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1. Assessment and Constraint of Mesozooplankton in CMIP6 Earth System Models

Author

Petrik, CM, Luo, JY, Heneghan, RF, Everett, JD, Harrison, CS, and Richardson, AJ

Subjects
Life Below Water, Climate Action, biogeochemical modeling, Earth system modeling, ecosystem modeling, emergent constraint, impacts of global change, zooplankton, Atmospheric Sciences, Geochemistry, Oceanography, Meteorology & Atmospheric Sciences
Published
2022

2. Pushing the limits in marine species distribution modelling: lessons from the land present challenges and opportunities

Author

Robinson, LM, Elith, J, Hobday, AJ, Pearson, RG, Kendall, BE, Possingham, HP, and Richardson, AJ

Subjects
Life Below Water, Aggregation, bioclimatic envelope model, competition, dispersal, ecological niche modelling, feeding, marine/terrestrial systems, ontogenetic shifts, prey, species distribution model, Physical Geography and Environmental Geoscience, Ecological Applications, Ecology
Abstract

Aim Species distribution models (SDMs) have been used to address a wide range of theoretical and applied questions in the terrestrial realm, but marine-based applications remain relatively scarce. In this review, we consider how conceptual and practical issues associated with terrestrial SDMs apply to a range of marine organisms and highlight the challenges relevant to improving marine SDMs. Location We include studies from both marine and terrestrial systems that encompass many geographic locations around the globe. Methods We first performed a literature search and analysis of marine and terrestrial SDMs in ISI Web of Science to assess trends and applications. Using knowledge from terrestrial applications, we critically evaluate the application of SDMs in marine systems in the context of ecological factors (dispersal, species interactions, aggregation and ontogenetic shifts) and practical considerations (data quality, alternative modelling approaches and model validation) that facilitate or create difficulties for model application. Results The relative importance of ecological factors to be considered when applying SDMs varies among terrestrial and marine organisms. Correctly incorporating dispersal is frequently considered an important issue for terrestrial models, but because there is greater potential for dispersal in the ocean, it is often less of a concern in marine SDMs. By contrast, ontogenetic shifts and feeding have received little attention in terrestrial SDM applications, but these factors are important to many marine SDMs. Opportunities also exist for applying more advanced SDM approaches in the marine realm, including mechanistic ecophysiological models, where water balance and heat transfer equations are simpler for some marine organisms relative to their terrestrial counterparts. Main conclusions SDMs have generally been under-utilized in the marine realm relative to terrestrial applications. Correlative SDM methods should be tested on a range of marine organisms, and we suggest further development of methods that address ontogenetic shifts and feeding interactions. We anticipate developments in, and cross-fertilization between, coupled correlative and process-based SDMs, mechanistic eco-physiological SDMs, and spatial population dynamic models for climate change and species invasion applications in particular. Comparisons of the outputs of different model types will provide insight that is useful for improved spatial management of marine species. © 2011 Blackwell Publishing Ltd.

Published
2011

3. Priorities for synthesis research in ecology and environmental science

Author

Halpern, BS, Halpern, BS, Boettiger, C, Dietze, MC, Gephart, JA, Gonzalez, P, Grimm, NB, Groffman, PM, Gurevitch, J, Hobbie, SE, Komatsu, KJ, Kroeker, KJ, Lahr, HJ, Lodge, DM, Lortie, CJ, Lowndes, JSS, Micheli, F, Possingham, HP, Ruckelshaus, MH, Scarborough, C, Wood, CL, Wu, GC, Aoyama, L, Arroyo, EE, Bahlai, CA, Beller, EE, Blake, RE, Bork, KS, Branch, TA, Brown, NEM, Brun, J, Bruna, EM, Buckley, LB, Burnett, JL, Castorani, MCN, Cheng, SH, Cohen, SC, Couture, JL, Crowder, LB, Dee, LE, Dias, AS, Diaz-Maroto, IJ, Downs, MR, Dudney, JC, Ellis, EC, Emery, KA, Eurich, JG, Ferriss, BE, Fredston, A, Furukawa, H, Gagné, SA, Garlick, SR, Garroway, CJ, Gaynor, KM, González, AL, Grames, EM, Guy-Haim, T, Hackett, E, Hallett, LM, Harms, TK, Haulsee, DE, Haynes, KJ, Hazen, EL, Jarvis, RM, Jones, K, Kandlikar, GS, Kincaid, DW, Knope, ML, Koirala, A, Kolasa, J, Kominoski, JS, Koricheva, J, Lancaster, LT, Lawlor, JA, Lowman, HE, Muller-Karger, FE, Norman, KEA, Nourn, N, O'Hara, CC, Ou, SX, Padilla-Gamino, JL, Pappalardo, P, Peek, RA, Pelletier, D, Plont, S, Ponisio, LC, Portales-Reyes, C, Provete, DB, Raes, EJ, Ramirez-Reyes, C, Ramos, I, Record, S, Richardson, AJ, Salguero-Gómez, R, Satterthwaite, EV, Schmidt, C, Schwartz, AJ, See, CR, Shea, BD, Smith, RS, Sokol, ER, Halpern, BS, Halpern, BS, Boettiger, C, Dietze, MC, Gephart, JA, Gonzalez, P, Grimm, NB, Groffman, PM, Gurevitch, J, Hobbie, SE, Komatsu, KJ, Kroeker, KJ, Lahr, HJ, Lodge, DM, Lortie, CJ, Lowndes, JSS, Micheli, F, Possingham, HP, Ruckelshaus, MH, Scarborough, C, Wood, CL, Wu, GC, Aoyama, L, Arroyo, EE, Bahlai, CA, Beller, EE, Blake, RE, Bork, KS, Branch, TA, Brown, NEM, Brun, J, Bruna, EM, Buckley, LB, Burnett, JL, Castorani, MCN, Cheng, SH, Cohen, SC, Couture, JL, Crowder, LB, Dee, LE, Dias, AS, Diaz-Maroto, IJ, Downs, MR, Dudney, JC, Ellis, EC, Emery, KA, Eurich, JG, Ferriss, BE, Fredston, A, Furukawa, H, Gagné, SA, Garlick, SR, Garroway, CJ, Gaynor, KM, González, AL, Grames, EM, Guy-Haim, T, Hackett, E, Hallett, LM, Harms, TK, Haulsee, DE, Haynes, KJ, Hazen, EL, Jarvis, RM, Jones, K, Kandlikar, GS, Kincaid, DW, Knope, ML, Koirala, A, Kolasa, J, Kominoski, JS, Koricheva, J, Lancaster, LT, Lawlor, JA, Lowman, HE, Muller-Karger, FE, Norman, KEA, Nourn, N, O'Hara, CC, Ou, SX, Padilla-Gamino, JL, Pappalardo, P, Peek, RA, Pelletier, D, Plont, S, Ponisio, LC, Portales-Reyes, C, Provete, DB, Raes, EJ, Ramirez-Reyes, C, Ramos, I, Record, S, Richardson, AJ, Salguero-Gómez, R, Satterthwaite, EV, Schmidt, C, Schwartz, AJ, See, CR, Shea, BD, Smith, RS, and Sokol, ER

Abstract

Synthesis research in ecology and environmental science improves understanding, advances theory, identifies research priorities, and supports management strategies by linking data, ideas, and tools. Accelerating environmental challenges increases the need to focus synthesis science on the most pressing questions. To leverage input from the broader research community, we convened a virtual workshop with participants from many countries and disciplines to examine how and where synthesis can address key questions and themes in ecology and environmental science in the coming decade. Seven priority research topics emerged: (1) diversity, equity, inclusion, and justice (DEIJ), (2) human and natural systems, (3) actionable and use-inspired science, (4) scale, (5) generality, (6) complexity and resilience, and (7) predictability. Additionally, two issues regarding the general practice of synthesis emerged: the need for increased participant diversity and inclusive research practices; and increased and improved data flow, access, and skill-building. These topics and practices provide a strategic vision for future synthesis in ecology and environmental science.

Published
2023

4. The Long road home : repatriation in Tasmania, 1916-1929

Author

Richardson, AJ

Subjects
Australian history
Abstract

This thesis examines the work of repatriation authorities in Tasmania after WWI, the returned soldiers' responses to the system, and the experiences of both the soldiers and the authorities in re-establishing returned men into society. Repatriation was one of the great problems facing Australian administrators after the Great War. The need to provide for the large numbers of returning soldiers and cater for their re-establishment into society was one of the most costly programs undertaken by the Commonwealth. Pryor, Lloyd, Rees, and Garton have all examined repatriation in Australia in a national context, while other authors have considered select repatriation policies on a regional basis. However, previous historians have failed to investigate the specific Tasmanian context of major Commonwealth repatriation policies such as the soldier land settlement scheme, employment, health services, and the political dimension of repatriation. This thesis focuses on the Tasmanian context to enable some comparison where applicable with Commonwealth outcomes of repatriation. To provide comparison and to examine repatriation policy and its implementation in Tasmania, this thesis focuses on the design and implementation of Commonwealth Repatriation poI icy during the latter half of the war, and assesses a decade of its post war performance of, in particular, policies such as health and employment. Returned soldiers' abilities to reassimilate successfully into the community were determined by two main factors. Firstly, Commonwealth health policy, treatment, and subsequent pensions were crucial to Tasmanian returned soldiers who suffered injuries caused or aggravated by their war service. Secondly and even more important was the need for meaningful employment and vocational opportunities and training. Employment and vocational training for returned men had the most immediate impact on their abilities to re-engage with society and support families; hence it was crucial to the success in their efforts to repatriate. One form of employment involved the Returned Soldier Land Settlement Scheme. It illustrated the provision of employment and vocational opportunities in Tasmania, and it suffered the highest failure rates in the Commonwealth in terms of soldiers vacated and of losses per head. Through the examination of legislation, departmental correspondence, individual cases, media reports and a State Royal Commission, the path of the scheme in Tasmania is explored. In understanding the design and implementation of Commonwealth repatriation polices and local responses to it, Tasmania's unique social and regional needs are highlighted. Repatriation in Tasmania largely confirms the broader national experience with some exceptions based on the State's comparatively isolated location, with the conclusion that Commonwealth policies. while at times adequate, could not hope to satisfy all the needs of the Tasmanian returned soldier.

Published
2023
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5. A global horizon scan of issues impacting marine and coastal biodiversity conservation

Author

Herbert-Read, JE, Thornton, A, Amon, DJ, Birchenough, SNR, Côté, IM, Dias, MP, Godley, BJ, Keith, SA, McKinley, E, Peck, LS, Calado, R, Defeo, O, Degraer, S, Johnston, EL, Kaartokallio, H, Macreadie, Peter, Metaxas, A, Muthumbi, AWN, Obura, DO, Paterson, DM, Piola, AR, Richardson, AJ, Schloss, IR, Snelgrove, PVR, Stewart, BD, Thompson, PM, Watson, GJ, Worthington, TA, Yasuhara, M, Sutherland, WJ, Herbert-Read, JE, Thornton, A, Amon, DJ, Birchenough, SNR, Côté, IM, Dias, MP, Godley, BJ, Keith, SA, McKinley, E, Peck, LS, Calado, R, Defeo, O, Degraer, S, Johnston, EL, Kaartokallio, H, Macreadie, Peter, Metaxas, A, Muthumbi, AWN, Obura, DO, Paterson, DM, Piola, AR, Richardson, AJ, Schloss, IR, Snelgrove, PVR, Stewart, BD, Thompson, PM, Watson, GJ, Worthington, TA, Yasuhara, M, and Sutherland, WJ

Published
2022

6. A global, historical database of tuna, billfish, and saury larval distributions

Author

Buenafe, KCV, Everett, JD, Dunn, DC, Mercer, J, Suthers, IM, Schilling, HT, Hinchliffe, C, Dabalà, A, Richardson, AJ, Buenafe, KCV, Everett, JD, Dunn, DC, Mercer, J, Suthers, IM, Schilling, HT, Hinchliffe, C, Dabalà, A, and Richardson, AJ

