Taxonomy, phylogeny, and biodiversity of Lumbrineridae (Annelida, Polychaeta) from the Central Pacific Clarion-Clipperton Zone

The DNA taxonomy of six species of the annelid family Lumbrineridae collected from the Clarion-Clipperton Zone (CCZ) in the Central Pacific, an area of potential mining interest for polymetallic nodules, is presented. Lumbrinerids are an ecologically important and understudied annelid family within the deep sea, with many species still undescribed. This study aims to document the taxonomy and biodiversity of the CCZ using specimens collected from the UK-1, OMS, and NORI-D exploration contract areas and Areas of Particular Environmental Interest. Species were identified through a combination of morphological and molecular phylogenetic analysis. We present informal species descriptions associated with voucher specimens, accessible through the Natural History Museum (London) collections, to improve future taxonomic and biodiversity studies of this region. Five taxa in this study had no morphological or genetic matches within the literature and therefore are possibly new to science, but their suboptimal morphological preservation prevented the formalisation of new species. The most abundant taxon Lumbrinerides cf. laubieri (NHM_0020) was compared with the holotype of Lumbrinerides laubieri Miura, 1980 from the deep Northeast Atlantic. Currently no reliable morphological characters separating the Pacific and Atlantic specimens have been found and molecular data from the Atlantic specimens was not available.publishedVersio

EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders

BACKGROUND: Genomic variant prioritisation is one of the most significant bottlenecks to mainstream genomic testing in healthcare. Tools to improve precision while ensuring high recall are critical to successful mainstream clinical genomic testing, in particular for whole genome sequencing where millions of variants must be considered for each patient. METHODS: We developed EyeG2P, a publicly available database and web application using the Ensembl Variant Effect Predictor. EyeG2P is tailored for efficient variant prioritisation for individuals with inherited ophthalmic conditions. We assessed the sensitivity of EyeG2P in 1234 individuals with a broad range of eye conditions who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we assessed the precision of EyeG2P in comparison with routine diagnostic approaches. For 10 additional individuals, we assessed the utility of EyeG2P for whole genome analysis. RESULTS: EyeG2P had 99.5% sensitivity for genomic variants previously identified as clinically relevant through routine diagnostic analysis (n=1234 individuals). Prospectively, EyeG2P enabled a significant increase in precision (35% on average) in comparison with routine testing strategies (p<0.001). We demonstrate that incorporation of EyeG2P into whole genome sequencing analysis strategies can reduce the number of variants for analysis to six variants, on average, while maintaining high diagnostic yield. CONCLUSION: Automated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders

Crop updates 2006 - Farming Systems

This session covers nineteen papers from different authors: SOIL AND NUTRIENT MANAGEMENT 1. Inve$tigating fertili$er inve$tment, Wayne Pluske, Nutrient Management Systems 2. KASM, the potassium in Agricultural System Model,Bill Bowden and Craig Scanlan, DAWA Northam and UWA, School of Earth and Geographical Sciences 3. Long term productivity and economic benefits of subsurface acidity management from surface and subsurface liming, Stephen Davies, Chris Gazey and Peter Tozer, Department of Agriculture 4. Furrow and ridges to prevent waterlogging, Dr Derk Bakker, Department of Agriculture 5. Nitrous oxide emissions from a cropped soil in Western Australia, Louise Barton1, David Gatter2, Renee Buck1, Daniel Murphy1, Christoph Hinz1and Bill Porter2 1School of Earth and Geographical Sciences, The University of Western Australia, 2Department of Agriculture GROWER DECISIONS 6. Managing the unmanageable, Bill Bowden Department of Agriculture 7. Review of climate model summaries reported in Department of Agriculture’s Season Outlook, Meredith Fairbanks, Department of Agriculture 8. Mapping the frost risk in Western Australia, Nicolyn Short and Ian Foster, Department of Agriculture 9. .35 kg/ha.day and other myths, James Fisher, Doug Abrecht and Mario D’Antuono, Department of Agriculture 10. Gaining with growers – Lessons from a successful alliance of WA Grower Groups, Tracey M. Gianatti, Grower Group Alliance 11. WA Agribusiness Trial Network Roundup – 2005, Paul Carmody, Local Farmer Group Network, UWA 12. Drivers of no-till adoption, Frank D’Emdenabc, Rick Llewellynabdand Michael Burtonb,aCRC Australian Weed Management; bSchool of Agricultural and Resource Economics, UWA. cDepartment of Agriculture, dCSIRO Sustainable Ecosystems, Adelaide PRODUCTION SYSTEMS, PRECISION AGRICULTURE AND SUSTAINABILITY 13. Maintaining wheat and lupin yields using phase pastures and shielded sprayers to manage increasing herbicide resistance, Caroline Peek, Nadine Eva, Chris Carter and Megan Abrahams, Department of Agriculture 14. Analaysis of a wheat-pasture rotation in the 330mm annual rainfall zone using the STEP model, Andrew Blake and Caroline Peek, Department of Agriculture 15. Response to winter drought by wheat on shallow soil with low seeding rate and wide row spacing, Paul Blackwell1, Sylvain Pottier2and Bill Bowden1 1 Department of Agriculture; 2Esitpa (France) 16. How much yield variation do you need to justify zoning inputs? Michael Robertson and Greg Lyle, CSIRO Floreat, Bill Bowden, Department of Agriculture; Lisa Brennan, CSIRO Brisbane 17. Automatic guidance and wheat row position: On-row versus between-row seeding at various rates of banded P fertilisers, Tony J. Vyn1, Simon Teakle2, Peter Norris3and Paul Blackwell4,1Purdue University, USA; 2Landmark; 3Agronomy for Profit; 4 Department of Agriculture 18. Assessing the sustainability of high production systems (Avon Agricultural Systems Project), Jeff Russell and James Fisher, Department of Agriculture, Roy Murray-Prior and Deb Pritchard, Muresk Institute; Mike Collins, ex WANTFA, 19. The application of precision agriculture techniques to assess the effectiveness of raised beds on saline land in WA, Derk Bakker, Greg Hamilton, Rob Hetherington, Andrew Van Burgel and Cliff Spann, Department of Agricultur

