CRC for Plant Biosecurity - travel report

2011 International Symposium on Grain Information technology (ISGIT2011)

CRICHTONA — Mon, 22 Oct 2012 21:48:06 +0000

YongLin Ren found the trip to China useful to share innovative results generated from the platform of grain storage and transportation digitalisation, such as collaboration with China, Japan and Canada on:

grain quality evaluation and management system
the use of smartphone can improve auditing, validation, chain of evidence and can increase the volume of data collected as well as its integrity through relational databases and seamless data transfer to corporate system
current research on the application of simulation technology in grain storage, and
insect oriented image and audio recognition and identification technology.

All of these R&D areas are innovative and have great potential for use of the internet, smartphone, digitalisation simulation, digitalisation image and audio technology in a new grain storage system, which will assist to establish a new modern and high efficient grain industry biosecurity system.

YongLin was joined by CRCNPB CEO Dr Simon McKirdy, Dr Shashi Sharma (director of plant biosecurity, DAFWA) and Rob Emery (Senior Entomology, DAFWA and Chinese visiting professor) on the trip in which they visited the Chinese Academy of Grain Science (CAGS) and Chinese Academy of Inspection and Quarantine (CAIQ) in Beijing.

The CRC and Chinese Academy of Grain Science have signed a collaborative agreement to work together in the future, and the Chinese Department of Inspection and Quarantine was planning to organise a senior delegation to visit Australia to sign a collaborative agreement as well.

During the visit to CAIQ, the delegation was also invited to visit the headquarters of the Chinese Quarantine Department and meet with Dr Wu Jinsheng, Director General of Science and Technology.

The delegation also spent two days visiting Northwest Agricultural and Forest University in Yangling. This university is the top Chinese agricultural and forest related central government funded university. The vice president, Professor Zhuo Zhong, met with the delegation. Prof. Zhuo would like to establish a long term relationship with the CRC and he hosted a dinner for the delegation. Finally, Prof. Zhuo decided to visit Australia during CRC 2012 Science Exchange to sign an agreement with CRC in Australia.

International Congress of Antibodies: Winning the Race for Antibody R & D

CRICHTONA — Tue, 12 Jun 2012 00:27:34 +0000

The three objectives of Andrew Geering's travel were to learn about new antibody technologies by attending the BIT 4th Annual International Congress of Antibodies-2012, to investigate collaborative research opportunities with Chinese scientists, and to visit the Beijing Genome Institute Headquarters at Shenzen near Hong Kong. Unfortunately, only three days before Andrew was to depart Australia, his contact at the Beijing Genome Institute (BGI) suddenly cancelled the planned visit as she had neglected the fact in previous discussions that the Institute was closed for three days for ‘Tomb sweeping ceremonies’. As flights and hotel accommodation had already been reserved and paid for, and because of the very late notice, it was difficult to cancel the stopover in Hong Kong. Nevertheless, the remaining objectives of the travel were successfully achieved.

Highlights of the conference were:

Talks by Drs Seth Blackshaw and Guozhen Liu, who although working on two different types of organism (humans and rice, respectively), have a common goal to produce monoclonal antibodies against every protein produced by their subject organism. To achieve this monumental task, high throughput protein expression and monoclonal production facilities have been set up. Interestingly, for both studies, yeast was the chosen in vitro protein expression system and using this system, a broad diversity of proteins were successfully expressed in soluble form (c. 95% success rate). Protein solubility has been a serious limiting factor to our research using E. coli as the expression system.
A talk by Dr Yan Chen (X-body Sciences) on a novel method of displaying scFvs on double-stranded (ds) DNA molecules instead of bacteriophages. Enrichment of scFvs during biopanning can then be analysed by 454 sequencing of the dsDNA molecule tags.
There were many trade displays from Chinese biotechnology providers offering a multitude of services and products. Many research needs can now be outsourced and the work done more cost and time-effectively by others. For example, many competing Chinese companies were offering next generation sequencing services (e.g. the Beijing Genome Institute, the South China Genome Center, the North China Genome Center, Bioyong Technologies (contact jiangwq@bioyong.com) and Novogene (contact jiangzhi@novogene.cn)). There were several companies offering protein expression and antibody production services (e.g. Sino Biological Inc. www.sinobiological.com, Beijing Protein Innovation Co., Ltd (www.proteomics.org.cn) and GenScript. Also of interest was a company called LightArray (www.lightarray.com) who have a novel protein detection system called ‘SearchLight Plus CCD Imaging & Analysis System’. SearchLight resembles an ELISA but detection is enabled using fluorescently labelled antibody conjugates. As different antibodies can be labelled with different fluorophores, it is possible to do 16 simultaneous detection assays.
Andrew presented the research findings of project CRC60107 in a lecture on day two of the conference.

