by more than 100 temporary broadband stations, have been analyzed and interpreted to quantify high-frequency earthquake ground motion in this subduction zone. We completely calibrated the excitation and attenuation of the ground motion in Central Chile. For the Ferrara sequence, we calculated moment tensor solutions for 20 events from MW 5.63 (the largest main event occurred on May 20 2012), down to MW 3.2 by a 1-D velocity model for the crust beneath the Pianura Padana, using all the geophysical and geological information available for the area. The PADANIA model allowed a numerical study on the characteristics of the ground motion in the thick sediments of the flood plain.

A cellular cleavage pathway for the Moloney murine leukemia virus precursor protein, Pr65$\rm\sp{gag}$: Identification of a new viral protein containing CAp30 and NCp10 sequences

The origin and structure of P55$\sp{\rm gag},$ a gag encoded polyprotein lacking the nucleocapsid protein, NCp10, have been explored. Evidence shows that P55$\sp{\rm gag}$ is formed by non-viral proteolytic cleavage of the Moloney murine leukemia virus (MoMuLV)gag precursor protein, Pr65$\sp{\rm gag}.$ P55$\sp{\rm gag}$ is produced in cells infected by a viral protease deletion mutant and by a recombinant murine sarcoma virus known to lack the protease gene, implying that a cellular protease is responsible for the cleavage. Structural and immunological studies show that the protein cleavage site is upstream of the CAp30-NCp10 viral proteolytic junction, implying that P55$\sp{\rm gag}$ lacks the carboxy-terminal residues of CAp30. During the course of studying P55$\sp{\rm gag},$ another protein was discovered, which I named nucleocapsid-related protein(NCRP). NCRP possesses the portion of CAp30 that is lacking in P55$\sp{\rm gag}.$ NCRP possesses antigenic epitopes present in CAp30 and NCp10. NCRP was observed in virus lysates and in nuclear lysates of MoMuLV infected cells; it was not detected in the cytoplasmic fractions of MoMuLV infected cells. Our results indicated that NCRP originates from Pr65$\sp{\rm gag},$ resulting from the same cellular proteolytic cleavage event that produces the viral cellular protein P55$\sp{\rm gag}.$ P55$\sp{\rm gag}$- and NCRP-like proteins also were observed in AKV murine leukemia virus (AKV MuLV) and feline leukemia virus (FeLV) infected cells and in their respective virus particles. The site of cleavage that yields P55$\sp{\rm gag}$ and NCRP is within the carboxy terminus of CAp30, likely within a motif highly conserved among mammalian type C retroviruses. This new motif, called the capsid conserved motif (CCM), overlaps a region containing both a possible bipartite nuclear targeting sequence and a region homologous with the U1 small nuclear ribonucleoprotein 70-kD protein. This domain, when intact, may act as a nuclear targeting sequence for the gag precursor proteins Pr65$\sp{\rm gag}$ and CAp30. Nuclei of cells infected with MoMuLV were examined for the presence of gag proteins. Both Pr65$\sp{\rm gag}$ and CAp30 were detected in the nuclear fraction of MoMuLV, AKV MuLV and FeLV infected cells. P55$\sp{\rm gag}$ was never detected in the nucleus of MoMuLV, AKV MuLV and FeLV infected cells or in their respective virus particles. I propose that NCRP may be involved in sequestering viral genomic RNA for the purposes of encapsidation and intracellular viral genomic RNA dimerization. ^

The Cenomanian/Turronian Boundary Event at ODP Hole 103-641A

Drilling at ODP Site 641 (on the western margin of Galicia Bank, off northwestern Spain) revealed a thin, but pronounced, interval of black shale and gray-green claystone. Our high-resolution study combines the sedimentology, micropaleontology (palynomorphs and others), organic and inorganic geochemistry, and isotopic values of this layer to demonstrate the distinct nature of the sediment and prove that the sequence represents the local sedimentary expression of the global Cenomanian/Turonian Oceanic Anoxic Event (OAE) of Schlanger and Jenkyns (1976), Arthur and Schlanger (1979), and Jenkyns (1980), also called the Cenomanian/Turonian Boundary Event (CTBE). The most striking evidence is that the strong positive d13C excursion characterizing the CTBE sequences in shallow areas can be traced into a pronounced deep-sea expression, thus providing a good stratigraphic marker for the CTBE in various paleosettings. The isotopic excursion at Site 641 coincides with an extremely enriched trace metal content, with values that were previously unknown for the Cretaceous Atlantic. Similar to other CTBE occurrences, the organic carbon content is high (up to 11%) and the organic matter is of dominantly marine origin (kerogen type II). The bulk mineralogy of the CTBE sediments does not differ significantly from the general trend of Cretaceous North Atlantic sediments (dominance of smectite and zeolite with minor amounts of illite and scattered palygorskite, kaolinite, and chlorite); thus, no evidence for either increased volcanic activity nor a drastic climatic change in the borderlands was found. Results from Site 641 are compared with the CTBE section found at Site 398, DSDP Leg 47B (Vigo Seamount at the southern end of the Galicia Bank).

