Comparison of dynamics of wildtype and V94M human UDP-galactose 4-epimerase-A computational perspective on severe epimerase-deficiency galactosemia

UDP-galactose 4'-epimerase (GALE) catalyzes the interconversion of UDP-galactose and UDP-glucose, an important step in galactose catabolism. Type III galactosemia, an inherited metabolic disease, is associated with mutations in human GALE. The V94M mutation has been associated with a very severe form of type III galactosemia. While a variety of structural and biochemical studies have been reported that elucidate differences between the wildtype and this mutant form of human GALE, little is known about the dynamics of the protein and how mutations influence structure and function. We performed molecular dynamics simulations on the wildtype and V94M enzyme in different states of substrate and cofactor binding. In the mutant, the average distance between the substrate and both a key catalytic residue (Tyr157) and the enzyme-bound NAD(+) cofactor and the active site dynamics are altered making substrate binding slightly less stable. However, overall stability or dynamics of the protein is not altered. This is consistent with experimental findings that the impact is largely on the turnover number (kcat), with less substantial effects on Km. Active site fluctuations were found to be correlated in enzyme with substrate bound to just one of the subunits in the homodimer suggesting inter-subunit communication. Greater active site loop mobility in human GALE compared to the equivalent loop in Escherichia coli GALE explains why the former can catalyze the interconversion of UDP-N-acetylgalactosamine and UDP-N-acetylglucosamine while the bacterial enzyme cannot. This work illuminates molecular mechanisms of disease and may inform the design of small molecule therapies for type III galactosemia.

Determining the response of African biota to climate change: using the past to model the future

Prediction of biotic responses to future climate change in tropical Africa tends to be based on two modelling approaches: bioclimatic species envelope models and dynamic vegetation models. Another complementary but underused approach is to examine biotic responses to similar climatic changes in the past as evidenced in fossil and historical records. This paper reviews these records and highlights the information that they provide in terms of understanding the local- and regional-scale responses of African vegetation to future climate change. A key point that emerges is that a move to warmer and wetter conditions in the past resulted in a large increase in biomass and a range distribution of woody plants up to 400–500 km north of its present location, the so-called greening of the Sahara. By contrast, a transition to warmer and drier conditions resulted in a reduction in woody vegetation in many regions and an increase in grass/savanna-dominated landscapes. The rapid rate of climate warming coming into the current interglacial resulted in a dramatic increase in community turnover, but there is little evidence for widespread extinctions. However, huge variation in biotic response in both space and time is apparent with, in some cases, totally different responses to the same climatic driver. This highlights the importance of local features such as soils, topography and also internal biotic factors in determining responses and resilience of the African biota to climate change, information that is difficult to obtain from modelling but is abundant in palaeoecological records.

In vitro viability of choroidal melanomata following pre-enucleation irradiation

In a group of eighteen patients with uveal melanomas, seven underwent low-dose pre-enucleation irradiation of approximately 2000 cGy. All the tumours were propagated in tissue culture and the growth characteristics of tumour cells from irradiated eyes were compared with tumour cells from non-irradiated eyes. Cultures were observed with phase-contrast microscopy, and radioactive thymidine labelling was used to study cell turnover. Although tissue samples from peripheral areas of irradiated tumours produced a mixture of viable and non-viable cells, with reduced ability to attach to substrate, central regions of irradiated tumours contained viable cells which propagated freely in tissue culture.

An ultrastructural study of retinal photoreceptor degeneration associated with bronchial carcinoma

We studied both eyes of a 66-year-old man with retinal degeneration and oat cell carcinoma of the bronchus. Retinal degeneration was most marked peripheral to the parafovea where photoreceptor cells and their outer segments were absent. Within the parafovea, photoreceptor cells remained but rod outer segments were absent and cone outer segments were fragmented and disorganized. The retinal pigment epithelium contained many immature melanin granules within melanolysosomes, suggesting abnormal melanin synthesis and resorption. We suggest that a pharmacologically active substance resembling a hormone produced by the tumor increased melanin synthesis in the pigment epithelium and that the increased melanin content in these cells compromised their ability to phagocytose and maintain normal turnover of photoreceptor outer segments. We believe these changes led to photoreceptor outer segment loss and subsequent degeneration of the photoreceptor cells.

