ERDMAS: An exemplar-driven institutional research data management and analysis strategy

Devising fit-for-purpose research data management strategies within a university is challenging. This is because the five ‘Vs’ for generated research data; its Volume, Variety, Velocity, Veracity and its Value must be constantly considered. Invariably, a combination of data V's for any given research endeavour determine how best to manage it appropriately addressing archiving, compliance, security, privacy, sharing, reuse and so forth. As such, institutions are faced with defining, shaping and refining strategies and practicies to ensure there are consistent and adequate research data management polices and guidelines in place for their researchers. FAIR data principles are very important for embracing open data opportunities, but more broadly, research data management practices need to be established in a comprehensive way. Additionally, new ICT options have rapidly become available where institutions can make considered choices on whether to continue to use ‘on prem’, private Cloud or public Cloud infrastructure. If a hybrid approach is adopted, then the potential impact on existing institutional research data management strategies must be continually assessed and revised accordingly. Getting the balance right between developing a relevant institutional policy on the one hand yet also dynamically catering for the eclectic research data management and analytics needs of researchers and their evolving interactions with external collaborators on the other, must be continually navigated. In this manuscript, an exemplar-driven research data management and analytics conceptual framework is introduced. A key feature of this framework is that it is couched in two dimensions. On one axis is the ‘standard’ linear approach of developing the research data management policy, guidelines, procedures, audit and risk assessment and an options matrix. Importantly, a second axis comprising a researcher-driven focus is introduced where exemplar research activities are used to define ‘classes’ of research data management and analysis requirements. This exemplar-driven dimension enables an ongoing system-wide comparative review to occur in parallel that can continually inform policy and guidelines refinement

BarleyVarDB: a database of barley genomic variation

Barley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation. It can be publicly accessible through the website at http://146.118.64.11/BarleyVar. This database mainly provides three sets of information. First, there are 57 754 224 single nuclear polymorphisms (SNPs) and 3 600 663 insertions or deletions (InDels) included in BarleyVarDB, which were identified from high-coverage whole genome sequencing of 21 barley germplasm, including 8 wild barley accessions from 3 barley evolutionary original centers and 13 barley landraces from different continents. Second, it uses the latest barley genome reference and its annotation information publicly accessible, which has been achieved by the International Barley Genome Sequencing Consortium (IBSC). Third, 522 212 whole genome-wide microsatellites/simple sequence repeats (SSRs) were also included in this database, which were identified in the reference barley pseudo-molecular genome sequence. Additionally, several useful web-based applications are provided including JBrowse, BLAST and Primer3. Users can design PCR primers to asses polymorphic variants deposited in this database and use a user-friendly interface for accessing the barley reference genome. We envisage that the BarleyVarDB will benefit the barley genetic research community by providing access to all publicly available barley genomic variation information and barley reference genome as well as providing them with an ultra-high density of SNP and InDel markers for molecular breeding and identification of functional genes with important agronomic traits in barley. Database URL: http://146.118.64.11/BarleyVa