Gene sequences of the lichen Cetraria aculeata

Lichens are symbioses between fungi (mycobionts) and photoautotrophic green algae or cyanobacteria (photobionts). Many lichens occupy large distributional ranges covering several climatic zones. So far, little is known about the large-scale phylogeography of lichen photobionts and their role in shaping the distributional ranges of lichens. We studied south polar, temperate and north polar populations of the widely distributed fruticose lichen Cetraria aculeata. Based on the DNA sequences from three loci for each symbiont, we compared the genetic structure of mycobionts and photobionts. Phylogenetic reconstructions and Bayesian clustering methods divided the mycobiont and photobiont data sets into three groups. An AMOVA shows that the genetic variance of the photobiont is best explained by differentiation between temperate and polar regions and that of the mycobiont by an interaction of climatic and geographical factors. By partialling out the relative contribution of climate, geography and codispersal, we found that the most relevant factors shaping the genetic structure of the photobiont are climate and a history of codispersal. Mycobionts in the temperate region are consistently associated with a specific photobiont lineage. We therefore conclude that a photobiont switch in the past enabled C. aculeata to colonize temperate as well as polar habitats. Rare photobiont switches may increase the geographical range and ecological niche of lichen mycobionts by associating them with locally adapted photobionts in climatically different regions and, together with isolation by distance, may lead to genetic isolation between populations and thus drive the evolution of lichens.

Haplotype and nucleotide characteristics of photobiont and mycobiont gene sequences in the lichen Cetraria aculeata

Lichens, symbiotic associations of fungi (mycobionts) and green algae or cyanobacteria (photobionts), are poikilohydric organisms that are particularly well adapted to withstand adverse environmental conditions. Terrestrial ecosystems of the Antarctic are therefore largely dominated by lichens. The effects of global climate change are especially pronounced in the maritime Antarctic and it may be assumed that the lichen vegetation will profoundly change in the future. The genetic diversity of populations is closely correlated to their ability to adapt to changing environmental conditions and to their future evolutionary potential. In this study, we present evidence for low genetic diversity in Antarctic mycobiont and photobiont populations of the widespread lichen Cetraria aculeata. We compared between 110 and 219 DNA sequences from each of three gene loci for each symbiont. A total of 222 individuals from three Antarctic and nine antiboreal, temperate and Arctic populations were investigated. The mycobiont diversity is highest in Arctic populations, while the photobionts are most diverse in temperate regions. Photobiont diversity decreases significantly towards the Antarctic but less markedly towards the Arctic, indicating that ecological factors play a minor role in determining the diversity of Antarctic photobiont populations. Richness estimators calculated for the four geographical regions suggest that the low genetic diversity of Antarctic populations is not a sampling artefact. Cetraria aculeata appears to have diversified in the Arctic and subsequently expanded its range into the Southern Hemisphere. The reduced genetic diversity in the Antarctic is most likely due to founder effects during long-distance colonization.

Metadata und statistic analysis of archael and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (Z1-Z3, all habitats)

DNA extraction was carried out as described on the MICROBIS project pages (http://icomm.mbl.edu/microbis ) using a commercially available extraction kit. We amplified the hypervariable regions V4-V6 of archaeal and bacterial 16S rRNA genes using PCR and several sets of forward and reverse primers (http://vamps.mbl.edu/resources/primers.php). Massively parallel tag sequencing of the PCR products was carried out on a 454 Life Sciences GS FLX sequencer at Marine Biological Laboratory, Woods Hole, MA, following the same experimental conditions for all samples. Sequence reads were submitted to a rigorous quality control procedure based on mothur v30 (doi:10.1128/AEM.01541-09) including denoising of the flow grams using an algorithm based on PyroNoise (doi:10.1038/nmeth.1361), removal of PCR errors and a chimera check using uchime (doi:10.1093/bioinformatics/btr381). The reads were taxonomically assigned according to the SILVA taxonomy (SSURef v119, 07-2014; doi:10.1093/nar/gks1219) implemented in mothur and clustered at 98% ribosomal RNA gene V4-V6 sequence identity. V4-V6 amplicon sequence abundance tables were standardized to account for unequal sampling effort using 1000 (Archaea) and 2300 (Bacteria) randomly chosen sequences without replacement using mothur and then used to calculate inverse Simpson diversity indices and Chao1 richness (doi:10.2307/4615964). Bray-Curtis dissimilarities (doi:10.2307/1942268) between all samples were calculated and used for 2-dimensional non metric multidimensional scaling (NMDS) ordinations with 20 random starts (doi:10.1007/BF02289694). Stress values below 0.2 indicated that the multidimensional dataset was well represented by the 2D ordination. NMDS ordinations were compared and tested using Procrustes correlation analysis (doi:10.1007/BF02291478). All analyses were carried out with the R statistical environment and the packages vegan (available at: http://cran.r-project.org/package=vegan), labdsv (available at: http://cran.r-project.org/package=labdsv), as well as with custom R scripts. Operational taxonomic units at 98% sequence identity (OTU0.03) that occurred only once in the whole dataset were termed absolute single sequence OTUs (SSOabs; doi:10.1038/ismej.2011.132). OTU0.03 sequences that occurred only once in at least one sample, but may occur more often in other samples were termed relative single sequence OTUs (SSOrel). SSOrel are particularly interesting for community ecology, since they comprise rare organisms that might become abundant when conditions change.16S rRNA amplicons and metagenomic reads have been stored in the sequence read archive under SRA project accession number SRP042162.