Acidic properties of nanolayered ZSM-5 zeolites

The acidic properties of nanolayered ZSM-5 zeolites synthesized with the aid of multiquaternary ammonium surfactants were investigated in detail. A substantial fraction of Al is present in highly dispersed form at extraframework positions indicative of the defective nature of the calcined nanolayered zeolites. Acidity characterization reveals that the Brønsted acid sites are similar in strength to those in bulk HZSM-5. Nanolayered zeolites contain a higher amount of Brønsted acid sites (BAS) at their external (mesopore) surface. Unilamellar zeolites have a higher concentration of external BA and silanol sites than multilamellar ones. The number of BAS in the nanolayered zeolites is considerably lower than the tetrahedral Al content, the difference increasing with nanolayer thickness. Except for one particular sample (nanolayered ZSM-5 synthesized from COH template), the total turnover of methanol normalized per BAS trends inversely with the concentration of BAS. There is no correlation with the concentration of external BAS. Catalyst deactivation due to coke mainly depends on the BAS concentration. A unilamellar ZSM-5 zeolite prepared using COH displayed substantially improved performance in terms of a much lower rate of coke deactivation in line with earlier data Choi et al. [10]. Since the acidic and textural properties of this zeolite did not differ significantly from the others, it remains to be determined why this zeolite performs so much better. © 2013 Elsevier Ltd. All rights reserved.

Biochemical characterisation of triose phosphate isomerase from the liver fluke Fasciola hepatica

Triose phosphate isomerase (TPI) catalyses the interconversion of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, a reaction in the glycolytic pathway. TPI from the common liver fluke, Fasciola hepatica, has been cloned, sequenced and recombinantly expressed in Escherichia coli. The protein has a monomeric molecular mass of approximately 28 kDa. Crosslinking and gel filtration experiments demonstrated that the enzyme exists predominantly as a dimer in solution. F. hepatica TPI is predicted to have a ß-barrel structure and key active site residues (Lys-14, His-95 and Glu-165) are conserved. The enzyme shows remarkable stability to both proteolytic degradation and thermal denaturation. The melting temperature, estimated by thermal scanning fluorimetry, was 67 °C and this temperature was increased in the presence of either dihydroxyacetone phosphate or glyceraldehyde 3-phosphate. Kinetic studies showed that F. hepatica TPI demonstrates Michaelis-Menten kinetics in both directions, with Km values for dihydroxyacetone phosphate and glyceraldehyde 3-phosphate of 2.3 mM and 0.66 mM respectively. Turnover numbers were estimated at 25,000 s(-1) for the conversion of dihydroxyacetone phosphate and 1900 s(-1) for the conversion of glyceraldehyde 3-phosphate. Phosphoenolpyruvate acts as a weak inhibitor of the enzyme. F. hepatica TPI has many features in common with mammalian TPI enzymes (e.g. ß-barrel structure, homodimeric nature, high stability and rapid kinetic turnover). Nevertheless, recent successful identification of specific inhibitors of TPI from other parasites, suggests that small differences in structure and biochemical properties could be exploited in the development of novel, species-specific inhibitors.

Fasciola hepatica:studies on vaccination of rats and mice with a surface antigen prepared from fluke homogenate by means of a monoclonal antibody

T1 tegumental antigen was isolated from a homogenate of eight- to 10-week-old Fasciola hepatica using a T1-specific monoclonal antibody bound to sepharose in an antibody-affinity column. Rats and mice were vaccinated with T1 antigen in Freund's complete adjuvant, and control groups received equivalent amounts of non-T1 antigen (eluted from the antibody-affinity column) or ovalbumin. On completion of the immunisation programme, serum samples were collected for ELISA and IFA testing. The animals were challenged by oral infection with F hepatica metacercariae or, for several vaccinated rats, by intraperitoneal transplantation of live adult flukes. At autopsy, worm-burden and liver damage was assessed for each animal and the condition of transplanted flukes was examined. Comparison of test and control groups of animals showed that neither T1 nor non-T1 antigens provided significant protection against challenge, although specific antibody responses against the appropriate sensitising antigen were engendered. Flukes transplanted to the peritoneal cavity of immunised rats survived without damage, although they became encased in hollow fibrous capsules of host origin. The results lend support to the pre-existing concept that glycocalyx turnover by discharge of T1 secretory bodies at the apical surface of migrating flukes provides an efficient means of protection for the parasite against host immunity.

