Epstein-Barr Virus Large Tegument Protein BPLF1 Contributes to Innate Immune Evasion through Interference with Toll-Like Receptor Signaling

Viral infection triggers an early host response through activation of pattern recognition receptors, including Toll-like receptors (TLR). TLR signaling cascades induce production of type I interferons and proinflammatory cytokines involved in establishing an anti-viral state as well as in orchestrating ensuing adaptive immunity. To allow infection, replication, and persistence, (herpes)viruses employ ingenious strategies to evade host immunity. The human gamma-herpesvirus Epstein-Barr virus (EBV) is a large, enveloped DNA virus persistently carried by more than 90% of adults worldwide. It is the causative agent of infectious mononucleosis and is associated with several malignant tumors. EBV activates TLRs, including TLR2, TLR3, and TLR9. Interestingly, both the expression of and signaling by TLRs is attenuated during productive EBV infection. Ubiquitination plays an important role in regulating TLR signaling and is controlled by ubiquitin ligases and deubiquitinases (DUBs). The EBV genome encodes three proteins reported to exert in vitro deubiquitinase activity. Using active site-directed probes, we show that one of these putative DUBs, the conserved herpesvirus large tegument protein BPLF1, acts as a functional DUB in EBV-producing B cells. The BPLF1 enzyme is expressed during the late phase of lytic EBV infection and is incorporated into viral particles. The N-terminal part of the large BPLF1 protein contains the catalytic site for DUB activity and suppresses TLR-mediated activation of NF-κB at, or downstream of, the TRAF6 signaling intermediate. A catalytically inactive mutant of this EBV protein did not reduce NF-κB activation, indicating that DUB activity is essential for attenuating TLR signal transduction. Our combined results show that EBV employs deubiquitination of signaling intermediates in the TLR cascade as a mechanism to counteract innate anti-viral immunity of infected hosts.

Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection

UNLABELLED: Burkholderia pseudomallei causes the potentially fatal disease melioidosis. It is generally accepted that B. pseudomallei is a noncommensal bacterium and that any culture-positive clinical specimen denotes disease requiring treatment. Over a 23-year study of melioidosis cases in Darwin, Australia, just one patient from 707 survivors has developed persistent asymptomatic B. pseudomallei carriage. To better understand the mechanisms behind this unique scenario, we performed whole-genome analysis of two strains isolated 139 months apart. During this period, B. pseudomallei underwent several adaptive changes. Of 23 point mutations, 78% were nonsynonymous and 43% were predicted to be deleterious to gene function, demonstrating a strong propensity for positive selection. Notably, a nonsense mutation inactivated the universal stress response sigma factor RpoS, with pleiotropic implications. The genome underwent substantial reduction, with four deletions in chromosome 2 resulting in the loss of 221 genes. The deleted loci included genes involved in secondary metabolism, environmental survival, and pathogenesis. Of 14 indels, 11 occurred in coding regions and 9 resulted in frameshift mutations that dramatically affected predicted gene products. Disproportionately, four indels affected lipopolysaccharide biosynthesis and modification. Finally, we identified a frameshift mutation in both P314 isolates within wcbR, an important component of the capsular polysaccharide I locus, suggesting virulence attenuation early in infection. Our study illustrates a unique clinical case that contrasts a high-consequence infectious agent with a long-term commensal infection and provides further insights into bacterial evolution within the human host.

IMPORTANCE: Some bacterial pathogens establish long-term infections that are difficult or impossible to eradicate with current treatments. Rapid advances in genome sequencing technologies provide a powerful tool for understanding bacterial persistence within the human host. Burkholderia pseudomallei is considered a highly pathogenic bacterium because infection is commonly fatal. Here, we document within-host evolution of B. pseudomallei in a unique case of human infection with ongoing chronic carriage. Genomic comparison of isolates obtained 139 months (11.5 years) apart showed a strong signal of adaptation within the human host, including inactivation of virulence and immunogenic factors, and deletion of pathways involved in environmental survival. Two global regulatory genes were mutated in the 139-month isolate, indicating extensive regulatory changes favoring bacterial persistence. Our study provides insights into B. pseudomallei pathogenesis and, more broadly, identifies parallel evolutionary mechanisms that underlie chronic persistence of all bacterial pathogens.

Bladder continence management in adult acquired brain injury

Purpose: Persistence of urinary incontinence post acquired brain injury (ABI) carries important prognostic significance. We undertook to document the incidence of urinary incontinence, its management and complications in rehabilitation inpatients following ABI and to assess adherence to post ABI bladder management guidelines. 