The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones

<p>Abstract</p> <p>Background</p> <p><it>Rhipicephalus (Boophilus) microplus (Rmi) </it>a major cattle ectoparasite and tick borne disease vector, impacts on animal welfare and industry productivity. In arthropod research there is an absence of a complete Chelicerate genome, which includes ticks, mites, spiders, scorpions and crustaceans. Model arthropod genomes such as <it>Drosophila </it>and <it>Anopheles </it>are too taxonomically distant for a reference in tick genomic sequence analysis. This study focuses on the <it>de-novo </it>assembly of two <it>R. microplus </it>BAC sequences from the understudied <it>R microplus </it>genome. Based on available <it>R. microplus </it>sequenced resources and comparative analysis, tick genomic structure and functional predictions identify complex gene structures and genomic targets expressed during tick-cattle interaction.</p> <p>Results</p> <p>In our BAC analyses we have assembled, using the correct positioning of BAC end sequences and transcript sequences, two challenging genomic regions. Cot DNA fractions compared to the BAC sequences confirmed a highly repetitive BAC sequence BM-012-E08 and a low repetitive BAC sequence BM-005-G14 which was gene rich and contained short interspersed elements (SINEs). Based directly on the BAC and Cot data comparisons, the genome wide frequency of the SINE Ruka element was estimated. Using a conservative approach to the assembly of the highly repetitive BM-012-E08, the sequence was de-convoluted into three repeat units, each unit containing an 18S, 5.8S and 28S ribosomal RNA (rRNA) encoding gene sequence (rDNA), related internal transcribed spacer and complex intergenic region.</p> <p>In the low repetitive BM-005-G14, a novel gene complex was found between to 2 genes on the same strand. Nested in the second intron of a large 9 Kb <it>papilin </it>gene was a <it>helicase </it>gene. This <it>helicase </it>overlapped in two exonic regions with the <it>papilin</it>. Both these genes were shown expressed in different tick life stage important in ectoparasite interaction with the host. Tick specific sequence differences were also determined for the <it>papilin </it>gene and the protein binding sites of the 18S subunit in a comparison to <it>Bos taurus</it>.</p> <p>Conclusion</p> <p>In the absence of a sequenced reference genome we have assembled two complex BAC sequences, characterised novel gene structure that was confirmed by gene expression and sequencing analyses. This is the first report to provide evidence for 2 eukaryotic genes with exon regions that overlap on the same strand, the first to describe <it>Rhipicephalinae papilin</it>, and the first to report the complete ribosomal DNA repeated unit sequence structure for ticks. The Cot data estimation of genome wide sequence frequency means this research will underpin future efforts for genome sequencing and assembly of the <it>R. microplus </it>genome.</p

Immunomic Investigation of Holocyclotoxins to Produce the First Protective Anti-Venom Vaccine Against the Australian Paralysis Tick, Ixodes holocyclus

Venom producing animals are ubiquitously disseminated among vertebrates and invertebrates such as fish, snakes, scorpions, spiders, and ticks. Of the ~890 tick species worldwide, 27 have been confirmed to cause paralysis in mammalian hosts. The Australian paralysis tick (Ixodes holocyclus) is the most potent paralyzing tick species known. It is an indigenous three host tick species that secretes potent neurotoxins known as holocyclotoxins (HTs). Holocyclotoxins cause a severe and harmful toxicosis leading to a rapid flaccid paralysis which can result in death of susceptible hosts such as dogs. Antivenins are generally polyclonal antibody treatments developed in sheep, horses or camels to administer following bites from venomous creatures. Currently, the methods to prevent or treat tick paralysis relies upon chemical acaricide preventative treatments or prompt removal of all ticks attached to the host followed by the administration of a commercial tick-antiserum (TAS) respectively. However, these methods have several drawbacks such as poor efficacies, non-standardized dosages, adverse effects and are expensive to administer. Recently the I. holocyclus tick transcriptome from salivary glands and viscera reported a large family of 19 holocyclotoxins at 38-99% peptide sequence identities. A pilot trial demonstrated that correct folding of holocyclotoxins is needed to induce protection from paralysis. The immunogenicity of the holocyclotoxins were measured using commercial tick antiserum selecting HT2, HT4, HT8 and HT11 for inclusion into the novel cocktail vaccine. A further 4 HTs (HT1, HT12, HT14 and HT17) were added to the cocktail vaccine to ensure that the sequence variation among the HT protein family was encompassed in the formulation. A second trial comparing the cocktail of 8 HTs to a placebo group demonstrated complete protection from tick challenge. Here we report the first successful anti-venom vaccine protecting dogs from tick paralysis

Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley

The TREAT-NMD DMD Global Database: analysis of more than 7,000 Duchenne muscular dystrophy mutations.

Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations)

Crop Updates 2002 - Pulse Research and Industry Development in Western Australia

This session covers seventy one papers from different authors: 1. 2001 PULSE INDUSTRY HIGHLIGHTS CONTRIBUTORS BACKGROUND 2001 REGIONAL ROUNDUP 2. Northern Agricultural Region, M. Harries, Department of Agriculture 3. Central Agricultural Region, R. French and I. Pritchard, Department of Agriculture 4. Great Southern and Lakes, N. Brandon, N. Runciman and S. White, Department of Agriculture 5. Esperance Mallee, M. Seymour, Department of Agriculture PULSE PRODUCTION AGRONOMY AND GENETIC IMPROVEMENT 6. Faba bean, P. White, Department of Agriculture 7. Germplasm evaluation, P. White, M. Seymour and M. Harries, Department of Agriculture 8. Variety evaluation, P. White, M. Harries, N. Brandon and M. Seymour, Department of Agriculture 9. Sowing rate and time of sowing, P. White, N. Brandon, M. Seymour and M. Harries, Department of Agriculture 10.Use of granular inoculum in the Great Southern, N. Brandon1, J. Howieson2 and R. Yates2 1Department of Agriculture, 2Centre for Rhizobium Studies, Murdoch University 11.Tolerance to post emergent herbicides, M. Seymour and M. Harries, Department of Agriculture 12.Herbicide tolerance of new varieties, H. Dhammu and T. Piper, Department of Agriculture Desi chickpea 13. Breeding highlights, T. Khan, Department of Agriculture 14. Variety evaluation, T. Khan and K. Regan, Department of Agriculture 15. Effect of genotype and environment on seed quality, N. Suizu1 and D. Diepeveen2 1School of Public Health, Curtin University of Technology 2Department of Agriculture 16. Seed discolouration, C. Veitch and P. White, Department of Agriculture 17. Foliar application on N increases seed yield and seed protein under terminal drought, J. Palta1,2, A. Nandwal3 and N. Turner1,2 , 1CSIRO Plant Industry, 2CLIMA, the University of Western Australia, 3Department of Botany, Haryana Agric University, Hisar, India 18. Tolerance to chilling at flowering, H. Clarke, CLIMA, The University of Western Australia 19. Molecular studies of ascochyta blight disease in chickpea, G. Dwyer1, H. Loo1, T. Khan2, K. Siddique3, M. Bellgard1 and M. Jones1 ,1WA State Agricultural Biotechnology Centre and Centre for Bioinformatics and Biological Computing, Murdoch University, 2Department of Agriculture, 3CLIMA, The University of Western Australia 20. Effect of row spacing and sowing rate on seed yield, G. Riethmuller and B. MacLeod, Department of Agriculture 21. Herbicide tolerance on marginal soil types, H. Dhammu and T. Piper, Department of Agriculture 22. Kabuli chickpea, K. Regan, Department of Agriculture 23. Variety and germplasm evaluation, T. Khan and K. Regan, Department of Agriculture 24. Premium quality kabuli chickpea development in the ORIA, K. Siddique1, K. Regan2, R. Shackles2 and P. Smith2 , 1 CLIMA, The University of Western Australia, 2Department of Agriculture 25. Evaluation of ascochylta resistant germplasm from Syria and Turkey, K. Siddique1, C. Francis1 and K. Regan2, 1CLIMA, University of Western Australia 2Department of Agriculture Field pea 26. Breeding highlights, T. Khan Department of Agriculture 27. Variety evaluation, T. Khan Department of Agriculture 28. Comparing the phosphorus requirement of field pea and wheat, M. Bolland and P. White, Department of Agriculture 29. Tolerance of field pea to post emergent herbicides, M. Seymour and N. Brandon, Department of Agriculture 30. Response of new varieties to herbicides, H. Dhammu and T. Piper, Department of Agriculture 31. Lentil, K. Regan, Department of Agriculture 32. Variety evaluation, K. Regan, N. Brandon, M. Harries and M. Seymour, Department of Agriculture 33. Interstate evaluation of advanced breeding lines developed in WA, K. Regan1, K. Siddique2 and M. Materne3, 1Department of Agriculture, 2CLIMA, University of Western Australia, 3Victorian Institute for Dryland Agriculture, Agriculture Victoria 34. Evaluation