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Genetics Otago
University of Otago Research Centre

Possums, and Pregnancy in a Pouch – Melanie Laird investigates a forgotten class of animals

 

Pest or Prize? – Melanie Laird explores Possum Pregnancy and Genetics

Paihamu (Brush Tail Possum)

The possum, at first glance, appears a pesky drab rodent. For kiwis, they are a reminder of the recklessness of early settlers’ preference for introducing game animals, over preserving our existing native wildlife. For Australians, they are an endemic animal of national significance, critically endangered, and far removed from their native habitats. Melanie Laird is doing fascinating research on an animal that everyone knows, but most people do not give much thought to, beyond whether it was big enough to dint your car upon becoming a roadkill victim.

New Zealand Bushtail possum

Melanie explained that for various reasons possums, and marsupials in general, have not been studied anywhere near the amount of mammals. Being Australian herself, Melanie is well acquainted with marsupials and has worked with them for a long time. Melanie explained, “there are a lot of unanswered questions in that, marsupials are a very unusual, but very understudied group of animals, and it is often assumed that they are the same as other mammals, but they are actually quite different. I work on brushtail possums because they are such an important economic pest and environmental pest. There is a lot of national interest in studying them more, and in working out ways of getting rid of them. This is good news for us because it means there is more money around to go back and look at the basic aspects of their biology. There is a lot of stuff that people want to do with possums. And there are a lot of applied aspects of pest control could work with possums.”

 

Gene Drives

Advances in genetic engineering have brought up the concept of what is called a ‘gene drive’, for pest eradication. Melanie explained, “if you wanted to get rid of an animal population in New Zealand, you could introduce individuals into the population that have a particular genetic ‘edit’ that is heritable, and always gets passed on to offspring.” New technologies such as CRISPR-CAS9, provide a means of doing this. “With something like CRISPR CAS-9, instead of normal Mendelian inheritance (where half of the offspring have a particular gene, and the other half do not) the genetic change that you make will be passed on to 100% of offspring.” If for example, a gene edit is introduced to make all males infertile, all male offspring of the introduced animals will be infertile, and the females will be carriers of male infertility. Melanie explained “that would keep going through the generations. In a small population, it does not take very many individuals before you have got effective extinction, where all of the males are infertile. Then there are only females. It would not take very many individuals if the population was small to begin with. But in a big population, you would need a lot of transgenic individuals added. Otherwise, the effect would be diluted—the rate of breeding of everybody else would outpace the breeding of the ones that you added.”

Brushtail Possum Embryo.

Melanie’s current research, therefore, looks at marsupial birth and development, as this is an area with very little research. We cannot expect to produce viable pest control interventions for possums when very little is known about their development. Melanie explained how “people ask ‘should we do this?’, and ‘should we do that?’, but the truth of it is that we do not know enough about them to know what will work.” Melanie is doing the basic research required to answer the questions of whether things like gene drives would even be possible. “Technically we do not know if things like gene drives would be possible [for marsupials], or even gene editing. That is one of the big unanswered questions about the work that I do: can you make a genetically modified marsupial? We do not know that yet… the normal ways of doing this…that we do pretty routinely to make transgenic mice and rats have not worked thus far for marsupials.

Melanie offered some reasons why marsupials are a relatively understudied group of animals. “There are many ways in which the marsupial develops differently during pregnancy [compared to regular mammalian pregnancies]. The length of pregnancy is incredibly short. Marsupials have a lot of quirks that have made [studying their development] very difficult. That means that we cannot make a marsupial cell line, for example. We cannot make transgenic marsupials for any research, in any application. They are used widely for research, and a lot of universities have colonies of them for different things. But if for example, we want to find out what a gene does in a marsupial, we have to knock it out in a mouse, and then extrapolate. Even worse, if it is a novel marsupial gene, we have to put it into a mouse, and see what happens. It is really, not a good way of figuring that out.”

