Whole-genome screening in ankylosing spondylitis: Evidence of non-MHC genetic-susceptibility loci

Ankylosing spondylitis (AS) is a common inflammatory arthritis predominantly affecting the axial skeleton. Susceptibility to the disease is thought to be oligogenic. To identify the genes involved, we have performed a genomewide scan in 185 families containing 255 affected sibling pairs. Two-point and multipoint nonparametric linkage analysis was performed. Regions were identified showing "suggestive" or stronger linkage with the disease on chromosomes 1p, 2q, 6p, 9q, 10q, 16q, and 19q. The MHC locus was identified as encoding the greatest component of susceptibility, with an overall LOD score of 15.6. The strongest non-MHC linkage lies on chromosome 16q (overall LOD score 4.7). These results strongly support the presence of non-MHC genetic-susceptibility factors in AS and point to their likely locations.

Whole-genome linkage analysis of rheumatoid arthritis susceptibility loci in 252 affected sibling pairs in the United Kingdom

Objective. To undertake a systematic wholegenome screen to identify regions exhibiting genetic linkage to rheumatoid arthritis (RA). Methods. Two hundred fifty-two RA-affected sibling pairs from 182 UK families were genotyped using 365 highly informative microsatellite markers. Microsatellite genotyping was performed using fluorescent polymerase chain reaction primers and semiautomated DNA sequencing technology. Linkage analysis was undertaken using MAPMAKER/SIBS for single-point and multipoint analysis. Results. Significant linkage (maximum logarithm of odds score 4.7 [P = 0.000003] at marker D6S276, 1 cM from HLA-DRB1) was identified around the major histocompatibility complex (MHC) region on chromosome 6. Suggestive linkage (P < 7.4 × 10-4) was identified on chromosome 6q by single- and multipoint analysis. Ten other sites of nominal linkage (P < 0.05) were identified on chromosomes 3p, 4q, 7p, 2 regions of 10q, 2 regions of 14q, 16p, 21q, and Xq by single-point analysis and on 3 sites (1q, 14q, and 14q) by multipoint analysis. Conclusion. Linkage to the MHC region was confirmed. Eleven non-HLA regions demonstrated evidence of suggestive or nominal linkage, but none reached the genome-wide threshold for significant linkage (P = 2.2 × 10-5). Results of previous genome screens have suggested that 6 of these regions may be involved in RA susceptibility.

Whole blood transcriptional profiling in ankylosing spondylitis identifies novel candidate genes that might contribute to the inflammatory and tissue-destructive disease aspects

Introduction: A number of genetic-association studies have identified genes contributing to ankylosing spondylitis (AS) susceptibility but such approaches provide little information as to the gene activity changes occurring during the disease process. Transcriptional profiling generates a 'snapshot' of the sampled cells' activity and thus can provide insights into the molecular processes driving the disease process. We undertook a whole-genome microarray approach to identify candidate genes associated with AS and validated these gene-expression changes in a larger sample cohort. Methods: A total of 18 active AS patients, classified according to the New York criteria, and 18 gender- and age-matched controls were profiled using Illumina HT-12 whole-genome expression BeadChips which carry cDNAs for 48,000 genes and transcripts. Class comparison analysis identified a number of differentially expressed candidate genes. These candidate genes were then validated in a larger cohort using qPCR-based TaqMan low density arrays (TLDAs). Results: A total of 239 probes corresponding to 221 genes were identified as being significantly different between patients and controls with a P-value <0.0005 (80% confidence level of false discovery rate). Forty-seven genes were then selected for validation studies, using the TLDAs. Thirteen of these genes were validated in the second patient cohort with 12 downregulated 1.3- to 2-fold and only 1 upregulated (1.6-fold). Among a number of identified genes with well-documented inflammatory roles we also validated genes that might be of great interest to the understanding of AS progression such as SPOCK2 (osteonectin) and EP300, which modulate cartilage and bone metabolism. Conclusions: We have validated a gene expression signature for AS from whole blood and identified strong candidate genes that may play roles in both the inflammatory and joint destruction aspects of the disease.