Abstract

Knowing the distribution of fish larvae can inform fisheries science and resource management in several ways by 1 providing information on spawning areas 2 identifying key areas to manage and conserve and 3 helping to understand how fish populations are affected by anthropogenic pressures such as overfishing and climate change With the expansion of industrial fishing activity after 1945 there was increased sampling of fish larvae to help better understand variation in fish stocks However large scale larval records are rare and often unavailable Here we digitize data from Nishikawa et al 1985 which were collected from 1956 1981 and are near global 50 N 50 S seasonal distribution maps of fish larvae of 18 mainly commercial pelagic taxa of the families Scombridae Xiphiidae Istiophoridae Scombrolabracidae and Scomberesocidae Data were collected from the Pacific Atlantic and Indian Oceans We present four seasonal 1 1 resolution maps per taxa representing larval abundance per grid cell and highlight some of the main patterns Data are made available as delimited text raster and vector files 2022 The Author s

Published
2022

8. Effect of a Once in 100-Year Flood on a Subtropical Coastal Phytoplankton Community

Author

Clementson, LA, Richardson, AJ, Rochester, WA, Oubelkheir, K, Liu, B, D’Sa, EJ, Gusmão, LFM, Ajani, P, Schroeder, T, Ford, PW, Burford, MA, Saeck, E, and Steven, ADL

Subjects
fungi, 0405 Oceanography, 0602 Ecology
Abstract

© Copyright © 2021 Clementson, Richardson, Rochester, Oubelkheir, Liu, D’Sa, Gusmão, Ajani, Schroeder, Ford, Burford, Saeck and Steven. Subtropical systems experience occasional severe floods, dramatically altering the phytoplankton community structure, in response to changes in salinity, nutrients, and light. This study examined the effects of a 1:100 year summer flood on the phytoplankton community in an Australian subtropical bay – Moreton Bay – over 48 weeks, from January to December 2011. Immediately after maximum flood levels were reached on the rivers flowing into the bay, the lowest salinity, and highest turbidity values, in more than a decade, were measured in the Bay and the areal extent of the flood-related parameters was also far greater than previous flood events. Changes in these parameters together with changes in Colored Dissolved Organic Matter (CDOM) and sediment concentrations significantly reduced the light availability within the water column. Despite the reduced light availability, the phytoplankton community responded rapidly (1–2 weeks) to the nutrients from flood inputs, as measured using pigment concentrations and cell counts and observed in ocean color satellite imagery. Initially, the phytoplankton community was totally dominated by micro-phytoplankton, particularly diatoms; however, in the subsequent weeks (up to 48-weeks post flood) the community changed to one of nano- and pico-plankton in all areas of the Bay not usually affected by river flow. This trend is consistent with many other studies that show the ability of micro-phytoplankton to respond rapidly to increased nutrient availability, stimulating their growth rates. The results of this study suggest that one-off extreme floods have immediate, but short-lived effects, on phytoplankton species composition and biomass as a result of the interacting and dynamic effects of changes in nutrient and light availability.

Published
2021

10. Mutualism promotes site selection in a large marine planktivore

Author

Armstrong, AO, Armstrong, AJ, Bennett, MB, Richardson, AJ, Townsend, KA, Everett, JD, Hays, Graeme, Pederson, H, Dudgeon, CL, Armstrong, AO, Armstrong, AJ, Bennett, MB, Richardson, AJ, Townsend, KA, Everett, JD, Hays, Graeme, Pederson, H, and Dudgeon, CL

Published
2021

11. A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus

Author

Hardcastle, AJ, Liskova, P, Bykhovskaya, Y, McComish, BJ, Davidson, AE, Inglehearn, CF, Li, X, Choquet, H, Habeeb, M, Lucas, SEM, Sahebjada, S, Pontikos, N, Lopez, KER, Khawaja, AP, Ali, M, Dudakova, L, Skalicka, P, Van Dooren, BTH, Geerards, AJM, Haudum, CW, Lo Faro, V, Tenen, A, Simcoe, MJ, Patasova, K, Yarrand, D, Yin, J, Siddiqui, S, Rice, A, Farraj, LA, Chen, Y-DI, Rahi, JS, Krauss, RM, Theusch, E, Charlesworth, JC, Szczotka-Flynn, L, Toomes, C, Meester-Smoor, MA, Richardson, AJ, Mitchell, PA, Taylor, KD, Melles, RB, Aldave, AJ, Mills, RA, Cao, K, Chan, E, Daniell, MD, Wang, JJ, Rotter, JI, Hewitt, AW, MacGregor, S, Klaver, CCW, Ramdas, WD, Craig, JE, Iyengar, SK, O'Brart, D, Jorgenson, E, Baird, PN, Rabinowitz, YS, Burdon, KP, Hammond, CJ, Tuft, SJ, Hysi, PG, Hardcastle, AJ, Liskova, P, Bykhovskaya, Y, McComish, BJ, Davidson, AE, Inglehearn, CF, Li, X, Choquet, H, Habeeb, M, Lucas, SEM, Sahebjada, S, Pontikos, N, Lopez, KER, Khawaja, AP, Ali, M, Dudakova, L, Skalicka, P, Van Dooren, BTH, Geerards, AJM, Haudum, CW, Lo Faro, V, Tenen, A, Simcoe, MJ, Patasova, K, Yarrand, D, Yin, J, Siddiqui, S, Rice, A, Farraj, LA, Chen, Y-DI, Rahi, JS, Krauss, RM, Theusch, E, Charlesworth, JC, Szczotka-Flynn, L, Toomes, C, Meester-Smoor, MA, Richardson, AJ, Mitchell, PA, Taylor, KD, Melles, RB, Aldave, AJ, Mills, RA, Cao, K, Chan, E, Daniell, MD, Wang, JJ, Rotter, JI, Hewitt, AW, MacGregor, S, Klaver, CCW, Ramdas, WD, Craig, JE, Iyengar, SK, O'Brart, D, Jorgenson, E, Baird, PN, Rabinowitz, YS, Burdon, KP, Hammond, CJ, Tuft, SJ, and Hysi, PG

Abstract

Keratoconus is characterised by reduced rigidity of the cornea with distortion and focal thinning that causes blurred vision, however, the pathogenetic mechanisms are unknown. It can lead to severe visual morbidity in children and young adults and is a common indication for corneal transplantation worldwide. Here we report the first large scale genome-wide association study of keratoconus including 4,669 cases and 116,547 controls. We have identified significant association with 36 genomic loci that, for the first time, implicate both dysregulation of corneal collagen matrix integrity and cell differentiation pathways as primary disease-causing mechanisms. The results also suggest pleiotropy, with some disease mechanisms shared with other corneal diseases, such as Fuchs endothelial corneal dystrophy. The common variants associated with keratoconus explain 12.5% of the genetic variance, which shows potential for the future development of a diagnostic test to detect susceptibility to disease.

Published
2021

13. Do age-related macular degeneration genes show association with keratoconus?

Author

Cao, K, Sahebjada, S, Richardson, AJ, Baird, PN, Cao, K, Sahebjada, S, Richardson, AJ, and Baird, PN

Abstract

BACKGROUND: Keratoconus (KC) is a common corneal condition with an unknown gender predominance. Although numerous studies have investigated the genetic component of KC, no specific genes have yet been attributed to the condition. We recently reported posterior segment changes occurring in the eyes of KC patients. However, it is not clear whether these changes are part of KC pathogenesis or reflect changes in anatomical features of the eye manifested by changes at the cornea. Given retinal changes represent the main characteristics observed in age-related macular degeneration (AMD) and that pleiotropy has been demonstrated between different eye diseases, we wished to assess if known AMD associated genes were also associated with KC. METHODS: A total of 248 KC subjects and 366 non-KC (control) subjects were recruited from public and private clinics in Melbourne for this analysis. Nineteen single nucleotide polymorphisms (SNPs) previously associated with AMD, including rs10490924 (ARMS2/HTRA1), rs10737680 (CFH), rs13278062 (TNFRSF10A), rs1864163 (CETP), rs2230199 (C3), rs3130783 (IER3/DDR1), rs334353 (TGFBR1), rs3812111 (COL10A1), rs429608 (C2/CFB), rs4420638 (APOE), rs4698775 (CFI), rs5749482 (TIMP3), rs6795735 (ADAMTS9), rs8017304 (RAD51B), rs8135665 (SLC16A8), rs920915 (LIPC), rs943080 (VEGFA), rs9542236 (B3GALTL) and rs13081855 (COL8A1/FILIP1L), were genotyped in this cohort. Logistic regression was applied to evaluate the association between these SNPs and KC on both genders together, as well as each gender separately. Linear regression was also applied to assess the association between SNPs and corneal curvature. Bonferroni correction was applied to adjust for multiple testing. RESULTS: Genotyping data were available for 18 SNPs. The SNP, rs6795735 (ADAMTS9) was significantly associated with KC (p = 3.5 × 10- 4) when both genders were assessed, whereas rs5749482 (TIMP3) was only associated in males (p = 7.7 × 10- 4) following Bonferroni multiple correction. Howev

Published
2019

14. Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration

Author

Waksmunski, AR, Grunin, M, Kinzy, TG, Igo, RP, Haines, JL, Bailey, JNC, Fritsche, LG, Igl, W, Grassmann, F, Sengupta, S, Bragg-Gresham, JL, Burdon, KP, Hebbring, SJ, Wen, C, Gorski, M, Kim, IK, Cho, D, Zack, D, Souied, E, Scholl, HPN, Bala, E, Lee, KE, Hunter, DJ, Sardell, RJ, Mitchell, P, Merriam, JE, Cipriani, V, Hoffman, JD, Schick, T, Lechanteur, YTE, Guymer, RH, Johnson, MP, Jiang, Y, Stanton, CM, Buitendijk, GHS, Zhan, X, Kwong, AM, Boleda, A, Brooks, M, Gieser, L, Ratnapriya, R, Branham, KE, Foerster, JR, Heckenlively, JR, Othman, M, Vote, BJ, Liang, HH, Souzeau, E, McAllister, IL, Isaacs, T, Hall, J, Lake, S, Mackey, DA, Constable, IJ, Craig, JE, Kitchner, TE, Yang, Z, Su, Z, Luo, H, Chen, D, Ouyang, H, Flagg, K, Lin, D, Mao, G, Ferreyra, H, Stark, K, von Strachwitz, CN, Wolf, A, Brandl, C, Rudolph, G, Olden, M, Morrison, MA, Morgan, DJ, Schu, M, Ahn, J, Silvestri, G, Tsironi, EE, Park, KH, Farrer, LA, Orlin, A, Brucker, A, Li, M, Curcio, CA, Mohand-Said, S, Sahel, J-A, Audo, I, Benchaboune, M, Cree, AJ, Rennie, CA, Goverdhan, S, Hagbi-Levi, S, Campochiaro, P, Katsanis, N, Holz, FG, Blond, F, Blanche, H, Deleuze, J-F, Truitt, B, Peachey, NS, Meuer, SM, Myers, CE, Moore, EL, Klein, R, Hauser, MA, Postel, EA, Courtenay, MD, Schwartz, SG, Kovach, JL, Scott, WK, Liew, G, Tan, AG, Gopinath, B, Merriam, JC, Smith, RT, Khan, JC, Shahid, H, Moore, AT, McGrath, JA, Laux, R, Brantley, MA, Agarwal, A, Ersoy, L, Caramoy, A, Langmann, T, Saksens, NTM, de Jong, EK, Hoyng, CB, Cain, MS, Richardson, AJ, Martin, TM, Blangero, J, Weeks, DE, Dhillon, B, van Duijn, CM, Doheny, KF, Romm, J, Klaver, CCW, Hayward, C, Gorin, MB, Klein, ML, Baird, PN, den Hollander, A, Fauser, S, Yates, JRW, Allikmets, R, Wang, JJ, Schaumberg, DA, Klein, BEK, Hagstrom, SA, Chowers, I, Lotery, AJ, Leveillard, T, Zhang, K, Brilliant, MH, Hewitt, AW, Swaroop, A, Chew, EY, Pericak-Vance, MA, DeAngelis, M, Stambolian, D, Iyengar, SK, Weber, BHF, Abecasis, GR, Heid, IM, Waksmunski, AR, Grunin, M, Kinzy, TG, Igo, RP, Haines, JL, Bailey, JNC, Fritsche, LG, Igl, W, Grassmann, F, Sengupta, S, Bragg-Gresham, JL, Burdon, KP, Hebbring, SJ, Wen, C, Gorski, M, Kim, IK, Cho, D, Zack, D, Souied, E, Scholl, HPN, Bala, E, Lee, KE, Hunter, DJ, Sardell, RJ, Mitchell, P, Merriam, JE, Cipriani, V, Hoffman, JD, Schick, T, Lechanteur, YTE, Guymer, RH, Johnson, MP, Jiang, Y, Stanton, CM, Buitendijk, GHS, Zhan, X, Kwong, AM, Boleda, A, Brooks, M, Gieser, L, Ratnapriya, R, Branham, KE, Foerster, JR, Heckenlively, JR, Othman, M, Vote, BJ, Liang, HH, Souzeau, E, McAllister, IL, Isaacs, T, Hall, J, Lake, S, Mackey, DA, Constable, IJ, Craig, JE, Kitchner, TE, Yang, Z, Su, Z, Luo, H, Chen, D, Ouyang, H, Flagg, K, Lin, D, Mao, G, Ferreyra, H, Stark, K, von Strachwitz, CN, Wolf, A, Brandl, C, Rudolph, G, Olden, M, Morrison, MA, Morgan, DJ, Schu, M, Ahn, J, Silvestri, G, Tsironi, EE, Park, KH, Farrer, LA, Orlin, A, Brucker, A, Li, M, Curcio, CA, Mohand-Said, S, Sahel, J-A, Audo, I, Benchaboune, M, Cree, AJ, Rennie, CA, Goverdhan, S, Hagbi-Levi, S, Campochiaro, P, Katsanis, N, Holz, FG, Blond, F, Blanche, H, Deleuze, J-F, Truitt, B, Peachey, NS, Meuer, SM, Myers, CE, Moore, EL, Klein, R, Hauser, MA, Postel, EA, Courtenay, MD, Schwartz, SG, Kovach, JL, Scott, WK, Liew, G, Tan, AG, Gopinath, B, Merriam, JC, Smith, RT, Khan, JC, Shahid, H, Moore, AT, McGrath, JA, Laux, R, Brantley, MA, Agarwal, A, Ersoy, L, Caramoy, A, Langmann, T, Saksens, NTM, de Jong, EK, Hoyng, CB, Cain, MS, Richardson, AJ, Martin, TM, Blangero, J, Weeks, DE, Dhillon, B, van Duijn, CM, Doheny, KF, Romm, J, Klaver, CCW, Hayward, C, Gorin, MB, Klein, ML, Baird, PN, den Hollander, A, Fauser, S, Yates, JRW, Allikmets, R, Wang, JJ, Schaumberg, DA, Klein, BEK, Hagstrom, SA, Chowers, I, Lotery, AJ, Leveillard, T, Zhang, K, Brilliant, MH, Hewitt, AW, Swaroop, A, Chew, EY, Pericak-Vance, MA, DeAngelis, M, Stambolian, D, Iyengar, SK, Weber, BHF, Abecasis, GR, and Heid, IM

