The development of techniques to distinguish species and strains of giardia : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University

Water supplies, in some rural areas of New Zealand, contain Giardia cysts. This is assumed to make the water unsuitable for human consumption. G. intestinalis and/or G. muris cysts may be present but are not distinguished by the standard test. G. muris infects rodents only so it is not infectious for humans. However G. intestinalis infects humans and a wide range of animals, but it is unclear if the strains which infect animals also infect humans. If G. intestinalis strains are host-specific, then since water in rural areas may contain cysts derived only from animal species it would follow that the water (even if G. muris and/or G. Intestinalis cysts were found) may not be infectious for humans. Investigation of host-specificity of G. intestinalis would be facilitated by a reliable test to distinguish strains of the organism and this thesis investigates the use of PCR for this purpose. A series of random primers were investigated for their ability to distinguish strains of G. intestinalis when used with a variety of PCR protocols. We found that several of these primers (especially GC50 at an annealing temperature of 35°C, and GC80 at an annealing temperature of 35°C) had the potential to distinguish strains. The differences seen were not large but this may be because some of the isolates were clonally related. Consequently we concluded that further modifications and extensions of PCR when applied to human and animal strains should distinguish strains and may have the potential to address the question of host-specificity. The major aim of the thesis however was to produce primers which when used in the PCR are capable of distinguishing G. muris from G. intestinalis. The same approach,ie the use of a random primer, was used to distinguish G. muris from G. intestinalis. Clear differences were seen but the non-specificity of the random primer would allow the organisms to be reliably distinguished only in the absence of other organisms. To avoid this lack of specificity an amplified band produced with G. muris DNA but not with G. intestinalis DNA was sequenced and a primer pair was selected. These primers were, in principle, long enough (21-mer and 23-mer) to be specific for the target DNA and were chosen so as to have matched melting temperatures. The selected primer pair amplified a sequence 307bp long, and the primer sequences were specific for the target species, namely G. muris. Thus in our hands using PCR this primer pair amplified DNA from the available strains of G. muris but failed to amplify DNA from any of seven G. intestinalis strains. Further work is required to establish both an optimal method for lysing cysts and to estimate the minimum number of cysts required to ensure that DNA is available for amplification. However, the availability of the G. muris -specific primers, along with the recently developed genus and G. intestinalis -specific primers should allow us to undertake investigations of water supplies to see if G. muris, G. intestinalis or both species are present. In the case of a small rural supply it would seem reasonable to accept the potability of water supplies containing G. muris only, as long as assurance could be given that G. intestinalis was not present

Expressive and Instrumental Voting: The Scylla and Charybdis of Constitutional Political Economy

Brennan and Hamlin (2002) note that expressive voting still holds at the constitutional phase. The argument, when taken to its necessary conclusion, proves quite problematic for Constitutional Political Economy. Veil mechanisms following Buchanan induce expressive voting at the constitutional phase, removing the normative benefits ascribed to the hypothetical unanimity principle. If the constitution is authored by a small group and the veil is thereby removed, instrumental considerations come to bear and the authors of the constitution establish themselves as Oligarch.expressive voting, constitutional political economy, Leviathan

Karst, GIS and geological hazard planning and management in Great Britain

The British Geological Survey (BGS) database of karst features for the United Kingdom include dolines, cave entrances, stream sinks, resurgences and building damage; data for approximately half of the country has so far been gathered. BGS makes and utilises digital geological map data, which includes lithological and stratigraphical information for bedrock and superficial deposits. By incorporating this digital map data with digital elevation slope models and karst data, BGS has generated a derived dataset assessing the likelihood of subsidence due to karst collapse. This dataset is informed and verified by the karst database and marketed as part of its GeoSure suite; the karst layer includes areas of limestone, chalk, gypsum and salt. It is currently used by environmental regulators, the insurance and construction industries plus the BGS semi-automated enquiry system. The karst database and GeoSure datasets can be combined and manipulated using GIS to make other datasets that deal with specific problems. Sustainable drainage systems, some of which use soak-aways into the ground are being encouraged in the UK, but in karst areas they can cause problems. Similarly, open loop ground source heat pumps may induce subsidence if installed in certain types of karst such as chalk with overlying sand deposits. Groundwater abstraction also has the potential to trigger subsidence in karst areas. GIS manipulation of the karst information will allow the UK to be zoned into areas suitable, or unsuitable, for such uses; it has the potential to become part of a suite of planning management tools for local and National Government to assess the long term sustainable use of the ground

Arabian adventures

The United Arab Emirates (UAE) is one of the world’s most rapidly urbanising countries. Despite the recent downturn in the economy, the region continues to undergo rapid development, particularly around Abu Dhabi and Dubai. Consequently the country is host to many major civil engineering projects including the world’s tallest building, artificial offshore islands, new international airports, metro systems and high-speed rail networks

