Program 4: National Research Infrastructure: National Facilities and Collections

The highlights, deliverables and performance of our National Research Facilities and National Biological Collections.

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Objectives and deliverables

CSIRO hosts National Research Infrastructure on behalf of the scientific community to assist with the delivery of research.

There are two types of National Research Infrastructure: National Research Facilities and National Biological Collections.

In addition, CSIRO hosts 30 other research facilities and over 30 national reference collections.

National Research Facilities are available for use by Australian and international researchers and are not restricted to CSIRO personnel.

National Biological Collections are similarly available to all researchers and are storehouses of information on Australia’s biodiversity.

They support a significant part of the country’s taxonomic, genetic, bio-geographical and ecological research and are a vital resource for conservation and research.

Program performance

The performance of CSIRO’s National Research Infrastructure Program is assessed through six key performance indicators. Table 2.13 provides a summary of progress. More detailed analysis and trend data follow the Table.

Table 2.13: Performance indicators for Program 4 – National Research Infrastructure.
Key performance indicator Target (and performance assessment) Performance
Utilisation of the National Research Infrastructure Maintain or increase CSIRO maintained the levels of availability and supported an increase in the use of the National Research Infrastructure under its custodianship.
Maintenance and operation of National Research Infrastructure Meet international standards Compliance with relevant Australian and International Standards was achieved. Initiatives to strengthen and enhance the maintenance and operation standards for all National Research Infrastructure were also undertaken in 2012–13.
Coverage of National Biological Collections Maintain or increase The coverage of Australian species in the National Biological Collections was maintained in line with previous years. The Australian National Fish Collection increased by two per cent from 2011–12.
Proportion of National Biological Collections digitised and available to the public Maintain or increase The proportion of the National Biological Collections digitised was maintained, with the exception of the National Wildlife Collection which increased by one per cent from 2011–12.
Response to national events Timely response CSIRO successfully launched a world-first vaccine for the Hendra virus – Equivac®. On behalf of the United Nations Food and Agriculture Organisation, the Australian Animal Health Laboratory (AAHL) also produced test kits to detect the new avian influenza strain among Asian poultry, which has now been supplied to laboratories in over 13 countries.
Scientific contributions in support of research Demonstrated high-quality contributions CSIRO’s National Research Infrastructure continues to provide significant support and opportunities for collaboration with Australian and international scientific communities. For example, an international team of astronomers used the Parkes telescope to detect enormous ‘geysers’ of gas in our Galaxy which has provided additional understanding of galaxy formation and evolution.

Green shading: indicates positive progress for the year and the target has been achieved. Yellow shading: indicates some challenges have occurred during the year, but they were managed. Red shading: indicates challenges have affected progress and resulted in the target not being achieved. White/no colour: indicates that this is the first year results have been recorded for this indicator therefore no trend can be observed.

National Research Facilities

CSIRO operates a range of specialised laboratories, scientific and testing equipment, and other research facilities. The three major National Research Facilities, classified as landmark facilities, are:

The Australian Animal Health Laboratory (AAHL)

AAHL is located in Geelong, Victoria and is a national centre of excellence in disease diagnosis, research and policy advice in animal health and human diseases of animal origin (zoonoses).

AAHL helps protect Australia’s billion-dollar livestock and aquaculture industries, and the general public, from exotic and emerging infectious diseases.

Maintenance and operation of National Research Infrastructure

Indicator: All National Research Infrastructure maintained and operated to international standard.

As a crucial part of Australia’s biosecurity infrastructure, maintaining the integrity of the AAHL high-containment facility and ensuring our preparedness in the event of an outbreak, requires continuous monitoring.

AAHL has therefore remained operational 24 hours a day, 365 days a year since the official opening in 1985.

AAHL PC4 Zoonosis Suite (previously called the AAHL Collaborative Biosecurity Research Facility) was used extensively during the testing and development of the Hendra virus vaccine that was released for provisional use in horses in late 2012.

The PC4 Zoonosis Suite is routinely used to investigate the comparative pathogenesis and immunology of Hendra and Nipah viruses in bats, and to perform routine national diagnostic testing procedures that require handling of the live Hendra virus (see Program 1 for more information about the Hendra vaccine).

To ensure best practice in aspects of biocontainment and to uphold the quality and integrity of our research, AAHL aims to maintain or exceed the many regulatory requirements.

AAHL continues to retain accreditation to ISO/IEC 17025:2005 and certification of its management system to AS/NZS ISO 9001:2008 and environmental management system to AS/NZS ISO 14001:2004.