Method: A retrospective chart survey of a convenience sample of consecutive admissions to two adult neurorehabilitation units Forster Green Hospital, Belfast, and the Scottish Brain Injury Rehabilitation Service, Edinburgh (SBIRSE). Bladder continence and management on transfer to and discharge from rehabilitation, trial removal of catheter, use of bladder drill, ultrasound investigation, anticholinergic medication and complications were recorded. 

Results: One hundred and forty six patients were identified. Seventy-seven (52.7%) were independent and continent of urine at rehabilitation admission and 109 (74.7%) on discharge. In all, 13 patients had urinary tract infection, 7 had urethral stricture and 1 developed haematuria whilst catheterised. Ultrasound of renal tracts was underused. Trial removal of catheter after transfer to rehabilitation occurred at a median of 10 days. 

Conclusions: Urinary continence was achieved in almost half of incontinent ABI patients during rehabilitation. There is potential for increased use of investigation of the renal tracts. Rehabilitation physicians should consider urethral stricture in the management of continence post ABI. 

Implications for Rehabilitation:

- Persisting urinary incontinence post ABI is associated with increased morbidity.

- Urethral stricture is an under-recognised complication after ABI and should be considered as a potential cause of incontinence in this patient group.

- Gains in urinary continence are seen in patients post ABI, managed with various interventions.

- Goal setting offers an opportunity to focus on bladder management rather than simply continence and may allow improvement in rate of appropriate investigation

Promoting Community Renewable Energy in a Corporate Energy World

Small-scale, decentralized and community-owned renewable energy is widely acknowledged to be a desirable feature of low carbon futures, but faces a range of challenges in the context of conventional, centralized energy systems. This paper draws on transition frameworks to investigate why the UK has been an inhospitable context for community-owned renewables and assesses whether anything fundamental is changing in this regard. We give particular attention to whether political devolution, the creation of elected governments for Scotland, Wales and Northern Ireland, has affected the trajectory of community renewables. Our analysis notes that devolution has increased political attention to community renewables, including new policy targets and support schemes. However, these initiatives are arguably less important than the persistence of key features of socio-technical regimes: market support systems for renewable energy and land-use planning arrangements that systemically favour major projects and large corporations, and keep community renewables to the margins. There is scope for rolling out hybrid pathways to community renewables, via joint ownership or through community benefit funds, but this still positions community energy as an adjunct to energy pathways dominated by large, corporate generation facilities

Role of capsular modified heptose in the virulence of Campylobacter jejuni

The Campylobacter jejuni capsular polysaccharide is important for virulence and often contains a modified heptose. In strain ATCC 700819 (a.k.a. NCTC 11168), the modified heptose branches off from the capsular backbone and is directly exposed to the environment. We reported previously that the enzymes encoded by wcaG, mlghB and mlghC are involved in heptose modification. Here, we show that inactivation of any of these genes leads to production of capsule lacking modified heptose and alters the transcription of other capsule modification genes differentially. Inactivation of mlghB or mlghC, but not of wcaG, decreased susceptibility to bile salts and abrogated invasion of intestinal cells. All mutants showed increased sensitivity to serum killing, especially wcaG::cat, and had defects in colonization and persistence in chicken intestine, but did not show significant differences in adhesion, phagocytosis and intracellular survival in murine macrophages. Together, our findings suggest that the capsular heptose modification pathway contributes to bacterial resistance against gastrointestinal host defenses and supports bacterial persistence via its role in serum resistance and invasion of intestinal cells. Our data further suggest a dynamic regulation of expression of this pathway in the gastrointestinal tract.

Reducing SCADA System Nuisance Alarms in the Water Industry in Northern Ireland

The advancement of telemetry control for the water industry has increased the difficulty of 14 managing large volumes of nuisance alarms (i.e. alarms that do not require a response). The aim 15 of this study was to identify and reduce the number of nuisance alarms that occur for Northern 16 Ireland (NI) Water by carrying-out alarm duration analysis to determine the appropriate length of 17 persistence (an advanced alarm management tool) that could be applied. All data was extracted 18 from TelemWeb (NI Water’s telemetry monitoring system) and analysed in Excel. Over a 6 19 week period, an average of 40,000 alarms occurred per week. The alarm duration analysis, which 20 has never been implemented before by NI Water, found that an average of 57% of NI Water 21 alarms had a duration of <5 minutes. Applying 5 minute persistence; therefore, could prevent an 22 average 26,816 nuisance alarms per week. Most of these alarms were from wastewater assets.