Social responsiveness scale-aided analysis of the clinical impact of copy number variations in autism

Recent array-based studies have detected a wealth of copy number variations (CNVs) in patients with autism spectrum disorders (ASD). Since CNVs also occur in healthy individuals, their contributions to the patient’s phenotype remain largely unclear. In a cohort of children with symptoms of ASD, diagnosis of the index patient using ADOS-G and ADI-R was performed, and the Social Responsiveness Scale (SRS) was administered to the index patients, both parents, and all available siblings. CNVs were identified using SNP arrays and confirmed by FISH or array CGH. To evaluate the clinical significance of CNVs, we analyzed three families with multiple affected children (multiplex) and six families with a single affected child (simplex) in which at least one child carried a CNV with a brain-transcribed gene. CNVs containing genes that participate in pathways previously implicated in ASD, such as the phosphoinositol signaling pathway (PIK3CA, GIRDIN), contactin-based networks of cell communication (CNTN6), and microcephalin (MCPH1) were found not to co-segregate with ASD phenotypes. In one family, a loss of CNTN5 co-segregated with disease. This indicates that most CNVs may by themselves not be sufficient to cause ASD, but still may contribute to the phenotype by additive or epistatic interactions with inherited (transmitted) mutations or non-genetic factors. Our study extends the scope of genome-wide CNV profiling beyond de novo CNVs in sporadic patients and may aid in uncovering missing heritability in genome-wide screening studies of complex psychiatric disorders

IgG glycosylation changes and MBL2 polymorphisms:associations with markers of systemic inflammation and joint destruction in rheumatoid arthritis

Objective. To examine whether IgG glycosylation changes and MBL2 genotypes are associated with systemic inflammation and joint destruction in rheumatoid arthritis (RA). Methods. IgG N-glycan content was determined from serum in 118 patients with RA by high-throughput glycan analysis using normal-phase high-pressure liquid chromatography. MBL2 extended genotypes (YA/YA, YA/XA, XA/XA, YA/YO, XA/YO, YO/YO) were determined. Systemic inflammation was assessed by serum levels of C-reactive protein (CRP), interleukin 6 (IL-6), and tumor necrosis factor-α (TNF-α). Joint destruction was assessed by total Sharp score (TSS) and alloplastic surgery records. Results. IgG hypogalactosylation was significantly correlated to IL-6 (Spearman’s rho = 0.32, p < 0.001), CRP (Spearman’s rho = 0.31, p < 0.001), TSS (Spearman’s rho = 0.25, p = 0.01), and alloplastic replacement of joints (Spearman’s rho = 0.18, p = 0.05). In multivariate analysis including age, CRP, anticitrullinated protein antibodies (ACPA), and other confounders, IgG hypogalactosylation was significantly associated with TSS (p = 0.014) and alloplastic joint replacement (OR 76.5, p = 0.041) in patients homozygous for the high expression MBL2 genotype YA/YA, but not in carriers of lower expression genotypes. Conclusion. Decreased galactosylation of IgG correlated to markers of inflammation, i.e., IL-6 and CRP. Only in patients homozygous for high expression of the MBL2 genotype YA/YA was IgG hypogalactosylation associated with markers of joint destruction. Our results suggest that inflammation-associated decreased galactosylation of IgG combined with high expression MBL2 genotypes are involved in the pathophysiology of RA.No Full Tex