AAHL expanded its function as an international proficiency testing provider in 2012 for exotic disease agents and has maintained accreditation to ISO/IEC17043.

The facility is operating with all of its facilities certified by the Department of Agriculture, Fisheries and Forestry, the Office of the Gene Technology Regulator and the Department of Health and Ageing’s Security Sensitive Biological Agent legislation.

The safety of staff is paramount at all times and a rigorous program of microbiological and safety training is provided throughout the year.

The Australia Telescope National Facility (ATNF)

ATNF is operated and managed by CSIRO’s Division of Astronomy and Space Science, is made up of radio telescopes at three observatories, near the towns of Parkes, Coonabarabran and Narrabri in New South Wales.

A fourth telescope, the next generation Australian Square Kilometre Array Pathfinder (ASKAP) is currently being developed at the Murchison Radio-astronomy Observatory in Western Australia.

All 36 antennas are now in place and are progressively being outfitted with radio-frequency receivers and commissioned.

ATNF also continues to maintain and upgrade its existing instrumentation. New wide bandwidth receivers, sensitive to radio signals in the four centimetre wavelength band, were installed on all antennas of the Australia Telescope Compact Array – this increases the sensitivity of the telescope to better pick-up faint sources of radio emission from across space.

A new Telescope Protection System was commissioned at the Parkes Telescope to ensure the telescope and its systems are safely protected.

The telescope is a massive piece of infrastructure (the dish is 300 tonnes) which has motors, gearboxes, brakes and moving parts. The protection system enables the safe and unattended operation of the telescope by remotely located observers.

Utilisation of the National Research Infrastructure

Indicator: Utilisation of the National Research Infrastructure (the number of loans, visitor days, research days, observation time or operation time).

The Mopra telescope is now operating under a new model, with funding from the National Astronomical Observatory of Japan, the University of New South Wales, and the University of Adelaide.

These groups support the operation of the telescope and are provided dedicated access in return. Infrastructure at the Mopra Observatory suffered significant damage in a bushfire in January 2013, but critical equipment was unharmed, and the telescope restored to operation in May.

The telescopes of the ATNF continue to be oversubscribed, see Table 2.14. International astronomers account for half the user community, with CSIRO staff and other Australian researchers sharing the remainder of the time.

Observing time is determined on scientific merit of the proposals received. Over 75 per cent (target is to exceed 70 per cent) of the time was allocated for astronomical observations on the Australia Telescope Compact Array and Parkes Telescope, with telescope maintenance, reconfigurations and changes accounting for almost 20 per cent of the time.

Time lost during scheduled observations due to equipment failure remained below five per cent, which is in line with other observatories. Over 100 papers using ATNF data were also published in refereed journals in 2012.

The Marine National Facility (MNF)

MNF is under the direction of an independent Steering Committee and managed by CSIRO’s Division of Marine and Atmospheric Research.

MNF is made up of a 66-metre blue-water research vessel, Southern Surveyor, a package of unique scientific equipment and a collection of 28 years of marine data.

It has the scientific, technical and administrative expertise required to safely and effectively manage an ocean-going research platform.

CSIRO is managing a major project to design and build a new state-of-the-art research vessel, the 94-metre RV Investigator, scheduled to be delivered in late 2013 to replace the Southern Surveyor.

Utilisation of the National Research Infrastructure

Indicator: Utilisation of the National Research Infrastructure (the number of loans, visitor days, research days, observation time or operation time).

MNF provided 203 days (58 per cent) of ship time grants out of 390 days requested by researchers.

Figure 2.21: Access to the Marine National Facility.

Show text description

This figure now includes transit voyages utilised for student training and opportunistic science and results in the slight increase in the days observed, see Figure 2.21. In addition, there were 21 research charter days.

Table 2.14: Utilisation of National Research Facilities46.
Access to National Research Infrastructure 2008–09 2009–10 2010–11 2011–12 2012–13
Australia Telescope National Facility*
Time allocated to observations (%) 76 75.3 72.4 73.6 76.7
Time lost to equipment failure (%) 3 2.9 3.1 2.7 2.7
Time allocated to CSIRO staff (%) 20 24 24 22 22
Time allocated to other Australian researchers (%) 30 23 25 21 28
Time allocated to international researchers (%) 50 53 51 57 50

*More information can be found in the ATNF’s Annual Report.

