Comparative Pathogenomics Reveals Horizontally Acquired Novel Virulence Genes in Fungi Infecting Cereal Hosts

Comparative analyses of pathogen genomes provide new insights into how pathogens have evolved common and divergent virulence strategies to invade related plant species. Fusarium crown and root rots are important diseases of wheat and barley world-wide. In Australia, these diseases are primarily caused by the fungal pathogen Fusarium pseudograminearum. Comparative genomic analyses showed that the F. pseudograminearum genome encodes proteins that are present in other fungal pathogens of cereals but absent in non-cereal pathogens. In some cases, these cereal pathogen specific genes were also found in bacteria associated with plants. Phylogenetic analysis of selected F. pseudograminearum genes supported the hypothesis of horizontal gene transfer into diverse cereal pathogens. Two horizontally acquired genes with no previously known role in fungal pathogenesis were studied functionally via gene knockout methods and shown to significantly affect virulence of F. pseudograminearum on the cereal hosts wheat and barley. Our results indicate using comparative genomics to identify genes specific to pathogens of related hosts reveals novel virulence genes and illustrates the importance of horizontal gene transfer in the evolution of plant infecting fungal pathogens

Uniform electroactive fiber-like micelle nanowires for organic electronics

AbstractMicelles formed by the self-assembly of block copolymers in selective solvents have attracted widespread attention and have uses in a wide variety of fields, whereas applications based on their electronic properties are virtually unexplored. Herein we describe studies of solution-processable, low-dispersity, electroactive fibre-like micelles of controlled length from π-conjugated diblock copolymers containing a crystalline regioregular poly(3-hexylthiophene) core and a solubilizing, amorphous regiosymmetric poly(3-hexylthiophene) or polystyrene corona. Tunnelling atomic force microscopy measurements demonstrate that the individual fibres exhibit appreciable conductivity. The fibres were subsequently incorporated as the active layer in field-effect transistors. The resulting charge carrier mobility strongly depends on both the degree of polymerization of the core-forming block and the fibre length, and is independent of corona composition. The use of uniform, colloidally stable electroactive fibre-like micelles based on common π-conjugated block copolymers highlights their significant potential to provide fundamental insight into charge carrier processes in devices, and to enable future electronic applications.</jats:p

Protocol for the Foot in Juvenile Idiopathic Arthritis trial (FiJIA): a randomised controlled trial of an integrated foot care programme for foot problems in JIA

&lt;b&gt;Background&lt;/b&gt;: Foot and ankle problems are a common but relatively neglected manifestation of juvenile idiopathic arthritis. Studies of medical and non-medical interventions have shown that clinical outcome measures can be improved. However existing data has been drawn from small non-randomised clinical studies of single interventions that appear to under-represent the adult population suffering from juvenile idiopathic arthritis. To date, no evidence of combined therapies or integrated care for juvenile idiopathic arthritis patients with foot and ankle problems exists. &lt;b&gt;Methods/design&lt;/b&gt;: An exploratory phase II non-pharmacological randomised controlled trial where patients including young children, adolescents and adults with juvenile idiopathic arthritis and associated foot/ankle problems will be randomised to receive integrated podiatric care via a new foot care programme, or to receive standard podiatry care. Sixty patients (30 in each arm) including children, adolescents and adults diagnosed with juvenile idiopathic arthritis who satisfy the inclusion and exclusion criteria will be recruited from 2 outpatient centres of paediatric and adult rheumatology respectively. Participants will be randomised by process of minimisation using the Minim software package. The primary outcome measure is the foot related impairment measured by the Juvenile Arthritis Disability Index questionnaire's impairment domain at 6 and 12 months, with secondary outcomes including disease activity score, foot deformity score, active/limited foot joint counts, spatio-temporal and plantar-pressure gait parameters, health related quality of life and semi-quantitative ultrasonography score for inflammatory foot lesions. The new foot care programme will comprise rapid assessment and investigation, targeted treatment, with detailed outcome assessment and follow-up at minimum intervals of 3 months. Data will be collected at baseline, 6 months and 12 months from baseline. Intention to treat data analysis will be conducted. A full health economic evaluation will be conducted alongside the trial and will evaluate the cost effectiveness of the intervention. This will consider the cost per improvement in Juvenile Arthritis Disability Index, and cost per quality adjusted life year gained. In addition, a discrete choice experiment will elicit willingness to pay values and a cost benefit analysis will also be undertaken

DNA addition or deletion is associated with a major karyotype polymorphism in the fungal phytopathogen Colletotrichum gloeosporioides

