GREAT EXPECTATIONS

Our series continues in which Australianscientists describe their journeys of professional

and personal development. Agnieszka Lichanska describes her varied work on blood, eyes and teeth.

Discovering the New Way

Agnieszka Lichanska.

The Beginnings I always enjoyed biology, loved the nature programs on TV

and would spend hours reading about plants and animals. Then in my last year of primary school, I learned about something that was to dominate my future study and work − DNA and genetics. The next step was obvious − I entered the biological-chemical stream in high school. It was hard work as we were expected to know material equivalent to the first year of university by year 11. At the beginning of year 12, I had to make a decision as what to study at university. In Poland you could select only one area, so the decision was tough. It came down to three: archaeology, medicine and biology. I did not have anyone to help me decide, but after careful consideration, I chose biology. During the first year of study I started a family, which disrupted my studies, and I ended up studying part-time for the first three years of university. Once I started to get on top of my studies, I moved, along with my husband and daughter, to Brisbane in 1989. I resumed my undergraduate studies two years later and went on to complete my Honours in 1994 and PhD in 1998, both at the Centre for Molecular and Cellular Biology (CMCB), now the Institute for Molecular Biosciences (IMB). After Honours in Professor David Hume's laboratory, I

decided to continue my postgraduate studies, but changed my project to a new exciting area of gene expression and development: examining embryonic macrophages. The aim was to characterise their phenotype and determine when they appear in the embryo. There were many challenges during the three years but also definite highlights, one of which was a trip to the 2nd Congress on Phagocytes in Pavia, Italy. I was quite nervous as I was invited to give an oral presentation; it was well-received and a great experience for the future. A second highlight was a trip to Professor Richard Maki's lab in San Diego at the Burnham Institute. I analysed knock-out mice deficient in the transcription factor PU-1 that were generated in his lab and were key to my project. It was very refreshing to be in a different lab and see the project from a different perspective. Setting up a new method and getting the results in six weeks was a challenge. Despite the fact that many people expected it not to work, I got the in situ hybridisation working without problems and obtained the results I needed to complete my project!

A Challenging Road through the Postdocs:from Sunny Queensland to Rainy Northern IrelandThere were other exciting events during my PhD, like

moving to a new lab. Despite this interruption, I managed to finish my work on time and submitted the thesis at 3.5 years with a couple of papers already published. The quality of the papers and my wide experience made for a strong basis to obtain a good postdoc position. I wanted to go overseas but that had to wait for a while, as immediately after submitting my thesis, I started working on the hepatitis B virus in Professor Graham Cooksley's lab at the Queensland Institute of Medical Research (QIMR). My husband was offered a visiting professorship at Queen's University in Belfast and we decided to take this opportunity. I got a job in the Departments of Medical Genetics and Ophthalmology, working in Dr Anne Hughes' group at the Belfast City Hospital as well as interacting closely with the clinical leader of the project, Dr Julie Silvestri. This group has done some excellent work previously on the genetics of eye disorders and really is one of the leading clinical groups working on eye diseases.

However, the transition was not all smooth. I was a bit lost at the beginning, as the labs in Belfast were smaller and the technical support was much more limited than those I was used to at CMCB and QIMR. The project was also quite tricky; it seemed that my ability to pick particularly difficult projects had followed me to the UK. There is no useful small animal model of macular degeneration for the simple reason that mice do not have maculae! This has greatly limited our progress, as the interpretation of expression patterns in mouse eyes was inherently limited. Another problem was the fact that diagnosis in humans occurs generally too late to catch the early changes in maculae. Therefore, there is still uncertainty as to what changes occur first during the disease process and which cells are first affected. I liked the project because of its challenges, including the high-throughput nature of the project, human library screening, P1-derived artificial chromosome (PAC) isolation and sequencing I was doing, with the added issue of managing the data. A visit to Cambridge helped me to manage the project much more efficiently and significantly improved my bioinformatics skills.

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"The important thing in science is not so much to obtain new facts as to discover new ways of

thinking about them." − Sir William Bragg

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A year and a half later I had narrowed down the region of interest to 2.5Mb and mapped it. I also generated a transcript map and it looked like we were a step away from naming the gene responsible. However, after sequencing some of the better candidates, we were still no closer to finding the culprit gene and with another 50 odd genes in the region, it could still take a while. This project led to my great interest in bioinformatics and I found a colleague with similar interests, David Simpson, with whom I have published a review on in silico positional cloning. The idea came out of conversations we had with clinicians who wanted to know more about the genetics and the tools they can use to clone disease-related genes. After mapping the region of central areolar choroidal

dystrophy, I decided to move on to an area that has always interested me, metabolism and diabetes. I therefore took the opportunity to join the group of Professor Alan Stitt to work on diabetic retinopathy. The project reignited my interest in metabolism and how it was linked to genetics and gene expression. This time the work was not high-throughput but was highly challenging in a different way. I was cloning a number of promoters out of PAC clones in order to get 0.6 to 3.0kb fragments into vectors with fluorescent tags for our studies. During this project I used a real time PCR instrument for the first time and became familiar with microarrays. It showed me new ways of doing experiments, instead of tedious Northern blots. If only I had known where those microarrays are going to lead me in the future...

