The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens

Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.

Overview of genomic and bioinformatic resources for Zymoseptoria tritici

Zymoseptoria tritici (syn. Mycosphaerella graminicola, Septoria tritici) is a haploid fungus belonging to the class Dothideomycetes. It is the causal agent of septoria leaf blotch - one of the world's most significant diseases of wheat. Here we review the genomic and bioinformatic resources that have been generated for Z. tritici. These include the whole-genome reference assembly for isolate IPO323, genome resequencing of alternate isolates, mitochondrial genome sequences, transcriptome sequences and expression data, and annotations of gene structure and function. We also highlight important advances in our fundamental knowledge of genome evolution and its effects on adaptation and pathogenicity in Z. tritici that have been facilitated by these resources.

Evaluation of a sequencing batch reactor sewage treatment rig for investigating the fate of radioactively labelled pharmaceuticals: Case study of propranolol

Pharmaceuticals are frequently detected in the aquatic environment, and have potentially damaging effects. Effluents from sewage treatment plants (STPs) are major sources of these substances. The use of sequencing batch reactor (SBR) STPs, involving cycling between aerobic and anoxic conditions to promote nitrification and denitrification, is increasing but these have yet to be understood in terms of removal of pharmaceutical residues. This study reports on the development of a laboratory rig to simulate a SBR. The rig was used to investigate the fate of radiolabelled propranolol. This is a commonly prescribed beta blocker, but with unresolved fate in STPs. The SBR rig (4.5 L) was operated on an 8 h batch cycle with settled sewage. Effective treatment was demonstrated, with clearly distinct treatment phases and evidence of nitrogen removal. Radiolabelled (14)C-propranolol was dosed into both single (closed) and continuous (flow-through) simulations over 13 SBR cycles. Radioactivity in CO2 off-gas, biomass and liquid was monitored, along with the characteristics of the sewage. This allowed apparent rate constants and coefficients for biodegradation and solid:water partitioning to be determined. Extrapolation from off-gas radioactivity measurements in the single dose 4-d study suggested that propranolol fell outside the definitions of being readily biodegradable (DegT50 = 9.1 d; 60% biodegradation at 12.0 d). During continuous dosing, 63-72% of propranolol was removed in the rig, but less than 4% of dose recovered as (14)CO2, suggesting that biodegradation was a minor process (Kbiol(M) L kg d(-1) = 22-49) and that adsorption onto solids dominated, giving rise to accumulations within biomass during the 17 d solid retention time in the SBR. Estimations of adsorption isotherm coefficients were different depending on which of three generally accepted denominators representing sorption sites was used (mixed liquor suspended solids, reactor COD or mass of waste activated sludge). With further development and evaluation, the rig developed for simulating SBR processes has potential to be used for informing better environmental risk assessments for those pharmaceuticals showing ambiguous results in field fate studies.

Interventions for the treatment of keratocystic odontogenic tumours

BACKGROUND

The keratocystic odontogenic tumours (KCOTs) account for between about 2% and 11% of all jaw cysts and can occur at any age. They are more common in males than females with a male:female ratio of approximately 2:1. Although they are benign, KCOTs are locally very aggressive and have a tendency to recur after treatment. Reported recurrence rates range from 3% to 60%. The traditional method for the treatment of most KCOTs is surgical enucleation. However, due to the lining of the cyst being delicate and the fact that they frequently recur, this method alone is not sufficient. Adjunctive surgical treatment has been proposed in addition to the surgical enucleation, such as removal of the peripheral bone (ostectomy) or resection of the cyst with surrounding bone (en-bloc) resection. Other adjunctive treatments proposed are: cryotherapy (freezing) with liquid nitrogen and the use of the fixative Carnoy's solution placed in the cyst cavity after enucleation; both of which attempt to address residual tissue to prevent recurrence.

OBJECTIVES

To assess the available evidence comparing the effectiveness of interventions for the treatment of KCOTs.

SEARCH METHODS

We searched the following electronic databases: the Cochrane Oral Health Group Trials Register (to 17 March 2015), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library, 2015, Issue 2), MEDLINE via Ovid (1946 to 17 March 2015) and EMBASE via Ovid (1980 to 17 March 2015). We searched the US National Institutes of Health Trials Register (http://clinicaltrials.gov) and the WHO Clinical Trials Registry Platform for ongoing trials. No restrictions were placed on the language or date of publication when searching the electronic databases.