Abstract

PURPOSE: Age-related macular degeneration (AMD) is the worldwide leading cause of blindness among the elderly. Although genome-wide association studies (GWAS) have identified AMD risk variants, their roles in disease etiology are not well-characterized, and they only explain a portion of AMD heritability. METHODS: We performed pathway analyses using summary statistics from the International AMD Genomics Consortium's 2016 GWAS and multiple pathway databases to identify biological pathways wherein genetic association signals for AMD may be aggregating. We determined which genes contributed most to significant pathway signals across the databases. We characterized these genes by constructing protein-protein interaction networks and performing motif analysis. RESULTS: We determined that eight genes (C2, C3, LIPC, MICA, NOTCH4, PLCG2, PPARA, and RAD51B) "drive" the statistical signals observed across pathways curated in the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and Gene Ontology (GO) databases. We further refined our definition of statistical driver gene to identify PLCG2 as a candidate gene for AMD due to its significant gene-level signals (P < 0.0001) across KEGG, Reactome, GO, and NetPath pathways. CONCLUSIONS: We performed pathway analyses on the largest available collection of advanced AMD cases and controls in the world. Eight genes strongly contributed to significant pathways from the three larger databases, and one gene (PLCG2) was central to significant pathways from all four databases. This is, to our knowledge, the first study to identify PLCG2 as a candidate gene for AMD based solely on genetic burden. Our findings reinforce the utility of integrating in silico genetic and biological pathway data to investigate the genetic architecture of AMD.

Published
2019

15. BioTIME: a database of biodiversity time series for the Anthropocene

Author

Dornelas, M, Antão, LH, Moyes, F, Bates, AE, Magurran, AE, Adam, D, Akhmetzhanova, AA, Appeltans, W, Arcos, JM, Arnold, H, Ayyappan, N, Badihi, G, Baird, AH, Barbosa, M, Barreto, TE, Bässler, C, Bellgrove, Alecia, Belmaker, J, Benedetti-Cecchi, L, Bett, BJ, Bjorkman, AD, Błażewicz, M, Blowes, SA, Bloch, CP, Bonebrake, TC, Boyd, S, Bradford, M, Brooks, AJ, Brown, JH, Bruelheide, H, Budy, P, Carvalho, F, Castañeda-Moya, E, Chen, CA, Chamblee, JF, Chase, TJ, Siegwart Collier, L, Collinge, SK, Condit, R, Cooper, EJ, Cornelissen, JHC, Cotano, U, Kyle Crow, S, Damasceno, G, Davies, CH, Davis, RA, Day, FP, Degraer, S, Doherty, Timothy, Dunn, TE, Durigan, G, Duffy, JE, Edelist, D, Edgar, GJ, Elahi, R, Elmendorf, SC, Enemar, A, Ernest, SKM, Escribano, R, Estiarte, M, Evans, BS, Fan, T-Y, Turini Farah, F, Loureiro Fernandes, L, Farneda, FZ, Fidelis, A, Fitt, R, Fosaa, AM, Daher Correa Franco, GA, Frank, GE, Fraser, WR, García, H, Cazzolla Gatti, R, Givan, O, Gorgone-Barbosa, E, Gould, WA, Gries, C, Grossman, GD, Gutierréz, JR, Hale, S, Harmon, ME, Harte, J, Haskins, G, Henshaw, DL, Hermanutz, L, Hidalgo, P, Higuchi, P, Hoey, A, Van Hoey, G, Hofgaard, A, Holeck, K, Hollister, RD, Holmes, R, Hoogenboom, M, Hsieh, C-H, Hubbell, SP, Huettmann, F, Huffard, CL, Hurlbert, AH, Macedo Ivanauskas, N, Janík, D, Jandt, U, Jażdżewska, A, Johannessen, T, Johnstone, J, Jones, J, Jones, FAM, Kang, J, Kartawijaya, T, Keeley, EC, Kelt, DA, Kinnear, R, Klanderud, K, Knutsen, H, Koenig, CC, Kortz, AR, Král, K, Kuhnz, LA, Kuo, C-Y, Kushner, DJ, Laguionie-Marchais, C, Lancaster, LT, Min Lee, C, Lefcheck, JS, Lévesque, E, Lightfoot, D, Lloret, F, Lloyd, JD, López-Baucells, A, Louzao, M, Madin, JS, Magnússon, B, Malamud, S, Matthews, I, McFarland, KP, McGill, B, McKnight, D, McLarney, WO, Meador, J, Meserve, PL, Metcalfe, DJ, Meyer, CFJ, Michelsen, A, Milchakova, N, Moens, T, Moland, E, Moore, J, Mathias Moreira, C, Müller, J, Murphy, G, Myers-Smith, IH, Myster, RW, Naumov, A, Neat, F, Nelson, JA, Paul Nelson, M, Newton, SF, Norden, N, Oliver, JC, Olsen, EM, Onipchenko, VG, Pabis, K, Pabst, RJ, Paquette, A, Pardede, S, Paterson, DM, Pélissier, R, Peñuelas, J, Pérez-Matus, A, Pizarro, O, Pomati, F, Post, E, Prins, HHT, Priscu, JC, Provoost, P, Prudic, KL, Pulliainen, E, Ramesh, BR, Mendivil Ramos, O, Rassweiler, A, Rebelo, JE, Reed, DC, Reich, PB, Remillard, SM, Richardson, AJ, Richardson, JP, van Rijn, I, Rocha, R, Rivera-Monroy, VH, Rixen, C, Robinson, KP, Ribeiro Rodrigues, R, de Cerqueira Rossa-Feres, D, Rudstam, L, Ruhl, H, Ruz, CS, Sampaio, EM, Rybicki, N, Rypel, A, Sal, S, Salgado, B, Santos, FAM, Savassi-Coutinho, AP, Scanga, S, Schmidt, J, Schooley, R, Setiawan, F, Shao, K-T, Shaver, GR, Sherman, S, Sherry, TW, Siciński, J, Sievers, C, da Silva, AC, Rodrigues da Silva, F, Silveira, FL, Slingsby, J, Smart, T, Snell, SJ, Soudzilovskaia, NA, Souza, GBG, Maluf Souza, F, Castro Souza, V, Stallings, CD, Stanforth, R, Stanley, EH, Mauro Sterza, J, Stevens, M, Stuart-Smith, R, Rondon Suarez, Y, Supp, S, Yoshio Tamashiro, J, Tarigan, S, Thiede, GP, Thorn, S, Tolvanen, A, Teresa Zugliani Toniato, M, Totland, Ø, Twilley, RR, Vaitkus, G, Valdivia, N, Vallejo, MI, Valone, TJ, Van Colen, C, Vanaverbeke, J, Venturoli, F, Verheye, HM, Vianna, M, Vieira, RP, Vrška, T, Quang Vu, C, Van Vu, L, Waide, RB, Waldock, C, Watts, D, Webb, S, Wesołowski, T, White, EP, Widdicombe, CE, Wilgers, D, Williams, R, Williams, SB, Williamson, M, Willig, MR, Willis, TJ, Wipf, S, Woods, KD, Woehler, EJ, Zawada, K, Zettler, ML, Hickler, T, Dornelas, M, Antão, LH, Moyes, F, Bates, AE, Magurran, AE, Adam, D, Akhmetzhanova, AA, Appeltans, W, Arcos, JM, Arnold, H, Ayyappan, N, Badihi, G, Baird, AH, Barbosa, M, Barreto, TE, Bässler, C, Bellgrove, Alecia, Belmaker, J, Benedetti-Cecchi, L, Bett, BJ, Bjorkman, AD, Błażewicz, M, Blowes, SA, Bloch, CP, Bonebrake, TC, Boyd, S, Bradford, M, Brooks, AJ, Brown, JH, Bruelheide, H, Budy, P, Carvalho, F, Castañeda-Moya, E, Chen, CA, Chamblee, JF, Chase, TJ, Siegwart Collier, L, Collinge, SK, Condit, R, Cooper, EJ, Cornelissen, JHC, Cotano, U, Kyle Crow, S, Damasceno, G, Davies, CH, Davis, RA, Day, FP, Degraer, S, Doherty, Timothy, Dunn, TE, Durigan, G, Duffy, JE, Edelist, D, Edgar, GJ, Elahi, R, Elmendorf, SC, Enemar, A, Ernest, SKM, Escribano, R, Estiarte, M, Evans, BS, Fan, T-Y, Turini Farah, F, Loureiro Fernandes, L, Farneda, FZ, Fidelis, A, Fitt, R, Fosaa, AM, Daher Correa Franco, GA, Frank, GE, Fraser, WR, García, H, Cazzolla Gatti, R, Givan, O, Gorgone-Barbosa, E, Gould, WA, Gries, C, Grossman, GD, Gutierréz, JR, Hale, S, Harmon, ME, Harte, J, Haskins, G, Henshaw, DL, Hermanutz, L, Hidalgo, P, Higuchi, P, Hoey, A, Van Hoey, G, Hofgaard, A, Holeck, K, Hollister, RD, Holmes, R, Hoogenboom, M, Hsieh, C-H, Hubbell, SP, Huettmann, F, Huffard, CL, Hurlbert, AH, Macedo Ivanauskas, N, Janík, D, Jandt, U, Jażdżewska, A, Johannessen, T, Johnstone, J, Jones, J, Jones, FAM, Kang, J, Kartawijaya, T, Keeley, EC, Kelt, DA, Kinnear, R, Klanderud, K, Knutsen, H, Koenig, CC, Kortz, AR, Král, K, Kuhnz, LA, Kuo, C-Y, Kushner, DJ, Laguionie-Marchais, C, Lancaster, LT, Min Lee, C, Lefcheck, JS, Lévesque, E, Lightfoot, D, Lloret, F, Lloyd, JD, López-Baucells, A, Louzao, M, Madin, JS, Magnússon, B, Malamud, S, Matthews, I, McFarland, KP, McGill, B, McKnight, D, McLarney, WO, Meador, J, Meserve, PL, Metcalfe, DJ, Meyer, CFJ, Michelsen, A, Milchakova, N, Moens, T, Moland, E, Moore, J, Mathias Moreira, C, Müller, J, Murphy, G, Myers-Smith, IH, Myster, RW, Naumov, A, Neat, F, Nelson, JA, Paul Nelson, M, Newton, SF, Norden, N, Oliver, JC, Olsen, EM, Onipchenko, VG, Pabis, K, Pabst, RJ, Paquette, A, Pardede, S, Paterson, DM, Pélissier, R, Peñuelas, J, Pérez-Matus, A, Pizarro, O, Pomati, F, Post, E, Prins, HHT, Priscu, JC, Provoost, P, Prudic, KL, Pulliainen, E, Ramesh, BR, Mendivil Ramos, O, Rassweiler, A, Rebelo, JE, Reed, DC, Reich, PB, Remillard, SM, Richardson, AJ, Richardson, JP, van Rijn, I, Rocha, R, Rivera-Monroy, VH, Rixen, C, Robinson, KP, Ribeiro Rodrigues, R, de Cerqueira Rossa-Feres, D, Rudstam, L, Ruhl, H, Ruz, CS, Sampaio, EM, Rybicki, N, Rypel, A, Sal, S, Salgado, B, Santos, FAM, Savassi-Coutinho, AP, Scanga, S, Schmidt, J, Schooley, R, Setiawan, F, Shao, K-T, Shaver, GR, Sherman, S, Sherry, TW, Siciński, J, Sievers, C, da Silva, AC, Rodrigues da Silva, F, Silveira, FL, Slingsby, J, Smart, T, Snell, SJ, Soudzilovskaia, NA, Souza, GBG, Maluf Souza, F, Castro Souza, V, Stallings, CD, Stanforth, R, Stanley, EH, Mauro Sterza, J, Stevens, M, Stuart-Smith, R, Rondon Suarez, Y, Supp, S, Yoshio Tamashiro, J, Tarigan, S, Thiede, GP, Thorn, S, Tolvanen, A, Teresa Zugliani Toniato, M, Totland, Ø, Twilley, RR, Vaitkus, G, Valdivia, N, Vallejo, MI, Valone, TJ, Van Colen, C, Vanaverbeke, J, Venturoli, F, Verheye, HM, Vianna, M, Vieira, RP, Vrška, T, Quang Vu, C, Van Vu, L, Waide, RB, Waldock, C, Watts, D, Webb, S, Wesołowski, T, White, EP, Widdicombe, CE, Wilgers, D, Williams, R, Williams, SB, Williamson, M, Willig, MR, Willis, TJ, Wipf, S, Woods, KD, Woehler, EJ, Zawada, K, Zettler, ML, and Hickler, T