For the remaining two days of the stay in Beijing, Andrew visited scientists in the Chinese Academy of Sciences. The first visit was to the Institute of Microbiological Sciences (IMS) where he met with Professor Cai Lei and members of his research group. Professor Cai heads a fungal evolution and systematics group. Professor Cai gave Andrew a tour around the Plant Disease Herbarium and also introduced him to Dr Xinyu Zhang, who is the bioinformatician for the fungal genomics group in the IMS. Dr Zhang has developed an ‘in house’ software pipeline for compiling and annotating fungal genomes.

After the IMS, Andrew visited the Beijing Institute of Genomics (BIG), not to be confused with the BGI. BIG and BGI were one and the same a few years ago but the BGI split off as a private company while BIG remained a public entity. At the BIG, Andrew met Dr Zhang Zhang (zhangzhang@big.ac.cn), a Professor in the “100-Talent” Program. Dr Zhang is a bioinformatician and a computer scientist and works on a diversity of projects including analysing the rice genome. The BIG has a surplus of next generation sequencing capacity, which could be used in the event of collaborative projects being developed between the BIG and the CRCNPB. Within the lifetime of the CRCNPB, whole genome shotgun sequencing will become routine for pathogen or pest identification, classification and diagnostic assay development.

The 2011 Field Crops Rust Symposium including Kansas State University and Texas A&M University visit

CRICHTONA — Fri, 20 Jan 2012 03:38:14 +0000

Jordan Bailey's travels took her to Kansas and Texas, to visit Kansas State University and Texas A&M and to attend the Field Crops Rust Symposium, hosted by the American Phytopathological Society, in San Antonio, Texas.

The visit to Kansas State included back to back meetings with everyone Professor Bowden thought Jordan might like to meet, and many who had expressed an interest in meeting her. Jordan had the chance to visit Jim Stack, previous director of their biosecurity research institute, who now heads up their diagnostic network program. One of his PhD students, Christian Cruz, was nice enough to show Jordan his work at the BRI on wheat blast resistance breeding - a disease which is not yet in North America but is currently devastating South America. At Christian’s lab at the BRI nothing can be taken in (not even your own underwear!). Jordan commented that you have to shower outside, which includes washing your hair, not much fun when it is -4oC outside; Jordan admired Christian for taking on the research.

At Texas A&M Jordan toured their quality control testing facilities, where grain samples are sent and graded on various characteristics. Their largest contract was in fact for corn, as the tortilla industry is so large. She also toured their Borlaug centre, agri-genomics facility and plant pathology laboratory where she met a number of very interesting and helpful staff and students.

The inoculating procedures and glasshouse setup at K-State and also Texas A&M mirror those at PBI, but Jordan noted a few differences that may influence Australia's setup. The most interesting practice at K-State that they have just started implementing, due to a new post doc there called Jamie Poland, is using QR codes. These codes are used by smart and are mainly seen in advertising. The barcodes are included with a plants I.D. tag and when scanned will tell you all the information associated with that particular line. If applied to the rust collection at PBI this would greatly aid the research done by the rust group potentially eliminating human error in record taking and easing communication between researchers and technicians.

The FCRS was Jordan's highlight of the trip. She was lucky enough to attend a seminar at K-State by Jack A. Bobo, a Senior Advisor at the Department of State. His seminar was on networking, it was perfect timing and Jordan thought his talk was fantastic. Jordan's favourite comment of his, which she thought was worth sharing, is that people always say that they feel guilty when asking someone for a favour. He asked, “Would you feel inconvenienced if asked to do a favour for someone?” Of course, all being generous members of the scientific community, we reply “No”. “Exactly”, he said, in fact, it makes you feel good doing something for someone else, even a complete stranger, so by not asking that someone to help you, you are depriving them of feeling good.

Jordan's poster was well liked and she looks forward to displaying it at the upcoming CRC science exchange in May 2012. The talks were all very interesting and gave Jordan a history of rust diseases in North America, as well as insight into rusts of hosts other than wheat. Of particular interest was an introductory seminar on an overview of the rust diseases from a phylogenetic perspective. Phylogenetics is a field that Jordan has always enjoyed and hopes to work in one day. After talking with Catherine Aime, the presenter, it seems that they are always looking for students interested in the field and later Jordan discovered that her lab at Louisiana State University is where Alistair McTaggart, a former CRC student, has just completed a post doc. It seems he has given CRC students a good name and Jordan looks forward to doing the same in the not too distant future.