Whole exome sequencing is an efficient and sensitive method for detection of germline mutations in patients with phaeochromcytomas and paragangliomas

Background Genetic testing is recommended when the probability of a disease-associated germline mutation exceeds 10%. Germline mutations are found in approximately 25% of individuals with phaeochromcytoma (PCC) or paraganglioma (PGL); however, genetic heterogeneity for PCC/PGL means many genes may require sequencing. A phenotype-directed iterative approach may limit costs but may also delay diagnosis, and will not detect mutations in genes not previously associated with PCC/PGL. Objective To assess whether whole exome sequencing (WES) was efficient and sensitive for mutation detection in PCC/PGL. Methods Whole exome sequencing was performed on blinded samples from eleven individuals with PCC/PGL and known mutations. Illumina TruSeq™ (Illumina Inc, San Diego, CA, USA) was used for exome capture of seven samples, and NimbleGen SeqCap EZ v3.0 (Roche NimbleGen Inc, Basel, Switzerland) for five samples (one sample was repeated). Massive parallel sequencing was performed on multiplexed samples. Sequencing data were called using Genome Analysis Toolkit and annotated using annovar. Data were assessed for coding variants in RET, NF1, VHL, SDHD, SDHB, SDHC, SDHA, SDHAF2, KIF1B, TMEM127, EGLN1 and MAX. Target capture of five exome capture platforms was compared. Results Six of seven mutations were detected using Illumina TruSeq™ exome capture. All five mutations were detected using NimbleGen SeqCap EZ v3.0 platform, including the mutation missed using Illumina TruSeq™ capture. Target capture for exons in known PCC/PGL genes differs substantially between platforms. Exome sequencing was inexpensive (<$A800 per sample for reagents) and rapid (results <5 weeks from sample reception). Conclusion Whole exome sequencing is sensitive, rapid and efficient for detection of PCC/PGL germline mutations. However, capture platform selection is critical to maximize sensitivity.

Characterisation of lignins isolated from sugarcane bagasse pretreated with acidified ethylene glycol and ionic liquids

Sugarcane bagasse pretreatment processes using acidified aqueous ethylene glycol (EG) and ionic liquids (ILs) have been reported recently. In this study, recovery of lignins from these processes was conducted, as well as determination of their physico-chemical properties. The amount of lignins recovered from 1-butyl-3-methylimidazolium chloride ([bmim]Cl) with HCl as a catalyst and [bmim][CH3SO3] was ∼42%, and ∼35%–36% by EG with HCl or H2SO4 as a catalyst, respectively. The isolated lignins were characterised using wet chemistry, spectroscopy and thermogravimetry analysis (TGA), and the results compared to soda lignin from NaOH pretreatment of bagasse. The IL and EG lignins contained no or trace amounts of carbohydrates, slightly lower hydrogen content but slightly higher oxygen contents than soda lignin. The IL and EG lignins contained more C-3 and C-5 reactive sites for Mannich reaction and had more p-hydroxypheny propane unit structures than soda lignin. Two-dimensional heteronuclear single quantum coherence (2D HSQC) nuclear magnetic resonance (NMR) identified the major substructural units in the lignins, and allowed differences among them to be studied. As EG lignins were extracted in very reactive environment, intermediate enol ethers were formed and led to cleavage reactions which were not apparent in the other lignins. 31P NMR and infra-red spectroscopy results showed that IL and EG lignins had lower total hydroxyl content than soda lignin, probably indicating that a higher degree of self-polymerisation occurred during bagasse pretreatment, despite the use of lower temperature and shorter reaction time. On the basis of the salient features of these lignins, potential applications were proposed.

Hybrid metaheuristic techniques for optimising sugarcane rail operations

Mixed integer programming and parallel-machine job shop scheduling are used to solve the sugarcane rail transport scheduling problem. Constructive heuristics and metaheuristics were developed to produce a more efficient scheduling system and so reduce operating costs. The solutions were tested on small and large size problems. High-quality solutions and improved CPU time are the result of developing new hybrid techniques which consist of different ways of integrating simulated annealing and Tabu search techniques.

Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging

Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by immersion for 1–14 d, with the exact time required dependent on the sample type and the experimental purposes. A single imaging set can be completed in 30–60 min. Image processing and analysis can take <1 d, but it is dependent on the number of samples in the data set. The CUBIC clearing protocol can process multiple samples simultaneously. We previously used CUBIC to image whole-brain neural activities at single-cell resolution using Arc-dVenus transgenic (Tg) mice. CUBIC informatics calculated the Venus signal subtraction, comparing different brains at a whole-organ scale. These protocols provide a platform for organism-level systems biology by comprehensively detecting cells in a whole organ or body.

Performance enhancement: A whole of person approach to first year dance students’ transition into tertiary training

The transition into university presents very particular challenges for students. The First Year Experience (FYE) is a transitional liminal phase, fraught with uncertainty, ripe with potential. The complexity inherent in this initial phase of tertiary education is well documented and continues to be interrogated. Providing timely and effective support and interventions for potentially at-risk first year students as they transition into tertiary study is a key priority for universities across the globe (Gale et al., 2015). This article outlines the evolution of an established and highly successful Transitional Training Program (TTP) for first year tertiary dance students, with particular reference to the 2015 iteration of the program. TTP design embraces three dimensions: physical training in transition, learning in transition, and teaching for transition, with an emphasis on developing and encouraging a mindset that enables information to be transferred into alternative settings for practice and learning throughout life. The aim of the 2015 TTP was to drive substantial change in first year Dance students’ satisfaction, connectedness, and overall performance within the Bachelor of Fine Arts (BFA) Dance course, through the development and delivery of innovative curriculum and pedagogical practices that promote the successful transition of dance students into their first year of university. The program targeted first year BFA Dance students through the integration of specific career guidance; performance psychology; academic skills support; practical dance skills support; and specialized curricula and pedagogy.