Habitat Isolation Reduces the Temporal Stability of Island Ecosystems in the Face of Flood Disturbance

Natural ecosystems are increasingly exposed to multiple anthropogenic stressors, including land-use change, deforestation, agricultural intensification, and urbanisation, all of which have led to widespread habitat fragmentation, which is also likely to be amplified further by predicted climate change. The potential interactive effects of these different stressors cannot be determined by studying each in isolation, although such synergies have been largely ignored in ecological field studies to date. Here, we use a model system of naturally fragmented islands in a braided river network, which is exposed to periodic inundation, to investigate the interactive effects of habitat isolation and flood disturbance. Food web structure was similar across the islands during periods of hydrological stability, but several key properties were altered in the aftermath of flood disturbance, based on distance of the islands from the regional source pool of species: taxon richness and mean food chain length declined with habitat isolation after flooding, while the proportion of basal species increased. Greater species turnover through time reflected the slower process of re-colonisation on the more distant islands following disturbance. Increased variability of several food web properties over a 1-year period highlighted the reduced temporal stability of isolated habitat fragments. Many of these effects reflected the differential successes of predator and prey species at re-colonising the islands: even though larger, more mobile consumers may reach the more distant islands first, they cannot establish populations until the lower trophic levels have successfully reassembled. These results highlight the susceptibility of fragmented ecosystems to environmental perturbations. © 2013 Elsevier Ltd.

Keratinocyte growth factor in acute lung injury to reduce pulmonary dysfunction--a randomised placebo-controlled trial (KARE):study protocol

Acute lung injury is a common, devastating clinical syndrome associated with substantial mortality and morbidity with currently no proven therapeutic interventional strategy to improve patient outcomes. The objectives of this study are to test the potential therapeutic effects of keratinocyte growth factor for patients with acute lung injury on oxygenation and biological indicators of acute inflammation, lung epithelial and endothelial function, protease:antiprotease balance, and lung extracellular matrix degradation and turnover.

Prevalence and Causes of Prescribing ErrorsL The PRescribing Outcomes for Trainee Doctors Engaged in Clinical Training (PROTECT) Study

Objectives: Study objectives were to investigate the prevalence and causes of prescribing errors amongst foundation doctors (i.e. junior doctors in their first (F1) or second (F2) year of post-graduate training), describe their knowledge and experience of prescribing errors, and explore their self-efficacy (i.e. confidence) in prescribing.

Method: A three-part mixed-methods design was used, comprising: prospective observational study; semi-structured interviews and cross-sectional survey. All doctors prescribing in eight purposively selected hospitals in Scotland participated. All foundation doctors throughout Scotland participated in the survey. The number of prescribing errors per patient, doctor, ward and hospital, perceived causes of errors and a measure of doctors’ self-efficacy were established.

Results: 4710 patient charts and 44,726 prescribed medicines were reviewed. There were 3364 errors, affecting 1700 (36.1%) charts (overall error rate: 7.5%; F1:7.4%; F2:8.6%; consultants:6.3%). Higher error rates were associated with : teaching hospitals (p,0.001), surgical (p = ,0.001) or mixed wards (0.008) rather thanmedical ward, higher patient turnover wards (p,0.001), a greater number of prescribed medicines (p,0.001) and the months December and June (p,0.001). One hundred errors were discussed in 40 interviews. Error causation was multi-factorial; work environment and team factors were particularly noted. Of 548 completed questionnaires (national response rate of 35.4%), 508 (92.7% of respondents) reported errors, most of which (328 (64.6%) did not reach the patient. Pressure from other staff, workload and interruptions were cited as the main causes of errors. Foundation year 2 doctors reported greater confidence than year 1 doctors in deciding the most appropriate medication regimen.

Conclusions: Prescribing errors are frequent and of complex causation. Foundation doctors made more errors than other doctors, but undertook the majority of prescribing, making them a key target for intervention. Contributing causes included work environment, team, task, individual and patient factors. Further work is needed to develop and assess interventions that address these.

Molecular mechanism and physiological role of active-deactive transition of mitochondrial complex I

The unique feature ofmitochondrial complex I is the so-called A/D transition (active-deactive transition). The A-form catalyses rapid oxidation of NADH by ubiquinone (k ~10 min) and spontaneously converts into the D-form if the enzyme is idle at physiological temperatures. Such deactivation occurs in vitro in the absence of substrates or in vivo during ischaemia, when the ubiquinone pool is reduced. The D-form can undergo reactivation given both NADH and ubiquinone availability during slow (k ~1-10 min) catalytic turnover(s). We examined known conformational differences between the two forms and suggested a mechanism exerting A/D transition of the enzyme. In addition, we discuss the physiological role of maintaining the enzyme in the D-form during the ischaemic period. Accumulation of the D-form of the enzyme would prevent reverse electron transfer from ubiquinol to FMN which could lead to superoxide anion generation. Deactivation would also decrease the initial burst of respiration after oxygen reintroduction. Therefore the A/D transition could be an intrinsic protective mechanism for lessening oxidative damage during the early phase of reoxygenation. Exposure of Cys of mitochondrially encoded subunit ND3 makes the Dform susceptible for modification by reactive oxygen species and nitric oxide metabolites which arrests the reactivation of the D-form and inhibits the enzyme. The nature of thiol modification defines deactivation reversibility, the reactivation timescale, the status of mitochondrial bioenergetics and therefore the degree of recovery of the ischaemic tissues after reoxygenation.