 

Melanie’s Path to Possums

Melanie hails from the central coast of New South Wales originally. She recalls that as a child “all I wanted to be when I grew up was whatever David Attenborough was. I was obsessed with bugs and plants and everything—I loved natural history. When I went to university, I did a science degree and completely fell in love with invertebrate and vertebrate anatomy, because that was about as close as I could find to being David Attenborough in a class, and I loved it.” When considering projects for her honour’s year, Melanie explained she had the opportunity to work with fat tail dannarts, an Australian marsupial. For her PhD, she explained, “I did a broad comparative study with Brushtail Possums and Tamar Wallabies, among different kinds of things, trying to understand the molecular changes (not genetics at that stage) that a marsupial uterus has to undergo to support a marsupial pregnancy.”

“I fell in love with marsupials doing that work, because they were fascinating, and I realised that even as an Australian, I knew very little about them, and other people did not appreciate them at all. When I finished my PhD, I saw that a job was going here to continue to work on marsupial biology. Not for the reason of understanding, protecting, or conserving them, but for getting rid of them.” This was fine with her, as any research into marsupials would be beneficial to them as a whole.

Melanie now works on the development of brushtail possum joeys. “We are interested in understanding how the germ cells (that go on to either: become the eggs; or the producers of sperm in an adult’s gonads) actually develop to that point, and what epigenetic changes have to occur to those cells…Immature germ cells start out with a set ‘pattern of methylation’. Very early in development, they completely lose their methylation. They then regain it again in such a way that the methylation pattern reflects the sex that the Joey will be. There will be female-related patterns or male-related patterns. If we want to do things with these cells or compare them for some other aspect, then we need to be aware of what differences in methylation there might be…The cells are undergoing an important process at the time when we think that they could be most easily edited or modified. We think this might be useful for gene editing. Even a week or two after the young is born, the immature sex cells still possess stem cell like characteristics. We could potentially use them in place of the embryonic stem cells that other techniques use to try to introduce a genetic change, we think.”

 

Obstacles to Overcome

Gene drives are a new concept and have not been tried on a large scale yet. There is potential for unintended side effects, as with any new technology. The biggest risk with a possum gene drive is that it could be too effective, and potentially put Australian possums at risk of extinction, as they are genetically identical to New Zealand possums. Scientists are all too aware of this risk and aware of the fact that robust safeguards and umpteen safety measures must be in place, in order to try something like this. I asked Melanie what she thinks the key reasons people might have trouble understanding new technologies like this are.

Comparison of the lining of the uterus during pregnancy in different marsupial species.

“It is a gut reaction in a lot of cases. However, because it is a theoretical concept, we as scientists do not have a good answer for this, the real issue is once you release a gene drive, how do you stop a gene drive? The best answer that we have, which is a terrible answer, is to produce another gene drive. That is not good enough. That is not fixing the problem. That is the problem with these technologies, especially in the minds of the public, but also a scientist’s concern too: once you open the box, you cannot close it. Saying yes to something is saying yes to basically everything. That is what it seems like. And there is a lot of concern, it is quite touching really as an Australian—one of the main things people say is, what about Australian possums? And I am like, oh you actually care about them, that is nice. In terms of the biosecurity laws and regulations, there is nothing in place yet for this, because it does not exist. The likelihood of something like that happening—of gene-edited possums with reduced fertility or whatever, ending up in Australia, and destroying the Australian population—is incredibly low. But if it did happen, the consequences could be unbelievably bad. At the moment, it is a risk we cannot take until we know that there is a way of stopping it, or mitigating it, or diluting it, or protecting Australian individuals in some other way. I think that is the main concern, you cannot do anything about it once you start that journey.”

In New Zealand, we are all too aware of the unintended consequences of large-scale conservation interventions. Mistakes were made by early colonists who introduced small rodents for sport, and then small carnivores to control the populations of those rodents when they became out of control. Melanie explained “we remember that stuff, and we know that that does not work. Unless there is a good way to stop it, then people are not likely to be on board.” This is a technology that could provide a viable solution to remedying the mistakes made by early settlers, and as such there can be no risk of making those same mistakes.