The multiple sclerosis whole blood mRNA transcriptome and genetic associations indicate dysregulation of specific T cell pathways in pathogenesis

Multiple sclerosis (MS) is an autoimmune disease with a genetic component, caused at least in part by aberrant lymphocyte activity. The whole blood mRNA transcriptome was measured for 99 untreated MS patients: 43 primary progressive MS, 20 secondary progressive MS, 36 relapsing remitting MS and 45 age-matched healthy controls. The ANZgene Multiple Sclerosis Genetics Consortium genotyped more than 300 000 SNPs for 115 of these samples. Transcription from genes on translational regulation, oxidative phosphorylation, immune synapse and antigen presentation pathways was markedly increased in all forms of MS. Expression of genes tagging T cells was also upregulated (P < 10-12) in MS. A T cell gene signature predicts disease state with a concordance index of 0.79 with age and gender as co-variables, but the signature is not associated with clinical course or disability. The ANZgene genome wide association screen identified two novel regions with genome wide significance: one encoding the T cell co-stimulatory molecule, CD40; the other a region on chromosome 12q13-14. The CD40 haplotype associated with increased MS susceptibility has decreased gene expression in MS (P < 0.0007). The second MS susceptibility region includes 17 genes on 12q13-14 in tight linkage disequilibrium. Of these, only 13 are expressed in leukocytes, and of these the expression of one, FAM119B, is much lower in the susceptibility haplotype (P tdthomlt; 10-14). Overall, these data indicate dysregulation of T cells can be detected in the whole blood of untreated MS patients, and supports targeting of activated T cells in therapy for all forms of MS.

Combined analysis of three whole genome linkage scans for Ankylosing Spondylitis

Objective. Ankylosing spondylitis (AS) is a debilitating chronic inflammatory condition with a high degree of familiality (λs=82) and heritability (>90%) that primarily affects spinal and sacroiliac joints. Whole genome scans for linkage to AS phenotypes have been conducted, although results have been inconsistent between studies and all have had modest sample sizes. One potential solution to these issues is to combine data from multiple studies in a retrospective meta-analysis. Methods: The International Genetics of Ankylosing Spondylitis Consortium combined data from three whole genome linkage scans for AS (n=3744 subjects) to determine chromosomal markers that show evidence of linkage with disease. Linkage markers typed in different centres were integrated into a consensus map to facilitate effective data pooling. We performed a weighted meta-analysis to combine the linkage results, and compared them with the three individual scans and a combined pooled scan. Results: In addition to the expected region surrounding the HLA-B27 gene on chromosome 6, we determined that several marker regions showed significant evidence of linkage with disease status. Regions on chromosome 10q and 16q achieved 'suggestive' evidence of linkage, and regions on chromosomes 1q, 3q, 5q, 6q, 9q, 17q and 19q showed at least nominal linkage in two or more scans and in the weighted meta-analysis. Regions previously associated with AS on chromosome 2q (the IL-1 gene cluster) and 22q (CYP2D6) exhibited nominal linkage in the meta-analysis, providing further statistical support for their involvement in susceptibility to AS. Conclusion: These findings provide a useful guide for future studies aiming to identify the genes involved in this highly heritable condition. . Published by on behalf of the British Society for Rheumatology.

Managing the impacts of sugarcane farming on the Great Barrier Reef: An evaluation of the implementation of the Polluter Pays Principle

This report provides an evaluation of the implementation of the Polluter Pays Principle (PPP) – a principle of international environmental law – in the context of pollution from sugarcane farming affecting Australia’s Great Barrier Reef (GBR). The research was part of an experiment to test methods for evaluating the effectiveness of environmental laws. Overall, we found that whilst the PPP is reflected to a limited extent in Australian law (more so in Queensland law, than at the national level), the behaviour one might expect in terms of implementing the principle was largely inadequate. Evidence of a longer term, explicit commitment to the PPP was particularly weak.