ND3, ND1 and 39 kDa subunits are more exposed in the de-active form of bovine mitochondrial complex I

An intriguing feature of mitochondrial complex I from several species is the so-called A/D transition, whereby the idle enzyme spontaneously converts from the active (A) form to the de-active (D) form. The A/D transition plays an important role in tissue response to the lack of oxygen and hypoxic deactivation of the enzyme is one of the key regulatory events that occur in mitochondria during ischaemia. We demonstrate for the first time that the A/D conformational change of complex I does not affect the macromolecular organisation of supercomplexes in vitro as revealed by two types of native electrophoresis. Cysteine 39 of the mitochondrially-encoded ND3 subunit is known to become exposed upon de-activation. Here we show that even if complex I is a constituent of the I + III + IV (S) supercomplex, cysteine 39 is accessible for chemical modification in only the D-form. Using lysine-specific fluorescent labelling and a DIGE-like approach we further identified two new subunits involved in structural rearrangements during the A/D transition: ND1 (MT-ND1) and 39 kDa (NDUFA9). These results clearly show that structural rearrangements during de-activation of complex I include several subunits located at the junction between hydrophilic and hydrophobic domains, in the region of the quinone binding site. De-activation of mitochondrial complex I results in concerted structural rearrangement of membrane subunits which leads to the disruption of the sealed quinone chamber required for catalytic turnover.

Review of Marine Spatial Planning Best Practice of Relevance to Ireland

Making room for new marine uses and safeguarding more traditional uses, without degrading the marine environment, will require the adoption of new integrated management strategies. Current management frameworks do not facilitate the integrated management of all marine activities occurring in one area. To address this issue, the government developed Harnessing Our Ocean Wealth – An Integrated Marine Plan (IMP) for Ireland. Harnessing Our Ocean
Wealth presents a ‘roadmap’ for adopting an integrated approach to marine governance and for achieving the Government’s ambitious targets for the maritime sector, including: exceeding €6.4 billion turnover annually by 2020, and doubling its contribution to GDP to 2.4% by 2030. As part of this roadmap, Harnessing Our Ocean Wealth endorses the development of an appropriate Marine Spatial Planning (MSP) Framework. One way to develop an MSP Framework is to learn from early adapters. Critical assessments of key
elements of MSP as implemented in early initiatives can serve to inform the development of an appropriate framework. The aim of this project is to contribute to the development of this framework by reporting on
MSP best practice relevant to Ireland. Case study selection and evaluation criteria are outlined in the next section. This is followed by a presentation of case study findings. The final section of the report focuses on outlining how the lessons could be transferred to the Irish context.

Selective Palladium-Catalysed Aerobic Oxidation of Alcohols

Palladium has a significant track record as a catalyst for a range of oxidation reactions and it has been explored for the selective oxidation of alcohols for many years. This chapter focuses on the two main types of aerobic Pd catalysts: heterogeneous and ligand-modulated systems. In the case of heterogeneous systems, the mechanistic understanding of these systems and the use of in situ and operando techniques to obtain this knowledge are discussed. The current state-of-the-art is also summarized in terms of catalytic performance and substrate scope for heterogeneous Pd-based catalysts. In terms of ligand-modulated systems, leading examples of molecular Pd(ii) catalysts which undergo direct O2 coupled turnover are highlighted. The catalyst performance for such catalysts is exemplified and mechanistic understanding for these molecular systems is discussed.

Resilience and Burnout in Child protection social work: Individual and organisational themes from a systematic literature review

Child protection social work is acknowledged as a very stressful occupation, with high turnover and poor retention of staff being a major concern. This paper highlights themes that emerged from findings of sixty-five articles that were included as part of a systematic literature review. The review focused on the evaluation of research findings, which considered individual and organisational factors associated with resilience or burnout in child protection social work staff. The results identified a range of individual and organisational themes for staff in child protection social work. Nine themes were identified in total. These are categorised under ‘Individual’ and ‘Organisational’ themes. Themes categorised as individual included personal history of maltreatment, training and preparation for child welfare, coping, secondary traumatic stress, compassion fatigue and compassion satisfaction. Those classified as organisational included workload, social support and supervision, organisational culture and climate, organisational and professional commitment, and job satisfaction or dissatisfaction. The range of factors is discussed with recommendations and areas for future research are highlighted.