Published
2018

16. A database of chlorophyll a in Australian waters

Author

Davies, CH, Ajani, P, Armbrecht, L, Atkins, N, Baird, ME, Beard, J, Bonham, P, Burford, M, Clementson, L, Coad, P, Crawford, C, Dela-Cruz, J, Doblin, MA, Edgar, S, Eriksen, R, Everett, JD, Furnas, M, Harrison, DP, Hassler, C, Henschke, N, Hoenner, X, Ingleton, T, Jameson, I, Keesing, J, Leterme, SC, James McLaughlin, M, Miller, M, Moffatt, D, Moss, A, Nayar, S, Patten, NL, Patten, R, Pausina, SA, Proctor, R, Raes, E, Robb, M, Rothlisberg, P, Saeck, EA, Scanes, P, Suthers, IM, Swadling, KM, Talbot, S, Thompson, P, Thomson, PG, Uribe-Palomino, J, Van Ruth, P, Waite, AM, Wright, S, Richardson, AJ, Davies, CH, Ajani, P, Armbrecht, L, Atkins, N, Baird, ME, Beard, J, Bonham, P, Burford, M, Clementson, L, Coad, P, Crawford, C, Dela-Cruz, J, Doblin, MA, Edgar, S, Eriksen, R, Everett, JD, Furnas, M, Harrison, DP, Hassler, C, Henschke, N, Hoenner, X, Ingleton, T, Jameson, I, Keesing, J, Leterme, SC, James McLaughlin, M, Miller, M, Moffatt, D, Moss, A, Nayar, S, Patten, NL, Patten, R, Pausina, SA, Proctor, R, Raes, E, Robb, M, Rothlisberg, P, Saeck, EA, Scanes, P, Suthers, IM, Swadling, KM, Talbot, S, Thompson, P, Thomson, PG, Uribe-Palomino, J, Van Ruth, P, Waite, AM, Wright, S, and Richardson, AJ

Abstract

© The Author(s) 2018. Chlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.

Published
2018

17. Corrigendum:A database of marine phytoplankton abundance, biomass and species composition in Australian waters (Scientific Data (2016) 3 (160043) DOI: 10.1038/sdata.2016.43)

Author

Davies, CH, Coughlan, A, Hallegraeff, G, Ajani, P, Armbrecht, L, Atkins, N, Bonham, P, Brett, S, Brinkman, R, Burford, M, Clementson, L, Coad, P, Coman, F, Davies, D, Dela-Cruz, J, Devlin, M, Edgar, S, Eriksen, R, Furnas, M, Hassler, C, Hill, D, Holmes, M, Ingleton, T, Jameson, I, Leterme, SC, Lønborg, C, McLaughlin, J, McEnnulty, F, McKinnon, AD, Miller, M, Murray, S, Nayar, S, Patten, R, Pausina, SA, Pritchard, T, Proctor, R, Purcell-Meyerink, D, Raes, E, Rissik, D, Ruszczyk, J, Slotwinski, A, Swadling, KM, Tattersall, K, Thompson, P, Thomson, P, Tonks, M, Trull, TW, Uribe-Palomino, J, Waite, AM, Yauwenas, R, Zammit, A, and Richardson, AJ

Subjects
TheoryofComputation_COMPUTATIONBYABSTRACTDEVICES, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries)
Abstract

© The Author(s) 2016. A series of errors in our database were brought to our attention by readers, and have been corrected in an updated version of this database, which is accessible via the AODN at the following link: https://portal.aodn.org.au/search?uuid =75f4f1fc-bee3-4498-ab71-aa1ab29ab2c0 The custodian details of several datasets were incorrect. These fields in the metadata table have been updated to correctly assign P744, P746, P748, and P778 to the Australian Antarctic Division, and P752 to the Royal Belgian Institute of Natural Sciences. Species names and functional group assignments have been changed for a small number of records to fix identified errors. Tripos brevis and Tripos arietinus were spelt incorrectly, and have been duly corrected. Pedinellaceae was wrongly assigned to dinoflagellate as a functional group, and has now been re-assigned to flagellate. The 'Naked flagellate' group has been renamed 'Flagellate' as there is some inconsistency in the use of the term 'Naked flagellate' and what precisely would be included. The functional group 'Other', has also been excluded as this contained data that was not necessarily phytoplankton but had been found in phytoplankton counts. The macroalgae Murrayella australica, Cladophora spp., Chlorohormidium sp., Eudorina spp., Tribonema spp., Chlorohormidium spp. were also removed. In addition to these corrections, three datasets have been extended to include more recently acquired data: P 597 IMOS Australian Continuous Plankton Recorder survey (ongoing dataset, 59089 new records as of 2016-08-31); P599 IMOS National Reference Stations (ongoing dataset, 14669 new records as of 2016-08-31); and P1068 Great Barrier Reef Expedition 1928-29 (new dataset, 1340 new records). Table 1 provides a summary of the overall change in database contents. (Table Presented). This dataset will continue to grow and will be regularly updated with new data and any further corrections to the data. Users can email imos-planktonatcsiro.au with any comments, which will be reviewed and included in future updates if applicable. The AODN portal will always direct the user to the most recent version, the original version will remain available at http://dx.doi.org/10.4225/69/ 56454b2ba2f79, and interim versions will be available on request.

Published
2017
Full Text
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19. Corrigendum: A database of marine phytoplankton abundance, biomass and species composition in Australian waters (Scientific Data (2016) 3 (160043) DOI: 10.1038/sdata.2016.43)

Author

Davies, CH, Coughlan, A, Hallegraeff, G, Ajani, P, Armbrecht, L, Atkins, N, Bonham, P, Brett, S, Brinkman, R, Burford, M, Clementson, L, Coad, P, Coman, F, Davies, D, Dela-Cruz, J, Devlin, M, Edgar, S, Eriksen, R, Furnas, M, Hassler, C, Hill, D, Holmes, M, Ingleton, T, Jameson, I, Leterme, SC, Lønborg, C, McLaughlin, J, McEnnulty, F, McKinnon, AD, Miller, M, Murray, S, Nayar, S, Patten, R, Pausina, SA, Pritchard, T, Proctor, R, Purcell-Meyerink, D, Raes, E, Rissik, D, Ruszczyk, J, Slotwinski, A, Swadling, KM, Tattersall, K, Thompson, P, Thomson, P, Tonks, M, Trull, TW, Uribe-Palomino, J, Waite, AM, Yauwenas, R, Zammit, A, Richardson, AJ, Davies, CH, Coughlan, A, Hallegraeff, G, Ajani, P, Armbrecht, L, Atkins, N, Bonham, P, Brett, S, Brinkman, R, Burford, M, Clementson, L, Coad, P, Coman, F, Davies, D, Dela-Cruz, J, Devlin, M, Edgar, S, Eriksen, R, Furnas, M, Hassler, C, Hill, D, Holmes, M, Ingleton, T, Jameson, I, Leterme, SC, Lønborg, C, McLaughlin, J, McEnnulty, F, McKinnon, AD, Miller, M, Murray, S, Nayar, S, Patten, R, Pausina, SA, Pritchard, T, Proctor, R, Purcell-Meyerink, D, Raes, E, Rissik, D, Ruszczyk, J, Slotwinski, A, Swadling, KM, Tattersall, K, Thompson, P, Thomson, P, Tonks, M, Trull, TW, Uribe-Palomino, J, Waite, AM, Yauwenas, R, Zammit, A, and Richardson, AJ

Abstract

© 2017 The Author(s). The authors regret that Sarah A. Pausina was omitted in error from the author list of the original version of this Data Descriptor. This omission has now been corrected in the HTML and PDF versions of this Data Descriptor, as well as the accompanying Corrigendum.