Crop Classification using Biologically-inspired Techniques with High Resolution Satellite Image

Remote sensing provides a lucid and effective means for crop coverage identification. Crop coverage identification is a very important technique, as it provides vital information on the type and extent of crop cultivated in a particular area. This information has immense potential in the planning for further cultivation activities and for optimal usage of the available fertile land. As the frontiers of space technology advance, the knowledge derived from the satellite data has also grown in sophistication. Further, image classification forms the core of the solution to the crop coverage identification problem. No single classifier can prove to satisfactorily classify all the basic crop cover mapping problems of a cultivated region. We present in this paper the experimental results of multiple classification techniques for the problem of crop cover mapping of a cultivated region. A detailed comparison of the algorithms inspired by social behaviour of insects and conventional statistical method for crop classification is presented in this paper. These include the Maximum Likelihood Classifier (MLC), Particle Swarm Optimisation (PSO) and Ant Colony Optimisation (ACO) techniques. The high resolution satellite image has been used for the experiments.

Sigastus weevil - an emerging pest of macadamias in north Queensland

A large weevil was found infesting macadamia nuts on the Atherton Tableland during the 1994/95 season. It was unrepresented in various Australian insect collections but thought to belong to the genus Sigastus. This paper reports some preliminary studies on its biology, pest status and control. From 4-6 weeks after first nut-set adult females commence laying single eggs through the husk, after first scarifying an oviposition site. The nut stalk is then cleaved leading to rapid abscission. Nuts were generally attacked up until hard shell formation. Weevil larvae consumed whole kernels, with % survival higher and larval duration shorter in larger nuts. Infestation rates increased with increasing nut diameter, reaching 72.8% of fallen nuts by mid-October. A crop loss of 30% could be attributed to weevils in an unsprayed orchard. However, adult weevils are very susceptible to both carbaryl and methidathion sprays. In addition, exposure of infested nuts to full sunlight over several weeks kills 100% of larvae. Crops should be surveyed for weevil damage from the 5-10 mm diameter stage until mid-December. Methidathion used as an initial spray for fruitspotting bugs should provide control. Organic growers are advised to sweep infested nuts into mown interrows where solarisation will kill larvae.

Abacá mosaic virus: a distinct strain of Sugarcane mosaic virus

Abacá mosaic virus (AbaMV) is related to members of the sugarcane mosaic virus subgroup of the genus Potyvirus. The ~2 kb 3′ terminal region of the viral genome was sequenced and, in all areas analysed, found to be most similar to Sugarcane mosaic virus (SCMV) and distinct from Johnsongrass mosaic virus (JGMV), Maize dwarf mosaic virus (MDMV) and Sorghum mosaic virus (SrMV). Cladograms of the 3′ terminal region of the NIb protein, the coat protein core and the 3′ untranslated region showed that AbaMV clustered with SCMV, which was a distinct clade and separate from JGMV, MDMV and SrMV. The N-terminal region of the AbaMV coat protein had a unique amino acid repeat motif different from those previously published for other strains of SCMV. The first experimental transmission of AbaMV from abacá (Musa textilis) to banana (Musa sp.), using the aphid vectors Rhopalosiphum maidis and Aphis gossypii, is reported. Polyclonal antisera for the detection of AbaMV in western blot assays and ELISA were prepared from recombinant coat protein expressed in E. coli. A reverse transcriptase PCR diagnostic assay, with microtitre plate colourimetric detection, was developed to discriminate between AbaMV and Banana bract mosaic virus, another Musa-infecting potyvirus. Sequence data, host reactions and serological relationships indicate that AbaMV should be considered a distinct strain of SCMV, and the strain designation SCMV-Ab is suggested.

Phenology of Carpophilus spp. (Coleoptera: Nitidulidae)in stone fruit orchards as determined by pheromone trapping: Implications for prediction of crop damage

Traps baited with synthetic aggregation pheromone and fermenting bread dough were used to monitor seasonal incidence and abundance of the ripening fruit pests, Carpophilus hemipterus (L.), C. mutilatus Erichson and C. davidsoni Dobson in stone fruit orchards in the Leeton district of southern New South Wales during five seasons (1991-96). Adult beetles were trapped from September-May, but abundance varied considerably between years with the amount of rainfall in December-January having a major influence on population size and damage potential during the canning peach harvest (late February-March). Below average rainfall in December-January was associated with mean trap catches of < 10 beetles/trap/week in low dose pheromone traps during the harvest period in 1991/92 and 1993/94 and no reported damage to ripening fruit. Rainfall in December-January 1992/93 was more than double the average and mean trap catches ranged from 8-27 beetles/week during the harvest period with substantial damage to the peach crop. December-January rainfall was also above average in 1994/95 and 1995/96 and means of 50-300 beetles/trap/week were recorded in high dose pheromone traps during harvest periods. Carpophilus spp. caused economic damage to peach crops in both seasons. These data indicate that it may be possible to predict the likelihood of Carpophilus beetle damage to ripening stone fruit in inland areas of southern Australia, by routine pheromone-based monitoring of beetle populations and summer temperatures and rainfall.