Characterisation of penA and tetM resistance genes of Neisseria gonorrhoeae isolated in southern Africa - epidemiological monitoring and resistance development

Objective. To investigate penA and tetM resistance gene variation of Neisseria gonorrhoeae in order to define gene types for epidemiological monitoring and resistance development. Design. Isolates of N. gonorrhoeae which were susceptible and resistant to penicillin and/or tetracycline were selected. Strains comprised South African isolates (22 from Bloemfontein, 13 from Transvaal, 20 from the Cape) and 15 Botswana and 4 Namibia isolates. The penA genes (2 kb) of all strains and tetM genes (765 bp) of 11 high-level tetracycline-resistant strains were amplified and restricted with Hpall. Results and conclusions. Twelve different Hpall fingerprint patterns were obtained from the 74 isolates analysed for penicillin-binding protein (PBP) 2 gene (penA) alterations. Focusing on the transpeptidase domain, 25 isolates (3 whole gene patterns, minimal inhibitory concentrations (MICs) ~ 0,03 - 0,125 ug/ml) had restriction sites equivalent to those previously described for a susceptible strain. Of the remaining 9 PBP 2 'gene groups, 25 strains fell into a designated group E. Penicillin/ penicillin + clavulanic acid MICs determined on these group E isolates gave a range of 0,125 - 2,0 ug/ml, although MICs against 4 strains were ~ 0,03 ug/ml. MICs of penicillin/penicillin + c1avulanic acid for the 24 isolates that contained altered PBP 2 transpeptidase gene regions not designated group E were only ~ 0,03 - 0,125 ug/ml. The lack of a Hpall restriction site at nucleotide 1934 in the PBP 2 gene of group E strains was indicative of a small terminal region of N. cinerea DNA. This gene block, which was found in all the southern African areas studied, appears to predispose isolates to increased penicillin resistance. The 25,2 MDa conjugative plasmid carrying the tetM resistance determinant was readily demonstrated in 11 Botswana Namibia isolates exhibiting high-level resistance to tetracycline (MICs > 16 ug/ml). The tetM gene was shown to be of the American type

Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities

This article describes the effect of re-interrogation of electron-transfer dissociation (ETD) data with newly developed analytical tools. MS/MS-based characterization of O-linked glycopeptides is discussed using data acquired from a complex mixture of O-linked glycopeptides, featuring mucin core 1-type carbohydrates with and without sialic acid, as well as after partial deglycosylation to leave only the core GalNAc units (Darula and Medzihradszky in Mol Cell Proteomics 8:2515, 2009). Information content of collision-induced dissociation spectra generated in collision cell (in QqTOF instruments) and in ion traps is compared. Interpretation of the corresponding ETD data using Protein Prospector is also presented. Search results using scoring based on the frequency of different fragment ions occurring in ETD spectra of tryptic peptides are compared with results obtained after ion weightings were adjusted to accommodate differential ion frequencies in spectra of differing charge states or cleavage specificities. We show that the improved scoring is more than doubled the glycopeptide assignments under very strict acceptance criteria. This study illustrates that “old” proteomic data may yield significant new information when re-interrogated with new, improved tools

The Sydney Triage to Admission Risk Tool (START) to predict Emergency Department Disposition: A derivation and internal validation study using retrospective state-wide data from New South Wales, Australia.

BACKGROUND: Disposition decisions are critical to the functioning of Emergency Departments. The objectives of the present study were to derive and internally validate a prediction model for inpatient admission from the Emergency Department to assist with triage, patient flow and clinical decision making. METHODS: This was a retrospective analysis of State-wide Emergency Department data in New South Wales, Australia. Adult patients (age ≥ 16 years) were included if they presented to a Level five or six (tertiary level) Emergency Department in New South Wales, Australia between 2013 and 2014. The outcome of interest was in-patient admission from the Emergency Department. This included all admissions to short stay and medical assessment units and being transferred out to another hospital. Analyses were performed using logistic regression. Discrimination was assessed using area under curve and derived risk scores were plotted to assess calibration. RESULTS: 1,721,294 presentations from twenty three Level five or six hospitals were analysed. Of these 49.38% were male and the mean (sd) age was 49.85 years (22.13). Level 6 hospitals accounted for 47.70% of cases and 40.74% of cases were classified as an in-patient admission based on their mode of separation. The final multivariable model including age, arrival by ambulance, triage category, previous admission and presenting problem had an AUC of 0.82 (95% CI 0.81, 0.82). CONCLUSION: By deriving and internally validating a risk score model to predict the need for in-patient admission based on basic demographic and triage characteristics, patient flow in ED, clinical decision making and overall quality of care may be improved. Further studies are now required to establish clinical effectiveness of this risk score model