Published
2017

20. Modeling what we sample and sampling what we model: Challenges for zooplankton model assessment

Author

Everett, JD, Baird, ME, Buchanan, P, Bulman, C, Davies, C, Downie, R, Griffiths, C, Heneghan, R, Kloser, RJ, Laiolo, L, Lara-Lopez, A, Lozano-Montes, H, Matear, RJ, McEnnulty, F, Robson, B, Rochester, W, Skerratt, J, Smith, JA, Strzelecki, J, Suthers, IM, Swadling, KM, van Ruth, P, Richardson, AJ, Everett, JD, Baird, ME, Buchanan, P, Bulman, C, Davies, C, Downie, R, Griffiths, C, Heneghan, R, Kloser, RJ, Laiolo, L, Lara-Lopez, A, Lozano-Montes, H, Matear, RJ, McEnnulty, F, Robson, B, Rochester, W, Skerratt, J, Smith, JA, Strzelecki, J, Suthers, IM, Swadling, KM, van Ruth, P, and Richardson, AJ

Abstract

© 2017 Everett, Baird, Buchanan, Bulman, Davies, Downie, Griffiths, Heneghan, Kloser, Laiolo, Lara-Lopez, Lozano-Montes, Matear, McEnnulty, Robson, Rochester, Skerratt, Smith, Strzelecki, Suthers, Swadling, van Ruth and Richardson. Zooplankton are the intermediate trophic level between phytoplankton and fish, and are an important component of carbon and nutrient cycles, accounting for a large proportion of the energy transfer to pelagic fishes and the deep ocean. Given zooplankton's importance, models need to adequately represent zooplankton dynamics. A major obstacle, though, is the lack of model assessment. Here we try and stimulate the assessment of zooplankton in models by filling three gaps. The first is that many zooplankton observationalists are unfamiliar with the biogeochemical, ecosystem, size-based and individual-based models that have zooplankton functional groups, so we describe their primary uses and how each typically represents zooplankton. The second gap is that many modelers are unaware of the zooplankton data that are available, and are unaccustomed to the different zooplankton sampling systems, so we describe the main sampling platforms and discuss their strengths and weaknesses for model assessment. Filling these gaps in our understanding of models and observations provides the necessary context to address the last gap-a blueprint for model assessment of zooplankton. We detail two ways that zooplankton biomass/abundance observations can be used to assess models: data wrangling that transforms observations to be more similar to model output; and observation models that transform model outputs to be more like observations. We hope that this review will encourage greater assessment of zooplankton in models and ultimately improve the representation of their dynamics.

Published
2017

21. Pancreatectomy is underused in NSW regions with low institutional surgical volumes: A population data linkage study

Author

Creighton, N, Walton, R, Roder, DM, Aranda, S, Richardson, AJ, Merrett, N, Currow, D, Creighton, N, Walton, R, Roder, DM, Aranda, S, Richardson, AJ, Merrett, N, and Currow, D

Abstract

© 2017 AMPCo Pty Ltd. Produced with Elsevier B.V. All rights reserved. Objective: To examine differences in the proportions of people diagnosed with pancreatic cancer who underwent pancreatectomy, post-operative outcomes and 5-year survival in different New South Wales administrative health regions of residence. Design, setting and participants: Retrospective analysis of NSW data on pancreatic cancer incidence and surgery, 2005e2013. Main outcome measures: The proportion of newly diagnosed patients with pancreatic cancer who were resected in each region; 90-day post-operative mortality; one-year post-operative survival; 5-year post-diagnosis survival. Results: 14% of people diagnosed with pancreatic cancer during 2010e2013 (431 of 3064) underwent pancreatectomy, an average of 108 resections per year. After adjusting for age, sex and comorbidities, the proportion that underwent resection varied significantly between regions, ranging between 8% and 21% (P<0.001). Higher resection rates were not associated with higher post-operative 90-day mortality or lower one-year survival (unadjusted and risk-adjusted analyses). Higher resection rates were associated with higher 5-year post-diagnosis survival: the mean survival in regions with resection rates below 10% was 3.4%, compared with 7.2% in regions with rates greater than 15% (unadjusted and adjusted survival analyses; P<0.001). There was a positive association between regional resection rate and the pancreatectomy volume of hospitals during 2005e2009. An additional 32 people would be resected annually if resection rates in low rate regions were increased to the 80th percentile regional resection rate (18%). Conclusion: There is significant geographic variation in the proportion of people with pancreatic cancer undergoing pancreatectomy, and the 5-year survival rate is higher in regions where this proportion is higher.

Published
2017

27. Auditory frequency discrimination in adult developmental dyslexics

Author

France, SJ, Rosner, BS, Hansen, PC, Calvin, C, Talcott, JB, Richardson, AJ, and Stein, JF

Subjects
Adult, Male, medicine.medical_specialty, Sound Spectrography, Experimental and Cognitive Psychology, Sensory system, Audiology, Developmental psychology, Dyslexia, Pitch Discrimination, Communication disorder, medicine, Memory span, Humans, Attention, Language disorder, General Psychology, Interstimulus interval, Frequency discrimination, medicine.disease, Sensory Systems, Developmental disorder, Mental Recall, Female, Psychology, Psychoacoustics
Abstract

Developmental dyslexics reportedly discriminate auditory frequency poorly. A recent study found no such deficit. Unlike its predecessors, however, it employed multiple exposures per trial to the standard stimulus. To investigate whether this affects frequency discrimination in dyslexics, a traditional two-interval same-different paradigm (2I_1A_X) and a variant with six A-stimuli per trial (2I_6A_X) were used here. Frequency varied around 500 Hz; interstimulus interval (ISI) ranged between 0 and 1,000 msec. Under 2I_1A_X, dyslexics always had larger just noticeable differences (JNDs) than did controls. Dyslexic and control JNDs were equal at shorter ISIs under 2I_6A_X, but dyslexics became worse than controls at longer ISIs. Signal detection analysis suggests that both sensory variance and trace variance are larger in dyslexics than in controls.

Published
2016
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33. Pancreatectomy is underused in NSW regions with low institutional surgical volumes: A population data linkage study

Author

Creighton, N, Walton, R, Roder, DM, Aranda, S, Richardson, AJ, Merrett, N, and Currow, D

Subjects
Aged, 80 and over, Male, Information Storage and Retrieval, Middle Aged, Survival Analysis, Pancreatic Neoplasms, Cohort Studies, Pancreatectomy, General & Internal Medicine, Humans, Female, New South Wales, Hospitals, High-Volume, Retrospective Studies, Aged
Abstract

© 2017 AMPCo Pty Ltd. Produced with Elsevier B.V. All rights reserved. Objective: To examine differences in the proportions of people diagnosed with pancreatic cancer who underwent pancreatectomy, post-operative outcomes and 5-year survival in different New South Wales administrative health regions of residence. Design, setting and participants: Retrospective analysis of NSW data on pancreatic cancer incidence and surgery, 2005e2013. Main outcome measures: The proportion of newly diagnosed patients with pancreatic cancer who were resected in each region; 90-day post-operative mortality; one-year post-operative survival; 5-year post-diagnosis survival. Results: 14% of people diagnosed with pancreatic cancer during 2010e2013 (431 of 3064) underwent pancreatectomy, an average of 108 resections per year. After adjusting for age, sex and comorbidities, the proportion that underwent resection varied significantly between regions, ranging between 8% and 21% (P

Published
2016

34. Short term heat acclimation improves the determinants of endurance performance and 5,000 m running performance in the heat

Author

James, CA, Richardson, AJ, Watt, PW, Willmott, AGB, Gibson, OR, and Maxwell, NS

Subjects
V̇O2max, Heat acclimation, Hyperthermia, Thermoregulation, Endurance
Abstract

This study investigated the effect of 5 days controlled hyperthermia heat acclimation (STHA) on the determinants of endurance performance and 5 km performance in runners, relative to the impairment afforded by moderate heat stress. A control group (CON), matched for total work and power output (2.7 W.kg-1), differentiated thermal and exercise contributions of STHA on exercise performance. Seventeen participants (10 STHA, 7 CON) completed graded exercise tests (GXT) in cool (13°C, 50% RH, pre training) and hot conditions (32°C, 60% RH, pre and post training), as well as 5 km time trials (TT) in the heat, pre and post training. STHA reduced resting (p=0.01) and exercising (p=0.04) TCORE alongside a smaller change in thermal sensation (p=0.04). Both groups improved the lactate threshold (LT, p=0.021), lactate turnpoint (LTP, p=0.005) and vV̇O2max (p=0.031) similarly. Statistical differences between training methods were observed in TT performance (STHA -6.2[5.5]%, CON; -0.6[1.7]%, p=0.029) and total running time during the GXT (STHA; +20.8[12.7]%, CON; +9.8[1.2]%, p=0.006). There were large mean differences in change in V̇O2max between STHA +4.0 (2.2) mL.kg-1.min-1 (7.3[4.0]%) and CON +1.9(3.7)mL.kg-1.min-1 (3.8[7.2]%). Running economy deteriorated following both training programmes (p=0.008). Similarly, RE was impaired in the cool GXT, relative to the hot GXT (p=0.004). STHA improved endurance running performance in comparison to work matched normothermic training, despite equality of adaptation for typical determinants of performance (LT, LTP, vV̇O2max). Accordingly, these data highlight the ergogenic effect of STHA, potentially via greater improvements in V̇O2max and specific thermoregulatory and associated thermal perception adaptations absent in normothermic training.

Published
2016

35. Multiallelic copy number variation in the complement component 4A (C4A) gene is associated with late-stage age-related macular degeneration (AMD)

Author

Grassmann, F, Cantsilieris, S, Schulz-Kuhnt, A-S, White, SJ, Richardson, AJ, Hewitt, AW, Vote, BJ, Schmied, D, Guymer, RH, Weber, BHF, Baird, PN, Grassmann, F, Cantsilieris, S, Schulz-Kuhnt, A-S, White, SJ, Richardson, AJ, Hewitt, AW, Vote, BJ, Schmied, D, Guymer, RH, Weber, BHF, and Baird, PN

Abstract

BACKGROUND: Age-related macular degeneration (AMD) is the leading cause of vision loss in Western societies with a strong genetic component. Candidate gene studies as well as genome-wide association studies strongly implicated genetic variations in complement genes to be involved in disease risk. So far, no association of AMD with complement component 4 (C4) was reported probably due to the complex nature of the C4 locus on chromosome 6. METHODS: We used multiplex ligation-dependent probe amplification (MLPA) to determine the copy number of the C4 gene as well as of both relevant isoforms, C4A and C4B, and assessed their association with AMD using logistic regression models. RESULTS: Here, we report on the analysis of 2645 individuals (1536 probands and 1109 unaffected controls), across three different centers, for multiallelic copy number variation (CNV) at the C4 locus. We find strong statistical significance for association of increased copy number of C4A (OR 0.81 (0.73; 0.89);P = 4.4 × 10(-5)), with the effect most pronounced in individuals over 78 years (OR 0.67 (0.55; 0.81)) and females (OR 0.77 (0.68; 0.87)). Furthermore, this association is independent of known AMD-associated risk variants in the nearby CFB/C2 locus, particularly in females and in individuals over 78 years. CONCLUSIONS: Our data strengthen the notion that complement dysregulation plays a crucial role in AMD etiology, an important finding for early intervention strategies and future therapeutics. In addition, for the first time, we provide evidence that multiallelic CNVs are associated with AMD pathology.

Published
2016

36. GWAS study using DNA pooling strategy identifies association of variant rs4910623 in OR52B4 gene with anti-VEGF treatment response in age-related macular degeneration

Author

Riaz, M, Lores-Motta, L, Richardson, AJ, Lu, Y, Montgomery, G, Omar, A, Koenekoop, RK, Chen, J, Muether, P, Altay, L, Schick, T, Fauser, S, Smailhodzic, D, van Asten, F, de Jong, EK, Hoyng, CB, Burdon, KP, MacGregor, S, Guymer, RH, den Hollander, AI, Baird, PN, Riaz, M, Lores-Motta, L, Richardson, AJ, Lu, Y, Montgomery, G, Omar, A, Koenekoop, RK, Chen, J, Muether, P, Altay, L, Schick, T, Fauser, S, Smailhodzic, D, van Asten, F, de Jong, EK, Hoyng, CB, Burdon, KP, MacGregor, S, Guymer, RH, den Hollander, AI, and Baird, PN

Abstract

Pooled DNA based GWAS to determine genetic association of SNPs with visual acuity (VA) outcome in anti-vascular endothelial growth factor (anti-VEGF) treated neovascular age-related macular degeneration (nAMD) patients. We performed pooled DNA based GWAS on 285 anti-VEGF treated nAMD patients using high density Illumina 4.3 M array. Primary outcome was change in VA in Early Treatment Diabetic Retinopathy Study (ETDRS) letters after 6 months of anti-VEGF treatment (patients who lost ≥5 ETDRS letters classified as non-responders and all remaining classified as responders). GWAS analysis identified 44 SNPs of interest: 37 with strong evidence of association (p < 9 × 10-8), 2 in drug resistance genes (p < 5 × 10-6) and 5 nonsynonymous changes (p < 1 × 10-4). In the validation phase, individual genotyping of 44 variants showed three SNPs (rs4910623 p = 5.6 × 10-5, rs323085 p = 6.5 × 10-4 and rs10198937 p = 1.30 × 10-3) remained associated with VA response at 6 months. SNP rs4910623 also associated with treatment response at 3 months (p = 1.5 × 10-3). Replication of these three SNPs in 376 patients revealed association of rs4910623 with poor VA response after 3 and 6 months of treatment (p = 2.4 × 10-3 and p = 3.5 × 10-2, respectively). Meta-analysis of both cohorts (673 samples) confirmed association of rs4910623 with poor VA response after 3 months (p = 1.2 × 10-5) and 6 months (p = 9.3 × 10-6) of treatment in nAMD patients.

