Effects of the 6th September 2002 earthquake: damage amplification in the south-eastern sector of Palermo explained by GIS technology

During the 6th September 2002 earthquake the highest damage level in Palermo was observed in the SE sector. This is a recent urbanization area where reinforced concrete structures predominate. A detailed analysis of soil properties in Palermo was carried out by City-GIS to investigate a possible role of nearsurface geology on earthquake effects. City-GIS is a tool dedicated to natural hazard evaluation in urban areas. The availability of high density of well log data (stratigraphic and geotechnical) allowed a realistic modeling of surface geology and physical-mechanical properties that control the seismic response. In wide zones of the above mentioned sector of Palermo, outcropping terrains are composed of thin calcarenite layers, lying above remarkably thick siltyclayey sands that overlay the Numidian Flysch, commonly considered the bedrock of Quaternary sediments. Since silty-clayey sands feature greater deformability properties (Young's modulus) and smaller resistance properties (undrained cohesion and shear resistance angle) than Numidian Flysch, these zones of the SE sector exhibit high values of the acoustic impedance contrast. Moreover, a quite wide portion of the study area, crossed by the Oreto River, is characterized by very thick alluvial deposits. Here, the significant lateral variations of the lithostratigraphic geometry may be an additional cause of strong site effects

Microtremor Measurements in the City of Palermo, Italy: Analysis of the Correlation between Local Geology and Damage

This study presents the results of 90 seismic ambient noise measurements in Palermo, the main city of Sicily (Italy). The dataset has been processed using the horizontal-to-vertical spectral ratio (HVNSR) technique and interpreted in terms of local geology, which is characterized by the presence of alluvial sediments of two riverbeds masked by urbanization since the seventeenth century. HVNSRs show significant variations in the study area: when the transition stiff to soft is crossed, a typical spectral peak appears in the HVNSRs, mostly in the frequency band 1–2 Hz, and exceeding a factor of 3 in amplitude. Using available information on subsurface geological structure, we compute theoretical 1D and 2D transfer functions. The resonance frequencies of soft soils obtained by HVNSR are well reproduced by the fundamental frequencies from numerical modeling. The distribution of frequency peaks of HVNSR and their amplitudes are also compared with the local damage caused by historical earthquakes. Previous studies demonstrated that damage variations in Palermo were controlled more by near-surface geology than building vulnerability. A uniform vulnerability is an ideal condition to test statistical methods and their capability in seeking correlation between HVNSR and potential damage due to local geological conditions. We apply two well-established multivariate statistical methodologies (factor analysis and canonical correlation) to the HVNSR dataset and macroseismic data (damage grades of the European macroseismic scale). Through these analyses we quantify the significance of the correlation between the HVNSR peak in the low-medium frequency range (0.5–3 Hz) and the occurrence of the highest damage grades. This approach allows us (1) to estimate the threshold value in the resulting linear combination of the HVNSR amplitudes, which separates zones of light damage from zones of significant damage, and therefore (2) to improve the spatial definition of potentially high hazard zones through a denser grid of microtremor measurements

Microtremor Measurements in the City of Palermo, Italy: Analysis of the Correlation with Local Geology and Damage

This study presents the results of 90 seismic ambient noise measurements in Palermo, the main city of Sicily (Italy). The dataset has been processed using the horizontal-to-vertical spectral ratio (HVNSR) technique and interpreted in terms of local geology, which is characterized by the presence of alluvial sediments of two river-beds masked by urbanization since the 17th century. HVNSRs show significant variations in the study area: when the transition stiff-to-soft is crossed, a typical spectral peak appears in the HVNSRs, mostly in the frequency band 1 to 2 Hz, and exceeding a factor of 3 in amplitude. Using available information on sub-surface geological structure we compute theoretical 1- and 2-D transfer functions. The resonance frequencies of soft soils obtained by HVNSR are well reproduced by the fundamental frequencies from numerical modeling. The distribution of frequency peaks of HVNSR and their amplitudes are also compared with the local damage caused by historical earthquakes. Previous studies demonstrated that damage variations in Palermo were controlled more by near-surface geology than building vulnerability. A uniform vulnerability is an ideal condition to test statistical methods and their capability in seeking correlation between HVNSR and potential damage due to local geological conditions. We apply two well-established multivariate statistical methodologies (factor analysis and canonical correlation) to the HVNSR dataset and macroseismic data (damage grades of the European Macroseismic Scale). Through these analyses we quantify the significance of the correlation between the HVNSR peak in the low-medium frequency range (0.5-3 Hz) and the occurrence of the highest damage grades. This approach allows us i) to estimate the threshold value in the resulting linear combination of the HVNSR amplitudes which separates zones of light damage from zones of significant damage, and therefore ii) to improve the spatial definition of potentially high hazard zones through a denser grid of microtremor measurements

