A markerless deletion method for genetic manipulation of Burkholderia cenocepacia and other multidrug-resistant gram-negative bacteria

Genetic manipulation of multidrug-resistant bacteria is often difficult and hinders progress in understanding their physiology and pathogenesis. This book chapter highlights advances in genetic manipulation of Burkholderia cenocepacia, which are also applicable to other members of the Burkholderia cepacia complex and multidrug-resistant gram-negative bacteria of other genera. The method detailed here is based on the I-SceI homing endonuclease system, which can be efficiently used for chromosomal integration, deletion, and genetic replacement. This system creates markerless mutations and insertions without leaving a genetic scar and thus can be reused successively to generate multiple modifications in the same strain.

Structure and thermal properties of salicylate-based-protic ionic liquids as new heat storage media. COSMO-RS structure characterization and modeling of heat capacities

During this research, we present a study on the thermal properties, such as the melting, cold crystallization, and glass transition temperatures as well as heat capacities from 293.15 K to 323.15 K of nine in-house synthesized protic ionic liquids based on the 3-(alkoxymethyl)-1H-imidazol-3-ium salicylate ([H-Im-C₁OC_n][Sal]) with n = 3–11. The 3D structures, surface charge distributions and COSMO volumes of all investigated ions are obtained by combining DFT calculations and the COSMO-RS methodology. The heat capacity data sets as a function of temperature of the 3-(alkoxymethyl)-1H-imidazol-3-ium salicylate are then predicted using the methodology originally proposed in the case of ionic liquids by Ge et al. 3-(Alkoxymethyl)-1H-imidazol-3-ium salicylate based ionic liquids present specific heat capacities higher in many cases than other ionic liquids that make them suitable as heat storage media and in heat transfer processes. It was found experimentally that the heat capacity increases linearly with increasing alkyl chain length of the alkoxymethyl group of 3-(alkoxymethyl)-1H-imidazol-3-ium salicylate as was expected and predicted using the Ge et al. method with an overall relative absolute deviation close to 3.2% for temperatures up to 323.15 K.

Elaborating Justice for Victims at the International Criminal Court: Beyond Rhetoric and the Hague

Justice for victims has often been invoked as the raison d’être of international criminal justice, by punishing perpetrators of international crimes. This article attempts to provide a more holistic account of justice for victims by examining victims’ needs, interests, and rights. The International Criminal Court itself includes participation, protection and reparation for victims, indicating they are important stakeholders. This article also suggests that victims are integral to the purpose of the ICC in ending impunity by ensuring transparency of proceedings. However, there are limits to the resources and capacity of the ICC, which can only investigate and prosecute selected crimes. To overcome this justice gap, this article directs the debate towards a victim-orientated agenda to complementarity, where state parties and the Assembly of State Parties should play a greater role in implementing justice for victims domestically. This victim-orientated complementarity approach can be achieved through new ASP guidelines on complementarity, expanding universal jurisdiction, or seeking enforcement and cooperation through regional and international bodies and courts, such asUniversal Periodic Review or the African Court’s International Criminal Law Section. In the end, ifwe are serious about delivering justice for victims we need to move beyond the rhetoric, with realistic expectations of what the ICC can achieve, and concentrate our attention to what states should bedoing to end impunity.

CULTURE AND CULTURE INDEPENDANT IDENTIFICATION OF BACTERIAL COMMUNITIES IN THE CYSTIC FIBROSIS RESPIRATORY TRACT

Introduction and Aims: The identification of complex chronic polymicrobial infections, such as those observed in the cystic fibrosis (CF) airways, are often a diagnostic challenge. Few studies have compared culture-dependent methods with molecular identification making it hard to describe bacterial communities in a comprehensive manner. The aim of the study is to compare four different methods with respect to their similarities and differences in detection of bacteria. Methods: We compared41 sputum samples fromroutine clinical-culture, extended-culture (aerobic and anaerobic), and molecular identification such as Roche 454-FLX Titanium and T-RFLP to assess concurrence between methodologies in detecting bacteria. The agreement between methodologies in detecting either absence or presence of bacterial taxa was assessed by Kappa (κ) statistics. Results: The majority of bacterial taxa identified by culture were also identified with molecular analysis. In total 2, 60, 25, and 179 different bacterial taxa were identified with clinical-culture, extended-culture, T-RFLP and 454-FLX respectively. Clinical-culture, extended-culture and T-RFLP were poor predictors of species richness when compared to 454-FLX (p < 0.0001). Agreement between methods for detecting Pseudomonas sp. and Burkholderia sp. was good with κ ≥ 0.7 [p < 0.0001] and κ ≥ 0.9 [p < 0.0001] respectively. Detection of anaerobic bacteria, such as Prevotella sp. and Veillonella sp., was moderate between extended-culture and 454-FLX with κ = 0.461 [p < 0.0001] and κ = 0.311 [p = 0.032] respectively, and good between T-RFLP and 454-FLX with κ = 0.577 [p < 0.0001] and κ = 0.808 [p < 0.0001] respectively. Agreement between methods for other main bacterial taxa, such as Staphylcoccus sp. and Streptococcus sp., was poor with only a moderate agreement for detection of Streptococcus sp. observed between T-RFLP and 454-FLX (κ = 0.221 [p = 0.024]). Conclusions: This study demonstrates the increased sensitivity culture-independent microbial identification such as the 454-FLX have over clinical-culture, extended-culture and T-RFLP methodologies. The extended-culture detected majority of the most prevalent bacterial taxa associated with chronic colonisation of the CF airways which were also detected by culture-independent methodologies. However, agreement between methods in detecting number of potentially relevant bacteria is largely lacking.

