by

Joanne Ernest

I began my PhD in 2010 with Dr Tony Gendall at La Trobe University, Melbourne. Tony’s group is using reverse genetics to investigate the physiological and cellular roles of two sodium/proton antiporters. These proteins affect cell differentiation and expansion, ro
ot length and lateral root development as well as subcellular trafficking. In my thesis I described the expression patterns of these antiporters in Arabidopsis, and described their role in trafficking seed proteins to a specialised storage vacuole in developing embryos. I presented some this work at two ComBio meetings (2012 and 2014), as well as the International Conference for Arabidopsis Research (ICAR) in 2013, the Australian Research Assembly on Brassicas (ARAB) in 2014, and the Agriculture Bioscience International Conference in 2015. A chapter of my thesis was published in 2015 in the journal of Plant and Cell Physiology (Ashnest et al. 2015).

Like many other PhD candidates, I began looking for a post doc fellowship about 6 months before submitting my thesis. I had applied for several advertised positions, but hadn’t been granted even an interview. Then in May of 2015, I met Dr Tim Sharbel at a free seminar at the AgriBio Systems Biology conference. Tim was in the process of moving his entire lab from Germany to Canada, and was recruiting post docs. Tim’s content and manner really impressed me, and when he mentioned that he was hiring, I decided on the spur of the moment that I would approach him about a job. I went to the ladies’ room and did the “power pose” for 2 minutes, then bravely walked up to Tim and introduced myself (he’s since told me that he had no idea how nervous I was…). We had a brief chat, and arranged to meet more comprehensively the next day. I remember going home and asking my husband, “how do you feel about Canada? Because I met this guy today…”

Tim and I chatted for about an hour the following morning. No pressure, I thought, but this is an interview! In the end it went really well; I had the skill set that Tim was looking for and we got along great. About a fortnight later, after Tim had read my CV and some positive emails from my referees, he offered me a job! There was a little more back and forth over contracts, and it took some time for us to arrange permits to work and live in Canada, and to pack up our home and all our things, but about 6 months later my husband, my cat and I were boarding a plane to Saskatoon. Now I’m living on the other side of the world, working with a wonderful team of people, and doing some really exciting science. I owe it all to the power pose and a moment of great bravery!

Author email: Dr Joanne Ernest  < joanne.ernest@gifs.ca>

Greenhouse Research Education Training Facility

By

Kathryn Dumschott

PhD Candidate, Centre for Carbon Water and Food, Faculty of Agriculture and Environment, University of Sydney

The ASPS travel award gave me the opportunity to present my research involving carbon accumulation and partitioning in the legume species Vicia faba (faba bean) at ComBio 2015. Legumes are vitally important for human nutrition and agricultural practices. As we face global population increases and the effects of climate change become evermore apparent, it is crucial to focus on improving legume tolerance to environmental stress. Plants rely on changes in metabolism and carbon allocation to adapt to and tolerate their changing environment. Understanding these responses on a physiological, chemical and molecular basis is crucial for developing improved breeding strategies. Being able to discuss my project provided me the opportunity to hone my presentation skills as well as share my research with the ComBio community. The diverse range and high quality of plant science research covered throughout ComBio2015 meant that every lecture and symposium was both unique and interesting. Overall, it was a great experience that broadened my view on all the research being done in Australia as well as in the international plant science community.

Contact: kathryn.dumschott@sydney.edu.au

“The interaction between the different cell types of the plant are controlled through complex physical, chemical and environmental signals”

The first half of 2016 has been a busy time for the study of whole plants. Several teams of researchers across the country have been awarded funding for questions at the whole plant scale as well as some significant recognition to individuals in the field.

Congratulations to Professor Peter Waterhouse from the Queensland University of Technology for his Laureate Fellowship to investigate how plants distinguish between ‘self’ and ‘non-self’ genes. The implications for this research certainly have broad repercussions for plant scale research, particularly among agricultural efforts to improve crop production.

Many other researchers across the country have had significant success in securing research funding for plant scale research with some common themes emerging. Management of plants in urban landscapes has been recognised twice in this years ARC Linkage programs. Dr Jie Li and the team at RMIT are focused on the management of trees in suburban environments and the unique challenges faced by soil conditions in close proximity to building structures. Again with a focus on trees in urban landscapes, Dr Stephen Livesley and the team at the University of Melbourne are investigating the role that urban tree plantings have on biodiversity and strategically address the management challenges faced by local councils in maintaining them. Both of these projects reflect the increasing recognition that plants are a critical component for society outside of natural and food production systems.