Ecological dynamics of extinct species in empty habitat networks. 1. The role of habitat pattern and quantity, stochasticity and dispersal

We examined a remnant host plant (Primula veris L.) habitat network that was last inhabited by the rare butterfly Hamearis lucina L. in north Wales in 1943, to assess the relative contribution of several spatial parameters to its regional extinction. We first examined relationships between P. veris characteristics and H. lucina eggs in surviving H. lucina populations, and used these to predict the suitability and potential carrying capacity of the habitat network in north Wales. This resulted in an estimate of roughly 4500 eggs (ca 227 adults). We developed a discrete space, discrete time metapopulation model to evaluate the relative contribution of dispersal distance, habitat and environmental stochasticity as possible causes of extinction. We simulated the potential persistence of the butterfly in the current network as well as in three artificial (historical and present) habitat networks that differed in the quantity (current and X3) and fragmentation of the habitat (current and aggregated). We identified that reduced habitat quantity and increased isolation would have increased the probability of regional extinction, in conjunction with environmental stochasticity and H. lucina's dispersal distance. This general trend did not change in a qualitative manner when we modified the ability of dispersing females to stay in, and find suitable habitats (by changing the size of the grid cells used in the model). Contrary to most metapopulation model predictions, system persistence declined with increasing migration rate, suggesting that the mortality of migrating individuals in fragmented landscapes may pose significant risks to system-wide persistence. Based on model predictions for the present landscape we argue that a major programme of habitat restoration would be required for a re-established metapopulation to persist for > 100 years.

Ecological dynamics of extinct species in empty habitat networks. 2. The role of host plant dynamics

This paper explores the relative effects of host plant dynamics and butterfly-related parameters on butterfly persistence. It considers an empty habitat network where a rare butterfly (Cupido minimus) became extinct in 1939 in part of its historical range in north Wales, UK. Surviving populations of the butterfly in southern Britain were visited to assess use of its host plant (Anthyllis vulneraria) in order to calibrate habitat suitability and carrying capacity in the empty network in north Wales. These data were used to deduce that only a portion ( similar to 19%) of the host plant network from north Wales was likely to be highly suitable for oviposition. Nonetheless, roughly 65,460 eggs (3273 adult equivalents) could be expected to be laid in north Wales, were the empty network to be populated at the same levels as observed on comparable plants in surviving populations elsewhere. Simulated metapopulations of C. minimus in the empty network revealed that time to extinction and patch occupancy were significantly influenced by carrying capacity, butterfly mean dispersal distance and environmental stochasticity, although for most reasonable parameter values, the model system persisted. Simulation outputs differed greatly when host plant dynamics was incorporated into the modelled butterfly dynamics. Cupido minimus usually went extinct when host plant were at low densities. In these simulations host plant dynamics appeared to be the most important determinant of the butterfly's regional extirpation. Modelling the outcome of a reintroduction programme to C. minimus variation at high quality locations, revealed that 65% of systems survived at least 100 years. Given the current amount of resources of the north Wales landscape, the persistence of C. minimus under a realistic reintroduction programme has a good chance of being successful, if carried out in conjunction with a host plant management programme.

A metapopulation model of species boundaries

The majority, if not all, species have a limited geographic range bounded by a distribution edge. Violent ecotones such as sea coasts clearly produce edges for many species; however such ecotones, while sufficient for the formation of an edge, are not always necessary. We demonstrate this by simulation in discrete time of a spatially structured finite size metapopulation subjected to a spatial gradient in per-unit-time population extinction probability together with spatially structured dispersal and recolonisation. We find that relatively sharp edges separating a homeland or main geographical range from an outland or zone of relatively sparse and ephemeral colonisation can form in gradual environmental gradients. The form and placing of the edge is an emergent property of the metapopulation dynamics. The sharpness of the edge declines with increasing dispersal distance, and is dependent on the relative scales of dispersal distance and gradient length. The space over which the edge develops is short relative to the potential species range. The edge is robust against changes in both the shape of the environmental gradient and to a lesser extent to alterations in the kind of dispersal operating. Persistence times in the absence of environmental gradients are virtually independent of the shape of the dispersal function describing migration. The common finding of bell shaped population density distributions across geographic ranges may occur without the strict necessity of a niche mediated response to a spatially autocorrelated environment.

Special condition wind power forecasting based on Gaussian process and similar historical data

Due to the variability of wind power, it is imperative to accurately and timely forecast the wind generation to enhance the flexibility and reliability of the operation and control of real-time power. Special events such as ramps, spikes are hard to predict with traditional methods using solely recently measured data. In this paper, a new Gaussian Process model with hybrid training data taken from both the local time and historic dataset is proposed and applied to make short-term predictions from 10 minutes to one hour ahead. A key idea is that the similar pattern data in history are properly selected and embedded in Gaussian Process model to make predictions. The results of the proposed algorithms are compared to those of standard Gaussian Process model and the persistence model. It is shown that the proposed method not only reduces magnitude error but also phase error.

