The epidemiology of the first wave of H1N1 influenza pandemic in Australia : a population-based study

Objectives: Following the recent H1N1 influenza pandemic we were able to describe seropositivity in a repre-sentative sample of adults prior to the availability of a specific vaccine.Methods: This cross-sectional serological study is set in the Barwon Statistical Division, Australia. Blood samples were collected from September 2009 through to May 2010, from 1184 individuals (569 men, 615 women; median age 61.7 years), randomly selected from electoral rolls. Serum was analysed for specific H1N1 immunity using a haemagglutina-tion inhibition test. A self-report provided information about symptoms, demographics and healthcare. Associations be-tween H1N1 infection, gender, households and occupation were determined using logistic regression, adjusting for age.Results: Of 1184 individuals, 129 (58 men, 71 women) were seropositive. Gender-adjusted age-specific prevalence was: 8.3% 20-29 years, 13.5% 30-39, 10.4% 40-49, 6.5% 50-59, 9.7% 60-69, 10.3% 70-79, 18.8% 80+. Standardised preva-lence was 10.3% (95%CI 9.6-11.0). No associations were detected between seropositivity and gender (OR=0.82, 95%CI 0.57-1.19) or being a healthcare worker (OR=1.43, 95%CI 0.62-3.29). Smokers (OR=1.86, 95%CI 1.09-3.15) and those socioeconomically disadvantaged (OR=2.52, 95%CI 1.24-5.13) were at increased risk. Among 129 seropositive individu-als, 31 reported symptoms that were either mild (n = 13) or moderate (time off work, doctor visit, n = 18). For age &lt;60, 39.6% of seropositive individuals reported symptoms, whereas the proportion was 13.2% for age 60+.Conclusions: Following the pandemic, the proportion of seropositive adults was low, but significant subclinical infection was found. Social disadvantage increased the likelihood of infection. The low symptom rate for older ages may relate to pre-existing immunity.<br /

Does an increase in body mass index over 10 years affect knee structure in a population-based cohort study of adult women?

Introduction : Although obesity is a modifiable risk factor for knee osteoarthritis (OA), the effect of weight gain on knee structure in young and healthy adults has not been examined. The aim of this study was to examine the relationship between body mass index (BMI), and change in BMI over the preceding 10-year period, and knee structure (cartilage defects, cartilage volume and bone marrow lesions (BMLs)) in a population-based sample of young to middle-aged females.Methods : One hundred and forty-two healthy, asymptomatic females (range 30 to 49 years) in the Barwon region of Australia, underwent magnetic resonance imaging (MRI) during 2006 to 2008. BMI measured 10 years prior (1994 to 1997), current BMI and change in BMI (accounting for baseline BMI) over this period, was assessed for an association with cartilage defects and volume, and BMLs.Results : After adjusting for age and tibial plateau area, the risk of BMLs was associated with every increase in one-unit of baseline BMI (OR 1.14 (95% CI 1.03 to 1.26) P = 0.009), current BMI (OR 1.13 (95% CI 1.04 to 1.23) P = 0.005), and per one unit increase in BMI (OR 1.14 (95% CI 1.03 to 1.26) P = 0.01). There was a trend for a one-unit increase in current BMI to be associated with increased risk of cartilage defects (OR 1.06 (95% CI 1.00 to 1.13) P = 0.05), and a suggestion that a one-unit increase in BMI over 10 years may be associated with reduced cartilage volume (-17.8 ml (95% CI -39.4 to 3.9] P = 0.10). Results remained similar after excluding those with osteophytes.Conclusions : This study provides longitudinal evidence for the importance of avoiding weight gain in women during early to middle adulthood as this is associated with increased risk of BMLs, and trend toward increased tibiofemoral cartilage defects. These changes have been shown to precede increased cartilage loss. Longitudinal studies will show whether avoiding weight gain in early adulthood may play an important role in diminishing the risk of knee OA.<br /

Glutamine repeat variants in human RUNX2 associated with decreased femoral neck BMD, broadband ultrasound attenuation and target gene transactivation

RUNX2 is an essential transcription factor required for skeletal development and cartilage formation. Haploinsufficiency of RUNX2 leads to cleidocranial displaysia (CCD) a skeletal disorder characterised by gross dysgenesis of bones particularly those derived from intramembranous bone formation. A notable feature of the RUNX2 protein is the polyglutamine and polyalanine (23Q/17A) domain coded by a repeat sequence. Since none of the known mutations causing CCD characterised to date map in the glutamine repeat region, we hypothesised that Q-repeat mutations may be related to a more subtle bone phenotype. We screened subjects derived from four normal populations for Q-repeat variants. A total of 22 subjects were identified who were heterozygous for a wild type allele and a Q-repeat variant allele: (15Q, 16Q, 18Q and 30Q). Although not every subject had data for all measures, Q-repeat variants had a significant deficit in BMD with an average decrease of 0.7SD measured over 12 BMD-related parameters (p = 0.005). Femoral neck BMD was measured in all subjects (&minus;0.6SD, p = 0.0007). The transactivation function of RUNX2 was determined for 16Q and 30Q alleles using a reporter gene assay. 16Q and 30Q alleles displayed significantly lower transactivation function compared to wild type (23Q). Our analysis has identified novel Q-repeat mutations that occur at a collective frequency of about 0.4%. These mutations significantly alter BMD and display impaired transactivation function, introducing a new class of functionally relevant RUNX2 mutants.<br /

