Geophysical measurements for site response investigation : preliminary results on the island of Malta

The main goal of this study is to investigate the dynamic properties of main lithotypes outcropping on the island of Malta and to evaluate the general features of the local seismic response through the combined use of geophysical methods based on Rayleigh waves and horizontal to vertical noise spectral ratios. These kind of studies have unfortunately never been undertaken in Malta and, therefore, no shear wave velocity values and fundamental frequency of outcropping lithotypes have been published. The proposed preliminary results represent a valid set of data useful for evaluating seismic hazard and risk for the Maltese islands. Even if the seismic activity around the archipelago is generally of low to moderate magnitude the islands in the past were struck by large events in Sicily and the Hellenic arc resulting in considerable damage.peer-reviewe

Evaluation of seismic site response in the Maltese archipelago

The investigation of local ground conditions is an important part of seismic hazard assessment (Fäh et al., 2003). It is now well–established that earthquake ground shaking is not only a function of the earth- quake magnitude and epicentral distance, but also of the site conditions, including soft layers in the sub–soil stratification and topographical features. Local geology can greatly alter the seismic waves from earthquakes by amplifying their amplitude, changing the frequency content and increasing the shaking duration during an earthquake (Kramer, 1996). In fact, several unconsolidated soft sites have suffered significantly greater damage than rock sites. One case was the 1985 Michoacán earthquake which showed low peak ground acceleration near the epicenter, yet caused severe damage in Mexico City, which is found more than 350 km away and is characterized by soft shallow sediments (Campillo et al., 1989).peer-reviewe

Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function

LNA (locked nucleic acids, i.e. oligonucleotides with a methyl bridge between the 2′ oxygen and 4′ carbon of ribose) and 2,6-diaminopurine were incorporated into 2′-O-methyl RNA pentamer and hexamer probes to make a microarray that binds unpaired RNA approximately isoenergetically. That is, binding is roughly independent of target sequence if target is unfolded. The isoenergetic binding and short probe length simplify interpretation of binding to a structured RNA to provide insight into target RNA secondary structure. Microarray binding and chemical mapping were used to probe the secondary structure of a 323 nt segment of the 5′ coding region of the R2 retrotransposon from Bombyx mori (R2Bm 5′ RNA). This R2Bm 5′ RNA orchestrates functioning of the R2 protein responsible for cleaving the second strand of DNA during insertion of the R2 sequence into the genome. The experimental results were used as constraints in a free energy minimization algorithm to provide an initial model for the secondary structure of the R2Bm 5′ RNA

The astrobiology primer: An outline of general knowledge - Version 1, 2006

Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genetic selection reveals the role of a buried, conserved polar residue

The burial of nonpolar surface area is known to enhance markedly the conformational stability of proteins. The contribution from the burial of polar surface area is less clear. Here, we report on the tolerance to substitution of Ser75 of bovine pancreatic ribonuclease (RNase A), a residue that has the unusual attributes of being buried, conserved, and polar. To identify variants that retain biological function, we used a genetic selection based on the intrinsic cytotoxicity of ribonucleolytic activity. Cell growth at 30°C, 37°C, and 44°C correlated with residue size, indicating that the primary attribute of Ser75 is its small size. The side-chain hydroxyl group of Ser75 forms a hydrogen bond with a main-chain nitrogen. The conformational stability of the S75A variant, which lacks this hydrogen bond, was diminished by ΔΔG = 2.5 kcal/mol. Threonine, which can reinstate this hydrogen bond, provided a catalytically active RNase A variant at higher temperatures than did some smaller residues (including aspartate), indicating that a secondary attribute of Ser75 is the ability of its uncharged side chain to accept a hydrogen bond. These results provide insight on the imperatives for the conservation of a buried polar residue