Texas A&M campus

Christian Cruz and Scott Rusk (BRI director) at the BRI training facility

K-State campus

ModSim 2011

CRICHTONA — Thu, 05 Jan 2012 05:41:07 +0000

Dr Hazel Parry attended ModSim 2011 in Perth, Western Australia, as a local (Australian) session chair during December 2011.

Dr Parry promoted the activities of the CRCNPB by giving a five minute introduction to the audience on the activities of the CRCNPB and how it had supported the session. She also promoted the activities of the CRC network B-DEMoN: Biosecurity Dispersal Ecology Modelling Network.

Prior to the meeting, Dr Parry encouraged attendance of CRCNPB members at this conference to give papers in this session.

The networking opportunities that were established by Dr Parry (an informal discussion session and a dinner) allowed plenty of time to discuss what was learnt from the presentations and to develop ideas. Much discussion focused on the relative merits of different dispersal modelling approaches, given particular research questions or hypotheses.

Specific methods with which to simulate dispersal, such as the application of dispersal kernals versus individual-based approaches was also discussed.

From this several ideas emerged to collaborate, both within the CRC and more widely. One example is to develop a proposal for a thematic issue of Environmental Modelling and Software journal on the subject of Spatial Population Modelling.

International collaboration opportunities for a number of participants in the CRCNPB were facilitated by the attendance of several international speakers and an international session chair. The session also fostered collaboration amongst existing CRCNPB participants interested in dispersal modelling for invasion ecology both with one another and with others outside the CRCNPB.

ModSim 2011

CRICHTONA — Thu, 05 Jan 2012 04:40:40 +0000

Dr Eelke Jongejans, from Radboud University, Nijmegen, the Netherlands, attended ModSim 2011 in Perth, Western Australia, as an international session chair in December 2011.

As part of ModSim, Dr Jongejans also presented a paper - Spatial dynamics of invasive Carduus thistles - which included research on plant invasion research and on biological control, with Carduus thistles as a case study.

Dr Jongejans explained in detail new modelling tools for analysing plant invasions and led discussions on plant dispersal and invasion biology and modelling.

Dr Jongejans found it insightful to listen to the various novel approaches for studying spatially-explicit population modelling, presented during the conference. Much discussion focused on the relative merits of different dispersal modelling approaches, given particular research questions or hypotheses.

Specific methods with which to simulate dispersal, such as the application of dispersal kernels versus individual-based approaches, was also discussed. From this several ideas emerged to collaborate, both within the CRC and more widely. One example is to develop a proposal for a thematic issue of Environmental Modelling and Software journal on the subject of Spatial Population Modelling.

The session fostered collaboration amongst existing CRCNPB participants interested in dispersal modelling for invasion ecology, both with one another and with others not involved in the CRC. The discussions during and after the session and the planned thematic issue should lead to joint research and publications, further building the cross-pollination of ideas among researchers working on plant dispersal and invasion.

International Society for Molecular Biology and Evolution Conference

CRICHTONA — Wed, 28 Sep 2011 05:17:30 +0000

Bo Zhang attended the International Society for Molecular Biology and Evolution Conference in Kyoto to present her PhD research on Russian Wheat Aphid Invasion Genetics.

Bo had a wonderful time in the conference, not only because of the opportunity to meet people working in field of molecular biology and evolution, but also as a stage for scientists presenting their ongoing research topics and results. The conference provided Bo with the opportunity to post her PhD results and to communicate with eminent researchers in this field of study.

With Nancy Moran as a plenary speaker and Japan as a centre for symbiont research, it presented a great opportunity for Bo to investigate the role of symbiont in invasion genetics. Bo discussed with Nancy the practicability and problems when using symbiont genes as the markers in Russian wheat aphid.

Nancy inspired Bo that symbiont genes in population genetic studies are usable to differentiate population clade and that it is also practical to test the invasive populations in area - as the founder effect and bottleneck would affect the natural selection when aphids are undertaking the gene drift and co-evolution in new environment.

Meanwhile, Bo found the research direction in Nancy’s lab very interesting, especially that biology and evolution of symbiont-aphid interaction was a breakthrough point to view the microbe-insect evolutionary research, which represents the most cutting edge proceedings in the field. Bo is also hoping to establish and evolve the future collaborations between researchers at QUT and CSIRO with Dr Moran’s group at Yale University. Furthermore, Bo talked with scientists research in invasion population genetics.

