Response to Mr. Batini’s comments on Davison (2018) Australas Plant Pathol 47:245–257

This reply refers to the comment available at https://doi.org/10.1007/s13313-018-0581-

Resolving confusions about jarrah dieback - don’t forget the plants

The name jarrah dieback has been used for two different disorders, leading to considerable confusion. It was coined in the 1940s to describe the sudden death of groups of jarrah (Eucalyptus marginata) trees in south western Western Australia, which occurred on poorly drained sites, following exceptionally heavy rainfall. In the 1960s these sites were shown to be infested by Phytophthora cinnamomi and jarrah deaths were attributed to it, even though it was only isolated from 5 % of sampled trees. Also the definition of jarrah dieback was expanded to include deaths of many other plants on infested sites, from which P. cinnamomi was more readily isolated. Jarrah trees die from severe water deficiency, indicating problems with water conduction through roots. Xylem vessel diameters vary along roots, being narrow at the root collar, while distally they are larger, providing water storage. Jarrah transpires vigorously during summer, accessing water at depth on sites with deep soil, but being more dependent on internally stored water when root systems are shallower. Following waterlogging, sapwood vessels become blocked with tyloses, reducing both conductivity and potential water storage; such trees may have insufficient water reserves for summer survival. In jarrah P. cinnamomi is unlikely to cause water deficiency because sapwood invasion is rapidly contained in healthy roots. Recent investigations into P. cinnamomi invasion and host responses in other plants show that it can potentially cause a vascular wilt in Banksia spp. and chronic, symptomless infections in herbaceous plants. Susceptibility to waterlogging damage, and/or mortality resulting from infection by P. cinnamomi can only be clarified by detailed knowledge of the hosts and their vulnerabilities. This is essential for making diagnoses, devising management strategies, and avoiding the confusions of the past

How Phytophthora cinnamomi became associated with the death of Eucalyptus marginata – the early investigations into jarrah dieback

The name jarrah dieback was used in the 1940s to describe a serious economic problem in the jarrah forest in the south west of Western Australia. This was the sudden death of groups of jarrah (Eucalyptus marginata) trees that occurred on previously logged sites that had a tendency to become waterlogged in winter. Although the cause was not determined at the time, from symptoms recorded in early investigations the most likely explanation is that the trees died as the result of waterlogging damage. In the 1960s it was shown that many of these sites were infested by the introduced oomycete Phytophthora cinnamomi and tree deaths, together with the deaths of many mid- and under-storey plants, were attributed to this pathogen. A chronology of the research, based on contemporary unpublished documents, shows that in 1968 the conclusion that P. cinnamomi caused jarrah deaths was not supported by the available evidence, because the work did not satisfy the first and fourth of Koch’s postulates. The evidence that P. cinnamomi killed many mid- and under-storey plants was much stronger. There are two problems that have been confused: the death of groups of jarrah trees (jarrah dieback) that is caused by waterlogging and the death of many mid- and under-storey plants (Phytophthora dieback) caused by P. cinnamomi infection

Comparison of sapwood invasion by three Phytophthora spp.in different hosts

Many Phytophthora spp. have recently been isolated from native vegetation in Western Australia. As their pathogenicity is often unknown, it is not possible to provide advice to land managers on the impact of site infestation on native plants and how these infestations should be managed. We describe a rapid screening method based on sapwood invasion that has been used to compare the pathogenicity of Phytophthora arenaria, P. cinnamomi and P. multivora. Radial invasion into the xylem of six banksias and three eucalypts was assessed in an excised branch assay in summer and winter. Branches were wound inoculated and invasion was assessed by plating from a strip of tissue cut across the stem at the inoculation point and at 40 mm above and below. A symptomless infection had established in both the bark and sapwood within 6 days. P. arenaria was only isolated from the strip of tissue at the inoculation point. P. cinnamomi was isolated from the sapwood of Banksia attenuata, B. burdettii, B. menziesii and B. speciosa 40 mm above or below the inoculation point in some experiments. P. multivora was isolated from B. speciosa 40 mm below the inoculation point in one experiment. Hyphae of both species were seen in both ray parenchyma cells and xylem vessels. The invasiveness of the Phytophthora spp. was compared on the two groups of hosts using scores for sapwood invasion at the inoculation point. For banksias, P. cinnamomi and P. multivora had significantly higher invasion scores on banksias than P. arenaria but were not significantly different to one another. There was no significant difference between the three Phytophthora spp. on the eucalypt hosts. Assessing sapwood invasion provides a rapid, inexpensive and biologically meaningful way of screening the many Phytophthora spp. that have been isolated from native vegetation