Participants included scientists from 18 Australian institutions including the:

  • Antarctic Climate and Ecosystems Cooperative Research Centre
  • Australian National University
  • Bureau of Meteorology
  • Museum and Art Gallery of the Northern Territory
  • Earthwatch
  • Geoscience Australia
  • James Cook University
  • Macquarie University
  • South Australian Research and Development Institute
  • University of New South Wales
  • University of Tasmania
  • University of Western Australia
  • University of Wollongong
  • collaborating scientists from institutions in China, Germany, Japan, New Zealand, Spain, the United Kingdom and the USA.

The development of the next generation of marine researchers was enhanced by enabling 33 students to experience scientific work at sea in the MNF’s Next Wave program.

This program enables institutions to propose training and education activities for onboard delivery that integrates with campus based studies, and provides a unique opportunity for early career researchers and students of marine science to experience the working environment of Australia’s only blue-water research vessel.

Maintenance and operation of National Research Infrastructure

Indicator: All National Research Infrastructure maintained and operated to international standard.

CSIRO is building a new state-of-the-art MNF research vessel RV Investigator to replace the current vessel Southern Surveyor.

The 42-year-old Southern Surveyor will continue research voyages until September 2013 and will then be decommissioned. The new vessel, RV Investigator, is nearing completion and is due in Hobart later in 2013 to commence a commissioning program.

Interest in the new vessel remains high with progress being reported to the public through a CSIRO blog .

National Biological Collections

Coverage of National Biological Collections

Indicator: Coverage of National Biological Collections (percentage of known species).

CSIRO is the custodian of four National Biological Collections:

  • Australian National Insect Collection (ANIC), specialising in terrestrial invertebrates
  • Australian National Wildlife Collection (ANWC), specialising in land vertebrates
  • Australian National Fish Collection (ANFC), specialising in marine fishes
  • Australian National Herbarium (ANH), specialising in our native plants and weeds

and over 20 smaller collections of interest that contribute to the discovery, inventory, understanding and conservation of Australia’s biological diversity.

The National Biological Collections provide up to 99 per cent coverage of Australian species (see Table 2.15), although in the national context the collections have focused on building strength in particular areas.

Table 2.15: Coverage of the National Biological Collections.
Proportion of diversity covered (%)
Collection 2009–10 2010–11 2011–12 2012–13
Australian National Insect Collection 70 70 70 70
Australian National Wildlife Collection Birds – 99 Other vertebrates – 55 Birds – 99 Other vertebrates – 55 Birds – 99 Other vertebrates – 55 Birds – 99 Other vertebrates – 55
Australian National Fish Collection 50 54 57 59
Australian National Herbarium 70 70 70 70

These collections are a vital resource for the provision of accurate and reliable information on species identification for biosecurity, conservation and the development of sustainable land and marine management systems.

The collections contribute to a range of national and international initiatives such as the Global Biodiversity Information Facility and the Intergovernmental Platform on Biodiversity and Ecosystem Services through staff participation and data provision.

They also contribute significantly to on-ground national biodiversity research initiatives such as Bush Blitz (Australian Biological Resources Study), the Biomes of Australian Soil Environments project (Bioplatforms Australia) and the High Rainfall Zone Biodiversity Project (Grains Research and Development Corporation (GRDC)).

In each case the collections make a crucial contribution by providing unique biodiversity reference datasets that represent the highest quality comprehensive, up-to-date, geocoded, biologically accurate, digitised inventories of Australian biodiversity assets.

The National Biological Collections continue to be widely accessed by a range of users. Metrics for 2012–13 remain largely comparable to those for the previous year.

Greater access to collections data via web portals such as the Atlas of Living Australia, Australia’s Virtual Herbarium and the Online Zoological Collections of Australian Museums has contributed to sustained demand for access to specimens by external researchers (see Table 2.16).

The creation of the Australian National Biological Collections Facility (ANBCF) Theme in 2012 has facilitated greater interaction between the individual collections, in both research and specimen management.

For example, the ANBCF is currently undertaking an evaluation of collection management software with a view to improving and integrating data management across the collections, as well as providing more secure long-term data management.

Similarly, a proposal to study the evolution of the biota of southern Papua New Guinea (and how it is related to that of northern Australia) is bringing together researchers and specimen data from across the major collections.

Pilot funding for the first 12 months of this work, focusing on plant biodiversity, has been secured from the Department of Sustainability, Environment, Water, Population and Communities.

This project will facilitate digitisation of New Guinea specimens in the ANBCF and deliver data to our regional neighbours for biodiversity inventory and environmental risk assessment. It will also provide opportunities for regional capability building biodiversity science.