In terms of genetic engineering for the purposes of gene editing, Melanie commented “Pest control is a grey area I think, where a lot of people are very against it, and I can completely understand why. But a lot of people are starting to think that what we are doing now is not the best, but we do not have any other alternatives. We should be at least investigating these other ideas.”

Ultimately, the success of this project will depend on the public’s trust in scientists.

“The reason that it has been such a rocky road for gene editing in New Zealand is that originally it was done in a way without any consultation with the public. Pretty much without the public’s awareness, and that does not look good—that you are behind closed doors doing this mad scientist thing. The public needs to be aware of all of this. It does not work if it is not transparent and open and flexible. I think scientists doing things in that way and expecting it to be fine is paternalistic in a way. It is saying that we as scientists know what you need, and we understand your needs better than you do, and we are more intelligent, and you should listen to what we have to say. That is very arrogant, but it is an easy identity to put on as a scientist. Things are a lot different now, but I think that that stuff leads to a real distrust of science and scientists, and what their agenda is.”

Fluorescence microscope image of developing oocytes (red) in a possum ovary.

I can completely understand people who are against it. Generally, it does not matter how much awareness there is, or how many facts you tell them about gene editing. I think the only thing that is going to change that, is if people who are against a technology understand that the people who are developing the technology, really do have their best interests at heart. Scientists are not going to assume those interests, they are going to actually ask what is needed, and they are going to do it in the safest way. They are not in it to discover something amazing at the expense of whatever, they are actually doing it because they are trying to benefit society, in the way that society wants to be benefitted, I would say that the attitudes have changed and that the awareness has increased, but what it is going to take is scientists being visible people and being open and transparent about what they are doing, and making sure that what they are doing is actually what is wanted and needed by society. It needs to be done in a way that is not unnecessarily risky, which is hard. But I think that we should all try to do that.”

 

Gene Drive in New Zealand?

I asked Melanie if she could give a general idea of the risk of total possum extinction, including an unintended consequence of wiping out Australian possums as well. “I would say that it would be low, but that we do not fully understand. It would depend on what was different about these newly introduced possums. If they were released into Australia, in an area with a small population, then the effect could be enormous. Possums are protected in Australia, and in the natural areas where they are supposed to be, their habitat has been threatened to an extent that the populations are in little fragments. You could effectively, with not very many individuals, cause a lot of damage. I do not know how many you would need, or how many could be transferred to Australia. I do not know what the likelihood of any of that is. But it is not inconceivable that a relatively small amount could do a lot of damage in an Australian population.”

Melanie and I discussed the regulations for animal studies and genetic studies in New Zealand, and whether they are appropriate. Melanie’s comprehensive understanding of the ethics involved in her research and its possible implications shone through here. It is reassuring that Melanie’s first line of thought is always scientific transparency and ethical conduct.

In her words “I would say that we have good regulation…You cannot do [genetic engineering] without a good reason for doing it. It has got to answer a really important question. We also cannot do it without a whole lot of safeguards…It is the same as working with animals…there is a lot of work to get permission to do that. There should be, because it is a privilege to work with animals. It is a privilege to do the research that we do. If we are not going to put in the work required to do that properly, then we should not be doing the work.”

Scanning electron microscope image of a pregnant marsupial uterus

“Scientists know the regulations are strict and very good, and I think the public would be quite surprised to know how hard it is for us to do the work that we do. They would probably be put at ease knowing how difficult it is to get permission to do work, and how little we can do—for good reason. However, if we can justify it well, and show how we are going to be able to do it safely, ideally with zero risk, then usually that research is allowed to go ahead. That is the way that it should be. Once it is going to impact the public, there are more of those regulatory levels to go through, where you have to prove ‘this’ before you can do ‘this’. You have to consult with people. As soon as what you do could affect something outside of the lab, then there are lots of regulations in place. We are also still working out what those regulations should look like because this stuff is new. New Zealand has done a really good job of allowing things but doing so very cautiously.”