Returning Home and Growing with Growth HormoneComing back to Brisbane was hard because the work

in Belfast was going well, and I had set up all the models for studying the advanced glycation endproduct effects in vitro. However, my husband had decided to return to continue his ARC Senior Research Fellowship. In 2002 I joined Professor Mike Water's group at IMB to work on gene arrays with growth hormone (GH) signalling models that were created in his lab. My bioinformatics and data-mining skills in particular were called upon for all the projects I have worked on in his lab. It was a great lab with a number

of great people, who helped me settle in and taught me quite a bit about GH and metabolism. During this postdoc I also started a collaboration with Dr Saso Ivanovski from the School of Dentistry on genetic mechanisms underlying periodontal regeneration. This has meant more microarrays and more analysis. But I enjoy this type of work, as it allows me to learn a lot about different genes, proteins, and biological systems. I also took on interesting work outside the research

area when I became a freelance writer for Lerner Publishing. I have contributed over 25 articles to various encyclopaedic publications by Lerner Publishing, which has actually helped me greatly with writing in a succinct and simple way and has taught me a lot of new information.

The New Way ForwardAt the end of 2005, I became the ASBMB State

Representative for Queensland. One of the main concerns is membership numbers of the Society, but also the fact that members are often quite unaware of the great resources that exist in some of the institutions and are holding back their own research because of lack of funding. I would like to bridge that problem by bringing people and the resources together.In 2005 I was offered a lecturer position in the School

of Dentistry. My collaborations with the members of the school have been going on for a few years already. My expertise is still in functional genomics and this is the area that my group is expanding upon. With three current Honours students, one co-supervised PhD student and a scholarship for another student, plus some strong collaborations nationally and internationally, the group is slowly picking up speed. However, my main interest is in metabolic diseases

and metabolism in general, particularly the use of the metabonomics platform to study changes in biofluid (saliva, urine or blood) composition induced by disease or genetic alterations. I am very pleased that after a year of hard work and trying to convince people that this is worth pursuing, we have completed our first project using urine from the GH receptor knock-in mouse. Working on this project with Horst Schirra from IMB

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My PhD graduation in 1998 was a family affair, with my husband (now lecturing physics at QUT) and my

daughter (now studying creative writing/journalism at QUT). It felt great to finish the hard 3.5 years of work.

Finding a new way on the wall can be tough, but

when you get to the top it feels great.

Rocksports is where I find the

greatest challenge apart

from the lab.

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has been a great experience and we both hope to go much further with the technique and studies. While the collection kept everyone entertained and challenged, the analysis once completed was worth all the effort. The year 2006 has started excitingly with me giving a

presentation at the World Microarray Congress (WMAC) in Vancouver about both GH models I have worked on. Continuing from there I was also invited to the IBC Discovery to Diagnostics conference in Boston this year to present the work on the biomarkers for obesity that we identified in the microarray analysis and confirmed and expanded in the metabonomics study. For me, this work initiates the systems biology approach, which I want to continue and expand by looking at other physiological models. My particular interest would be to work on mouse models of human metabolic diseases. I would like to combine that approach with human data to integrate what we know about metabolism.As someone said to me the other day, I always pick the

daisies. My projects have always been difficult but I never stepped away from the challenge. However, it has had one big downside: publications are not coming out as fast as I would like because the array projects in particular take quite a while to finish. Studying metabolism requires a broad knowledge of a

number of areas and is one of the most exciting areas to work in. Joining single nucleotide polymorphism typing and gene expression profiling with metabolic profiling is the new way that I want to go forward. The main aim now

is to find the best place to do this work. Such studies will allow us to determine the probability of an individual developing a particular metabolic condition, and to prevent it by appropriate diet or drug management. We all are trying to be healthier, however some of us have a much faster metabolism while others struggle to keep the weight off. The future of such studies is not only in actually doing them, but also in total automation of the process so that the methods can be used in diagnostics.

Beginning of the new group at the Dental School, University of Queensland (2005). From left: Saso Ivanovski, Yvonne Chang, Hao Choy, Thor Friis, Illo Streimann, two

visitors and Agnieszka in the front on the right.

GREAT EXPECTATIONS