Foliar fungi of the enigmatic desert plant Welwitschia mirabilis show little adaptation to their unique host plant

Foliar fungi, especially endophytic fungi, constitute an important part of the microbiome of plants. Yet little is known about the composition of these communities. In this study, we isolated fungi from leaf tissues of the desert plant Welwitschia mirabilis to determine the culturable diversity of the foliar fungal community. The isolated fungal taxa, which grouped into 17 distinct lineages, were identified by sequencing elongation factor 1 alpha, beta-tubulin 1, beta-tubulin 2 and the internal transcribed spacer region. The culturable community was mainly composed of cosmopolitan fungal genera despite the unique taxonomic position of the plant and its geographic isolation. To test for endemism in two of the common fungal genera, Alternaria and Aureobasidium, we built haplotype networks using a global data set. Even this broad data set showed little evidence for specialisation within this unique host or its geographical location. The data suggest that the culturable members of communities of leaf-associated fungi in habitats with little plant coverage, such as the Namib Desert, are mainly established by long-distance aerially distributed fungal inocula and few of these taxa co-evolve with the host within the habitat.Significance: The culturable members of fungal communities associated with an ecological and evolutionary isolated plant have not co-speciated with their hosts, but to a large extent are composed of globally distributed fungal species. Harsh environmental conditions and the geographic isolation of host plants seem to favour ubiquitous fungal species over more specialist fungal species

Ab initio derivation of model energy density functionals

I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results

Foliar fungi of the enigmatic desert plant Welwitschia mirabilis show little adaptation to their unique host plant

Foliar fungi, especially endophytic fungi, constitute an important part of the microbiome of plants. Yet little is known about the composition of these communities. In this study, we isolated fungi from leaf tissues of the desert plant Welwitschia mirabilis to determine the culturable diversity of the foliar fungal community. The isolated fungal taxa, which grouped into 17 distinct lineages, were identified by sequencing elongation factor 1 alpha, beta-tubulin 1, beta-tubulin 2 and the internal transcribed spacer region. The culturable community was mainly composed of cosmopolitan fungal genera despite the unique taxonomic position of the plant and its geographic isolation. To test for endemism in two of the common fungal genera, Alternaria and Aureobasidium, we built haplotype networks using a global data set. Even this broad data set showed little evidence for specialisation within this unique host or its geographical location. The data suggest that the culturable members of communities of leaf-associated fungi in habitats with little plant coverage, such as the Namib Desert, are mainly established by long-distance aerially distributed fungal inocula and few of these taxa co-evolve with the host within the habitat. SIGNIFICANCE : • The culturable members of fungal communities associated with an ecological and evolutionary isolated plant have not co-speciated with their hosts, but to a large extent are composed of globally distributed fungal species. • Harsh environmental conditions and the geographic isolation of host plants seem to favour ubiquitous fungal species over more specialist fungal species.The Department of Science and Technology (DSI)–National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology (CTHB) and the University of Pretoria.http://www.sajs.co.zaam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Legionella pneumophila Infection of Drosophila S2 Cells Induces Only Minor Changes in Mitochondrial Dynamics.

During infection of cells by Legionella pneumophila, the bacterium secretes a large number of effector proteins into the host cell cytoplasm, allowing it to alter many cellular processes and make the vacuole and the host cell into more hospitable environments for bacterial replication. One major change induced by infection is the recruitment of ER-derived vesicles to the surface of the vacuole, where they fuse with the vacuole membrane and prevent it from becoming an acidified, degradative compartment. However, the recruitment of mitochondria to the region of the vacuole has also been suggested by ultrastructural studies. In order to test this idea in a controlled and quantitative experimental system, and to lay the groundwork for a genome-wide screen for factors involved in mitochondrial recruitment, we examined the behavior of mitochondria during the early stages of Legionella pneumophila infection of Drosophila S2 cells. We found that the density of mitochondria near vacuoles formed by infection with wild typeLegionella was not different from that found in dotA– mutant-infected cells during the first 4 hours after infection. We then examined 4 parameters of mitochondrial motility in infected cells: velocity of movement, duty cycle of movement, directional persistence and net direction. In the 4 hours following infection, most of these measures were indistinguishable between wild type and dotA−.infection. However, wild type Legionella did induce a modest shift in the velocity distribution toward faster movement compared dotA− infection, and a small downward shift in the duty cycle distribution. In addition, wild type infection produced mitochondrial movement that was biased in the direction of the bacterial vacuole relative to dotA-, although not enough to cause a significant accumulation within 10 um of the vacuole. We conclude that in this host cell, mitochondria are not strongly recruited to the vacuole, nor is their motility dramatically affected