of germplasm from overseas and local projects, K. Regan1, J. Clements2, K.H.M. Siddique2 and C. Francis21Department of Agriculture, 2CLIMA, University of Western Australia 35. Evaluation of breeding lines developed in WA, K. Regan1, J. Clements2, K.H.M. Siddique2 and C. Francis21Department of Agriculture, 2CLIMA, University of Western Australia 36. Productivity and yield stability in Australia and Nepal, C. Hanbury, K. Siddique and C. Francis, CLIMA, the University of Western Australia Vetch 37. Germplasm evaluation, M. Seymour1, R. Matic2 and M. Tate3, 1Department of Agriculture, 2South Australian Research and Development Institute, 3University of Adelaide, Waite Campus 38. Tolerance of common vetch to post emergent herbicides, M. Seymour and N. Brandon, Department of Agriculture Narbon bean 39. Removing narbon bean from wheat, M. Seymour, Department of Agriculture 40. Tolerance to low rates of Roundup and Sprayseed, M. Seymour, Department of Agriculture 41. Lathyrus development, C. Hanbury, CLIMA, the University of Western Australia 42. Poultry feeding trials, C. Hanbury1 and B. Hughes2 ,1CLIMA, the University of Western Australia,2Pig and Poultry Production Institute, South Australia Pulse Species 43. Species time of sowing, B. French, Department of Agriculture 44. High value pulses in the Great Southern, N. Brandon and N. Runciman, Department of Agriculture 45. Time of Harvest for improved seed yields of pulses, G. Riethmuller and B. French, Department of Agriculture 46. Phosphate acquisition efficiency of pulse crops, P. Rees, Plant Biology, Faculty of Natural and Agricultural Sciences UWA DEMONSTRATION OF PULSES IN THE FARMING SYSTEM 47. Howzat desi chickpea in the northern region, M. Harries, Department of Agriculture 48. Field pea harvest losses in the Great Southern and Esperance region, N. Brandon and M. Seymour, Department of Agriculture 49. Timing of crop topping in field pea, N. Brandon and G. Riethmuller, Department of Agriculture DISEASE AND PEST MANAGEMENT 50. Ascochyta blight of chickpea, B. MacLeod, M. Harries and N. Brandon, Department of Agriculture 51. Evaluation of Australian management packages, 52. Screening foliar fungicides 53. Row spacing and row spraying 54. Ascochyta management package for 2002, B. MacLeod, Department of Agriculture 55. Epidemiology of aschochyta and botrytis disease of pulses, J. Galloway and B. MacLeod, Department of Agriculture 56. Ascochyta blight of chickpea 57. Black spot of field pea 58. Ascochyta blight of faba bean 59. Ascochyta blight of lentil 60. Botrytis grey mould of chickpea 61. Black spot spread: Disease models are based in reality, J. Galloway, Department of Agriculture 62. Black spot spread: Scaling-up field data to simulate ‘Bakers farm’, M. Salam, J. Galloway, A. Diggle and B. MacLeod, Department of Agriculture 63. Pulse disease diagnostics, N. Burges and D. Wright, Department of Agriculture Viruses in pulses 64. Incidence of virus diseases in chickpea, J. Hawkes1, D. Thackray1 and R. Jones1,2, 1CLIMA, The University of Western Australia 2Department of Agriculture Insect pests 65. Risk assessment of aphid feeding damage on pulses, O. Edwards, J. Ridsdill-Smith, and R. Horbury, CSIRO Entomology 66. Optimum spray timing to control aphid feeding damage of faba bean, F. Berlandier, Department of Agriculture 67. Incorporation of pea weevil resistance into a field pea variety, O. Byrne1 and D. Hardie2, 1CLIMA, The University of Western Australia, 2Department of Agriculture 68. Screening wild chickpea species for resistance to Helicoverpa, T. Ridsdill-Smith1 and H. Sharma2,1CSIRO, Entomology, 2ICRISAT, Hyderabad 69. Field strategies to manage the evolution of pea weevil resistance in transgenic field pea, M. de Sousa Majer1, R. Roush2, D. Hardie3, R. Morton4 and T. Higgins4, 1Curtin University of Technology, 2Waite Campus, University of Adelaide, 3Department of Agriculture, 4CSIRO Plant Industry, Canberra 70. ACKNOWLEDGMENTS 71. Appendix 1: Summary of previous result