Some of the most fundamental questions related to whole plant research pertain to the development of plant architecture. Professor John Bowman and the team at Monash University have secured ARC Discovery funding to investigate the development of plant architecture and how it is regulated. Also in the ARC Discovery scheme, Dr Gavin Flematti and the team at the University of Western Australia secured support to investigate the role of a yet to be characterised hormone in seed germination and seedling development whilst Dr Oliver van Aiken (also at the University of Western Australia) secured ARC Discovery funding to investigate the touch response in plants. Combined, these topics illustrate that there is still so much to learn about the fundamental nature of plants.

One of the most significant ways for researchers to develop their research activities is through the award of Discovery Early Career Researcher Award (DECRA) also from the ARC. These awards enable early career researchers to pursue questions and foster research programs with long lasting repercussions. This year we have three DECRA awardees in the field of plant science. Dr Simon Williams (Australian National University) is working on protecting wheat from necrotropic fungi, Dr Reena Narsai (LaTrobe University) is working to improve germination rates in cereals and Dr Stefane Wege (University of Adelaide) is investigating how plants acquire and cope with chloride. Congratulations to Simon, Reena and Stefane on their achievement. The scope of the projects no doubt reflects the importance of plant health to our environmental, economic and social welfare.

There are many events on the horizon for ‘whole plant’ scientists. One of the best places to check for upcoming events is the ASPS website under the ‘events’ tab (https://www.asps.org.au/events). Of particular note for whole plant research is the upcoming phenotyping workshop being held in Canberra from the 18^th-23^rd September. In recent years, advancements in high throughput phenotyping have been rapid and there is no better place to learn about these developments than this workshop.

Overseas there are many upcoming conferences as usual during the northern hemisphere summer period. Of particular note is the 17^th International Photosynthesis conference held in Maastricht (Netherlands) this year from the 7^th -12^th August (http://www.ps2016.com). Also The European Plant Biology congress is in Prague (Czech Repuplic) from the 26-30^th June (http://www.europlantbiology2016.org) with a great array of topics on the agenda. Every year the ASPS support numerous scientists to attend conferences such as these, particularly useful for those ECR and PhD students seeking to broaden their profile and make links with international researchers.

On a final note, please let me know of any major achievements by whole plant researchers that might otherwise go unrecognised. I am particularly interested in hearing from achievements by PhD or early career researchers that may not get recognition via the regular avenues. I would be delighted to help raise the profile of people (or teams) who are making major achievements across any aspect of ‘whole plant’ research.

Dr Andrew Merchant

Australian Research Council Future Fellow

Senior Lecturer in Plant Metabolism

Faculty of Agriculture and the Environment

University of Sydney

(andrew.merchant@sydney.edu.au)

By Belinda Worland

PhD Candidate in the School of Agriculture & Food Sciences at The University of Queensland

ComBio 2015 was the very first scientific conference I had attended since starting my PhD at The University of Queensland in early 2015. I was able to immerse myself for a week in a diversity of lectures and symposia covering topics of both general and specific interest related to plant biology. Two symposia in particular caught my attention. Both were on nitrogen nutrition and crop genetics focussing on maize. My undergraduate research and my PhD relate to nitrogen use in sorghum, a close relative of maize. I was familiar with the published work of Dr. Darren Plett and Dr. Julie Dechorgnat, however their research overview added a new depth of understanding that will facilitate my own discoveries. It was also exciting to see some very interesting unpublished research being presented. During the poster sessions and social events, I was able to meet these speakers and ask many questions while discussing their work. This is just one example of my ComBio 2016 experience I shared with fellow ASPS students. It was a great event to meet and interact with some of the people who have inspired and continue to motivate my own scientific interests and investigations.

For further information please email: belinda.worland@uqconnect.edu.au

PhD Candidate, Centre for Carbon Water and Food, Faculty of Agriculture and Environment

The University of Sydney

As an ASPS travel grant recipient I was able to attend ComBio 2015 to present research from a collaborative project between the University of Sydney and Forschungszentrum Jülich. The mobile nuclear magnetic resonance sensor (mNMR) recently developed at the Bio- and Geosciences Research Institute (IBG-2) at Forschungszentrum Jülich in Germany allows the non-invasive, real-time measurement of water status and dry matter accumulation during seed development. My PhD research focuses on the impact of drought and nutrient deficiency on photosynthetic capacity in common bean and the conversion of this energy into yield, particularly the nutritional quality of yield. Plant phenotyping technologies have an important role to play in this area and are evolving quickly to provide real time information about plant growth and development. It is an exciting field and it was great to share my research with the scientific community at ComBio.