SELECTION CRITERIA

Randomised controlled trials comparing one modality of intervention with another with or without adjunctive treatment for the treatment of KCOTs. Adults, over the age of 18 with a validated diagnosis of solitary KCOTs arising in the jaw bones of the maxilla or mandible. Patients with known Gorlin syndrome were to be excluded.

DATA COLLECTION AND ANALYSIS

Review authors screened trials for inclusion. Full papers were obtained for relevant and potentially relevant trials. If data had been extracted, it would have been synthesised using the fixed-effect model, if substantial clinical diversity were identified between studies we planned to use the random-effects model with studies grouped by action provided there were four or more studies included in the meta-analysis, and we would have explored the heterogeneity between the included studies.

MAIN RESULTS

No randomised controlled trials that met the inclusion criteria were identified.

AUTHORS' CONCLUSIONS

There are no published randomised controlled trials relevant to this review question, therefore no conclusions could be reached about the effectiveness or otherwise of the interventions considered in this review. There is a need for well designed and conducted randomised controlled trials to evaluate treatments for KCOTs.

First-in-human trial of the safety, pharmacokinetics and immunogenicity of a PEGylated anti-CD40L antibody fragment (CDP7657) in healthy individuals and patients with systemic lupus erythematosus

OBJECTIVE

The objective of this paper is to investigate the safety, pharmacokinetics (PK) and immunogenicity of CDP7657, a PEGylated anti-CD40L antibody fragment, in healthy individuals and patients with systemic lupus erythematosus (SLE).

METHODS

This randomized, double-blind, single-dose, dose-escalation phase I study consisted of two parts. In part 1, 28 healthy individuals received CDP7657 IV (0.004-5 mg/kg) or placebo. In part 2, 17 patients with SLE received CDP7657 IV (5-60 mg/kg) or placebo. The CDP7657:placebo ratio was 3:1.

RESULTS

Adverse events (AEs) were reported by 76% of healthy individuals and 100% of patients with SLE treated with CDP7657; most were mild or moderate in intensity. Two healthy individuals reported serious AEs (SAEs), one of which was considered treatment related (infusion-related reaction; 5 mg/kg cohort). One patient with SLE (60 mg/kg cohort) experienced three SAEs, one of which was considered treatment related (herpes zoster infection). No thromboembolic events were reported. CPD7657 exposure increased in a dose-proportional manner. Low anti-CDP7657 antibody titres were detected in the majority of CDP7657-treated participants with no apparent impact on the PK of CDP7657.

CONCLUSION

Single doses of CDP7657 showed predictable PK in healthy individuals and patients with SLE and were well tolerated, with no safety signals of concern. These findings support further investigation of CDP7657 as a therapy for SLE.

Mixtures as a fungicide resistance management tactic

We have reviewed the experimental and modeling evidence on the use of mixtures of fungicides of differing modes of action as a resistance management tactic. The evidence supports the following conclusions. 1. Adding a mixing partner to a fungicide that is at-risk of resistance (without lowering the dose of the at-risk fungicide) reduces the rate of selection for fungicide resistance. This holds for the use of mixing partner fungicides that have either multi-site or single-site modes of action. The resulting predicted increase in the effective life of the at-risk fungicide can be large enough to be of practical relevance. The more effective the mixing partner (due to inherent activity and/or dose), the larger the reduction in selection and the larger the increase in effective life of the at-risk fungicide. 2. Adding a mixing partner while lowering the dose of the at-risk fungicide reduces the selection for fungicide resistance, without compromising effective disease control. The very few studies existing suggest that the reduction in selection is more sensitive to lowering the dose of the at-risk fungicide than to increasing the dose of the mixing partner. 3. Although there are very few studies, the existing evidence suggests that mixing two at-risk fungicides is also a useful resistance management tactic. The aspects that have received too little attention to draw generic conclusions about the effectiveness of fungicide mixtures as resistance management strategies are as follows: (i) the relative effect of the dose of the two mixing partners on selection for fungicide resistance, (ii) the effect of mixing on the effective life of a fungicide (the time from introduction of the fungicide mode of action to the time point where the fungicide can no longer maintain effective disease control), (iii) polygenically determined resistance, (iv) mixtures of two at-risk fungicides, (v) the emergence phase of resistance evolution and the effects of mixtures during this phase, and (vi) monocyclic diseases and nonfoliar diseases. The lack of studies on these aspects of mixture use of fungicides should be a warning against overinterpreting the findings in this review.