Melanie and I also discussed the ways that laypersons and the general public can be sure the information they are receiving is correct. There is a lot happening in the field of genetics, and consequently a lot of literature. This also means that there is a lot of misunderstanding, and misinformation circulated. Melanie observed “I wish that everyone could be trained to think critically the way that scientists are. What I would advise is that, if something does not sound, right, check another source.

Melanie provided a great analogy, explaining “the most important thing to be aware of is your own lens through which you see the world. A lot of people never become aware of that. That is what critical thinking is—it is being aware of the lens, the bias, or the subjectivity of the person who is giving you that information. Always being aware of that as much as possible can really help you to understand.

If everybody could do that more often, take those lenses off, or see when other people are wearing them, then we would definitely be able to be more rational about the way that we do things. There is a lot of stuff around at the moment which preys on people’s doubts and weaknesses. But people would have more confidence and less doubt, if they had that ability to discern good information from bad, or at least relatively impartial information from propaganda. I wish everyone could think critically, I wish that we were all trained in this.”

Melanie is a diligent and compassionate scientist. It is reassuring to know that research in a sensitive area such as this, is taking place under the guise of a rational scientist, working for society, and with a solid ethical and moral foundation. I asked Melanie what she would most like to be remembered for, and her response was well in line with her attitude to science.

“I suppose as someone who, whatever they did, they did it with integrity. And also, someone who really tried to bring a bit more kindness and empathy, especially into science, which does not have a whole lot of that. That would be really nice. I am working on that.”

 

Written by Don Sinclair 

Images Supplied by Melanie Laird

 

 

New Profile Series Coming Soon

Don Sinclair is an aspiring Science Communicator with a background in Engineering, and an interest in healthcare and conservation. Over the last few months, Don met with researchers associated with Genetics Otago. They discussed their personal achievements and stories, their research, and some lessons they have learned throughout their careers.

The goals of this were to shine a light on:

  • The research that is taking place within GO, how far genetics research has come, the new possibilities being explored, and the hangover of fear that is often associated with genetics research.
  • The dynamic, intelligent, resourceful, and varied lives and personalities of researchers.

These are the people that are laying the foundations of a new generation of research in medicine and conservation, each has their unique and compelling projects, and each has their own story.

If you would like to get in touch with Don you can reach him via Linkedin.

Come back this Friday 26th February at 1pm for the first of five profiles that will be published weekly.

Alumni Series: Nadia Preitner

For Genetic Counsellor Nadia Preitner, a willingness “to go where my interests lay” has taken her halfway around the world—and to a fulfilling role that unites genetic know-how with patient well-being.

Yet it’s been a surprising journey for the Otago graduate, from laid-back New Zealand to cosmopolitan Switzerland and flamboyant France, to her current position in loud and lively London.

“I’ve chosen things that I enjoy, rather than following a firm path,” Nadia explains, “and that’s how I’ve ended up with the interesting career I have now.”

Originally intending to study biomedical sciences at Otago, Nadia instead found herself drawn towards genetics. “I found the programme so broad, from Arabidopsis [a flowering plant used as a model genetic organism] to humans,” she says. “Though I was always more interested in human genetics.”

She also loved to travel and, once armed with an Honours degree in genetics, eventually ended up as a research assistant in a university hospital laboratory in Switzerland. While there, and still not entirely sure what career path to take, she bumped into a Genetic Counsellor.

“That’s when I had a ‘eureka moment’,” she says. “Genetic counselling seemed a career with a perfect mix of genetics and patient care.”

Already fluent in French, she enrolled in a Master’s degree in Genetic Counselling in Marseille, followed by jobs in Burgundy and Switzerland. Finally, in late 2018, she took up her current role working for a Regional Genetics Service, in North West London.