This year the Australian National Insect Collection (ANIC) experienced a considerable increase in demand for beetle tissue resulting from a high-profile project documenting this mega-diverse group. ANIC research days have also significantly increased with several collaborators visiting for six months and longer.

Table 2.16: Combined utilisation of National Biological Collections.
Use of National Biological Collections 2008–09 2009–10 2010–11 2011–12 2012–13
Number of specimens dispatched 7,800 29,300 25,925 15,548 13,660
Outward going loans 138 147 193 157 153
Tissue samples sent 3,300 3,800 4,447 3,819 2,415
Tissue sample grants 79 44 40 43 74
Number of visitors hosted 155 186 336 267 238
Total visitor research days 403 713 551 800 1,066
Number of tours hosted 47 57 70 52 67
Total number of visitors on tours 535 597 1,266 363 586

Digitisation of collections

Proportion of National Biological Collections digitised

Indicator: Proportion of National Biological Collections digitised and available to the public.

The proportion of specimen level material digitised in the four collections ranges from five to 100 per cent, see Table 2.17.

Digitisation activity in the ANIC is focused on databasing and imaging the most scientifically valuable specimens and is value-adding to research projects by making taxonomic and phylogenetic information available online. Imaging of whole insect drawers has continued. Images and data are delivered to and accessible through the Atlas of Living Australia (ALA) .

The ANWC’s collections of birds, mammals, reptiles and amphibians comprise dried skins, skeletal specimens, whole specimens in alcohol and eggs. They have been almost completely digitised, even as the collection grows. Four thousand files of bird vocalisations from the Sound Library are available for download from the ALA.

The ANFC specimen data is 100 per cent digitised. Approximately 65 per cent of these data are available publicly through the Online Zoological Collections of Australian Museums [external link] and the ALA.

The majority of ANH Australian specimen records are digitised, with 100 per cent available through Australia’s Virtual Herbarium [external link] and the ALA.

Preparation for a new project to digitise ANH specimens from Papua New Guinea has also commenced. All type collections are now being imaged as part of a joint initiative across Australian herbaria, funded by the Mellon Foundation.

Demonstrated response to national events

Indicator: Demonstrated response to national events.

November 2012 saw the successful launch of Equivac® – the Hendra virus vaccine. AAHL has worked in close partnership with Zoetis Australia (formerly Pfizer Animal Health), the Uniformed Services University of the Health Sciences and the Henry M Jackson Foundation for the Advancement of Military Medicine to bring this discovery from the laboratory to market, for use in horses by registered veterinarians (more in Program 1).

On behalf of the United Nations Food and Agriculture Organisation, AAHL has also delivered as an international reference laboratory for animal influenzas, producing reagent test kits to detect the new avian influenza strain A (H7N9) amongst Asian poultry.

These test kits have now been supplied to laboratories in over 13 countries.

Table 2.17: Digitisation of the National Biological Collections.
Proportion of collection digitised (%)
Collection 2009–10 2010–11 2011–12 2012–13
Australian National Insect Collection 2.9 5 5 5
Australian National Wildlife Collection (excluding sound collection) 86 91 91 92
Australian National Fish Collection 100 100 100 100
Australian National Herbarium 76 76 76 76

Scientific contributions in support of research

Indicator: Demonstrated high-quality scientific contributions in support of National Research Flagships, CSIRO Core Research and external users.

Dr Jean-Bernard Duchemin, CSIRO Research Scientist, working in AAHL’s high-containment insectary.

This section highlights some of the high-quality scientific contributions made by the National Facilities and Collections in 2012–13.

Australian Animal Health Laboratory

During 2012–13, AAHL researchers reported a world-first discovery that mosquitoes can mount an immune response to zoonotic viruses, such as West Nile virus, by secreting specific antiviral proteins when infected by the virus.

This foundational discovery establishes the possibility that vector-borne diseases transmitted by insects might be counteracted by modifying the insect’s own immune system, or that these newly-discovered antiviral proteins produced by insects could form the basis for new classes of antiviral drugs.

Australia Telescope National Facility

An international team of astronomers used the Parkes telescope to detect enormous ‘geysers’ of gas in our galaxy.

These massive outflows of charged particles, which emanate from the centre of our galaxy and stretch more than halfway across the sky, correspond with regions of gamma-ray emission detected with NASA’s Fermi space telescope in 2010, which were dubbed the ‘Fermi Bubbles’.

The research was reported in the science magazine Nature and provides us with additional understanding of galaxy formation and evolution.