An analysis of the attitudes of dental patients attending general dental practice in Galway

AIM: To describe the patterns of dental attendance and attitudes towards tooth loss of general dental practice patients in Galway.

OBJECTIVES: 1. To determine the pattern of adult dental attendance in general practices in Galway; and, 2. To examine the oral health attitudes of these patients.

METHOD: Questionnaires were distributed to 311 consecutive adult patients in the waiting rooms of ten general dental practices in Galway, which were randomly selected from the telephone directory.

RESULTS: A total of 254 of the 311 questionnaires distributed were fully completed, returned and included in the results, giving a response rate of 81.7%. A total of 59% of dentate participants attended their dentist for annual or biannual examinations compared to 23% of edentate patients. Some 10.5% of medical card holders and 0.5% of non-medical card holders were edentulous.

CONCLUSIONS: The data from the survey indicated that medical card holders in Galway were more likely to be edentulous than nonmedical card holders. Edentate patients were less likely to be regular dental attenders than dentate patients.

Investigating Approaches to Three-Dimensional Printing of Hydroxyapatite Scaffolds for Bone Regeneration

This study investigated the feasibility of manufacturing hydroxyapatite (HA)-based scaffolds using 3D printing technology by incorporating different binding additives, such as maltodextrin and polyvinyl alcohol (PVOH), into the powder formulation. Different grades of PVOH were evaluated in terms of their impact on the printing quality. Results showed that scaffolds with high architectural accuracy in terms of the design and excellent green compressive strength were obtained when the PVOH (high viscosity) was used as the binding additive for HA.

Activity and coke formation of nickel and nickel carbide in dry reforming: A deactivation scheme from density functional theory

Dry reforming is a promising reaction to utilise the greenhouse gases CO2 and CH4. Nickel-based catalysts are the most popular catalysts for the reaction, and the coke formation on the catalysts is the main obstacle to the commercialisation of dry reforming. In this study, the whole reaction network of dry reformation on both flat and stepped nickel catalysts (Ni(111) and Ni(211)) as well as nickel carbide (flat: Ni3C(001); stepped: Ni3C(111)) is investigated using density functional theory calculations. The overall reaction energy profiles in the free energy landscape are obtained, and kinetic analyses are utilised to evaluate the activity of the four surfaces. By careful examination of our results, we find the following regarding the activity: (i) flat surfaces are more active than stepped surfaces for the dry reforming and (ii) metallic nickel catalysts are more active than those of nickel carbide, and therefore, the phase transformation from nickel to nickel carbide will reduce the activity. With respect to the coke formation, the following is found: (i) the coke formation probability can be measured by the rate ratio of CH oxidation pathway to C oxidation pathway (r(CH)/r(C)) and the barrier of CO dissociation, (ii) on Ni(111), the coke is unlikely to form, and (iii) the coke formations on the stepped surfaces of both nickel and nickel carbide can readily occur. A deactivation scheme, using which experimental results can be rationalised, is proposed. 

The influence of microbial factors on the susceptibility of bacteria to photocatalytic destruction

The role that bacterial factors play in determining how bacteria respond to photocatalytic degradation is becoming increasingly recognised. Fimbriae which are thin, proteinaceous cell surface structures produced by many enterobacteria are generally considered to be important bacterial virulence determinants in the host. Recent studies, however, suggest that their expression may be increased during times of environmental stress to protect them against factors such as nutrient depletion and oxidation. In this study bacteria were grown under defined culture conditions to promote the expression of type 1 fimbriae and subjected to photocatalytic treatment. Results showed that Escherichia coli grown under conditions to express type 1 fimbriae were more resistant to photocatalytic destruction than control cultures, taking 75 min longer to be destroyed. Curli fimbriae are also known to play a role in environmental protection of bacteria and they are associated with biofilm production. The ability of the E. coli strain to produce curli fimbriae was confirmed and biofilms were grown and subjected to photocatalytic treatment. Biofilm destruction by photocatalysis was assessed using a resazurin viability assay and a loss of cell viability was demonstrated within 30 min treatment time. This study suggests that intrinsic bacterial factors may play a role in determining an organism’s response to photocatalytic treatment and highlights their importance in this disinfection process.