Illustration by Poppy Ollerenshaw Whittle

“I wanted to broaden my experience, and work in a country where the profession is more established” she says.

The job—which combines professional counselling skills with a specialist knowledge of medical genetics—is fundamentally about “empowering people to make decisions,” Nadia says.

“Genetic counsellors communicate health and genetic information to patients and families,” she explains, working in a wide range of areas such as hereditary cancer, prenatal diagnosis and family planning.

“For many people, the results of genetic testing can be life-changing. Genetic counsellors help individuals to realise choices about testing and medical management, and support them throughout this process.”

And while the work can often be challenging, at its heart are real human beings, Nadia says. “You have the privilege of working with people at a time that can be very difficult.”

Although like health professionals across the world, Nadia’s work has been disrupted by the Covid pandemic, she says in normal times “one of the beautiful things about this job is exposure to different people and cultures”.

Yet despite loving London, Nadia does now have one firm path she’d like to follow.

“I would really like to move closer to home and one day work in Aotearoa.”

Written by Mick Whittle
Images Supplied by Nadia Preitner

Alumni Series: Bryony Leeke

A resident colony of South American opossums is not what you’d expect to find in the imposing-sounding Francis Crick Institute in the heart of London.

Yet the institute (named after the Nobel Prize-winning co-discoverer of DNA’s double helix) is also home to Otago genetics graduate Bryony Leeke, who reckons “the Crick” is nothing like most people’s image of a genetics laboratory.

Illustration by Poppy Ollerenshaw Whittle

According to Bryony, it’s full of an amazing array of international researchers, working on an incredible range of projects. (And this, of course, includes a typical down-to-earth friendly Kiwi like Bryony herself!)

As for the opossums: Bryony’s just completed her PhD investigating the embryonic development of these South American marsupials (a distant relative of New Zealand’s own introduced possums). While it’s been mainly pure research—“finding out how nature works”—studies like this do have important practical spin-offs, Bryony says.

For example, as many diseases are now thought to be the result of the wrong genes being turned on or off, she explains, a greater understanding “of how genes are being controlled in development” has crucial implications for human health.

Indeed, Bryony’s next position will be as a postdoctoral researcher at the London Institute of Medical Science, investigating how early development is genetically controlled and, in particular, how an embryo ‘knows’ when and how to turn on specific genes.

However, working in a prestigious international genetics lab was not really on Bryony’s radar when she first enrolled for a zoology and genetics degree at Otago. Indeed, tracing the route Bryony followed to the Crick is almost a metaphorical mirror of the developmental pathways she’s ended up studying.

There were, for instance, clear genetic and environmental influences in her early life. Originally from Porirua, Bryony obviously inherited her parents’ love of the great outdoors, including annual family tramps up the Orongorongo Valley near Wellington at Christmas. This early exposure to nature—plus an inspirational biology teacher at high school—naturally led her towards the life sciences at university.

At this stage, though, she didn’t yet have a specific career goal in mind. “I was curiosity-driven, studying science simply for the sake of it,” she says. (Metaphorically, you might say she was still at the ‘pluripotent’ stage, capable of heading in any number of directions.)

But her next major inspiration came when she chose to focus on genetics for her Honours year. “The awesome thing was the researchers from different disciplines and the cross-specialism exposure” she says. “It’s what made me want to go on with genetics.”

A research project working on gene expression in zebrafish quickly followed, in a lab overseen by Professor Julia Horsfield. The next pivotal moment came during a ‘coffee with the boss’, Julia’s regular informal get-togethers with individual junior researchers. With Bryony toying with the idea of becoming a teacher, Julia encouraged her instead to carry on with genetics and then make a decision. It proved good advice (again, like a metaphorical intervention in early development).

After “loads more lab work”, Bryony started seriously thinking about a PhD overseas—“partly for the adventure, and partly to expand experiences and opportunities,” she says

Already aware of “the then-being-built” Francis Crick Institute (this was in 2015), she applied for a position—and, after an “intense but fun selection process” in London, was accepted. And the rest, as they say, is history. Well, not really: who knows what new pathways may open in Bryony’s developing genetics career.