Governing principles can guide fungicide-resistance management tactics

Fungicide-resistance management would be more effective if principles governing the selection of resistant strains could be determined and validated. Such principles could then be used to predict whether a proposed change to a fungicide application program would decrease selection for resistant strains. In this review, we assess a governing principle that appears to have good predictive power. The principle states that reducing the product of the selection coefficient (defined as the difference between the per capita rate of increase of the sensitive and resistant strains) and the exposure time of the pathogen to the fungicide reduces the selection for resistance. We show that observations as well as modeling studies agree with the predicted effect (i.e., that a specific change to a fungicide program increased or decreased selection or was broadly neutral in its effect on selection) in 84% of the cases and that only 5% of the experimental results contradict predictions. We argue that the selection coefficient and exposure time principle can guide the development of resistance management tactics.

Antibiotics for the prophylaxis of bacterial endocarditis in dentistry

BACKGROUND

Infective endocarditis is a severe infection arising in the lining of the chambers of the heart with a high mortality rate.Many dental procedures cause bacteraemia and it was believed that this may lead to bacterial endocarditis (BE) in a few people. Guidelines in many countries have recommended that prior to invasive dental procedures antibiotics are administered to people at high risk of endocarditis. However, recent guidance by the National Institute for Health and Care Excellence (NICE) in England and Wales has recommended that antibiotics are not required.

OBJECTIVES

To determine whether prophylactic antibiotic administration, compared to no such administration or placebo, before invasive dental procedures in people at risk or at high risk of bacterial endocarditis influences mortality, serious illness or the incidence of endocarditis.

SEARCH METHODS

The following electronic databases were searched: the Cochrane Oral Health Group's Trials Register (to 21 January 2013), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2012, Issue 12), MEDLINE via OVID (1946 to 21 January 2013) and EMBASE via OVID (1980 to 21 January 2013). We searched for ongoing trials in the US National Institutes of Health Trials Register (http://clinicaltrials.gov) and the metaRegister of Controlled Trials (http://www.controlled-trials.com/mrct/). No restrictions were placed on the language or date of publication when searching the electronic databases.

SELECTION CRITERIA

Due to the low incidence of BE it was anticipated that few if any trials would be located. For this reason, cohort and case-control studies were included where suitably matched control or comparison groups had been studied. The intervention was the administration of antibiotic, compared to no such administration, before a dental procedure in people with an increased risk of BE. Cohort studies would need to follow those individuals at increased risk and assess outcomes following any invasive dental procedures, grouping by whether prophylaxis was received or not. Included case-control studies would need to match people who had developed endocarditis (and who were known to be at increased risk before undergoing an invasive dental procedure preceding the onset of endocarditis) with those at similar risk but who had not developed endocarditis. Outcomes of interest were mortality or serious adverse events requiring hospital admission; development of endocarditis following any dental procedure in a defined time period; development of endocarditis due to other non-dental causes; any recorded adverse events to the antibiotics; and cost implications of the antibiotic provision for the care of those patients who developed endocarditis.

DATA COLLECTION AND ANALYSIS

Two review authors independently selected studies for inclusion then assessed risk of bias and extracted data from the included study.

MAIN RESULTS

No randomised controlled trials (RCTs), controlled clinical trials (CCTs) or cohort studies were included. One case-control study met the inclusion criteria. It collected all the cases of endocarditis in the Netherlands over two years, finding a total of 24 people who developed endocarditis within 180 days of an invasive dental procedure, definitely requiring prophylaxis according to current guidelines, and who were at increased risk of endocarditis due to a pre-existing cardiac problem. This study included participants who died because of the endocarditis (using proxies). Controls attended local cardiology outpatient clinics for similar cardiac problems, had undergone an invasive dental procedure within the past 180 days, and were matched by age with the cases. No significant effect of penicillin prophylaxis on the incidence of endocarditis could be seen. No data were found on other outcomes.

AUTHORS' CONCLUSIONS

There remains no evidence about whether antibiotic prophylaxis is effective or ineffective against bacterial endocarditis in people at risk who are about to undergo an invasive dental procedure. It is not clear whether the potential harms and costs of antibiotic administration outweigh any beneficial effect. Ethically, practitioners need to discuss the potential benefits and harms of antibiotic prophylaxis with their patients before a decision is made about administration.