The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes

Background: The anaerobic spirochete Brachyspira pilosicoli colonizes the large intestine of various species of birds and mammals, including humans. It causes ''intestinal spirochetosis'', a condition characterized by mild colitis, diarrhea and reduced growth. This study aimed to sequence and analyse the bacterial genome to investigate the genetic basis of its specialized ecology and virulence. Methodology/Principal Findings: The genome of B. pilosicoli 95/1000 was sequenced, assembled and compared with that of the pathogenic Brachyspira hyodysenteriae and a near-complete sequence of Brachyspira murdochii. The B. pilosicoli genome was circular, composed of 2,586,443 bp with a 27.9 mol% G+C content, and encoded 2,338 genes. The three Brachyspira species shared 1,087 genes and showed evidence of extensive genome rearrangements. Despite minor differences in predicted protein functional groups, the species had many similar features including core metabolic pathways. Genes distinguishing B. pilosicoli from B. hyodysenteriae included those for a previously undescribed bacteriophage that may be useful for genetic manipulation, for a glycine reductase complex allowing use of glycine whilst protecting from oxidative stress, and for aconitase and related enzymes in the incomplete TCA cycle, allowing glutamate synthesis and function of the cycle during oxidative stress. B. pilosicoli had substantially fewer methyl-accepting chemotaxis genes than B. hyodysenteriae and hence these species are likely to have different chemotactic responses that may help to explain their different host range and colonization sites. B. pilosicoli lacked the gene for a new putative hemolysin identified in B. hyodysenteriae WA1. Both B. pilosicoli and B. murdochii lacked the rfbBADC gene cluster found on the B. hyodysenteriae plasmid, and hence were predicted to have different lipooligosaccharide structures. Overall, B. pilosicoli 95/1000 had a variety of genes potentially contributing to virulence. Conclusions/Significance: The availability of the complete genome sequence of B. pilosicoli 95/1000 will facilitate functional genomics studies aimed at elucidating host-pathogen interactions and virulence

De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes

Background Euphorbia fischeriana is an important medicinal plant found in Northeast China. The plant roots contain many medicinal compounds including 12-deoxyphorbol-13-acetate, commonly known as prostratin that is a phorbol ester from the tigliane diterpene series. Prostratin is a protein kinase C activator and is effective in the treatment of Human Immunodeficiency Virus (HIV) by acting as a latent HIV activator. Latent HIV is currently the biggest limitation for viral eradication. The aim of this study was to sequence, assemble and annotate the E. fischeriana transcriptome to better understand the potential biochemical pathways leading to the synthesis of prostratin and other related diterpene compounds. Results In this study we conducted a high throughput RNA-seq approach to sequence the root transcriptome of E. fischeriana. We assembled 18,180 transcripts, of these the majority encoded protein-coding genes and only 17 transcripts corresponded to known RNA genes. Interestingly, we identified 5,956 protein-coding transcripts with high similarity (>=75%) to Ricinus communis, a close relative to E. fischeriana. We also evaluated the conservation of E. fischeriana genes against EST datasets from the Euphorbeacea family, which included R. communis, Hevea brasiliensis and Euphorbia esula. We identified a core set of 1,145 gene clusters conserved in all four species and 1,487 E. fischeriana paralogous genes. Furthermore, we screened E. fischeriana transcripts against an in-house reference database for genes implicated in the biosynthesis of upstream precursors to prostratin. This identified 24 and 9 candidate transcripts involved in the terpenoid and diterpenoid biosyntehsis pathways, respectively. The majority of the candidate genes in these pathways presented relatively low expression levels except for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (HDS) and isopentenyl diphosphate/dimethylallyl diphosphate synthase (IDS), which are required for multiple downstream pathways including synthesis of casbene, a proposed precursor to prostratin. Conclusion The resources generated in this study provide new insights into the upstream pathways to the synthesis of prostratin and will likely facilitate functional studies aiming to produce larger quantities of this compound for HIV research and/or treatment of patients

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria

Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20–40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research