Yet while it’s already taken her in unimagined directions—“I thought I’d be doing something more outdoorsy, but I’ve found molecular biology so fascinating”—Bryony does have one eventual goal in mind: “I’d love to end up back in New Zealand.”

Good on ya, mate!

Watch Bryony in Action

 

Written by Mick Whittle

Photos Supplied by Bryony Leeke

Alumni Series: Tamsin Jones

What’s in a name? Well, if it’s the name of a gene then certain things are really useful—that it’s unique and memorable, say, or has a short form that’s easy to pronounce.1

And who actually names genes? (It’s a question that few of us likely ever think to ask.) Someone must—after all, just imagine the mess if we all used different names for the same common genes.

If fact, that mystery ‘someone’ might well be former Otago genetics student Tamsin Jones, who’s now a Gene Nomenclature Advisor (the name says it all, right?) at the European Bioinformatics Institute.2

At first glance, Tamsin’s role, as part of a seven-strong nomenclature committee, seems straightforward: “We’re looking to give everyone a shared language to work with,” she says.

“For the most part, once people understand why we [the committee] exist, it makes sense,” Tamsin says; indeed, “minimising confusion” is crucial in areas like human health that impact directly on people’s lives.

Yet there’s also much more to it than that.

For example, what if different researchers in different parts of the world independently discover the same new genes? Or if known genes are later found to have other, more significant functions? Who brings all this information together or, as importantly, ensures it’s readily shared with others?

You guessed it: it’s biocurators3 like Tamsin who help collect, annotate and validate the huge volumes of genetic information accumulating in this ever-growing field.

“Essentially, it’s the job of synthesising research-generated data and summarising key findings,” she says. Creating and maintaining databases (e.g., genenames.org) to disseminate this information is also an invaluable part of the biocurator’s role. (While we all appreciate the convenience of information at our fingertips, how many of us pause to consider how it so ‘magically’ appears?)

Illustration by Poppy Ollerenshaw Whittle

“Someone has to put that data there in the first place,” Tamsin points out. And, she says, they’re always happy to receive feedback and suggestions from researchers and database users.

Yet how did Auckland-born Tamsin end up in such a curious job?

Inspired by the then-on-going Human Genome Project plus the “amazing and exciting” popular science books she read (such as Matt Ridley’s ‘Genome’), she enrolled at Otago to study anatomy and genetics. Next came postgraduate lab work on limb development in frogs before a switch to studying the genetics of insects, initially at Otago and then at grad school Harvard, where she ended up teaching undergraduate genetics.

But she “felt drawn to a biocuration career path” when helping annotate the genomes of insects such as the milkweed bug (the laboratory model for sap-sucking agricultural pests). So when an interesting position came up in Europe, she readily swapped Cambridge, Massachusetts for Cambridge, England—first as the curator of FlyBase (“an amazing resource that summarises all the research on fruit flies) and then in her current role at EBI.

Although the day-to-day job involves a lot of (sometimes “diplomatic”) engagement with researchers, a few oddballs do crop up, Tamsin says. For instance, devising a new symbol for the ‘gastric intrinsic factor’ gene or GIF due to web search confusion with other, non-genetic GIFs; or renaming the inappropriately-labelled ‘DOPEY’ genes after their role in cognitive impairment was recognised.

And it’s the type of work that won’t come to an end any time soon. With the human genome, for instance,  while “we think we have most of the protein coding genes,” that still leaves a vast number “where we don’t yet know their role,” Tamsin says. And then, of course, there’s the non-human world, where historically different naming systems have been used with different species.

Given her wider background in evolutionary biology, therefore, Tamsin’s also taken on the task “of trying to harmonise gene names across vertebrates … to bring them in line with humans”.

With classic Kiwi understatement, she reckons “it would be nice if they [the common genes] all had the same names”.