The conference helped me improve my confidence and communication skills through having interesting discussions with other researchers about the future applications of the mNMR sensor technology. I am now determined to write up a manuscript sooner rather than later! Being exposed to a broad scope of research presented at COMBIO that is beyond what I would normally explore has made me excited about the possibilities awaiting me as a young member of the Australian plant science community. I am very grateful to the Australian Society of Plant Scientists for providing an opportunity to travel to ComBio in 2015.

R.N. Robertson Travelling Fellowship Report by Nicole Dakin

(School of Chemistry and Biochemistry, University of Western Australia)

At first, you wouldn’t think there was much connection between a snow-covered forest in Germany, and a sunny salt lake in Australia. My PhD project investigates C₄ photosynthesis in Tecticornia, a genus of succulents native to Australian salt lakes (Photo 1). Through the support of the R.N. Robertson Travelling Fellowship, I travelled to Mainz, Germany to complete part of my research, supervised by Dr. Gudrun Kadereit at the Johannes Gutenberg Universität Mainz.

Photo 1: Tecticornia indica subsp. bidens, a C4 species. An example of a vegetative article is shown.

Tecticornia is a genus in the family Chenopodiaceae. These plants are halophytes, and the majority of species are endemic to Western Australia. Tecticornia species have highly reduced features, an adaptation to the harsh conditions in which they live. Their stems and leaves are fused into cylindrical structures called vegetative articles (see photograph included). Their flowers are embedded in these vegetative articles, with only the stamens visible. This leaves few morphological features to identify species, and discerning between species can be challenging. In addition, hybridisation and variation in ploidy levels are common. Previous phylogenetic studies have found low genetic diversity between species. The phylogeny of the genus remains unresolved, and the relationships among the species are not clear.

Tecticornia currently includes two C₄ species and 39 C₃ species. These C₄ species among a large number of C₃ species make it an interesting genus for studying the steps in the evolution of C₄ photosynthesis. The evolution of C₄ photosynthesis involves changes in anatomy, protein localisation, and expression, and my PhD project sets out to study these steps in Tecticornia. However, before these studies can be completed, the C₃ species most closely related to the C₄ species must be identified.

My aim during my time in Germany was to use the external transcribed spacer (ETS) region as a nuclear marker to construct a phylogeny of the genus. Previous studies have used chloroplast markers and the internal transcribed spacer region (ITS) marker, and information from the ETS marker would further contribute to resolving the phylogeny of the genus.

A question I was asked a lot was “Why would a Western Australian student, studying a Western Australian genus, come to Germany?” Members of the Kadereit lab (Photo 2) are experts in the family Chenopodiaceae, conducting studies into the phylogenetics, biogeography, anatomy, and taxonomy of a wide range of species in this family. Members of the lab have completed studies into particular genera, and broader-scale studies of the family, and have integrated these studies with their extensive knowledge of the biology of the plants.

Photo 2: Ice-skating with Gudrun, and other students from the Kadereit lab.

I learnt how to extract total DNA from dried herbarium tissue, amplify the ETS fragment, and determine sequences from over 70 samples. These sequences were aligned, and I was taught how to use various programs to construct phylogenetic trees. The phylogenetic reconstruction was a lot more challenging than first expected. The amplification of paralogous sequences caused unusual branch lengths in the first trees constructed, and conflict between trees using different markers. Some samples had to be repeated with different primer pairs to obtain the orthologous sequences. The amplification of paralogues is an unusual problem, and is thought to be due to recent hybridisation between species.

The ETS phylogeny, combined with the ITS marker, had greater resolution compared to previous studies. A number of well-supported clades could be seen, dividing the genus into groups. The position of the C₄ species indicates they form a separate clade. The phylogeny revealed that the Tecticornia are a very young C₄ lineage. A rapid diversification and hybridisation, as seen from the paralogous sequences, make it a challenging genus to fully resolve. The information from this phylogeny will help choose further markers to fully resolve the species relationships in the genus.

Photo 3. A snow-covered scene in the Lennebergwald forest, Mainz.

I was also able to connect my findings with other studies. For example I was able to fit my phylogeny into a larger ETS phylogeny of a subfamily of Chenopodiaceae. My study, as well as increasing knowledge of Tecticornia, will also be valuable in resolving relationships across the whole family. I also picked up skills in hydrating dry herbarium material, and sectioning it to look at the anatomy; a difficult task for succulent tissue.

