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The Taipan Galaxy Survey: Scientific Goals and Observing Strategy
- Elisabete da Cunha, Andrew M. Hopkins, Matthew Colless, Edward N. Taylor, Chris Blake, Cullan Howlett, Christina Magoulas, John R. Lucey, Claudia Lagos, Kyler Kuehn, Yjan Gordon, Dilyar Barat, Fuyan Bian, Christian Wolf, Michael J. Cowley, Marc White, Ixandra Achitouv, Maciej Bilicki, Joss Bland-Hawthorn, Krzysztof Bolejko, Michael J. I. Brown, Rebecca Brown, Julia Bryant, Scott Croom, Tamara M. Davis, Simon P. Driver, Miroslav D. Filipovic, Samuel R. Hinton, Melanie Johnston-Hollitt, D. Heath Jones, Bärbel Koribalski, Dane Kleiner, Jon Lawrence, Nuria Lorente, Jeremy Mould, Matt S. Owers, Kevin Pimbblet, C. G. Tinney, Nicholas F. H. Tothill, Fred Watson
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- Journal:
- Publications of the Astronomical Society of Australia / Volume 34 / 2017
- Published online by Cambridge University Press:
- 24 October 2017, e047
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- Article
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The Taipan galaxy survey (hereafter simply ‘Taipan’) is a multi-object spectroscopic survey starting in 2017 that will cover 2π steradians over the southern sky (δ ≲ 10°, |b| ≳ 10°), and obtain optical spectra for about two million galaxies out to z < 0.4. Taipan will use the newly refurbished 1.2-m UK Schmidt Telescope at Siding Spring Observatory with the new TAIPAN instrument, which includes an innovative ‘Starbugs’ positioning system capable of rapidly and simultaneously deploying up to 150 spectroscopic fibres (and up to 300 with a proposed upgrade) over the 6° diameter focal plane, and a purpose-built spectrograph operating in the range from 370 to 870 nm with resolving power R ≳ 2000. The main scientific goals of Taipan are (i) to measure the distance scale of the Universe (primarily governed by the local expansion rate, H0) to 1% precision, and the growth rate of structure to 5%; (ii) to make the most extensive map yet constructed of the total mass distribution and motions in the local Universe, using peculiar velocities based on improved Fundamental Plane distances, which will enable sensitive tests of gravitational physics; and (iii) to deliver a legacy sample of low-redshift galaxies as a unique laboratory for studying galaxy evolution as a function of dark matter halo and stellar mass and environment. The final survey, which will be completed within 5 yrs, will consist of a complete magnitude-limited sample (i ⩽ 17) of about 1.2 × 106 galaxies supplemented by an extension to higher redshifts and fainter magnitudes (i ⩽ 18.1) of a luminous red galaxy sample of about 0.8 × 106 galaxies. Observations and data processing will be carried out remotely and in a fully automated way, using a purpose-built automated ‘virtual observer’ software and an automated data reduction pipeline. The Taipan survey is deliberately designed to maximise its legacy value by complementing and enhancing current and planned surveys of the southern sky at wavelengths from the optical to the radio; it will become the primary redshift and optical spectroscopic reference catalogue for the local extragalactic Universe in the southern sky for the coming decade.
5 - Investigating bacterial microevolution through next generation sequencing
- from Part I - Next Generation Phylogenetics
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- By Josephine M. Bryant, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK, Simon R. Harris, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Edited by Peter D. Olson, Natural History Museum, London, Joseph Hughes, University of Glasgow, James A. Cotton
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- Book:
- Next Generation Systematics
- Published online:
- 05 June 2016
- Print publication:
- 16 June 2016, pp 101-120
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Summary
Introduction
There is no doubt that since 1995 when the first two bacterial genomes were fully sequenced, Haemophilus influenzae (Fleischmann et al. 1995) and Mycoplasma genitalium (Fraser et al. 1995), our understanding of bacterial pathogens has benefited hugely from the wealth of information provided by high-quality reference bacterial genomes. Over the past 20 years, comparative analyses of these reference genomes has unravelled many of the mechanisms of pathogenicity. However, we are now in the age of NGS, which has revolutionized the field of comparative genomics, allowing evolutionary adaptations to be placed in a more resolved phylogenetic framework, and the emergence of virulence, pathogenicity and antibiotic resistance to be reconstructed far more accurately. The fine-scale resolution and low cost of NGS permit investigations of genome variation at an unprecedented scale, within an individual species or even at the level of individual disease outbreaks or bacterial populations within a patient. Furthermore, simple tweaks to the methodologies can provide a wealth of functional information that, when placed in a phylogenetic context, drives our understanding of pathogen biology even further forward. Here, we provide a review of recent progress in the field of bacterial genomics, and its impact both clinically and intellectually on our knowledge of bacterial pathogens.
Historical context: molecular typing of bacteria
To understand the evolution and spread of bacterial pathogens, it is essential to not only discriminate between species, but also have the ability to discriminate at the subspecies level. Researchers across all fields of microbiology depend on molecular typing techniques in order to obtain the resolution to investigate population structure (Maiden et al. 1998), molecular evolution (Feil et al. 1999), epidemiological tracking (Foley et al. 2009) and phenotypic variation (Brown et al. 2010). Furthermore, molecular typing techniques are instrumental in the clinical setting to provide precise diagnoses of infections (Goering et al. 2013). Traditional molecular typing techniques typically depend on the sequencing of a small number of loci. The speed and process by which these loci evolve vary depending on the bacteria in question, each bringing its own advantages and limitations. For Mycobacterium tuberculosis, which causes TB, variable number tandem repeats (VNTRs) and insertion sequences (IS elements), including IS6110, are typically used as the typing loci because they have a relatively high genetic turnover, allowing some level of discrimination in what is an extremely clonal pathogen with a very slow mutation rate.