Designing a physical activity parenting course : parental views on recruitment, content and delivery

Background Many children do not engage in sufficient levels of physical activity (PA) and spend too much time screen-viewing (SV). High levels of SV (e.g. watching TV, playing video games and surfing the internet) and low levels of PA have been associated with adverse health outcomes. Parenting courses may hold promise as an intervention medium to change children’s PA and SV. The current study was formative work conducted to design a new parenting programme to increase children’s PA and reduce their SV. Specifically, we focussed on interest in a course, desired content and delivery style, barriers and facilitators to participation and opinions on control group provision. Methods In-depth telephone interviews were conducted with thirty two parents (29 female) of 6–8 year olds. Data were analysed thematically. An anonymous online survey was also completed by 750 parents of 6–8 year old children and descriptive statistics calculated. Results Interview participants were interested in a parenting course because they wanted general parenting advice and ideas to help their children be physically active. Parents indicated that they would benefit from knowing how to quantify their child’s PA and SV levels. Parents wanted practical ideas of alternatives to SV. Most parents would be unable to attend unless childcare was provided. Schools were perceived to be a trusted source of information about parenting courses and the optimal recruitment location. In terms of delivery style, the majority of parents stated they would prefer a group-based approach that provided opportunities for peer learning and support with professional input. Survey participants reported the timing of classes and the provision of childcare were essential factors that would affect participation. In terms of designing an intervention, the most preferred control group option was the opportunity to attend the same course at a later date. Conclusions Parents are interested in PA/SV parenting courses but the provision of child care is essential for attendance. Recruitment is likely to be facilitated via trusted sources. Parents want practical advice on how to overcome barriers and suggest advice is provided in a mutually supportive group experience with expert input

The switch between acute and persistent paramyxovirus infection caused by single amino acid substitutions in the RNA polymerase P subunit

Paramyxoviruses can establish persistent infections both in vitro and in vivo, some of which lead to chronic disease. However, little is known about the molecular events that contribute to the establishment of persistent infections by RNA viruses. Using parainfluenza virus type 5 (PIV5) as a model we show that phosphorylation of the P protein, which is a key component of the viral RNA polymerase complex, determines whether or not viral transcription and replication becomes repressed at late times after infection. If the virus becomes repressed, persistence is established, but if not, the infected cells die. We found that single amino acid changes at various positions within the P protein switched the infection phenotype from lytic to persistent. Lytic variants replicated to higher titres in mice than persistent variants and caused greater infiltration of immune cells into infected lungs but were cleared more rapidly. We propose that during the acute phases of viral infection in vivo, lytic variants of PIV5 will be selected but, as the adaptive immune response develops, variants in which viral replication can be repressed will be selected, leading to the establishment of prolonged, persistent infections. We suggest that similar selection processes may operate for other RNA viruses

Can we trust “Magnitude-based inference”?

Since the times and works of William Sealy Gosset (1876-1937) and Ronald Aylmer Fisher (1890-1962), imperfections of conventional null-hypothesis significance testing and in particular, use of P-values to evaluate such testing (invariably referred to as inferential statistics), have been well recognised (Wilkinson, 1999; Wasserstein and Lazar, 2016). Attempts have been made to identify alternatives. For example, Cohen's effect sizes (Cohen 1988) and region of practical equivalence procedure (ROPE) (Kruschke, 2014). A more recent alternative is magnitude-based inference (MBI) (Hopkins and Baterham, 2016) although unlike others, MBI has created considerable controversy when reporting the results of studies (almost exclusively used in the field of sport and exercise science). Instead of defining research effects as “significant” based on P-values (using traditional hypothesis testing), MBI uses terms such as “implementable” and “substantial” based on two constraints called the “risk of harm” and the “chance of benefit”. However, concerns have been raised about the MBI approach. Stanford statistician Kristin Sainani was so concerned about the consequences of using MBI that she wrote a formal analysis of the MBI method. Published in MSSE (Sainani, 2018) her paper showed that, depending on sample size and thresholds for harm/benefit, MBI produces false positive rates that can be two to six times greater than those using traditional hypothesis testing. A finding, she claims, that makes MBI less reliable.Published versio

