Methylmercury Production in Two Northern Fen Peatlands

Northern peatlands provide conditions favourable for sulphate reducing bacteria, microorganisms responsible for producing methylmercury, an aquatic pollutant. An expected climate driven shift from moss- to sedge-dominance may alter mercury biogeochemistry. Observations from a moss-dominated poor fen and sedge-dominated intermediate fen were used to compare methylmercury to assess if contrasting plant communities, nutrients status and/or hydrologic regime control production. Chapter 2 compared porewater methylmercury and ancillary chemistry across two Northern Ontario fens. The lower water table, greater dissolved organic carbon, and lower pH in the poor fen resulted in 3.1 times greater methylmercury. Chapter 3, riparian zones in intermediate fen were evaluated to see if groundwater nutrient supply controlled methylmercury production and transport. Rather than groundwater supply, riparian zones with lower and greater water table fluctuations resulted in greater available sulphate and enhanced methylmercury. The proximity (≤ 2 m) of riparian zones to stream waters facilitated methylmercury transport to surface waters

Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis

The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species.Peer reviewe

Rapid differentiation of Staphylococcus aureus, Staphylococcus epidermidis and other coagulase-negative staphylococci and meticillin susceptibility testing directly from growth-positive blood cultures by multiplex real-time PCR

This study evaluated a multiplex real-time PCR method specific for the mecA, femA-SA and femA-SE genes for rapid identification of Staphylococcus aureus, Staphylococcus epidermidis and non-S. epidermidis coagulase-negative staphylococci (CoNS), and meticillin susceptibility testing directly in positive blood cultures that grew Gram-positive cocci in clusters. A total of 100 positive blood cultures produced: 39 S. aureus [12 meticillin-resistant S. aureus (MRSA), 31 % of all the S. aureus]; 30 S. epidermidis (56.6 % of the CoNS), 8 Staphylococcus capitis (15.1 %), 3 Staphylococcus saprophyticus (5.7 %), 4 Staphylococcus hominis (7.5 %), 3 Staphylococcus haemolyticus (5.7 %), 2 Staphylococcus warneri (3.8 %), 1 Staphylococcus cohnii (1.9 %) and 2 unidentified Staphylococcus spp. (3.8 %); and 1 Micrococcus luteus in pure culture. Two blood cultures had no growth on subculture and five blood cultures grew mixed CoNS. For the 95 blood cultures with pure growth or no growth on subculture, there was very good agreement between real-time PCR and the BD Phoenix identification system for staphylococcal species categorization in S. aureus, S. epidermidis and non-S. epidermidis CoNS and meticillin-resistance determination (Cohen's unweighted kappa coefficient κ=0.882). All MRSA and meticillin-susceptible S. aureus were correctly identified by mecA amplification. PCR amplification of mecA was more sensitive for direct detection of meticillin-resistant CoNS in positive blood cultures than testing with the BD Phoenix system. There were no major errors when identifying staphylococcal isolates and their meticillin susceptibility within 2.5 h. Further studies are needed to evaluate the clinical benefit of using such a rapid test on the consumption of glycopeptide antibiotics and the alteration of empiric therapy in the situation of positive blood cultures growing staphylococci, and the respective clinical outcomes

Identification of clinical isolates of - Hemolytic Streptococci by 16S rRNA gene sequencing, matrix-assisted laser desorption ionization - time of flight mass spectrometry using MALDI biotyper, and conventional phenotypic methods: a comparison

Fifty-six α-hemolytic streptococcal isolates were identified using MALDI Biotyper MS (Bruker Daltonics), API 20 Strep (bioMérieux), and BD Phoenix (Becton, Dickinson). The gold standard for identification was 16S rRNA gene sequence analysis with 16S-23S rRNA intergenic spacer sequencing. The following percentages of isolates were correctly identified to the species level: MALDI Biotyper, 46%; BD Phoenix, 35%; and API 20 Strep, 26%

Rapid differentiation of Staphylococcus aureus, Staphylococcus epidermidis and other coagulase-negative staphylococci and methicillin susceptibility testing directly from growth positive blood cultures by multiplex real-time PCR