At this conference, Bo learned novel methods of analysis, original figures of illustration, and the way of telling a scientific story, which she can incorporate into research and publications, leading to better outcomes for Australian plant biosecurity, particularly with respect to managing an invasive pest like Russian wheat aphid.

The conference was a window for Bo to see the evolutionary science in a new manner. She found her understanding of evolution was so narrow and limited previously. It's not as simple as phylogeny trees from bacteria to great apes, but the steps on development of depth and width in genes and all organisms.

As Bo is in the final year of her PhD study, the conference also presented a great opportunity for her to meet and speak to future potential postdoctoral employers. It was an extremely valuable conference in Bo's early scientific experience both on PhD research and future career.

Ninth Australian Banana Industry Congress

CRICHTONA — Tue, 02 Aug 2011 05:09:09 +0000

Rachel Meldrum represented the CRCNPB when she attended the Ninth Australian Banana Industry Congress during June 2011. Rachel presented her PhD research project on Fusarium oxysporum f.sp. cubense tropical race 4 (Foc TR4), a disease of great importance to Australian banana growers.

The information Rachel presented was related to improving the use of surface sterilants – used for decontaminating footwear, machinery and farm tools – thus the research was able to provide information regarding on-field management techniques for this destructive pathogen.

Rachel also participated in a Fusarium meeting at the Queensland Department of Employment, Economic Development and Innovation (DEEDI) at Maroochy Research Station. This meeting was held to discuss the future of banana Fusarium research and how Rachel's research may fit into the future development of this industry.

Participating in both the Fusarium meeting and Banana congress enabled Rachel to establish national and international collaborative networks which will benefit both current and future research.

Rachel said attendance at the Banana Congress gave her a greater understanding of the banana industry and the potential for future research activities and that discussing her research project enabled a greater understanding by industry on this pathogen.

Rachel said she anticipated that this interaction would lead to collaborations with people who also have an interest in the industry’s future.

Biosecurity model for exotic and non exotic plant parasitic nematodes

CRICHTONA — Tue, 02 Aug 2011 02:15:04 +0000

Sunil Singh travelled to Darwin to attend the 4th Asian conference on plant pathology, which was run concurrently with the 18th biennial Australasian Plant Pathology Society conference from the 26-29 April, 2011.

The conference was attended by close to 400 participants from over 30 different countries and included a wide range of presentations focussed around the theme New Frontiers in Plant Pathology for Asia and Oceania.

There was a good mix of presentations covering:

disease management
plant pathogen interactions
soil borne diseases
biosecurity
epidemiology
new technologies
alternatives to chemical control
cereal pathology
disease surveys
virology
forest pathology
tropical horticulture
training
extension and technology transfer
prokaryotic pathogens, and
population genetics.

Biosecurity was a popular issue discussed throughout the conference and presentations covered various aspects such as risk assessment methods, biosecurity policy, sampling methods, detection and diagnostic tests and incursion management.

Sunil thought the presentations were of a high quality and provided him with the opportunity to learn a lot over the three days. He met with other nematologists, plant pathologists and students and learnt about other projects while also discussing his own. Sunil's presentation on Biosecurity model for exotic and non-exotic plant parasitic nematodes was well received by the audience and the feedback was very encouraging.

Sunil also had discussions with other researchers working on risk assessment methods and exchanged ideas on how to address uncertainties in the risk assessment process (what do we do about the unknowns?). In addition he was able to talk to representatives from the Australian Quarantine Inspection Service and the Department of Agriculture, Fisheries and Forestry, who showed a keen interest in the project and the findings. The conference also provided good networking opportunities and Sunil said it was a pleasure to meet people with whom he had been conversing via emails or phone prior to the conference.

The conference program included several workshops, with Sunil attending the workshop on Nematology in the Asia-Pacific: new and old threats to plants. The one day pre conference workshop provided an opportunity to have a focussed group discussion on nematode problems in the Asia-Pacific and discuss nematodes in more detail.

There were presentations on current and emerging nematode pests in Australia, Fiji, Indonesia, China and Australasia. Two relatively less widespread root-knot nematode species, Meloidogyne graminicola and Meloidogyne enterolobii, were identified as emerging nematode pests in China and are of potential biosecurity significance to Australia and countries where the species are not present yet.

The workshop also included a farm visit to see the damage caused by root-knot nematodes (Meloidogyne spp.) on okra (Abelmoschus esculentus) in the Northern Territory. Overall the conference and workshop were a success.