Multidisciplinary investigations using historical data, specific experimental surveys, numerical simulations and earthquake data to assess seismic hazard in a densely urbanized city: the study case of Palermo

The city of Palermo (southern Italy) was severely damaged in the past by moderate-magnitude earthquakes located tens of kilometres offshore. The historical monumental heritage and the high density of population motivated large efforts for the seismic risk assessment. We present the geological and seismological studies performed in downtown Palermo as a study case to show how the complexity of an urban environment can be approached with multidisciplinary investigations. Downtown Palermo is characterized by sea deposits in the coastal zone and the alluvial deposits of two rivers (Papireto and Kemonia) of about 150 m width, which were buried and filled during the XVII century. The difficulty of surface geological surveys was compensated through an analysis of aerial photos and more than 2000 borehole data organized in the City-GIS of the Department of Geology and Geodesy of the University of Palermo. A previous study on the well-documented historical damage indicated the major role played by the two river valleys and the sea deposits in controlling the damage distribution, above the assumption of a fairly homogeneous vulnerability of the existing buildings in downtown. To test the feasibility of using ambient noise for recognizing the presence of alluvial deposits in a densely urbanized environment, a large microtremor measurement campaign was performed in Palermo across several profiles. The frequency peaks inferred from the horizontal-to-vertical spectral ratio were compared with numerical simulations to assess the seismic velocity profile and the soil stratigraphy. Moreover, noise data were analyzed through a statistical approach to establish a possible correlation between damage, resonance frequency and amplitude, and geology. After the moderate earthquake of September 6, 2002 (Mw=5.9, 50 km far away), the analysis of the aftershock sequence provided a well documented estimate of the variation of ground motion within the city in the case of linear soil response. Using these aftershocks we computed also synthetic accelerograms of the main shock through Empirical Green’s Functions that provided ground accelerations as large as 50 gals, consistently with the documented EMS-98 intensity. Synthetic accelerograms showed a large variability of horizontal ground motion within the city (a factor of 3 – 4) that confirms the role of local geology in causing an increase of the seismic hazard on sea and alluvial deposits. Finally, we discuss the comparison between the acceleration response spectra calculated for different soil categories and the design elastic spectra provided by EC8

A Variable Region within the Genome of Streptococcus pneumoniae Contributes to Strain-Strain Variation in Virulence

The bacterial factors responsible for the variation in invasive potential between different clones and serotypes of Streptococcus pneumoniae are largely unknown. Therefore, the isolation of rare serotype 1 carriage strains in Indigenous Australian communities provided a unique opportunity to compare the genomes of non-invasive and invasive isolates of the same serotype in order to identify such factors. The human virulence status of non-invasive, intermediately virulent and highly virulent serotype 1 isolates was reflected in mice and showed that whilst both human non-invasive and highly virulent isolates were able to colonize the murine nasopharynx equally, only the human highly virulent isolates were able to invade and survive in the murine lungs and blood. Genomic sequencing comparisons between these isolates identified 8 regions >1 kb in size that were specific to only the highly virulent isolates, and included a version of the pneumococcal pathogenicity island 1 variable region (PPI-1v), phage-associated adherence factors, transporters and metabolic enzymes. In particular, a phage-associated endolysin, a putative iron/lead permease and an operon within PPI-1v exhibited niche-specific changes in expression that suggest important roles for these genes in the lungs and blood. Moreover, in vivo competition between pneumococci carrying PPI-1v derivatives representing the two identified versions of the region showed that the version of PPI-1v in the highly virulent isolates was more competitive than the version from the less virulent isolates in the nasopharyngeal tissue, blood and lungs. This study is the first to perform genomic comparisons between serotype 1 isolates with distinct virulence profiles that correlate between mice and humans, and has highlighted the important role that hypervariable genomic loci, such as PPI-1v, play in pneumococcal disease. The findings of this study have important implications for understanding the processes that drive progression from colonization to invasive disease and will help direct the development of novel therapeutic strategies