Published
2016

37. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Author

Fritsche, LG, Igl, W, Bailey, JNC, Grassmann, F, Sengupta, S, Bragg-Gresham, JL, Burdon, KP, Hebbring, SJ, Wen, C, Gorski, M, Kim, IK, Cho, D, Zack, D, Souied, E, Scholl, HPN, Bala, E, Lee, KE, Hunter, DJ, Sardell, RJ, Mitchell, P, Merriam, JE, Cipriani, V, Hoffman, JD, Schick, T, Lechanteur, YTE, Guymer, RH, Johnson, MP, Jiang, Y, Stanton, CM, Buitendijk, GHS, Zhan, X, Kwong, AM, Boleda, A, Brooks, M, Gieser, L, Ratnapriya, R, Branham, KE, Foerster, JR, Heckenlively, JR, Othman, MI, Vote, BJ, Liang, HH, Souzeau, E, McAllister, IL, Isaacs, T, Hall, J, Lake, S, Mackey, DA, Constable, IJ, Craig, JE, Kitchner, TE, Yang, Z, Su, Z, Luo, H, Chen, D, Hong, O, Flagg, K, Lin, D, Mao, G, Ferreyra, H, Starke, K, von Strachwitz, CN, Wolf, A, Brandl, C, Rudolph, G, Olden, M, Morrison, MA, Morgan, DJ, Schu, M, Ahn, J, Silvestri, G, Tsironi, EE, Park, KH, Farrer, LA, Orlin, A, Brucker, A, Li, M, Curcio, CA, Mohand-Said, S, Sahel, J-M, Audo, I, Benchaboune, M, Cree, AJ, Rennie, CA, Goverdhan, SV, Grunin, M, Hagbi-Levi, S, Campochiaro, P, Katsanis, N, Holz, FG, Blond, F, Blanche, H, Deleuze, J-F, Igo, RP, Truitt, B, Peachey, NS, Meuer, SM, Myers, CE, Moore, EL, Klein, R, Hauser, MA, Postel, EA, Courtenay, MD, Schwartz, SG, Kovach, JL, Scott, WK, Liew, G, Tan, AG, Gopinath, B, Merriam, JC, Smith, RT, Khan, JC, Shahid, H, Moore, AT, McGrath, JA, Laux, R, Brantley, MA, Agarwal, A, Ersoy, L, Caramoy, A, Langmann, T, Saksens, NTM, de Jong, EK, Hoyng, CB, Cain, MS, Richardson, AJ, Martin, TM, Blangero, J, Weeks, DE, Dhillon, B, van Duijn, CM, Doheny, KF, Romm, J, Klaver, CCW, Hayward, C, Gorin, MB, Klein, ML, Baird, PN, den Hollander, AI, Fauser, S, Yates, JRW, Allikmets, R, Wang, JJ, Schaumberg, DA, Klein, BEK, Hagstrom, SA, Chowers, I, Lotery, AJ, Leveillard, T, Zhang, K, Brilliant, MH, Hewitt, AW, Swaroop, A, Chew, EY, Pericak-Vance, MA, DeAngelis, M, Stambolian, D, Haines, JL, Iyengar, SK, Weber, BHF, Abecasis, GR, Heid, IM, Fritsche, LG, Igl, W, Bailey, JNC, Grassmann, F, Sengupta, S, Bragg-Gresham, JL, Burdon, KP, Hebbring, SJ, Wen, C, Gorski, M, Kim, IK, Cho, D, Zack, D, Souied, E, Scholl, HPN, Bala, E, Lee, KE, Hunter, DJ, Sardell, RJ, Mitchell, P, Merriam, JE, Cipriani, V, Hoffman, JD, Schick, T, Lechanteur, YTE, Guymer, RH, Johnson, MP, Jiang, Y, Stanton, CM, Buitendijk, GHS, Zhan, X, Kwong, AM, Boleda, A, Brooks, M, Gieser, L, Ratnapriya, R, Branham, KE, Foerster, JR, Heckenlively, JR, Othman, MI, Vote, BJ, Liang, HH, Souzeau, E, McAllister, IL, Isaacs, T, Hall, J, Lake, S, Mackey, DA, Constable, IJ, Craig, JE, Kitchner, TE, Yang, Z, Su, Z, Luo, H, Chen, D, Hong, O, Flagg, K, Lin, D, Mao, G, Ferreyra, H, Starke, K, von Strachwitz, CN, Wolf, A, Brandl, C, Rudolph, G, Olden, M, Morrison, MA, Morgan, DJ, Schu, M, Ahn, J, Silvestri, G, Tsironi, EE, Park, KH, Farrer, LA, Orlin, A, Brucker, A, Li, M, Curcio, CA, Mohand-Said, S, Sahel, J-M, Audo, I, Benchaboune, M, Cree, AJ, Rennie, CA, Goverdhan, SV, Grunin, M, Hagbi-Levi, S, Campochiaro, P, Katsanis, N, Holz, FG, Blond, F, Blanche, H, Deleuze, J-F, Igo, RP, Truitt, B, Peachey, NS, Meuer, SM, Myers, CE, Moore, EL, Klein, R, Hauser, MA, Postel, EA, Courtenay, MD, Schwartz, SG, Kovach, JL, Scott, WK, Liew, G, Tan, AG, Gopinath, B, Merriam, JC, Smith, RT, Khan, JC, Shahid, H, Moore, AT, McGrath, JA, Laux, R, Brantley, MA, Agarwal, A, Ersoy, L, Caramoy, A, Langmann, T, Saksens, NTM, de Jong, EK, Hoyng, CB, Cain, MS, Richardson, AJ, Martin, TM, Blangero, J, Weeks, DE, Dhillon, B, van Duijn, CM, Doheny, KF, Romm, J, Klaver, CCW, Hayward, C, Gorin, MB, Klein, ML, Baird, PN, den Hollander, AI, Fauser, S, Yates, JRW, Allikmets, R, Wang, JJ, Schaumberg, DA, Klein, BEK, Hagstrom, SA, Chowers, I, Lotery, AJ, Leveillard, T, Zhang, K, Brilliant, MH, Hewitt, AW, Swaroop, A, Chew, EY, Pericak-Vance, MA, DeAngelis, M, Stambolian, D, Haines, JL, Iyengar, SK, Weber, BHF, Abecasis, GR, and Heid, IM

Abstract

Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Published
2016

38. A database of marine phytoplankton abundance, biomass and species composition in Australian waters

Author

Davies, CH, Coughlan, A, Hallegraeff, G, Ajani, P, Armbrecht, L, Atkins, N, Bonham, P, Brett, S, Brinkman, R, Burford, M, Clementson, L, Coad, P, Coman, F, Davies, D, Dela-Cruz, J, Devlin, M, Edgar, S, Eriksen, R, Furnas, M, Hassler, C, Hill, D, Holmes, M, Ingleton, T, Jameson, I, Leterme, SC, Lønborg, C, McLaughlin, J, McEnnulty, F, McKinnon, AD, Miller, M, Murray, S, Nayar, S, Patten, R, Pritchard, T, Proctor, R, Purcell-Meyerink, D, Raes, E, Rissik, D, Ruszczyk, J, Slotwinski, A, Swadling, KM, Tattersall, K, Thompson, P, Thomson, P, Tonks, M, Trull, TW, Uribe-Palomino, J, Waite, AM, Yauwenas, R, Zammit, A, Richardson, AJ, Davies, CH, Coughlan, A, Hallegraeff, G, Ajani, P, Armbrecht, L, Atkins, N, Bonham, P, Brett, S, Brinkman, R, Burford, M, Clementson, L, Coad, P, Coman, F, Davies, D, Dela-Cruz, J, Devlin, M, Edgar, S, Eriksen, R, Furnas, M, Hassler, C, Hill, D, Holmes, M, Ingleton, T, Jameson, I, Leterme, SC, Lønborg, C, McLaughlin, J, McEnnulty, F, McKinnon, AD, Miller, M, Murray, S, Nayar, S, Patten, R, Pritchard, T, Proctor, R, Purcell-Meyerink, D, Raes, E, Rissik, D, Ruszczyk, J, Slotwinski, A, Swadling, KM, Tattersall, K, Thompson, P, Thomson, P, Tonks, M, Trull, TW, Uribe-Palomino, J, Waite, AM, Yauwenas, R, Zammit, A, and Richardson, AJ

Abstract

There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels.

Published
2016

40. Corrigendum: A database of marine phytoplankton abundance, biomass and species composition in Australian waters (Scientific Data (2016) 3 (160043) DOI: 10.1038/sdata201643))

Author

Davies, CH, Coughlan, A, Hallegraeff, G, Ajani, P, Armbrecht, L, Atkins, N, Bonham, P, Brett, S, Brinkman, R, Burford, M, Clementson, L, Coad, P, Coman, F, Davies, D, Dela-Cruz, J, Devlin, M, Edgar, S, Eriksen, R, Furnas, M, Hassler, C, Hill, D, Holmes, M, Ingleton, T, Jameson, I, Leterme, SC, Lønborg, C, McLaughlin, J, McEnnulty, F, McKinnon, AD, Miller, M, Murray, S, Nayar, S, Patten, R, Pausina, SA, Pritchard, T, Proctor, R, Purcell-Meyerink, D, Raes, E, Rissik, D, Ruszczyk, J, Slotwinski, A, Swadling, KM, Tattersall, K, Thompson, P, Thomson, P, Tonks, M, Trull, TW, Uribe-Palomino, J, Waite, AM, Yauwenas, R, Zammit, A, Richardson, AJ, Davies, CH, Coughlan, A, Hallegraeff, G, Ajani, P, Armbrecht, L, Atkins, N, Bonham, P, Brett, S, Brinkman, R, Burford, M, Clementson, L, Coad, P, Coman, F, Davies, D, Dela-Cruz, J, Devlin, M, Edgar, S, Eriksen, R, Furnas, M, Hassler, C, Hill, D, Holmes, M, Ingleton, T, Jameson, I, Leterme, SC, Lønborg, C, McLaughlin, J, McEnnulty, F, McKinnon, AD, Miller, M, Murray, S, Nayar, S, Patten, R, Pausina, SA, Pritchard, T, Proctor, R, Purcell-Meyerink, D, Raes, E, Rissik, D, Ruszczyk, J, Slotwinski, A, Swadling, KM, Tattersall, K, Thompson, P, Thomson, P, Tonks, M, Trull, TW, Uribe-Palomino, J, Waite, AM, Yauwenas, R, Zammit, A, and Richardson, AJ