Making the user more efficient: Design for sustainable behaviour

User behaviour is a significant determinant of a product’s environmental impact; while engineering advances permit increased efficiency of product operation, the user’s decisions and habits ultimately have a major effect on the energy or other resources used by the product. There is thus a need to change users’ behaviour. A range of design techniques developed in diverse contexts suggest opportunities for engineers, designers and other stakeholders working in the field of sustainable innovation to affect users’ behaviour at the point of interaction with the product or system, in effect ‘making the user more efficient’. Approaches to changing users’ behaviour from a number of fields are reviewed and discussed, including: strategic design of affordances and behaviour-shaping constraints to control or affect energyor other resource-using interactions; the use of different kinds of feedback and persuasive technology techniques to encourage or guide users to reduce their environmental impact; and context-based systems which use feedback to adjust their behaviour to run at optimum efficiency and reduce the opportunity for user-affected inefficiency. Example implementations in the sustainable engineering and ecodesign field are suggested and discussed

Electron Capture Dissociation Mass Spectrometry of Tyrosine Nitrated Peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification.Here, we have investigated the electron capture dissociation (ECD) and collision-induced association (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains

The Effect of Using an Inappropriate Protein Database for Proteomic Data Analysis

A recent study by Bromenshenk et al., published in PLoS One (2010), used proteomic analysis to identify peptides purportedly of Iridovirus and Nosema origin; however the validity of this finding is controversial. We show here through re-analysis of a subset of this data that many of the spectra identified by Bromenshenk et al. as deriving from Iridovirus and Nosema proteins are actually products from Apis mellifera honey bee proteins. We find no reliable evidence that proteins from Iridovirus and Nosema are present in the samples that were re-analyzed. This article is also intended as a learning exercise for illustrating some of the potential pitfalls of analysis of mass spectrometry proteomic data and to encourage authors to observe MS/MS data reporting guidelines that would facilitate recognition of analysis problems during the review process

Affordances, constraints and information flows as ‘leverage points’ in design for sustainable behaviour

Copyright @ 2012 Social Science Electronic PublishingTwo of Donella Meadows' 'leverage points' for intervening in systems (1999) seem particularly pertinent to design for sustainable behaviour, in the sense that designers may have the scope to implement them in (re-)designing everyday products and services. The 'rules of the system' -- interpreted here to refer to affordances and constraints -- and the structure of information flows both offer a range of opportunities for design interventions to in fluence behaviour change, and in this paper, some of the implications and possibilities are discussed with reference to parallel concepts from within design, HCI and relevant areas of psychology

A new mode of chemical reactivity for metal-free hydrogen activation by Lewis acidic boranes

We herein explore whether tris(aryl)borane Lewis acids are capable of cleaving H2 outside of the usual Lewis acid/base chemistry described by the concept of “frustrated Lewis pairs” (FLPs). Instead of a Lewis base we use a chemical reductant to generate stable radical anions of two highly‐hindered boranes: tris(3,5‐dinitromesityl)borane and tris(mesityl)borane. NMR spectroscopic characterization reveals that the corresponding borane radical anions activate (cleave) dihydrogen, whilst EPR spectroscopic characterization, supported by computational analysis, reveals the intermediates along the hydrogen activation pathway for the first time. This radical–based, redox pathway involves homolytic cleavage of H2, in contrast to conventional models of FLP chemistry which invoke a heterolytic cleavage pathway. This represents a new mode of chemical reactivity for hydrogen activation by borane Lewis acids

Breaking Up the C Complex Spliceosome Shows Stable Association of Proteins with the Lariat Intron Intermediate

Spliceosome assembly requires several structural rearrangements to position the components of the catalytic core. Many of these rearrangements involve successive strengthening and weakening of different RNA∶RNA and RNA∶proteins interactions within the complex. To gain insight into the organization of the catalytic core of the spliceosome arrested between the two steps of splicing chemistry (C complex), we investigated the effects of exposing C complex to low concentrations of urea. We find that in the presence of 3M urea C complex separates into at least three sub-complexes. One sub-complex contains the 5′exon, another contains the intron-lariat intermediate, and U2/U5/U6 snRNAs likely comprise a third sub-complex. We purified the intron-lariat intermediate sub-complex and identified several proteins, including U2 snRNP and PRP19 complex (NTC) components. The data from our study indicate that U2 snRNP proteins in C complex are more stably associated with the lariat-intron intermediate than the U2 snRNA. The results also suggest a set of candidate proteins that hold the lariat-intron intermediate together in C complex. This information is critical for further interpreting the complex architecture of the mammalian spliceosome