Crop Updates - 2003 Lupins

This session covers twenty one papers from different authors LUPIN ISSUES AND R & D DIRECTIONS Mark Sweetingham, Department of Agriculture ACKNOWLEDGEMENTS VARIETIES AND BREEDING New lupin line for release – WALAN2141, Bevan J, Buirchell, Mark Sweetingham, Geoff Thomas, Amelia McLarty, Harmohinder Dhammu and CVT and Lupin Breeding teams, Department of Agriculture Lupin variety trial, Martin Harries and Wayne Parker, Department of Agriculture Herbicide tolerance of new lupins, Harmohinder S. Dhammu, Terry Piper and David Nicholson, Department of Agriculture YELLOW AND ALBUS LUPINS Selection for high lupin yield under terminal drought, Jairo A. Palta1&2, Neil C. Turner1&2 Bob French2&3 and Bevan Buirchell2&3 , 1CSIRO Plant Industry, Floreat, WA, 2CLIMA, University of Western Australia, Crawley, WA, 3Department of Agriculture Outcrossing and isolation distance in yellow lupins, Kedar Adhikari, Bevan Buirchell and Katia Stefanova, Department of Agriculture Development of aphid tolerant yellow lupins in Western Australia, Kedar Adhikari, Bevan Buirchell, Mark Sweetingham and Françoise Berlandier, Department of Agriculture ESTABLISHMENT Development of anthracnose resistant albus lupins for Western Australia, Kedar Adhikari, Bevan Buirchell, Mark Sweetingham and Geoff Thomas, Department of Agriculture Lupin sowing methods for improved yields, Glen Riethmuller, Department of Agriculture Moisture delving = more reliable lupin establishment, Paul Blackwell and Wayne Parker, Department of Agriculture Effect of time of sewing, plant density and row orientation on lupins at various row spacings, Geoff Fosbery, Farm Focus Consultants, Bill Crabtree, Crabtree Consulting and Tracy Gilham, WANTFA Influence of row spacing on water stress and water use of lupins, Bob French and Laurie Wahlsten, Department of Agriculture AGRONOMY Effect on lupin protein and yield from variety, planting time and seed rate, Pierre Fievez, Pierre Fievez and Associates Lupin row cropping: herbicides to band, shield design and economics, Mike Collins, WANTFA and John Holmes, 4 Farmers Harvest options for narrow leaf lupins, Martin Harries and Dirranie Kirby, Department of Agriculture NUTRITION Additional nutrients on lupin yield and protein, Pierre Fievez, Pierre Fievez and Associates Demonstrating the effect of phosphorous placement on yields of narrow leaf lupin and yellow lupin on high phosphorus retention soils, Martin Harries and Wayne Parker, Department of Agriculture PESTS AND DISEASES How far are anthracnose spores spread by rain splash? Geoff Thomas, Mark Sweetingham and Ken Adcock, Department of Agriculture Height of cereal stubble affects spread of lupin anthracnose, Geoff Thomas, Bill MacLeod and Ken Adcock, Department of Agriculture Controlling non-necrotic strains of bean yellow mosaic virus in lupins by cultural methods, Roger Jones and Rohan Prince, Department of Agriculture, and Centre for Legumes in Mediterranean Agriculture MARKET DEVELOPMENT Australian sweet lupin – is it the next human health food? Stuart Johnson, Deakin University; Ramon Hall, ARC SPIRT PhD Scholar; Madeleine Ball, University of Tasmania; Sofia Sipsas and David Petterson; Department of Agriculture CONTACT DETAILS FOR PRINCIPAL AUTHOR

The Southern Ocean mixed layer and its boundary fluxes: Fine-scale observational progress and future research priorities

