Seismic Design of Tialings Dam An Overview of its Evolution and New Challenges

This paper first provides an overview of the evolution of tailings dam engineering over the years. It then highlights key factors affecting seismic performance of tailings dams: such as site seismicity, foundation and damfill geotechnical characteristics, dam design, construction, operation and decommissioning, seismic slope stability, and dam rehabilitation. Finally, it reviews some of the recent trends that lead to new challenges to the engineering profession. These challenges include: coping with heightened public concern about dam safety; balancing potential conflict between seismic and environmental requirements; and addressing issues introduced by globalisation of the mining industry. Institutional responses and technological tools available to meet these challenges are outlined

Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.

BackgroundEvery genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology.ResultsWe analyze a previously uncharacterized Pfam protein family called DUF4424 [Pfam:PF14415]. The recently solved three-dimensional structure of the protein lpg2210 from Legionella pneumophila provides the first structural information pertaining to this family. This protein additionally includes the first representative structure of another Pfam family called the YARHG domain [Pfam:PF13308]. The Pfam family DUF4424 adopts a 19-stranded beta-sandwich fold that shows similarity to the N-terminal domain of leukotriene A-4 hydrolase. The YARHG domain forms an all-helical domain at the C-terminus. Structure analysis allows us to recognize distant similarities between the DUF4424 domain and individual domains of M1 aminopeptidases and tricorn proteases, which form massive proteasome-like capsids in both archaea and bacteria.ConclusionsBased on our analyses we hypothesize that the DUF4424 domain may have a role in forming large, multi-component enzyme complexes. We suggest that the YARGH domain may play a role in binding a moiety in proximity with peptidoglycan, such as a hydrophobic outer membrane lipid or lipopolysaccharide

Assessing U.S. Food Wastage and Opportunities for Reduction

Reducing food wastage is one of the key strategies to combat hunger and sustainably feed the world. We present a comprehensive analysis of available data, despite uncertainties due to data limitation, indicating that the U.S. loses at least 150 million metric tonnes (MMT) of food between farm and fork annually, of which about 70 MMT is edible food loss. Currently, \u3c2% of the edible food loss is recovered for human consumption. A reasonably-attainable goal of food waste reduction at the source by 20% would save more food than the annual increase in total food production and would feed millions of people. This is an opportunity of significant magnitude, offering food security and resource and environmental benefits with few negatives. Seizing this opportunity requires technological innovation, policy intervention, and public outreach. This U.S.-based analysis is pertinent to other mid- to high-income countries

Subglacial sediments: A regional geological template for ice flow in West Antarctica

We use aerogeophysical data to estimate the distribution of marine subglacial sediments and fault“bounded sedimentary basins beneath the West Antarctic Ice Sheet (WAIS). We find that significant ice flow occurs exclusively in regions covered by subglacial sediments. The onsets and lateral margins of ice streams coincide with the limit of marine sediments. Lateral margins are also consistently linked with fault“bounded basins. We predict that the inland migration of ice streams B and C 1 towards the ice divide outside the region covered by marine or rift sediments is unlikely. The subglacial geology has the potential to modulate the dynamic evolution of the ice streams and the WAIS

The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes

<p>Abstract</p> <p>Background</p> <p>Many Gram-positive lactic acid bacteria (LAB) produce anti-bacterial peptides and small proteins called bacteriocins, which enable them to compete against other bacteria in the environment. These peptides fall structurally into three different classes, I, II, III, with class IIa being pediocin-like single entities and class IIb being two-peptide bacteriocins. Self-protective cognate immunity proteins are usually co-transcribed with these toxins. Several examples of cognates for IIa have already been solved structurally. <it>Streptococcus pyogenes</it>, closely related to LAB, is one of the most common human pathogens, so knowledge of how it competes against other LAB species is likely to prove invaluable.</p> <p>Results</p> <p>We have solved the crystal structure of the gene-product of locus Spy_2152 from <it>S. pyogenes</it>, (PDB:<ext-link ext-link-id="2fu2" ext-link-type="pdb">2fu2</ext-link>), and found it to comprise an anti-parallel four-helix bundle that is structurally similar to other bacteriocin immunity proteins. Sequence analyses indicate this protein to be a possible immunity protein protective against class IIa or IIb bacteriocins. However, given that <it>S. pyogenes </it>appears to lack any IIa pediocin-like proteins but does possess class IIb bacteriocins, we suggest this protein confers immunity to IIb-like peptides.</p> <p>Conclusions</p> <p>Combined structural, genomic and proteomic analyses have allowed the identification and <it>in silico </it>characterization of a new putative immunity protein from <it>S. pyogenes</it>, possibly the first structure of an immunity protein protective against potential class IIb two-peptide bacteriocins. We have named the two pairs of putative bacteriocins found in <it>S. pyogenes </it>pyogenecin 1, 2, 3 and 4.</p

Incidence and Predictors of Drug-Eluting Stent Fracture in Human Coronary Artery A Pathologic Analysis

ObjectivesThe aim of this study was to perform pathologic assessment on stent fracture.BackgroundClinically, stent fracture has been reported in 1% to 2% of patients after drug-eluting stent (DES) implantation.MethodsHigh-contrast film-based radiographs of 177 consecutive lesions from the CVPath DES autopsy registry were reviewed. Stent fracture was graded as I (single-strut fracture), II (≥2 struts), III (≥2 struts with deformation), IV (with transection without gap), and V (with transection causing gap in stent segment). The incidence of adverse pathologic findings (thrombosis and restenosis) was assessed histologically.ResultsStent fracture was documented in 51 lesions (29%; grade I = 10, II = 14, III = 12, IV = 6, and V = 9). Lesions with stent fracture had longer duration after implantation (172 days [interquartile range (IQR) 31 to 630 days] vs. 44 days [IQR 7 to 270 days], p = 0.004), a higher rate of Cypher (Cordis Corp., Miami Lakes, Florida) stent usage (63% vs. 36%, p = 0.001), longer stent length (30.0 mm [IQR 22.0 to 40.0 mm] vs. 20.0 mm [IQR 14.0 to 27.3 mm], p < 0.0001), and a higher rate of overlapping stents (45% vs. 22%, p = 0.003). Although fracture with grade I to IV did not have significant impact on the occurrence of adverse pathologic findings such as thrombosis and restenosis, 67% of the grade V fracture lesions were associated with adverse pathologic findings at fracture sites. Longer stent length, use of Cypher, and longer duration of implant were identified as independent risk factors of stent fracture by logistic regression analysis.ConclusionsThe incidence of stent fracture was 29% lesions at autopsy, which is much higher than clinically reported. A high rate of adverse pathologic findings was observed in lesions with grade V stent fracture, whereas fracture with grade I to IV did not have a significant impact on the pathological outcome

Microbial community drivers of PK/NRP gene diversity in selected global soils

Background The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils. Results Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP. Conclusions The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites

Pfam: clans, web tools and services

Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://pfam.cgb.ki.se/)

Rfam: updates to the RNA families database

Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/