Abstract

© The Author(s) 2016. A series of errors in our database were brought to our attention by readers, and have been corrected in an updated version of this database, which is accessible via the AODN at the following link: https://portal.aodn.org.au/search?uuid =75f4f1fc-bee3-4498-ab71-aa1ab29ab2c0 The custodian details of several datasets were incorrect. These fields in the metadata table have been updated to correctly assign P744, P746, P748, and P778 to the Australian Antarctic Division, and P752 to the Royal Belgian Institute of Natural Sciences. Species names and functional group assignments have been changed for a small number of records to fix identified errors. Tripos brevis and Tripos arietinus were spelt incorrectly, and have been duly corrected. Pedinellaceae was wrongly assigned to dinoflagellate as a functional group, and has now been re-assigned to flagellate. The 'Naked flagellate' group has been renamed 'Flagellate' as there is some inconsistency in the use of the term 'Naked flagellate' and what precisely would be included. The functional group 'Other', has also been excluded as this contained data that was not necessarily phytoplankton but had been found in phytoplankton counts. The macroalgae Murrayella australica, Cladophora spp., Chlorohormidium sp., Eudorina spp., Tribonema spp., Chlorohormidium spp. were also removed. In addition to these corrections, three datasets have been extended to include more recently acquired data: P 597 IMOS Australian Continuous Plankton Recorder survey (ongoing dataset, 59089 new records as of 2016-08-31); P599 IMOS National Reference Stations (ongoing dataset, 14669 new records as of 2016-08-31); and P1068 Great Barrier Reef Expedition 1928-29 (new dataset, 1340 new records). Table 1 provides a summary of the overall change in database contents. (Table Presented). This dataset will continue to grow and will be regularly updated with new data and any further corrections to the data. Users can email imos-planktonatcsiro

Published
2016

41. Demography and interannual variability of salp swarms (Thalia democratica)

Author

Henschke, N, Everett, JD, Doblin, MA, Pitt, KA, Richardson, AJ, and Suthers, IM

Subjects
Marine Biology & Hydrobiology
Abstract

Swarms of the pelagic tunicate, Thalia democratica, form during spring, but the causes of the large interannual variability in the magnitude of salp swarms are unclear. Changes in asexual reproduction (buds per chain) of T. democratica populations in the coastal waters of south-east Australia (32-35°S) were observed in three austral springs (October 2008-2010). T. democratica abundance was significantly higher in 2008 (1,312 individuals m-3) than 2009 and 2010 (210 and 92 individuals m-3, respectively). There was a significant negative relationship (linear regression, r 2 = 0.61, F 1,22 = 33.83, P < 0.001) between abundance and asexual reproduction. Similarly, relative growth rates declined with decreasing abundance. Generalised additive mixed modelling showed that T. democratica abundance was significantly positively related to preferred food >2 μm in size (P < 0.05) and negatively related to the proportion of non-salp zooplankton (P < 0.001). Salp swarm magnitude, growth, and asexual reproduction may depend on the abundance of larger phytoplankton (prymnesiophytes and diatoms) and competition with other zooplankton. © 2013 Springer-Verlag Berlin Heidelberg.

Published
2014

42. Increased heat shock protein 90 (hsp90) expression leads to increased apoptosis in the monoblastoid cell line U937 following induction with TNF-alpha and cycloheximide: a possible role in immunopathology

Author

Galea-Lauri, J, Richardson, AJ, Latchman, DS, and Katz, DR

Subjects
Immunology, Immunology and Allergy
Abstract

In this study, we examined the hypothesis that heat shock proteins (hsp) (such as hsp72 and hsp90) are implicated in the regulation of forms of cell injury that lead to programmed cell death. The monoblastoid cell line U937 has been used as a model system. For hsp90, which is not heat inducible in this cell line, we used stable U937 transfectants that either hyperexpress or hypoexpress the protein. For hsp72 (which is reproducibly induced in all three cell lines to relatively high levels of expression), we studied U937 cells before and after heat shock. We showed that apoptosis does occur in the monoblast/mononuclear phagocyte lineage, and that it could be induced in vitro by serum deprivation, UV light, or TNF-alpha in combination with cycloheximide (cx). However, an excess of hsp90 is associated with increased apoptosis when the cells are treated with a combination of TNF-alpha and cx but not when they are exposed to UV B radiation. This was complemented by the finding that reduced hsp90 levels correlate with protection against apoptosis in the TNF-alpha- and cx-treated cells. Furthermore, new synthesis of hsp72 does not protect against apoptosis. Thus, hsp90 levels may play a role in controlling the part played by mononuclear phagocytes in immunopathology.

Published
1996
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43. IMOS National Reference Stations: A continental-wide physical, chemical and biological coastal observing system

Author

Lynch, TP, Morello, EB, Evans, K, Richardson, AJ, Rochester, W, Steinberg, CR, Roughan, M, Thompson, P, Middleton, JF, Feng, M, Sherrington, R, Brando, V, Tilbrook, B, Ridgway, K, Allen, S, Doherty, P, Hill, K, Moltmann, TC, Lynch, TP, Morello, EB, Evans, K, Richardson, AJ, Rochester, W, Steinberg, CR, Roughan, M, Thompson, P, Middleton, JF, Feng, M, Sherrington, R, Brando, V, Tilbrook, B, Ridgway, K, Allen, S, Doherty, P, Hill, K, and Moltmann, TC

Abstract

Sustained observations allow for the tracking of change in oceanography and ecosystems, however, these are rare, particularly for the Southern Hemisphere. To address this in part, the Australian Integrated Marine Observing System (IMOS) implemented a network of nine National Reference Stations (NRS). The network builds on one long-term location, where monthly water sampling has been sustained since the 1940s and two others that commenced in the 1950s. In-situ continuously moored sensors and an enhanced monthly water sampling regime now collect more than 50 data streams. Building on sampling for temperature, salinity and nutrients, the network now observes dissolved oxygen, carbon, turbidity, currents, chlorophyll a and both phytoplankton and zooplankton. Additional parameters for studies of ocean acidification and bio-optics are collected at a sub-set of sites and all data is made freely and publically available. Our preliminary results demonstrate increased utility to observe extreme events, such as marine heat waves and coastal flooding; rare events, such as plankton blooms; and have, for the first time, allowed for consistent continental scale sampling and analysis of coastal zooplankton and phytoplankton communities. Independent water sampling allows for cross validation of the deployed sensors for quality control of data that now continuously tracks daily, seasonal and annual variation. The NRS will provide multi-decadal time series, against which more spatially replicated short-term studies can be referenced, models and remote sensing products validated, and improvements made to our understanding of how large-scale, long-term change and variability in the global ocean are affecting Australia's coastal seas and ecosystems. The NRS network provides an example of how a continental scaled observing systems can be developed to collect observations that integrate across physics, chemistry and biology.

Published
2014

44. Association of the Hepatocyte Growth Factor Gene with Keratoconus in an Australian Population

Author

Morishita, R, Sahebjada, S, Schache, M, Richardson, AJ, Snibson, G, Daniell, M, Baird, PN, Morishita, R, Sahebjada, S, Schache, M, Richardson, AJ, Snibson, G, Daniell, M, and Baird, PN

Abstract

PURPOSE: A previous study has indicated suggestive association of the hepatocyte growth factor (HGF) gene with Keratoconus. We wished to assess this association in an independent Caucasian cohort as well as assess its association with corneal curvature. PARTICIPANTS: Keratoconus patients were recruited from private and public clinics in Melbourne, Australia. Non-keratoconic individuals were identified from the Genes in Myopia (GEM) study from Australia. A total of 830 individuals were used for the analysis including 157 keratoconic and 673 non keratoconic subjects. METHODS: Tag single nucleotide polymorphisms (tSNPs) were chosen to encompass the hepatocyte growth factor gene as well as 2 kb upstream of the start codon through to 2 kb downstream of the stop codon. Logistic and linear regression including age and gender as covariates were applied in statistical analysis with subsequent Bonferroni correction. RESULTS: Ten tSNPs were genotyped. Following statistical analysis and multiple testing correction, a statistically significant association was found for the tSNP rs2286194 {p = 1.1×10-(3) Odds Ratio 0.52, 95% CI--0.35, 0.77} for keratoconus. No association was found between the 10 tSNPs and corneal curvature. CONCLUSIONS: These findings provide additional evidence of significant association of the HGF gene with Keratoconus. This association does not appear to act through the corneal curvature route.

Published
2014

45. Comparative ecology of the copepods Calanoides carinatus and Calanus agulhensis - the influence of temperature and food

Author

Huggett, JA, Richardson, AJ, Field, JG, Department of Biological Sciences, and Faculty of Science

Subjects
cell size, copepods, food concentration, digestive, oral, and skin physiology, southern Benguela, temperature, egg production, Calanoides carinatus, Calanus agulhensis, Agulhas Bank
Abstract

Hypotheses regarding temperature, food abundance and food size were tested to explore niche separation between Calanoides carinatus, an abundant copepod in the cool and food-rich southern Benguela upwelling system, and Calanus agulhensis, the dominant copepod on the warmer, relatively food-poor Agulhas Bank off the south coast of South Africa. Under non-limiting food conditions, egg production by both species increased linearly with temperatures between 9°C and 18°C. Egg production by C. carinatus was relatively faster at 21°C, but was offset by greater mortality. Both species showed similar functional responses to food concentration in the field, reaching satiation at ∼15mg Chl a m−3, or ∼3–4ppm. Food abundance was the most important predictor of egg production, whether measured as Chl a or as particle volume. Both species preferred larger particles that dominated the biomass peak, but particle size appeared more important for C. carinatus, with increasingly faster rates of egg production as the proportion of large cells (>10μm) exceeded 50%, and slower ingestion of small (

Published
2007

47. Proof of Concept, Randomized, Placebo-Controlled Study of the Effect of Simvastatin on the Course of Age-Related Macular Degeneration

Author

Wedrich, A, Guymer, RH, Baird, PN, Varsamidis, M, Busija, L, Dimitrov, PN, Aung, KZ, Makeyeva, GA, Richardson, AJ, Lim, L, Robman, LD, Wedrich, A, Guymer, RH, Baird, PN, Varsamidis, M, Busija, L, Dimitrov, PN, Aung, KZ, Makeyeva, GA, Richardson, AJ, Lim, L, and Robman, LD

Abstract

BACKGROUND: HMG Co-A reductase inhibitors are ubiquitous in our community yet their potential role in age-related macular degeneration (AMD) remains to be determined. OBJECTIVES: To evaluate the effect of simvastatin on AMD progression and the effect modification by polymorphism in apolipoprotein E (ApoE) and complement factor H (CFH) genes. DESIGN: A proof of concept double-masked randomized controlled study. PARTICIPANTS: 114 participants aged 53 to 91 years, with either bilateral intermediate AMD or unilateral non-advanced AMD (with advanced AMD in fellow eye), BCVA ≥ 20/60 in at least one eye, and a normal lipid profile. INTERVENTION: Simvastatin 40 mg/day or placebo, allocated 1:1. MAIN OUTCOME MEASURES: Progression of AMD either to advanced AMD or in severity of non-advanced AMD. Results. The cumulative AMD progression rates were 70% in the placebo and 54% in the simvastatin group. Intent to treat multivariable logistic regression analysis, adjusted for age, sex, smoking and baseline AMD severity, showed a significant 2-fold decrease in the risk of progression in the simvastatin group: OR 0.43 (0.18-0.99), p = 0.047. Post-hoc analysis stratified by baseline AMD severity showed no benefit from treatment in those who had advanced AMD in the fellow eye before enrolment: OR 0.97 (0.27-3.52), p = 0.96, after adjusting for age, sex and smoking. However, there was a significant reduction in the risk of progression in the bilateral intermediate AMD group compared to placebo [adjusted OR 0.23 (0.07-0.75), p = 0.015]. The most prominent effect was observed amongst those who had the CC (Y402H) at risk genotype of the CFH gene [OR 0.08 (0.02-0.45), p = 0.004]. No evidence of harm from simvastatin intervention was detected. CONCLUSION/SIGNIFICANCE: Simvastatin may slow progression of non-advanced AMD, especially for those with the at risk CFH genotype CC (Y402H). Further exploration of the potential use of statins for AMD, with emphasis on genetic subgroups, is warranted.