The Eucalyptus stem canker pathogen Teratosphaeria zuluensis detected in seed samples

The global spread of Eucalyptus pathogens is thought to be facilitated by the trade in seed for the establishment of new plantations and breeding programmes. In this study we used highthroughput amplicon sequencing to elucidate whether this might be true for the Eucalyptus stem pathogen Teratosphaeria zuluensis in South Africa. DNA libraries were obtained for seed-capsules, clean seed, one-month-old seedlings grown in a phytotron, plants grown in vitro in a tissue culture facility as well as leaves and stems of three-month-old seedlings exposed to a Eucalyptus plantation environment. The DNA libraries were sequenced using high-throughput Illumina MiSeq and 454 technologies. Sequencing revealed the presence of several OTUs in the Botryosphaeriaceae, Mycosphaerellaceae and Teratosphaeriaceae in seed and seed-capsules and amongst these, OTUs that cluster close to T. zuluensis. OTUs from the Mycosphaerellaceae were also recovered from seedlings grown in a phytotron, in vitro propagated seedlings and those exposed to the plantation environment. The results support the view that important Eucalyptus pathogens, including T. zuluensis, can be spread via the trade in seed.National Research Foundation of South Africa (Grant specific unique reference number (UID83924).Tree Protection Co-operative Program (TPCP), the THRIP initiative of the Department of Trade and Industry and the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) based in the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa.http://forestry.oxfordjournals.org2017-07-31hb2016GeneticsMicrobiology and Plant PathologyPlant Production and Soil Scienc

Maternal effects on phenotype, resistance and the structuring of fungal communities in Eucalyptus grandis

The environmental experience of plants can modulate the development of the offspring and their interactions with other organisms. These effects, generally known as maternal effects, occur through seed provisioning and epigenetic modifications. This study considers the influence of differing environments of maternal plants on their progeny and their biotic interactions. Seeds were collected from two Eucalyptus grandis clonal seed orchards having different abiotic and biotic conditions. Seed and seedling development, and seedling responses to pest infestation and pathogen inoculation were measured. Finally, fungal communities in the foliage of the seedlings were assessed using a metabarcoding approach. The percentage of seed germination and height of seedlings were influenced by the maternal environments. Seedlings from one of the maternal environments were significantly more resistant to a pathogen than seedlings from the other. The composition and diversity of fungal communities also differed between the offspring from the two maternal environments. We found that the differences in the maternal environment affected the progeny performance and resistance. Moreover, we show for the first time that the maternal environment can influence the structure of fungal communities in the foliage in the subsequent generation.The Claude Leon Foundation, University of Pretoria, the Tree Protection Co-operative Programme, and the Genome Research Institute at the University of Pretoria.http://www.elsevier.com/locate/envexpbot2018-08-30hj2017Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Construction and Testing of orfA +/- FIV Reporter Viruses

Single cycle reporter viruses that preserve the majority of the HIV-1 genome, long terminal repeat-promoted transcription and Rev-dependent structural protein expression are useful for investigating the viral life cycle. Reporter viruses that encode the viral proteins in cis in this way have been lacking for feline immunodeficiency virus (FIV), where the field has used genetically minimized transfer vectors with viral proteins supplied in trans. Here we report construction and use of a panel of single cycle FIV reporter viruses that express fluorescent protein markers. The viruses can be produced to high titer using human cell transfection and can transduce diverse target cells. To illustrate utility, we tested versions that are (+) and (-) for OrfA, an FIV accessory protein required for replication in primary lymphocytes and previously implicated in down-regulation of the primary FIV entry receptor CD134. We observed CD134 down-regulation after infection with or without OrfA, and equivalent virion production as well. These results suggest a role for FIV proteins besides Env or OrfA in CD134 down-regulation

What are we measuring? A critique of range of motion methods currently in use for Dupuytren's disease and recommendations for practice