This study evaluated a multiplex real-time PCR method specific for the mecA, femA-SA and femA-SE genes for rapid identification of Staphylococcus aureus, Staphylococcus epidermidis and non-S. epidermidis coagulase-negative staphylococci (CoNS), and meticillin susceptibility testing directly in positive blood cultures that grew Gram-positive cocci in clusters. A total of 100 positive blood cultures produced: 39 S. aureus [12 meticillin-resistant S. aureus (MRSA), 31 % of all the S. aureus]; 30 S. epidermidis (56.6 % of the CoNS), 8 Staphylococcus capitis (15.1 %), 3 Staphylococcus saprophyticus (5.7 %), 4 Staphylococcus hominis (7.5 %), 3 Staphylococcus haemolyticus (5.7 %), 2 Staphylococcus warneri (3.8 %), 1 Staphylococcus cohnii (1.9 %) and 2 unidentified Staphylococcus spp. (3.8 %); and 1 Micrococcus luteus in pure culture. Two blood cultures had no growth on subculture and five blood cultures grew mixed CoNS. For the 95 blood cultures with pure growth or no growth on subculture, there was very good agreement between real-time PCR and the BD Phoenix identification system for staphylococcal species categorization in S. aureus, S. epidermidis and non-S. epidermidis CoNS and meticillin-resistance determination (Cohen's unweighted kappa coefficient κ=0.882). All MRSA and meticillin-susceptible S. aureus were correctly identified by mecA amplification. PCR amplification of mecA was more sensitive for direct detection of meticillin-resistant CoNS in positive blood cultures than testing with the BD Phoenix system. There were no major errors when identifying staphylococcal isolates and their meticillin susceptibility within 2.5 h. Further studies are needed to evaluate the clinical benefit of using such a rapid test on the consumption of glycopeptide antibiotics and the alteration of empiric therapy in the situation of positive blood cultures growing staphylococci, and the respective clinical outcomes

Decreasing Interface Defect Densities via Silicon Oxide Passivation at Temperatures Below 450 C

Low-temperature (LT) passivation methods ( 700oC). Therefore, the LT passivation of SiOx/Si has been, since long, a research topic to improve applications performance. Here, we demonstrate that a LT (<450oC) ultrahigh-vacuum (UHV) treatment is a potential method that can be combined with current state-of-the-art processes in a scalable way, to decrease the defect densities at the SiOx/Si interfaces. The studied LT-UHV approach includes a combination of wet chemistry followed by UHV-based heating and pre-oxidation of silicon surfaces. The controlled oxidation during the LT-UHV treatment is found to provide an until now not reported crystalline Si oxide phase. This crystalline SiOx phase can explain the observed decrease in the defect density by halve. Furthermore, the LT-UHV treatment can be applied in a complementary, post-treatment way to ready components to decrease electrical losses. The LT-UHV treatment has been found to decrease the detector leakage current by factor of two.Peer reviewe

Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis

The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species

Meric et al. 2015 GBE: 83 novel Staphylococcus epidermidis genome assemblies

ZIP archive containing contigs for 83 whole genome sequences of S. epidermidis. Metadata is attached to the Dryad submission. Contact: Prof Samuel Sheppard [email protected]

Corneal astigmatism and aberrations after combined femtosecond-assisted phacoemulsification and arcuate keratotomy: 2 years result

Conformal blocks are the central ingredient of the conformal bootstrap programme. We elaborate on our recent observation that uncovered a relation with wave functions of an integrable Calogero-Sutherland Hamiltonian in order to develop a systematic theory of conformal blocks. Our main goal here is to review central ingredients of the Heckman-Opdam theory for scattering states of Calogero-Sutherland models with special emphasis to the relation with scalar 4-point blocks. We will also discuss a number of direct consequences for conformal blocks, including a new series expansion for blocks of arbitrary complex spin and a complete analysis of their poles and residues. Applications to the Froissart-Gribov formula for conformal field theory, as well as extensions to spinning blocks and defects are briefly discussed before we conclude with an outlook on forthcoming work concerning algebraic consequences of integrability