Bosonic excitations of the AdS4 Reissner-Nordstrom black hole

We study the long-lived modes of the charge density and energy density correlators in the strongly-coupled, finite density field theory dual to the AdS4 Reissner-Nordstrom black hole. For small momenta q<<\mu, these correlators contain a pole due to sound propagation, as well as a pole due to a long-lived, purely imaginary mode analogous to the \mu=0 hydrodynamic charge diffusion mode. As the temperature is raised in the range T\lesssim\mu, the sound attenuation shows no significant temperature dependence. When T\gtrsim\mu, it quickly approaches the \mu=0 hydrodynamic result where it decreases like 1/T. It does not share any of the temperature-dependent properties of the 'zero sound' of Landau Fermi liquids observed in the strongly-coupled D3/D7 field theory. For such small momenta, the energy density spectral function is dominated by the sound mode at all temperatures, whereas the charge density spectral function undergoes a crossover from being dominated by the sound mode at low temperatures to being dominated by the diffusion mode when T \mu^2/q. This crossover occurs due to the changing residue at each pole. We also compute the momentum dependence of these spectral functions and their corresponding long-lived poles at fixed, low temperatures T<<\mu.Comment: 33 pages, 21 figures, 6 animation

Bi-allelic Variants in TKFC Encoding Triokinase/FMN Cyclase Are Associated with Cataracts and Multisystem Disease

We report an inborn error of metabolism caused by TKFC deficiency in two unrelated families. Rapid trio genome sequencing in family 1 and exome sequencing in family 2 excluded known genetic etiologies, and further variant analysis identified rare homozygous variants in TKFC. TKFC encodes a bifunctional enzyme involved in fructose metabolism through its glyceraldehyde kinase activity and in the generation of riboflavin cyclic 4′,5′-phosphate (cyclic FMN) through an FMN lyase domain. The TKFC homozygous variants reported here are located within the FMN lyase domain. Functional assays in yeast support the deleterious effect of these variants on protein function. Shared phenotypes between affected individuals with TKFC deficiency include cataracts and developmental delay, associated with cerebellar hypoplasia in one case. Further complications observed in two affected individuals included liver dysfunction and microcytic anemia, while one had fatal cardiomyopathy with lactic acidosis following a febrile illness. We postulate that deficiency of TKFC causes disruption of endogenous fructose metabolism leading to generation of by-products that can cause cataract. In line with this, an affected individual had mildly elevated urinary galactitol, which has been linked to cataract development in the galactosemias. Further, in light of a previously reported role of TKFC in regulating innate antiviral immunity through suppression of MDA5, we speculate that deficiency of TKFC leads to impaired innate immunity in response to viral illness, which may explain the fatal illness observed in the most severely affected individual

Bovine colostrum supplementation and upper respiratory symptoms during exercise training: a systematic review and meta-analysis of randomised controlled trials

Abstract Background Bovine colostrum is proposed as a nutritional countermeasure to the risk of upper respiratory symptoms (URS) during exercise training. The aim of this systematic review and meta-analysis was to estimate the size of the effect of bovine colostrum supplementation on URS. Methods Databases (CDSR, CENTRAL, Cinahl, ClinicalTrials.gov, Current Controlled Trials, DARE, EMBASE, Medline, PROSPERO and Web of Science) of published, unpublished and ongoing studies were searched for randomised controlled trials of healthy adults (≥18 years), evaluating the effect of oral bovine colostrum supplementation compared to a concurrent control group on URS. Results Five trials (152 participants) met the inclusion criteria, all of which involved individuals involved in regular exercise training. Over an 8–12 week follow-up period, bovine colostrum supplementation when compared to placebo significantly reduced the incidence rate of URS days (rate ratio 0.56, 95 % confidence intervals 0.43 to 0.72, P value < 0.001) and URS episodes (0.62, 0.40 to 0.99, P value = 0.04) by 44 and 38 % respectively. There were limited data and considerable variation in results of included studies for duration of URS episodes hence a meta-analysis of this outcome was deemed inappropriate. The risk of bias assessment in this review was hindered by poor reporting practices of included studies. Due to incomplete reporting of study methods, four of the five studies were judged to have a moderate or high risk of overall bias. Our findings must be interpreted in relation to quantity and quality of the available evidence. Conclusions The present systematic review and meta-analysis provides evidence that bovine colostrum supplementation may be effective in preventing the incidence of URS days and episodes in adults engaged in exercise training. The fact that the majority of included studies did not report significant effects on URS outcomes mitigates concerns about publication bias. The point estimates of the random-effects meta-analyses are greater than the smallest clinically important difference, but the low precision of the individual study estimates means the evidence presented in this review needs to be followed up with an appropriately designed and adequately powered, randomised control trial