Human Perception of Laughter from Context-free Whole Body Motion Dynamic Stimuli

Laughter is a ubiquitous social signal in human interactions yet it remains understudied from a scientific point of view. The need to understand laughter and its role in human interactions has become more pressing as the ability to create conversational agents capable of interacting with humans has come closer to a reality. This paper reports on three aspects of the human perception of laughter when context has been removed and only the body information from the laughter episode remains. We report on ability to categorise the laugh type and the sex of the laugher; the relationship between personality factors with laughter categorisation and perception; and finally the importance of intensity in the perception and categorisation of laughter.

Predictive Factors for Local Control in Primary and Metastatic Lung Tumours after Four to Five Fraction Stereotactic Ablative Body Radiotherapy: A Single Institution's Comprehensive Experience

AIMS: We report the outcomes of a large lung stereotactic ablative body radiotherapy (SABR) programme for primary non-small cell lung cancer (NSCLC) and pulmonary metastases. The primary study aim was to identify factors predictive for local control.

MATERIALS AND METHODS: In total, 311 pulmonary tumours in 254 patients were treated between 2008 and 2011 with SABR using 48-60 Gy in four to five fractions. Local, regional and distant failure data were collected prospectively, whereas other end points were collected retrospectively. Potential clinical and dosimetric predictors of local control were evaluated using univariate and multivariate analyses.

RESULTS: Of the 311 tumours, 240 were NSCLC and 71 were other histologies. The 2 year local control rate was 96% in stage I NSCLC, 76% in colorectal cancer (CRC) metastases and 91% in non-lung/non-CRC metastases. Predictors of better local control on multivariate analysis were non-CRC tumours and a larger proportion of the planning target volume (PTV) receiving ≥100% of the prescribed dose (higher PTV V100). Among the 45 CRC metastases, a higher PTV V100 and previous chemotherapy predicted for better local control.

CONCLUSIONS: Lung SABR of 48-60 Gy/four to five fractions resulted in high local control rates for all tumours except CRC metastases. Covering more of the PTV with the prescription dose (a higher PTV V100) also resulted in superior local control.

Arsenic uptake and accumulation in rice (Oryza sativa L.) irrigated with contaminated water

Long-term use of arsenic contaminated groundwater to irrigate crops, especially paddy rice (Oryza sativa L.) has resulted in elevated soil arsenic levels in Bangladesh. There is, therefore, concern regarding accumulation of arsenic in rice grown on these soils. A greenhouse pot experiment was conducted to evaluate the impact of arsenic-contaminated irrigation water on the growth and uptake of arsenic into rice grain, husk, straw and root. There were altogether 10 treatments which were a combination of five arsenate irrigation water concentrations (0-8 mg As l^-1) and two soil phosphate amendments. Use of arsenate containing irrigation water reduced plant height, decreased rice yield and affected development of root growth. Arsenic concentrations in all plant parts increased with increasing arsenate concentration in irrigation water. However, arsenic concentration in rice grain did not exceed the maximum permissible limit of 1.0 mg As kg^-1. Arsenic accumulation in rice straw at very high levels indicates that feeding cattle with such contaminated straw could be a direct threat for their health and also, indirectly, to human health via presumably contaminated bovine meat and milk. Phosphate application neither showed any significant difference in plant growth and development, nor in As concentrations in plant parts.

Electrochemical promotion of catalysis using solid-state proton-conducting membranes

A solid-state electrochemical reactor with ceramic proton-conducting membrane has been used to study the effect of electrochemically induced hydrogen spillover on the catalytic activity of platinum during ethylene oxidation. Suitable proton-conducting electrolyte membranes (Gd-doped BaPrO ₃ (BPG) and Y-doped BaZrO₃ (BZY)) were fabricated. These materials were chosen because of their protonic conductivity in the operational temperature region of the reaction (400-700 °C). The BZY-based electrochemical cell was used to investigate the open-circuit voltage (OCV) dependence on H₂ partial pressure with comparison being made to the theoretical OCV as predicted by the Nernst equation. Furthermore, the BZY pellets were used to study the effect of proton transfer of the catalytic activity of platinum during ethylene oxidation. The reaction was found to exhibit electrochemical promotion at 400 °C and to be electrophilic in nature, i.e. proton addition to the platinum surface resulted in an increase in reaction rate. At higher temperatures, the rate was not affected, within experimental error, by proton addition or removal. Under similar conditions, AC impedance showed that there was a large overall cell resistance at 400 °C with significantly decreased resistance at higher temperatures. It is possible that there could be a relationship between large cell resistances and the onset of electrochemical promotion in this system but there is, as yet, no conclusive evidence for this. © 2003 Elsevier B.V. All rights reserved.