Contributors
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- By Jennifer Alvarez, Ananda B. Amstadter, Metin Başoğlu, David M. Benedek, Charles C. Benight, George A. Bonanno, Evelyn J. Bromet, Richard A. Bryant, Barbara Lopes Cardozo, M. L. Somchai Chakkraband, Claude Chemtob, Roman Cieslak, Lauren M. Conoscenti, Joan M. Cook, Judith Cukor, Carla Kmett Danielson, JoAnn Difede, Charles DiMaggio, Anja J.E. Dirkzwager, Cristiane S. Duarte, Jon D. Elhai, Diane L. Elmore, Yael L.E. Errera, Julian D. Ford, Carol S. Fullerton, Sandro Galea, Freya Goodhew, Neil Greenberg, Lindsay Greene, Linda Grievink, Michael J. Gruber, Sumati Gupta, Johan M. Havenaar, Alesia O. Hawkins, Clare Henn-Haase, Kimberly Eaton Hoagwood, Christina W. Hoven, Sabra S. Inslicht, Krzysztof Kaniasty, Ronald C. Kessler, Rachel Kimerling, Richard V. King, Rolf J. Kleber, Jessica Mass Levitt, Brett T. Litz, Maria Livanou, Katelyn P. Mack, Paula Madrid, Shira Maguen, Paul Maguire, Donald J. Mandell, Charles R. Marmar, Andrea R. Maxwell, Shannon E. McCaslin, Alexander C. McFarlane, Thomas J. Metzler, Summer Nelson, Yuval Neria, Elana Newman, Thomas C. Neylan, Fran H. Norris, Carol S. North, Lawrence A. Palinkas, Benjaporn Panyayong, Maria Petukhova, Betty Pfefferbaum, Marleen Radigan, Beverley Raphael, James Rodriguez, G. James Rubin, Kenneth J. Ruggiero, Ebru Şalcıoğlu, Nancy A. Sampson, Arieh Y. Shalev, Bruce Shapiro, Laura M. Stough, Prawate Tantipiwatanaskul, Warunee Thienkrua, Phebe Tucker, J. Blake Turner, Robert J. Ursano, Bellis van den Berg, Peter G. van der Velden, Frits van Griensven, Miranda Van Hooff, Edward Waldrep, Philip S. Wang, Simon Wessely, Leslie H. Wind, C. Joris Yzermans, Heidi M. Zinzow
- Edited by Yuval Neria, Columbia University, New York, Sandro Galea, University of Michigan, Ann Arbor, Fran H. Norris
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- Book:
- Mental Health and Disasters
- Published online:
- 07 May 2010
- Print publication:
- 20 July 2009, pp xi-xvi
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The effects of [K+]o on regional differences in electrical characteristics of ventricular myocytes in guinea-pig
- Xiaoping Wan*, Simon M. Bryant, George Hart
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- Journal:
- Experimental Physiology / Volume 85 / Issue 6 / November 2000
- Published online by Cambridge University Press:
- 10 January 2001, pp. 769-774
- Print publication:
- November 2000
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Altering [K+]o might have different effects on action potential duration (APD) in myocytes from different regions. Therefore, the effects of [K+]o on regional differences in action potential characteristics were investigated in sub-endocardial, mid-myocardial and sub-epicardial myocytes isolated from the base of guinea-pig left ventricular free wall using three different [K+]o (2.7, 5.4 and 8.1 mM KCl). Action potentials were recorded using the switch-clamp technique at 0.5 Hz. Increasing [K+]o from 2.7 to 8.1 mM shortened the action potential duration to 90 % repolarization (APD90; mean APD90 values in sub-endocardial, mid-myocardial and sub-epicardial myocytes were, respectively, 295 +- 9, 286 +- 9 and 266 +- 8 ms in 2.7 mM [K+]o, 270 +- 7, 255 +- 7 and 215 +- 7 ms in 5.4 mM [K+]o, 234 +- 7, 212 +- 10 and 155 +- 8 ms in 8.1 mM [K+]o), depolarized the resting potential, and reduced the amplitude of the action potential. The effect of increasing [K+]o on action potential characteristics was more pronounced in sub-epicardial myocytes than in sub-endocardial and mid-myocardial myocytes. The regional differences in APD90 in 5.4 mM [K+]o were increased in 8.1 mM [K+]o and abolished in 2.7 mM [K+]o. In conclusion, changing [K+]o produces more pronounced effects on action potentials in sub-epicardial myocytes than in sub-endocardial myocytes, modifying the normal heterogeneity of action potentials. The differences in the response of sub-epicardium and sub-endocardium to [K+]o may contribute to the flattening or inversion of the T wave commonly seen in patients presenting with hypokalaemia and the upright and tall T waves observed in electrocardiograms recorded during hyperkalaemia, although the underlying ionic currents remain to be determined.