The ‘geysers of gas’ (pale blue) from the Galactic Centre. The background image is the whole Milky Way at the same scale. © Ettore Carretti, CSIRO (radio image); S-PASS survey team (radio data); Axel Mellinger, Central Michigan University (optical image); Eli Bressert, CSIRO (composition)

Marine National Facility

The new MNF vessel, Investigator, is nearing completion and will greatly increase Australia’s research capability. © Chris Dickinson

Following underwater landslides of marine sediment off Queensland’s southern coast in 2008, University of Sydney researchers onboard the MNF research vessel, Southern Surveyor, studied the sea floor to determine the potential for future tsunami-forming landslide events in this region.

The Southern Surveyor was also instrumental in finding a wreck site which enabled the New South Wales Government to identify the MV Limerick, which was sunk by torpedo in 1943.

In addition, CSIRO deployed and serviced Integrated Marine Observing System deep sea moorings in the Southern Ocean, Timor Passage and the Indian Ocean, in partnership with the University of Tasmania.

The moorings monitor conditions in the ocean and atmosphere from year to year. Information collected from these moorings is used to improve the understanding and prediction of climate change processes on a national and global scale.

Later in 2013, arrival of the new MNF vessel Investigator will greatly increase the scientific capability for Australian marine researchers and their international collaborators to work in the furthest reaches of our vast marine estate, including to the Antarctic ice edge, with larger teams covering many fields of research.

Honorary Research Fellow, Dr Marianne Horak, has uncovered the mechanism responsible for the scribbles on the scribbly-gum and described 11 new species of scribbly-gum moth (Ogmograptis sp.)

Australian National Insect Collection

During 2012–13, ANIC researchers, using taxonomy, which describes new species and how they relate to each other in a classification, produced revised information on various insect groups.

Working with organisations such as the British Natural History Museum and the Chinese Academy of Sciences, CSIRO scientists looked at the evolution of fruit flies, thrips and beetles using molecular genetic datasets.

The highly-anticipated taxonomic revision of the iconic Australian scribbly-gum moth made a significant impact in international journals and through social media outlets.

ANIC researchers were the first to uncover the way in which the scribbles are made by moth larvae, along with the biology and lifecycle of the moths responsible.

In the process they described eleven new species of moth and redefined how scribbly-gum moths fit into the moth family tree.

Australian National Wildlife Collection

Wandering Whistling-Duck Dendrocygna eytoni, which has featured in ANWC research on genetic connectivity between northern Australia and Papua New Guinea. © Julian Robinson

A long-running theme of the ANWC’s research is the past and present genetic connections between the closely-related faunas of Australia and our nearest neighbour Papua New Guinea.

CSIRO scientists are researching species of waterfowl and savanna birds in both countries to understand the complexity of these genetic connections.

Additionally, waterbirds are believed to be a primary reservoir of viruses involved in the transmission of avian influenza.

CSIRO is building critically important partnerships with Papua New Guinean researchers and students to better understand links between biodiversity and human health.

Yellowstripe Scad (Smooth-tailed Travally). © William White

Australian National Fish Collection

During 2012–13, the ANFC provided support and taxonomic and imaging expertise to projects such as CSIRO’s Guide to Mesopelagic Fishes of the Southern Tasman Sea, and the recently launched FishMap .

FishMap, a collaboration between CSIRO’s Wealth from Oceans Flagship and the ALA, is an online spatial mapping and identification tool for Australian marine fishes (about 4,500 species).

FishMap is already being used by Australian Fisheries Management Authority and the Department of Sustainability, Environment, Water, Population and Communities to assist management objectives.

Australian National Herbarium

CSIRO’s Bronwyn Collins taking high-resolution images of herbarium type specimens for the Global Plants Initiative project.

ANH has been actively involved this year in the JSTOR (journal storage) Global Plants Initiative, a community-contributed online database of high-resolution images of plant type specimens for scientific researchers, conservationists and others engaged in studying the world’s plant biodiversity.

Type specimens act as a reference point for plant names and are of critical importance in determining their correct application and use.

The ANH holds over 9,000 type specimens, dating back as far as the late 18th century. Digital imaging of these collections allows researchers worldwide ready access, while minimising the risk of damage to these fragile and irreplaceable specimens.

Herbarium staff also led a GRDC-funded project to examine the effects of cropping intensification on biodiversity in the high rainfall cropping zone of south-east and south-west Australia to develop management strategies to maximise species persistence.

  1. Figures are determined for ATNF observing semesters so that, for example, the 2012–13 figures apply to the period 1 April 2012 to 31 March 2013.


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