A Functional Genomics Approach to Establish the Complement of Carbohydrate Transporters in Streptococcus pneumoniae

The aerotolerant anaerobe Streptococcus pneumoniae is part of the normal nasopharyngeal microbiota of humans and one of the most important invasive pathogens. A genomic survey allowed establishing the occurrence of twenty-one phosphotransferase systems, seven carbohydrate uptake ABC transporters, one sodium∶solute symporter and a permease, underlining an exceptionally high capacity for uptake of carbohydrate substrates. Despite high genomic variability, combined phenotypic and genomic analysis of twenty sequenced strains did assign the substrate specificity only to two uptake systems. Systematic analysis of mutants for most carbohydrate transporters enabled us to assign a phenotype and substrate specificity to twenty-three transport systems. For five putative transporters for galactose, pentoses, ribonucleosides and sulphated glycans activity was inferred, but not experimentally confirmed and only one transport system remains with an unknown substrate and lack of any functional annotation. Using a metabolic approach, 80% of the thirty-two fermentable carbon substrates were assigned to the corresponding transporter. The complexity and robustness of sugar uptake is underlined by the finding that many transporters have multiple substrates, and many sugars are transported by more than one system. The present work permits to draw a functional map of the complete arsenal of carbohydrate utilisation proteins of pneumococci, allows re-annotation of genomic data and might serve as a reference for related species. These data provide tools for specific investigation of the roles of the different carbon substrates on pneumococcal physiology in the host during carriage and invasive infection

Contribution of a genomic accessory region encoding a putative cellobiose phosphotransferase system to virulence of Streptococcus Pneumoniae

Streptococcus pneumoniae (the pneumococcus) is a formidable human pathogen, responsible for massive global morbidity and mortality. The ability to utilize carbohydrates in a variety of host niches appears to be integral to pneumococcal pathogenesis. In this study we investigated a genomic island, which includes a ROK family protein, a putative cellobiose phosphotransferase system (PTS) and a putative sulfatase. This accessory region is widespread in the pneumococcus in strains of various serotypes and levels of virulence. We have performed simple bioinformatic analysis of the region and investigated its role in vivo in 2 strains with markedly different virulence profiles (WCH206 of serotype 3, ST180; Menzies5 of serotype 11A, ST662). Deleting and replacing the entire island with an antibiotic resistance cassette caused the virulent serotype 3 strain to become attenuated in a murine pneumonia/sepsis model. Further mutants were constructed and used to show that various components of the island contribute significantly to the fitness of WCH206 in a variety of niches of this model, including the nasopharynx, ears and blood, but especially in the lungs. In addition, the island conferred a competitive advantage in nasopharyngeal colonization for the serotype 11A strain, which was essentially avirulent in the pneumonia/sepsis model. The contribution of this island to both pathogenesis and colonization may explain why this accessory region is widespread in the pneumococcus.Lauren J. McAllister, Abiodun D. Ogunniyi, Uwe H. Stroeher and James C. Pato

Genome-based analysis of pneumococcal virulence factors: the quest for novel vaccine antigens and drug targets

Efforts to develop cheaper and more effective vaccines against Streptococcus pneumoniae have been greatly facilitated by access to the genome sequence for this organism. Targeted searches of the genome sequence, as well as techniques to identify genes essential for survival of the pathogen in vivo, have yielded promising new candidate vaccine antigens.James C. Paton, and Philippe Giammarinarohttp://www.elsevier.com/wps/find/journaldescription.cws_home/424100/description#descriptio