I used my free time to explore the city of Mainz. There was a beautiful forest close to where I was staying (Photo 3), and many museums and historical sites (Photo 4). Mainz, located on the Rhine River, has a rich history, and is the birthplace of Johannes Gutenberg, inventor of the first printing press.

Photo 4. Exploring the markets in the centre of Mainz.

Thank you to Gudrun Kadereit for her mentorship and teaching, and thank you to my other supervisors: Martha Ludwig from the University of Western Australia, and Kelly Shepherd, and Terry MacFarlane from the Western Australian Herbarium. Thank you to Silvia Wienken and Max Lauterbach, and the members of the Kadereit lab who gave me advice and help during my stay: Michael Pirie, Uschi Martine, Katherina Bohley, and Denise Schmidt. And thank you to the ASPS for the honour of receiving the R.N. Robertson Travelling Fellowship, and allowing me to undertake this research.

Email: nicole.dakin@research.uwa.edu.au

by Wending Li

ASPS Travel Awards Recipients for ComBio2015

PhD candidate, Centre for Carbon, Water and Food, Faculty of Agriculture and Environment, The University of Sydney

My research focuses on understanding ammonium transport in maize. In agricultural plant production, nitrogen fertilisers are used widely where ~10¹¹ kg of nitrogen fertilizers are used annualy (Glass, 2003). The cultivation of cereals (wheat, maize, barley, rice) requires a significant amount of nitrogen fertiliser. Unfortunately, cereal N fertiliser use is poor, where only 30-50% of the total N applied is actually used for the production of the final grain yield (Raun and Johnson, 1999; Tilman et al., 2002). Low nitrogen use efficiencies can result in the loss of nitrogen into the environment, which causes water and soil pollution as well as greenhouse gas production (Masclaux-Daubresse et al., 2010). In addition, the waste of nitrogen fertilizers also gives rise to financial losses to the farmers, a significant cost in the production cycle. Therefore, improving plant nitrogen use efficiency (NUE) is an important strategy to overcome many of these constraints. One direction in enhancing NUE in plants is to increase the efficiency of root N transport processes. This includes, the proteins involved in the uptake of nitrogen from the soil as well as the internal storage and redistribution of nitrogen required to support growth and final seed yield and quality (Garnett et al., 2009).

Ammonium is a major form of nitrogen absorbed by plants and can be redistributed through high and low affinity pathways. The physiological and molecular activities of high-affinity ammonium transporters have been examined in numerous plant species, which belong to the AMT/MEP/Rhesus superfamily. Conversely, molecular information about low-affinity ammonium transport systems remains limited. Recently, our lab has discovered a new family of low affinity ammonium transport proteins called AMF1 (ammonium facilitator 1) (Chiasson et al., 2014). Through sequence homology, we found two AMF1 homologs in maize, which are ZmAMF1;1 and ZmAMF1;2. I have been investigating the function of these two genes in maize as well as using heterologous expression systems (yeast and Xenopus laevis oocytes) to define their functional relevance in nitrogen transport and overall plant growth. In maize, I’ve observed ZmAMF1 is induced by nitrogen starvation in roots, while both ZmAMF1 and ZmAMF2 are preferentially expressed in the shoots. The cellular location of both genes is currently being identified using a native promoter::GUS fusion construct transformed into the dwarf maize inbred line Gaspe. I have undertaken a reverse genetics approach in maize using a collection of Mu transposon insertion lines within exon and promoter loci of either ZmAMF1 or ZmAMF2 (provided by B. Meeley, DuPont Pioneer). We have progressed the transposon lines through a series of backcrosses to B73 and Gaspe using a diagnostic PCR screening assay. Mutant plants containing perturbations in ammonium transport in maize are undergoing characterisation. This project will contribute to a better understanding of the role AMF1 proteins in plant N transport and metabolism, including their role as low-affinity ammonium transporters. Our research will improve our understanding of nitrogen uptake and redistribution in plants, whiles also establishing new strategies to improve nitrogen use efficiency, plant growth and development.