Interactions between the upper ocean and air-ice-ocean fluxes in the Southern Ocean play a critical role in global climate by impacting the overturning circulation and oceanic heat and carbon uptake. Remote and challenging conditions have led to sparse observational coverage, while ongoing field programmes often fail to collect sufficient information in the right place or at the time-space scales required to constrain the variability occurring in the coupled ocean-atmosphere system. Only within the last 10 years have we been able to directly observe and assess the role of the fine-scale ocean and rapidly evolving atmospheric marine boundary layer on the upper limb of the Southern Ocean's overturning circulation. This review summarizes advances in mechanistic understanding, arising in part from observational programmes using autonomous platforms, of the fine-scale processes (1-100 km, hours-seasons) influencing the Southern Ocean mixed layer and its variability. We also review progress in observing the ocean interior connections and the coupled interactions between the ocean, atmosphere and cryosphere that moderate air-sea fluxes of heat and carbon. Most examples provided are for the ice-free Southern Ocean, while major challenges remain for observing the ice-covered ocean. We attempt to elucidate contemporary research gaps and ongoing/future efforts needed to address them. This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'

Rapid semi-automated quantitative multiplex tandem PCR (MT-PCR) assays for the differential diagnosis of influenza-like illness

<p>Abstract</p> <p>Background</p> <p>Influenza A, including avian influenza, is a major public health threat in developed and developing countries. Rapid and accurate detection is a key component of strategies to contain spread of infection, and the efficient diagnosis of influenza-like-illness is essential to protect health infrastructure in the event of a major influenza outbreak.</p> <p>Methods</p> <p>We developed a multiplexed PCR (MT-PCR) assay for the simultaneous diagnosis of respiratory viruses causing influenza-like illness, including the specific recognition of influenza A haemagglutinin subtypes H1, H3, and H5. We tested several hundred clinical specimens in two diagnostic reference laboratories and compared the results with standard techniques.</p> <p>Results</p> <p>The sensitivity and specificity of these assays was higher than individual assays based on direct antigen detection and standard PCR against a range of control templates and in several hundred clinical specimens. The MT-PCR assays provided differential diagnoses as well as potentially useful quantitation of virus in clinical samples.</p> <p>Conclusions</p> <p>MT-PCR is a potentially powerful tool for the differential diagnosis of influenza-like illness in the clinical diagnostic laboratory.</p