Published
2013

48. Identification of a rare coding variant in complement 3 associated with age-related macular degeneration

Author

Zhan, X, Larson, DE, Wang, C, Koboldt, DC, Sergeev, YV, Fulton, RS, Fulton, LL, Fronick, CC, Branham, KE, Bragg-Gresham, J, Jun, G, Hu, Y, Kang, HM, Liu, D, Othman, M, Brooks, M, Ratnapriya, R, Boleda, A, Grassmann, F, von Strachwitz, C, Olson, LM, Buitendijk, GHS, Hofman, A, van Duijn, CM, Cipriani, V, Moore, AT, Shahid, H, Jiang, Y, Conley, YP, Morgan, DJ, Kim, IK, Johnson, MP, Cantsilieris, S, Richardson, AJ, Guymer, RH, Luo, H, Ouyang, H, Licht, C, Pluthero, FG, Zhang, MM, Zhang, K, Baird, PN, Blangero, J, Klein, ML, Farrer, LA, DeAngelis, MM, Weeks, DE, Gorin, MB, Yates, JRW, Klaver, CCW, Pericak-Vance, MA, Haines, JL, Weber, BHF, Wilson, RK, Heckenlively, JR, Chew, EY, Stambolian, D, Mardis, ER, Swaroop, A, Abecasis, GR, Zhan, X, Larson, DE, Wang, C, Koboldt, DC, Sergeev, YV, Fulton, RS, Fulton, LL, Fronick, CC, Branham, KE, Bragg-Gresham, J, Jun, G, Hu, Y, Kang, HM, Liu, D, Othman, M, Brooks, M, Ratnapriya, R, Boleda, A, Grassmann, F, von Strachwitz, C, Olson, LM, Buitendijk, GHS, Hofman, A, van Duijn, CM, Cipriani, V, Moore, AT, Shahid, H, Jiang, Y, Conley, YP, Morgan, DJ, Kim, IK, Johnson, MP, Cantsilieris, S, Richardson, AJ, Guymer, RH, Luo, H, Ouyang, H, Licht, C, Pluthero, FG, Zhang, MM, Zhang, K, Baird, PN, Blangero, J, Klein, ML, Farrer, LA, DeAngelis, MM, Weeks, DE, Gorin, MB, Yates, JRW, Klaver, CCW, Pericak-Vance, MA, Haines, JL, Weber, BHF, Wilson, RK, Heckenlively, JR, Chew, EY, Stambolian, D, Mardis, ER, Swaroop, A, and Abecasis, GR

Abstract

Macular degeneration is a common cause of blindness in the elderly. To identify rare coding variants associated with a large increase in risk of age-related macular degeneration (AMD), we sequenced 2,335 cases and 789 controls in 10 candidate loci (57 genes). To increase power, we augmented our control set with ancestry-matched exome-sequenced controls. An analysis of coding variation in 2,268 AMD cases and 2,268 ancestry-matched controls identified 2 large-effect rare variants: previously described p.Arg1210Cys encoded in the CFH gene (case frequency (fcase) = 0.51%; control frequency (fcontrol) = 0.02%; odds ratio (OR) = 23.11) and newly identified p.Lys155Gln encoded in the C3 gene (fcase = 1.06%; fcontrol = 0.39%; OR = 2.68). The variants suggest decreased inhibition of C3 by complement factor H, resulting in increased activation of the alternative complement pathway, as a key component of disease biology.

Published
2013

49. A rare functional haplotype of the P2RX4 and P2RX7 genes leads to loss of innate phagocytosis and confers increased risk of age-related macular degeneration

Author

Gu, BJ, Baird, PN, Vessey, KA, Skarratt, KK, Fletcher, EL, Fuller, SJ, Richardson, AJ, Guymer, RH, Wiley, JS, Gu, BJ, Baird, PN, Vessey, KA, Skarratt, KK, Fletcher, EL, Fuller, SJ, Richardson, AJ, Guymer, RH, and Wiley, JS

Abstract

Age-related macular degeneration (AMD) is a leading cause of blindness in Western countries and is diagnosed by the clinical appearance of yellow subretinal deposits called drusen. Genetic changes in immune components are clearly implicated in the pathology of this disease. We have previously shown that the purinergic receptor P2X7 can act as a scavenger receptor, mediating phagocytosis of apoptotic cells and insoluble debris. We performed a genetic association study of functional polymorphisms in the P2RX7 and P2RX4 genes in a cohort of 744 patients with AMD and 557 age-matched Caucasian control subjects. The P2X4 Tyr315Cys variant was 2-fold more frequent in patients with AMD compared to control subjects, with the minor allele predicting susceptibility to disease. Pairwise linkage disequilibrium was observed between Tyr315Cys in the P2RX4 gene and Gly150Arg in the P2RX7 gene, and these two minor alleles formed a rare haplotype that was overrepresented in patients with AMD (n=17) compared with control subjects (n=3) (odds ratio 4.05, P=0.026). Expression of P2X7 (wild type or variant 150Arg) in HEK293 cells conferred robust phagocytosis toward latex beads, whereas coexpression of the P2X7 150Arg with P2X4 315Cys variants almost completely inhibited phagocytic capacity. Fresh human monocytes harboring this heterozygous 150Arg-315Cys haplotype showed 40% reduction in bead phagocytosis. In the primate eye, immunohistochemistry indicated that P2X7 and P2X4 receptors were coexpressed on microglia and macrophages, but neither receptor was seen on retinal pigment epithelial cells. These results demonstrate that a haplotype including two rare variants in P2RX7 and P2RX4 confers a functional interaction between these two variant receptors that impairs the normal scavenger function of macrophages and microglia. Failure of this P2X7-mediated phagocytic pathway may impair removal of subretinal deposits and predispose individuals toward AMD.

Published
2013

50. Seven new loci associated with age-related macular degeneration

Author

Fritsche, LG, Chen, W, Schu, M, Yaspan, BL, Yu, Y, Thorleifsson, G, Zack, DJ, Arakawa, S, Cipriani, V, Ripke, S, Igo, RP, Buitendijk, GHS, Sim, X, Weeks, DE, Guymer, RH, Merriam, JE, Francis, PJ, Hannum, G, Agarwal, A, Armbrecht, AM, Audo, I, Aung, T, Barile, GR, Benchaboune, M, Bird, AC, Bishop, PN, Branham, KE, Brooks, M, Brucker, AJ, Cade, WH, Cain, MS, Campochiaroll, PA, Chan, C-C, Cheng, C-Y, Chew, EY, Chin, KA, Chowers, I, Clayton, DG, Cojocaru, R, Conley, YP, Cornes, BK, Daly, MJ, Dhillon, B, Edwards, A, Evangelou, E, Fagemess, J, Ferreyra, HA, Friedman, JS, Geirsdottir, A, George, RJ, Gieger, C, Gupta, N, Hagstrom, SA, Harding, SP, Haritoglou, C, Heckenlively, JR, Hoz, FG, Hughes, G, Ioannidis, JPA, Ishibashi, T, Joseph, P, Jun, G, Kamatani, Y, Katsanis, N, Keilhauer, CN, Khan, JC, Kim, IK, Kiyohara, Y, Klein, BEK, Klein, R, Kovach, JL, Kozak, I, Lee, CJ, Lee, KE, Lichtner, P, Lotery, AJ, Meitinger, T, Mitchell, P, Mohand-Saied, S, Moore, AT, Morgan, DJ, Morrison, MA, Myers, CE, Naj, AC, Nakamura, Y, Okada, Y, Orlin, A, Ortube, MC, Othman, MI, Pappas, C, Park, KH, Pauer, GJT, Peachey, NS, Poch, O, Priya, RR, Reynolds, R, Richardson, AJ, Ripp, R, Rudolph, G, Ryu, E, Sahel, J-A, Schaumberg, DA, Scholl, HPN, Schwartz, SG, Scott, WK, Shahid, H, Sigurdsson, H, Silvestri, G, Sivakumaran, TA, Smith, RT, Sobrin, L, Souied, EH, Stambolian, DE, Stefansson, H, Sturgill-Short, GM, Takahashi, A, Tosakulwong, N, Truitt, BJ, Tsironi, EE, Uitterlinden, AG, van Duijn, CM, Vijaya, L, Vingerling, JR, Vithana, EN, Webster, AR, Wichmann, H-E, Winkler, TW, Wong, TY, Wright, AF, Zelenika, D, Zhang, M, Zhao, L, Zhang, K, Klein, ML, Hageman, GS, Lathrop, GM, Stefansson, K, Allikmets, R, Baird, PN, Gorin, MB, Wang, JJ, Klaver, CCW, Seddon, JM, Pericak-Vance, MA, Iyengar, SK, Yates, JRW, Swaroop, A, Weber, BHF, Kubo, M, DeAngelis, MM, Leveillard, T, Thorsteinsdottir, U, Haines, JL, Farrer, LA, Heid, IM, Abecasis, GR, Fritsche, LG, Chen, W, Schu, M, Yaspan, BL, Yu, Y, Thorleifsson, G, Zack, DJ, Arakawa, S, Cipriani, V, Ripke, S, Igo, RP, Buitendijk, GHS, Sim, X, Weeks, DE, Guymer, RH, Merriam, JE, Francis, PJ, Hannum, G, Agarwal, A, Armbrecht, AM, Audo, I, Aung, T, Barile, GR, Benchaboune, M, Bird, AC, Bishop, PN, Branham, KE, Brooks, M, Brucker, AJ, Cade, WH, Cain, MS, Campochiaroll, PA, Chan, C-C, Cheng, C-Y, Chew, EY, Chin, KA, Chowers, I, Clayton, DG, Cojocaru, R, Conley, YP, Cornes, BK, Daly, MJ, Dhillon, B, Edwards, A, Evangelou, E, Fagemess, J, Ferreyra, HA, Friedman, JS, Geirsdottir, A, George, RJ, Gieger, C, Gupta, N, Hagstrom, SA, Harding, SP, Haritoglou, C, Heckenlively, JR, Hoz, FG, Hughes, G, Ioannidis, JPA, Ishibashi, T, Joseph, P, Jun, G, Kamatani, Y, Katsanis, N, Keilhauer, CN, Khan, JC, Kim, IK, Kiyohara, Y, Klein, BEK, Klein, R, Kovach, JL, Kozak, I, Lee, CJ, Lee, KE, Lichtner, P, Lotery, AJ, Meitinger, T, Mitchell, P, Mohand-Saied, S, Moore, AT, Morgan, DJ, Morrison, MA, Myers, CE, Naj, AC, Nakamura, Y, Okada, Y, Orlin, A, Ortube, MC, Othman, MI, Pappas, C, Park, KH, Pauer, GJT, Peachey, NS, Poch, O, Priya, RR, Reynolds, R, Richardson, AJ, Ripp, R, Rudolph, G, Ryu, E, Sahel, J-A, Schaumberg, DA, Scholl, HPN, Schwartz, SG, Scott, WK, Shahid, H, Sigurdsson, H, Silvestri, G, Sivakumaran, TA, Smith, RT, Sobrin, L, Souied, EH, Stambolian, DE, Stefansson, H, Sturgill-Short, GM, Takahashi, A, Tosakulwong, N, Truitt, BJ, Tsironi, EE, Uitterlinden, AG, van Duijn, CM, Vijaya, L, Vingerling, JR, Vithana, EN, Webster, AR, Wichmann, H-E, Winkler, TW, Wong, TY, Wright, AF, Zelenika, D, Zhang, M, Zhao, L, Zhang, K, Klein, ML, Hageman, GS, Lathrop, GM, Stefansson, K, Allikmets, R, Baird, PN, Gorin, MB, Wang, JJ, Klaver, CCW, Seddon, JM, Pericak-Vance, MA, Iyengar, SK, Yates, JRW, Swaroop, A, Weber, BHF, Kubo, M, DeAngelis, MM, Leveillard, T, Thorsteinsdottir, U, Haines, JL, Farrer, LA, Heid, IM, and Abecasis, GR

Abstract

Age-related macular degeneration (AMD) is a common cause of blindness in older individuals. To accelerate the understanding of AMD biology and help design new therapies, we executed a collaborative genome-wide association study, including >17,100 advanced AMD cases and >60,000 controls of European and Asian ancestry. We identified 19 loci associated at P < 5 × 10(-8). These loci show enrichment for genes involved in the regulation of complement activity, lipid metabolism, extracellular matrix remodeling and angiogenesis. Our results include seven loci with associations reaching P < 5 × 10(-8) for the first time, near the genes COL8A1-FILIP1L, IER3-DDR1, SLC16A8, TGFBR1, RAD51B, ADAMTS9 and B3GALTL. A genetic risk score combining SNP genotypes from all loci showed similar ability to distinguish cases and controls in all samples examined. Our findings provide new directions for biological, genetic and therapeutic studies of AMD.

Published
2013

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