Background: Range of motion is the most frequently reported measure used in practice to evaluate outcomes. A goniometer is the most reliable tool to assess range of motion yet, the lack of consistency in reporting prevents comparison between studies. The aim of this study is to identify how range of motion is currently assessed and reported in Dupuytren’s disease literature. Following analysis recommendations for practice will be made to enable consistency in future studies for comparability. This paper highlights the variation in range of motion reporting in Dupuytren’s disease. Methods: A Participants, Intervention, Comparison, Outcomes and Study design format was used for the search strategy and search terms. Surgery, needle fasciotomy or collagenase injection for primary or recurrent Dupuytren’s disease in adults were included if outcomes were monitored using range of motion to record change. A literature search was performed in May 2013 using subject heading and free-text terms to also capture electronic publications ahead of print. In total 638 publications were identified and following screening 90 articles met the inclusion criteria. Data was extracted and entered onto a spreadsheet for analysis. A thematic analysis was carried out to establish any duplication, resulting in the final range of motion measures identified. Results: Range of motion measurement lacked clarity, with goniometry reportedly used in only 43 of the 90 studies, 16 stated the use of a range of motion protocol. A total of 24 different descriptors were identified describing range of motion in the 90 studies. While some studies reported active range of motion, others reported passive or were unclear. Eight of the 24 categories were identified through thematic analysis as possibly describing the same measure, ‘lack of joint extension’ and accounted for the most frequently used. Conclusions: Published studies lacked clarity in reporting range of motion, preventing data comparison and meta-analysis. Percentage change lacks context and without access to raw data, does not allow direct comparison of baseline characteristics. A clear description of what is being measured within each study was required. It is recommended that range of motion measuring and reporting for Dupuytren’s disease requires consistency to address issues that fall into 3 main categories:- Definition of terms Protocol statement Outcome reportin

SHAPE analysis of the FIV Leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization

Feline immunodeficiency virus (FIV) infects many species of cat, and is related to HIV, causing a similar pathology. High-throughput selective 2′ hydroxyl acylation analysed by primer extension (SHAPE), a technique that allows structural interrogation at each nucleotide, was used to map the secondary structure of the FIV packaging signal RNA. Previous studies of this RNA showed four conserved stem–loops, extensive long-range interactions (LRIs) and a small, palindromic stem–loop (SL5) within the gag open reading frame (ORF) that may act as a dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Our analyses of wild-type (wt) and mutant RNAs suggest that although the four conserved stem–loops are static structures, the 5′ and 3′ regions previously shown to form LRI also adopt an alternative, yet similarly conserved conformation, in which the putative DIS is occluded, and which may thus favour translational and splicing functions over encapsidation. SHAPE and in vitro dimerization assays were used to examine SL5 mutants. Dimerization contacts appear to be made between palindromic loop sequences in SL5. As this stem–loop is located within the gag ORF, recognition of a dimeric RNA provides a possible mechanism for the specific packaging of genomic over spliced viral RNAs

Optimal functional outcome measures for assessing treatment for Dupuytren's disease: A systematic review and recommendations for future practice

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Ball et al.; licensee BioMed Central Ltd.Background: Dupuytren's disease of the hand is a common condition affecting the palmar fascia, resulting in progressive flexion deformities of the digits and hence limitation of hand function. The optimal treatment remains unclear as outcomes studies have used a variety of measures for assessment. Methods: A literature search was performed for all publications describing surgical treatment, percutaneous needle aponeurotomy or collagenase injection for primary or recurrent Dupuytren’s disease where outcomes had been monitored using functional measures. Results: Ninety-one studies met the inclusion criteria. Twenty-two studies reported outcomes using patient reported outcome measures (PROMs) ranging from validated questionnaires to self-reported measures for return to work and self-rated disability. The Disability of Arm, Shoulder and Hand (DASH) score was the most utilised patient-reported function measure (n=11). Patient satisfaction was reported by eighteen studies but no single method was used consistently. Range of movement was the most frequent physical measure and was reported in all 91 studies. However, the methods of measurement and reporting varied, with seventeen different techniques being used. Other physical measures included grip and pinch strength and sensibility, again with variations in measurement protocols. The mean follow-up time ranged from 2 weeks to 17 years. Conclusions: There is little consistency in the reporting of outcomes for interventions in patients with Dupuytren’s disease, making it impossible to compare the efficacy of different treatment modalities. Although there are limitations to the existing generic patient reported outcomes measures, a combination of these together with a disease-specific questionnaire, and physical measures of active and passive individual joint Range of movement (ROM), grip and sensibility using standardised protocols should be used for future outcomes studies. As Dupuytren’s disease tends to recur following treatment as well as extend to involve other areas of the hand, follow-up times should be standardised and designed to capture both short and long term outcomes