Religion, pragmatic fundamentalism and the transformation of the Northern Ireland conflict

Since 11 September 2001, the religious dimension of conflict has been the focus of increasing attention. In The Clash of Civilizations, Huntington has identified the West in religious-cultural terms, as Christian with a dominant democratic culture emphasizing tolerance, moderation and consensus. The persistence of conflict in Northern Ireland among 'White' Protestant and Catholic Christians undermines this simplistic argument and demands a more subtle understanding of the role of religion and fundamentalism in contemporary conflict. Modernization theory - which is echoed among some theorists of globalization - had predicted the declining importance of religion as the world became industrialized and increasingly interconnected. This is echoed by those who argue that the Northern Ireland conflict is 'ethno-national' and dismiss the role of religion. On the other hand, others have claimed that the conflict is religious and stress the role of Protestant fundamentalism. This article draws on new evidence from Northern Ireland of the complex and subtle ways in which religion impacts on the conflict there, incorporating insights about the pragmatism of fundamentalist Protestants and how religious actors are contributing to conflict transformation. This analysis leads to three broader conclusions about understanding conflicts with religious dimensions. First, the complexity of religion must be understood, and this includes a willingness to recognize the adaptability of fundamentalisms to particular contexts. Second, engaging with fundamentalists and taking their grievances seriously opens up possibilities for conflict transformation. Third, governments and religious actors within civil society can play complementary roles in constructing alternative (religious) ideologies and structures as part of a process of transformation. In a world in which the impact of religion is persistent, engaging with the religious dimension is a vital part of a broader-based strategy for dealing with conflict. © 2008 Journal of Peace Research.

Religion and Transformation in South Africa? Institutional and Discursive Change in a Charismatic Congregation

A number of Christian churches in South Africa have proclaimed their commitment to reconciliation and the elimination of unjust inequalities. This study analyses how these commitments are being worked out at the micro-level of a congregation. Using an ethnographic approach, I explore how a charismatic congregation in Cape Town has changed from being nearly all-white to being more inclusive. I explore links between individual, cognitive identity change and institutional change; and consider the discourses which justify change, including their emphasis on 'unity in diversity' and 'restitution'. I outline the limitations of change, including the persistence of 'racialised' leadership structures and the discursive privileging of unity over restitution. This allows us to understand how micro-level changes take place, to explore their potentialities and limitations, and to apply these insights to other contexts.

Characterization of nontypable Haemophilus influenzae isolates recovered from adult patients with underlying chronic lung disease reveals genotypic and phenotypic traits associated with persistent infection

Nontypable Haemophilus influenzae (NTHi) has emerged as an important opportunistic pathogen causing infection in adults suffering obstructive lung diseases. Existing evidence associates chronic infection by NTHi to the progression of the chronic respiratory disease, but specific features of NTHi associated with persistence have not been comprehensively addressed. To provide clues about adaptive strategies adopted by NTHi during persistent infection, we compared sequential persistent isolates with newly acquired isolates in sputa from six patients with chronic obstructive lung disease. Pulse field gel electrophoresis (PFGE) identified three patients with consecutive persistent strains and three with new strains. Phenotypic characterisation included infection of respiratory epithelial cells, bacterial self-aggregation, biofilm formation and resistance to antimicrobial peptides (AMP). Persistent isolates differed from new strains in showing low epithelial adhesion and inability to form biofilms when grown under continuous-flow culture conditions in microfermenters. Self-aggregation clustered the strains by patient, not by persistence. Increasing resistance to AMPs was observed for each series of persistent isolates; this was not associated with lipooligosaccharide decoration with phosphorylcholine or with lipid A acylation. Variation was further analyzed for the series of three persistent isolates recovered from patient 1. These isolates displayed comparable growth rate, natural transformation frequency and murine pulmonary infection. Genome sequencing of these three isolates revealed sequential acquisition of single-nucleotide variants in the AMP permease sapC, the heme acquisition systems hgpB, hgpC, hup and hxuC, the 3-deoxy-D-manno-octulosonic acid kinase kdkA, the long-chain fatty acid transporter ompP1, and the phosphoribosylamine glycine ligase purD. Collectively, we frame a range of pathogenic traits and a repertoire of genetic variants in the context of persistent infection by NTHi.

The prevalence of pica in tuberous sclerosis complex

Background: Pica and Tuberous sclerosis complex (TSC) are rare disorders. We carried out a population survey of pica in our TSC patient population.

Findings: Pica was identified in four percent of cases of TSC. It was associated with adult onset or persistence into adulthood, epilepsy, severe learning difficulties and anaemia.

Conclusions: Pica in TSC is a rare disorder and a coherent history may be difficult to obtain from patients. The prevalence of pica is likely to be underdiagnosed. Pica is a recognised feature in adults with TSC and prompt recognition of this disorder should allow better management of patients with TSC.