Subterranean glacial spillways: an example from the karst of South Wales, UK

Many karst areas in the UK have been glaciated one or more times during the last 0.5 Ma, yet there are few documented examples of caves in these regions being affected by glacial processes other than erosion. The karst of South Wales is one area where sub or pro-glacial modification of pre-existing caves is thought to occur. Evidence from the Ogof Draenen cave system suggests that caves can sometimes act as subterranean glacial ‘underspill’ channels for melt-water. This cave, one of the longest in Britain with a surveyed length of over 70 km, underlies the interfluve between two glaciated valleys. Sediment fills and speleo-morphological observations indicate that melt-water from a high level glacier in the Afon Lwyd valley (>340m asl) filled part of the cave and over-spilled into the neighbouring Usk valley, temporarily reversing non-glacial groundwater flow directions in the cave. It is suggested that this may have occurred during a Middle Pleistocene glaciation

Geology of the Greywell area, Basingstoke, Hampshire

This report gives a brief account of the geology of the Greywell area near Basingstoke, Hampshire. The Greywell area lies approximately 8 km east-south-east of Basingstoke, and is located on the 1:50 000 scale geological map sheet 284 (Basingstoke). The area was last completely mapped during the six-inch survey of the Basingstoke district, which was published in 1897 (Figures 1 and 2). A partial revision of the Chalk outcrop was undertaken in 2007 by K A Booth, but did not include the Palaeogene outcrop. The published geological map is based on the 1897 six-inch survey of the Basingstoke district (Figures 1 and 2). Consequently the map does not show the new Chalk lithostratigraphy, nor is the bedrock related to modern topographical contours. Thus there is considerable uncertainty in the location of the Chalk- Palaeogene contact in the Greywell area. As part of a groundwater modelling investigation in the Whitewater River catchment, focussed on the Greywell pumping station, BGS was asked by the client (Jacobs Engineering) to undertake a partial revision of the Basingstoke geological map sheet around the Whitewater valley. The present survey was commissioned to obtain additional field data and combine that with borehole records and topographic data to provide a more accurate indication of the Chalk– Palaeogene boundary. The area between Up Nately, Greywell, North Warnborough and Odiham was resurveyed in mid September 2012 by A R Farrant, in particular focussing on the Chalk– Palaeogene boundary, including a zone up to 0.5 km either side of the contact. Superficial deposits were also mapped, but no additional boreholes or sections were excavated or logged. Existing BGS records including old field-slips, borehole records and historic maps, along with information on the Greywell Canal Tunnel from the Surrey & Hampshire Canal Society (see http://www.basingstoke-canal.org.uk/engineering/tunnels.htm) were also used in the compilation of the new line work. Fieldwork was undertaken by a standard walkover survey with a soil auger. The new line-work is shown in Figures 3, and also in Figures 5 and 6 at the end of the report

Model metadata report for HS2 area 1 (Great Missenden to Aylesbury)

This report describes the 3D geological model of HS2 (High Speed 2 rail link) Area 1 (Great Missenden to Aylesbury), created by Dr Andrew Farrant with support from Steve Thorpe and Ricky Terrington. The model was created as part of a set of nine geological models that cover the proposed HS2 rail route from the end of the HS2 London model to Birmingham and the West Coast Main Line near Lichfield. The models were funded from the NERC/BGS Science Budget to promote BGS modelling and geological interpretation services to this important infrastructure project and to test methodologies and procedures for creating geological models by multiple compilers. The report describes the model construction and purpose, with spatial limits and scale, sources of information, data processing, workflow, decisions, assumptions, rules and limitations, together with images of the model

Hayek, Mill and the Liberal Tradition

This book considers the relationship between Hayek and Mill, taking issues with Hayek’s criticism of Mill and providing a broader perspective of the liberal tradition. Featuring contributions from the likes of Ross Emmett, Leon Montes and Robert Garnett, these chapters ask whether Hayek had an accurate reading of the ideas of Mill and Smith, as well as considering themes such as sympathy and analytical egalitarianism that play a large part in the liberal tradition, but less in work of Hayek These chapters argue that addition of these key ideas to the Hayekian corpus leads to a far broader understanding of the liberal tradition than that provided by Hayek Introduction, Andrew Farrant , 1.Hayek and the Liberal Tradition, 1. Is Friedrich Hayek rowing Adam Smith’s boat, Leon Montes , 2. F. A. Hayek’s Sympathetic Agents, David M. Levy and Sandra Peart , 3. Discussion and the Evolution of Institutions in a Liberal Democracy: Frank Knight Joins the Debate, Ross Emmett , 2. Pushing the Boundaries of the Liberal Tradition? , 4. Hayek, Mill, and the Problem of Institutional Change?, Andrew Farrant , 5. A Socialist Spontaneous Order, Theodore A. Burczak , 6. Hayek and Philanthropy: A Classical Liberal Road Not (Yet) Taken, Robert Garnet