Greenhouse 2011 Conference

CRICHTONA — Tue, 02 Aug 2011 01:12:56 +0000

The Greenhouse 2011 Conference was held from the 4-8 April in Cairns, Queensland. A total of 474 delegates attended, with Kyla Finlay attending on behalf of the CRCNPB.

The conference featured 29 keynote speakers/panelists, 150 presentations, 90 climate science posters and 11 exhibitors. PDF copies of all the presentations have been made available by the conference organisers (http://www.greenhouse2011.com/presentations).

The conference theme focused on the latest findings in the science of climate change and many of the key note presentations detailed the most up-to-date information including:

the earth’s warming impact on sea level rise
climatic uncertainties such as clouds, aerosols, water vapour and feedbacks
where we stand with national climate change projections, and
an update on Professor Garnaut’s Climate Change review.

Relevant up-to-date information is necessary for incorporation into our studies on the impacts of climate change on pests and diseases; research that is part of the CRCs Preparedness and Prevention Research Program.

An integral part of our climate change research involves optimizing surveillance strategies and determining potential new invasions pathways for emergency pests and pathogens. Part of this is analysis of extreme weather events in association with climate change, which was a strong focus in the conference, including presentations on tropical cyclones in the Atlantic and Australian regions, extreme precipitation events and storm surges.

Many papers were presented on the impact of climate change on Pacific Islands and the risks and opportunities faced by these small island nations. Examination of some of the drivers and potential impacts of climate change on these islands are very relevant to pest and disease incursion research and biosecurity contingency planning.

The Asia Pacific Network (APN) for Global Change Research was an exhibitor at the conference, which gave me the opportunity to showcase our collaborative work with India and Bangladesh under the APN program and the involvement of the CRCNPB in this research. A poster entitled “The effects of climate change on potato late blight in India, Bangladesh and Australia” was displayed throughout the conference.

Interestingly, it has recently been recognised that even though the scientific evidence is overwhelming, there is more skepticism regarding the cause and impact for climate change. Several sessions explored this disconnect between the science and the practitioners who use the information to develop adaptation strategies and the reasons behind it. One of the stated objectives of the CRCNPB's project is the development of tools to inform industry and government and enhance contingency planning for pest and disease responses to climate change. These lessons are invaluable for creating effective policy from the climate change research.

This conference was an excellent opportunity to network with Australian and international researchers. Discussions were held with potential collaborators from the Centre for Australian Weather and Climate Research and the WMO Expert Team on Climate Change Impacts of Tropical Cyclones on increased biosecurity incursion risks due to these extreme weather events and climate impacts on small island nations.

The next Greenhouse Conference will be held in 2013.

Canadian Food Inspection Agency Science Symposium

CRICHTONA — Wed, 29 Jun 2011 04:41:21 +0000

As a representative of CSIRO Ecosystem Sciences and the CRCNPB, Darren travelled to Ontario to take up an invitation to present at the Canadian Food Inspection Agency (CFIA) Science Symposium entitled Better Models - Better Assessments: The Use of Models in Plant Health and Biotechnology Risk Assessment. This symposium was hosted by the CFIA’s Plant and Biotechnology Risk Assessment Unit, and took place at the Lord Elgin Hotel in Ottawa on 22-23 February 2011.

The two-day meeting presented an excellent opportunity to discuss the work being done by the CRCNPB - Understanding and responding to the risks associated with climate change and plant biosecurity (CRC10071) - with respect to the development, assessment and communication of pest risk models to diverse government and community stakeholders. The paper Darren presented was very well received. Darren was dismayed to note the number of presentations involving the use of inappropriate methods for pest risk assessment. This situation highlights the need for ongoing scientific discourse on the issues, pitfalls and solutions for pest risk assessment.

One standout positive benefit of this meeting was the discussions that Darren had with Town Peterson form Kansas University. Town is an experienced and influential ecological modeller. Darren and Twon found a great deal of common ground understanding the scientific problems with model transferability: in Town's case for exploring climate change impacts on species of conservation concern, and in Darren's for assessing pest risk on different continents, and under future climates. Town invited Darren to visit his lab to collaborate on addressing several vexing issues in ecological niche modelling.

A second benefit of this visit was the opportunity to harness some of the effort that CFIA will expend on writing up this workshop, and using it as a contribution to the Practitioner’s Guide for pest Risk Modelling and Mapping. This is an initiative of the CRCNPB and the International Pest Risk Modelling Workgroup.