Crop Updates 2005 - Cereals

This session covers thirty six papers from different authors: WHEAT AGRONOMY 1. Optimum sowing time of new wheat varieties in Western Australia, Darshan Sharma, Brenda Shackley, Mohammad Amjad, Christine M. Zaicou-Kunesch and Wal Anderson, Department of Agriculture 2. Wheat varieties updated in ‘Flowering Calculator’: A model predicting flowering time, B. Shackley, D. Tennant, D. Sharma and C.M. Zaicou-Kunesch, Department of Agriculture 3. Plant populations for wheat varieties, Christine M. Zaicou-Kunesch, Wal Anderson, Darshan Sharma, Brenda Shackley and Mohammad Amjad, Department of Agriculture 4. New wheat cultivars response to fertiliser nitrogen in four major agricultural regions of Western Australia, Mohammad Amjad, Wal Anderson, Brenda Shackley, Darshan Sharma and Christine Zaicou-Kunesch, Department of Agriculture 5. Agronomic package for EGA Eagle Rock, Steve Penny, Department of Agriculture 6. Field evaluation of eastern and western wheats in large-scale farmer’s trials, Mohammad Amjad, Ben Curtis and Veronika Reck, Department of Agriculture 7. New wheat varieties for a changing environment, Richard Richards, CSIRO Plant Industry; Canberra 8. Farmers can profitably minimise exposure to frost! Garren Knell, Steve Curtin and David Sermon, ConsultAg 9. National Variety Trials, Alan Bedggood, Australian Crops Accreditation System; Horsham 10. Preharvest-sprouting tolerance of wheat in the field, T.B. Biddulph1, T.L. Setter2, J.A. Plummer1 and D.J. Mares3; 1Plant Biology; FNAS, University of Western Australia; 2Department of Agriculture, 3School of Agriculture and Wine, University of Adelaide 11. Waterlogging induces high concentration of Mn and Al in wheat genotypes in acidic soils, H. Khabaz-Saberi, T. Setter, I. Waters and G. McDonald, Department of Agriculture 12. Agronomic responses of new wheat varieties in the Northern Agricultural Region, Christine M. Zaicou-Kunesch and Wal Anderson, Department of Agriculture 13. Agronomic responses of new wheat varieties in the Central Agricultural Region of WA, Darshan Sharma, Steve Penny and Wal Anderson, Department of Agriculture 14. EGA Eagle Rock tolerance to metribuzin and its mixtures, Harmohinder Dhammu, David Nicholson and Chris Roberts, Department of Agriculture 15. Herbicide tolerance of new bread wheats, Harmohinder Dhammu1 and David Nicholson2, Department of Agriculture NUTRITION 16. The impact of fertiliser placement, timing and rates on nitrogen-use efficiency, Stephen Loss, CSBP Ltd 17. Cereals deficient in potassium are most susceptible to some leaf diseases, Ross Brennan and Kith Jayasena, Department of Agriculture 18. Responses of cereal yields to potassium fertiliser type, placement and timing, Eddy Pol, CSBP Limited 19. Sulphate of Potash, the potash of choice at seeding, Simon Teakle, United Farmers Co-operative 20. Essential disease management for successful barley production, K. Jayasena, R. Loughman, C. Beard, B. Paynter, K. Tanaka, G. Poulish and A. Smith, Department of Agriculture 21. Genotypic differences in potassium efficiency of wheat, Paul Damon and Zed Rengel, Faculty of Natural and Agricultural Sciences, University of Western Australia 22. Genotypic differences in potassium efficiency of barley, Paul Damon and Zed Rengel, Faculty of Natural and Agricultural Sciences, University of Western Australia 23. Investigating timing of nitrogen application in wheat, Darshan Sharma and Lionel Martin, Department of Agriculture, and Muresk Institute of Agriculture, Curtin University of Technology 24. Nutrient timing requirements for increased crop yields in the high rainfall cropping zone, Narelle Hill, Ron McTaggart, Dr Wal Anderson and Ray Tugwell, Department of Agriculture DISEASES 25. Integrate strategies to manage stripe rust risk, Geoff Thomas, Robert Loughman, Ciara Beard, Kith Jayasena and Manisha Shankar, Department of Agriculture 26. Effect of primary inoculum level of stripe rust on variety response in wheat, Manisha Shankar, John Majewski and Robert Loughman, Department of Agriculture 27. Disease resistance update for wheat varieties in WA, M. Shankar, J.M. Majewski, D. Foster, H. Golzar, J. Piotrowski and R. Loughman, Department of Agriculture 28. Big droplets for wheat fungicides, Rob Grima, Agronomist, Elders 29. On farm research to investigate fungicide applications to minimise leaf disease impacts in wheat, Jeff Russell and Angie Roe, Department of Agriculture, and Farm Focus Consultants PESTS 30. Rotations for nematode management, Vivien A. Vanstone, Sean J. Kelly, Helen F. Hunter and Mena C. Gilchrist, Department of Agriculture 31. Investigation into the adaqyacy of sealed farm silos in Western Australia to control phosphine-resistant Rhyzopertha dominica, C.R. Newman, Department of Agriculture 32.Insect contamination of cereal grain at harvest, Svetlana Micic and Phil Michael, Department of Agriculture 33. Phosure – Extending the life of phosphine, Gabrielle Coupland and Ern Kostas, Co-operative Bulk Handling SOIL 34. Optimum combinations of ripping depth and tine spacing for increasing wheat yield, Mohammed Hamza and Wal Anderson, Department of Agriculture 35. Hardpan penetration ability of wheat roots, Tina Botwright Acuña and Len Wade, School of Plant Biology, University of Western Australia MARKETS 36. Latin America: An emerging agricultural powerhouse, Ingrid Richardson, Food and Agribusiness Research, Rabobank; Sydne

Somatic cancer genetics in the UK: real-world data from phase I of the Cancer Research UK Stratified Medicine Programme

Introduction: Phase I of the Cancer Research UK Stratified Medicine Programme (SMP1) was designed to roll out molecular pathology testing nationwide at the point of cancer diagnosis, as well as facilitate an infrastructure where surplus cancer tissue could be used for research. It offered a non-trial setting to examine common UK cancer genetics in a real-world context. Methods: A total of 26 sites in England, Wales and Scotland, recruited samples from 7814 patients for genetic examination between 2011 and 2013. Tumour types involved were breast, colorectal, lung, prostate, ovarian cancer and malignant melanoma. Centralised molecular testing of surplus material from resections or biopsies of primary/metastatic tissue was performed, with samples examined for 3–5 genetic alterations deemed to be of key interest in site-specific cancers by the National Cancer Research Institute Clinical Study groups. Results: 10 754 patients (98% of those approached) consented to participate, from which 7814 tumour samples were genetically analysed. In total, 53% had at least one genetic aberration detected. From 1885 patients with lung cancer, KRAS mutation was noted to be highly prevalent in adenocarcinoma (37%). In breast cancer (1873 patients), there was a striking contrast in TP53 mutation incidence between patients with ductal cancer (27.3%) and lobular cancer (3.4%). Vast inter-tumour heterogeneity of colorectal cancer (1550 patients) was observed, including myriad double and triple combinations of genetic aberrations. Significant losses of important clinical information included smoking status in lung cancer and loss of distinction between low-grade and high-grade serous ovarian cancers. Conclusion: Nationwide molecular pathology testing in a non-trial setting is feasible. The experience with SMP1 has been used to inform ongoing CRUK flagship programmes such as the CRUK National Lung MATRIX trial and TRACERx

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data