Thermal stability of intralipid optical phantoms

We investigated the stability of light transmission through Intralipid-based optical phantoms in the wavelength range of 400-950 nm at temperatures between 35 and 70 °C. Optical phantoms are materials commonly used to simulate the light scattering and absorption properties of biological materials. These simulations require the phantom to be optically stable. We demonstrate that the scattering properties of Intralipid remain stable at higher temperatures, varying less than 0.5%. We also present results that show this is not the case for absorption below 700 nm at 35 and 70 °C, with greater instability at 70 °C. For example, at 500 nm, the light intensity transmitted through 15 mm of Intralipid dropped 39% over 12 h. We demonstrate that oxidation of fatty acids in Intralipid could account for this effect and show, by flushing the system continuously with nitrogen gas, the instability is reduced.

A Delphi approach to define learning outcomes and assessment

AIM

The aim of this study was to use a Delphi process for curriculum revision facilitating staff collaboration and curriculum 'alignment' in the orthodontic specialist training programme in Cardiff.

METHOD

A 2-round modified Delphi process was employed to achieve consensus amongst a heterogeneous panel with regard to the learning outcomes and assessment methods, which initially were defined according to formal directives and local initiatives. The panel comprised of nine staff members (five consultants, a professor, a reader, a lecturer and a student) who were working in the orthodontic department in Cardiff and involved in the process of curriculum revision.

RESULTS

The response rate to the questionnaires was 77.8%. The staff members' consensus achieved in the Delphi process was 98.4% for the learning outcomes and assessment. The results of the Delphi process provided a list of outcomes and their appropriate assessment methods for the specialist orthodontist in Cardiff.

DISCUSSION AND CONCLUSION

The results show that the Delphi process was an efficient and cost-effective technique to achieve consensus of opinion on the learning outcomes and the assessment methods for the specialist orthodontist as part of the process of curriculum revision in Cardiff.

Genomic tillage and the harvest of fungal phytopathogens

Genome sequencing has been carried out on a small selection of major fungal ascomycete pathogens. These studies show that simple models whereby pathogens evolved from phylogenetically related saprobes by the acquisition or modification of a small number of key genes cannot be sustained.The genomes show that pathogens cannot be divided into three clearly delineated classes (biotrophs, hemibiotrophs and necrotrophs) but rather into a complex matrix of categories each with subtly different properties. It is clear that the evolution of pathogenicity is ancient, rapid and ongoing. Fungal pathogens have undergone substantial genomic rearrangements that can be appropriately described as 'genomic tillage'. Genomic tillage underpins the evolution and expression of large families of genes - known as effectors - that manipulate and exploit metabolic and defence processes of plants so as to allow the proliferation of pathogens.

The possible relevance of the expression of MHC antigens and of EGF receptor in aggressive oral tumours

In this study the intensity of expression of major histocompatibility complex (MHC) class I and II antigens, adhesion molecule i.e. ICAM-1, epidermal growth factor receptor i.e. EGFr, T cell marker and cytokeratin were compared in oral squamous cell carcinoma (OSCC) and in the benign ameloblastoma of the jaws. The results showed that: a) There was strong expression of both monomorphic and of polymorphic class I MHC antigens (90% of cases) in both basal and suprabasal cells of controls from normal mucose. b) Whereas up to 4% of OSCCs and 27% of ameloblastomas showed complete loss of monomorphic class I antigens, the frequency of polymorphic class I abnormalities was even more marked in both tumour types. c) Strong expression of class II MHC antigens and of ECFr was observed in the basal cells of most normal controls. d) Both class II (50% of cases) and ICAM-1 (30% of cases) showed strong expression in OSCC but not in ameloblastoma. The statistical values between OSCC and normal basal cells for class II and ICAM-1 were not significant whilst the corresponding values for OSCC compared with ameloblastoma were p<0.001 and p<0.001. In the case of OSCC, there were a large number of infiltrating T cells expressing activation marker i.e. class II antigen. e) Strong expression of EGFr was seen in more than 90% of the OSCC cases compared with only 16% of ameloblastomas (0.01<p>0.001). Our working hypothesis to explain these abnormalities is that although both tumour types (more so in the case of ameloblastoma) have in place an escape mechanism from the immune system, the overexpression of EGFr in OSCC may in part be responsible for the more aggressive behaviour of the malignancy compared with the locally invasive but benign ameloblastoma.