A 1.2 Mb minichromosome resolved by pulsed-field electrophoresis was present in two independent race 3 isolates of Colletotrichum gloeosporioides causing Type B anthracnose specifically on Stylosanthes guianensis cv. Graham in Australia. This chromosome was absent in duplicate isolates representing races 1, 2 and 4 which infect other S. guianensis cultivars. A gene library was prepared specifically from the 1.2 Mb mini-chromosome and ten independent DNA clones unique to this chromosome were identified by differential hybridisation to whole chromosome probes. All of the ten selected probes hybridised only to the 1.2 Mb minichromosome unique to the race 3 isolates but not to any chromosome in isolates of the other races. These ten probes also hybridised only to restriction-digested DNA of race 3 and were thus both chromosome- and strain-specific for Type B C. gloeosporioides. Hybridisation analysis of NotI fragments of the 1.2 Mb minichromosome with these sequences indicated that they were not tightly clustered on the chromosome. These data demonstrate that the variation in the occurrence of the 1.2 Mb minichromosome did not arise by rearrangement of the genome of a progenitor strain but involved either large scale deletion or addition of DNA. The 1.2 Mb minichromosome did not contain a cloned high-copy-number repeat sequence present on all other mini- and maxichromosomes, suggesting addition from a genetically distinct strain. All ten chromosome-specific DNA probes hybridised to a 2.0 Mb chromosome in all races of C. gloeosporioides causing Type A anthracnose on Stylosanthes spp. including S. guianensis. Restriction fragment length polymorphism analysis demonstrated that only 15% of the hybridising restriction fragments of the Type A 2.0 Mb chromosome and the 1.2 Mb Type B race 3 minichromosome were identical. This indicated that it is unlikely that the 1.2 Mb minichromosome of the race 3 Type B pathogen was recently introgressed from-the Type A pathogen

Mini-chromosomes of Colletotrichum spp. infecting several host species in various countries

Pulsed-field gel electrophoresis was used to screen 52 isolates of Colletotrichum spp. for the presence of mini-chromosomes in the size range 200–1200 kb. Mini-chromosomes were observed in all isolates of C. gloeosporioides, and in Australian isolates of C. crassipes, C. dematium and C. truncatum, but not in C. musae, C. lindemuthianum and C. trifolii. The mini-chromosome complements of 36 isolates of C. gloeosporioides from the host genus Stylosanthes were investigated. These isolates were obtained in eight countries from Africa, South East Asia and South America and were from six species of Stylosanthes. Two classes of C. gloeosporioides were discerned on the basis of mini-chromosome content, the first class (Mtype 1) had less than six mini-chromosomes and the other class, (Mtype 2) had greater than six mini-chromosomes including one of 600 kb in size. There was no correlation between Mtype and disease symptom produced, pathogen biotype and the host species and country of origin. These results contrast previous correlations of Mtype with disease symptom, pathogen biotype and host range reported for isolates from Stylosanthes in Australia and suggest that a greater genetic diversity exists in pathogen populations outside Australia

Molecular cloning and characterisation of peroxidases from buffel grass (Cenchrus ciliaris L.)

Buffel grass (Cenchrus ciliaris L.) peroxidase cDNAs were isolated by hybridisation to an oligonucleotide from a conserved region of all plant peroxidases and a peroxidase cDNA clone from wheat. The 36 clones isolated were classified into one homogenous and three apparently heterogenous groups by cross-hybridisation and sequence homologies. Nine cDNAs were subcloned, partially sequenced and identified as peroxidase homologues by the presence of conserved sequences. Two full-length clones (PX7 and PX18) were completely sequenced and the deduced protein sequences revealed between 38% and 77% homology to other plant peroxidases. The mRNAs corresponding to five peroxidase cDNAs were analysed by northern analysis, to test for tissue specific or wound inducible expression. The peroxidases encoded by three clones, including PX7 and PX18, were expressed preferentially in leaves. The other two clones showed a marked wound response in leaves. No clone was strongly expressed in stems. Southern blot analysis indicated that PX18 is coded for by a single copy gene, whereas PX7 is represented in the buffel grass genome by five or six copies. This indicates the complexity of the buffel grass peroxidase gene family with respect to identification of peroxidase genes implicated in defence or developmental lignification

Distribution and relationship of chromosome-specific dispensable DNA sequences in diverse isolates of Colletotrichum gloeosporioides

DNA hybridization probes specific to a dispensable 1 2 Mb chromosome identified in some isolates of biotype B of Colletotrichum gloeosporioides pathogenic on the legume Stylosanthes guianensis were used to assess the distribution and chromosomal location of homologous sequences in a diverse collection of other Colletotrichum isolates. Homologous sequences were not detected in isolates representing C. lindemuthianum, C. musae, C. crassipes, C. trifolii, C. dematium and C. truncatum but were in some C. gloeosporioides isolates. Thus these sequences were not conserved in the genus and deleted in some C. gloeosporioides strains. Partly homologous DNA sequences were detected in genetically distinct biotypes of C. gloeosporioides pathogenic on hosts other than Stylosanthes, which suggests that these DNA sequences may have evolved within the species C. gloeasporioides prior to host specialization. Highly homologous chromosomes were identified in some isolates of the fungus from Stylosanthes from outside Australia including one isolate from the Philippines which appeared to have a 1.2 Mb chromosome almost identical to that of Australian biotype B strains. The DNA probes revealed a range of sizes of homologous chromosomes in other strains of C. gloeosporioides but in general the chromosome-specific DNA probes were linked, suggesting a common origin with subsequent gross chromosomal rearrangement or exchange. The possibility that the chromosome-specific markers may be useful diagnostic probes for biotype B isolates virulent on S. guianensis cv. Graham was tested using 10 new isolates with this virulence phenotype and three of these isolates lacked both the chromosome and the DNA sequence homology. This suggests that the 1.2 Mb mini-chromosome is not associated with race-specificity The significance of these results for the origin and function of dispensable chromosomes in C. gloeosporioides is discussed