Reference:

Chiasson DM, Loughlin PC, Mazurkiewicz D, Mohammadidehcheshmeh M, Fedorova EE, Okamoto M, McLean E, Glass AD, Smith SE, Bisseling T (2014) Soybean SAT1 (Symbiotic Ammonium Transporter 1) encodes a bHLH transcription factor involved in nodule growth and NH4+ transport. Proceedings of the National Academy of Sciences 111: 4814-4819

Garnett T, Conn V, Kaiser BN (2009) Root based approaches to improving nitrogen use efficiency in plants. Plant, cell & environment 32: 1272-1283

Glass AD (2003) Nitrogen use efficiency of crop plants: physiological constraints upon nitrogen absorption. Critical Reviews in Plant Sciences 22: 453-470

Masclaux-Daubresse C, Daniel-Vedele F, Dechorgnat J, Chardon F, Gaufichon L, Suzuki A (2010) Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture. Annals of Botany 105: 1141-1157

Raun WR, Johnson GV (1999) Improving nitrogen use efficiency for cereal production. Agronomy Journal 91: 357-363

Tilman D, Cassman KG, Matson PA, Naylor R, Polasky S (2002) Agricultural sustainability and intensive production practices. Nature 418: 671-677

By Dr. Zhengyu (Allen) Wen

ComBio 2015 was well above my expectation. As a plant physiologist interesting in ion transporter research, I had previosuly attended conferences relevant to my area of expertise and found myself comfortable enjoying the science. ComBio is a combined conference covering multiple fields of science and I had some minor trouble submitting my abstract to the relevant plenary that best aligned with my research topic, which did make me wonder about the scope of science that was to follow. But as the conference began, I realized that the 2015 ComBio was going to provide a big and pleasant experience. Professor Martin Caffrey’s lecture discussed new insights into protein structural biology and how it can effect protein function, which was very interesting from a structural biology perspective. I learn’t that there were new ways to crystallise a protein. Given the current difficulties in crystallizing ion transporters, this new method could potentially be used to solve the structure of ion transporters relevant to my research program. I also learn’t a lot from the epigenetics talks, which could pave new ways for crop biofortification and modification. Overall, ComBio2015 truly broadened my view in science, pushing me to think big.

by Dr. Matthew Tucker

ARC Future Fellow at The University of Adelaide

It’s been a busy start to the year in terms of conferences and workshops relevant to plant research. The bi-annual Plant Reproduction meeting was held from the 18^th to 23^rd of March at the University of Arizona in Tucson. The conference brings together experts from diverse fields stretching all the way from meristem development through to sporogenesis, pollen tube attraction, fertilisation, embryogenesis, endosperm development and fruit growth. The ultimate aim of the conference is to describe fundamental research from model species, such as the discovery of genes, mechanisms and biochemical pathways, which might be used to address current and future challenges in crop reproduction and yield. The conference was well attended with approximately 220 attendees, and the quality of data presented was amazing. Australian attendees included researchers from CSIRO Agriculture, The University of Adelaide and the ACPFG. The highlights were talks from Minako Ueda from the University of Nagoya, who showed stunning videos of fluorescently-tagged Arabidopsis egg cells developing into zygotes, Noni Franklin-Tong from the University of Birmingham, who described her work on transferring the self-incompatibility system from poppy into Arabidopsis, and Li Yuan from UC Davis who won an award for his talk on a histidine kinases that controls central cell development in the Arabidopsis female gametophyte. The discovery of genes controlling or inducing apomixis in maize, Taraxacum and Pennisetum was also a major breakthrough. It was clear from the talks that CRISPR/Cas9 and ChipSeq are now standard techniques in the field, while the capacity to isolate, profile and study previously inaccessible cell types through fluorescence assisted cell sorting (FACS) and microdissection is also rapidly progressing. The next plant Reproduction meeting will be held in Japan in 2018, and I would strongly recommend attending what always proves to be a collaborative, interactive and socially enjoyable meeting.

Photos of the Tucson desert moon, the famed Dr Minako Ueda with the author, the packed conference and Tetsuya Higashiyama introducing the next Plant Reproduction meeting.

Another excellent CSIRO workshop was recently held from the 19^th-21^st April in Kiama on the NSW south coast. The workshop, also sponsored by the ASPS, brought together Australian and International researchers from the field of Crop Developmental Genetics to discuss old and new strategies for the improvement of crop yield. Cereal crops such as wheat, barley and sorghum were discussed in addition to research on lupins, canola, tomato and legumes. Talks from international speakers including Jorge Dubcovsky from UC Davis, Junko Kyozuka from Tohoku University, Thorsten Schnurrbusch from IPK Gatersleben and Yuval Eshed from the Weizmann Institute were highlights, while students from CSIRO, ANU, the Universities of Adelaide, Queensland and Monash confirmed that the future of plant developmental genetics in Australia is in good hands. The intention was to use this workshop as a springboard for further collaborative research and meetings; plant developmental genetics is a relatively small field that provides so much promise for translating fundamental discoveries directly into breeding outcomes. As part of this I plan to update the ASPS Plant Development page to include information about the field and the research being undertaken in Australia, hopefully this will act as a useful resource for both students and researchers.