 

Written by Mick Whittle

Photo Supplied by Tamsin Jones

 

1 For instance, the gene name ‘cytotoxic T-lymphocyte-associated protein 4’ tells us something useful about its function, while the corresponding symbolCTLA4, is much easier to say. 

2  More precisely, Tamsin’s a GNA with HGNC at EMBL-EBI. Or, in translation, a Gene Nomenclature Advisor with the Human Genome Organisation Gene Nomenclature Committee at the European Molecular Biology Laboratory—European Bioinformatics Institute. We’re unsure whether there are  Organisation Nomenclature Advisors who come up with these names …

Talking of names, what a wonderful one biocurator is—literally a ‘custodian of life’. And it’s a sign of the newness of the field that the term was only coined around 2006.

 

Alumni Series – Jared Fudge

A love of plants hasn’t led Otago-born Jared Fudge down the garden path; it has, though, taken him along some curious byways, from the chic streets of Geneva to London’s famous Abbey Road.

Indeed, Jared’s journey signposts some of the more intriguing directions that a genetics career can go.

Raised on a farm in Waikouaiti—and inheriting a green thumb from his horticulturally-inclined grandparents—it was little wonder that Jared chose to study botany at the University of Otago.

At that point, though, his motivation was quite straightforward. “I was curious about science,” he says, “and I wanted to know how the living world worked.”

But the more he learned about plant ecology, the more he wanted to find out about plant physiology, about how they functioned at the fundamental molecular level.

Jared’s interest blossomed (almost literally) during a plant biotechnology Masters, seeking to understand how plants ‘perceive’ day length and the winter cold—and hence when to flower—from a molecular genetics perspective.

And while this prepared the ground for further academic study, the seeds for a suitable doctoral project had already been sown during a “compelling” undergraduate course on harnessing plant metabolism to benefit human health.

With over two billion people suffering micronutrient deficiencies—“over-represented in low- and middle-income countries reliant on a single staple crop”—biotechnology offered a possible means to boost micronutrient levels and thus improve the well-being of “some of the poorest people in the world”.

Or as Jared explains, “It seemed a cool way of helping people while still studying plants.”

This idea came to fruition with a PhD at the University of Geneva, Switzerland, looking at genetic ways to ‘biofortify’ important crops such as rice and cassava. (Rice and the starchy root vegetable cassava are major staple foods in the developing world, and in the absence of a more varied diet both can lead to nutrient deficiencies.)

The research facilities in Geneva were incredible, Jared says, as too was the accommodation on offer; in contrast to Dunedin’s student flats, he now ended up in an 18th century apartment on the swish Rue des Granges, in the heart of the old city of Geneva.

Illustration by Poppy Ollerenshaw Whittle

“It was another world and took a while to get used to it.”

Apart from these pleasant surprises, though, and despite this being his first time in Europe, Jared reckons adapting to his new life wasn’t difficult—well, apart from an initial language problem. Although almost everyone spoke English, “they just weren’t used to hearing a Kiwi accent,” he says, “so I had to become a bit more BBC.”

Then, after several busy years in a Geneva genetics lab and a spell writing up his thesis on the Sunshine Coast in Australia, it was time for a change. Less than a week after his PhD defence, Jared was settling in as a commissioning editor with the journal Frontiers in Plant Science in London. And while his initial Abbey Road address wasn’t quite as elegant as in Geneva, thanks to the Beatles it was at least as memorable.

“So far, it’s been an enjoyable experience in publishing,” Jared says. Having just become an assistant editor with the prestigious journal Current Biology, also in London, he’s now looking forward to getting “back closer to the science”. Yet he’s still got an earthy Otago attitude to his favourite subject.

“If you care about food,” Jared says, “you should care about plant genetics.”

Written by Mick Whittle

Image supplied by Jared Fudge

Alumni Series

Genetics is a broad field with global opportunity. To highlight this, in the coming weeks, we will be publishing a series of posts written by Mick Whittle about a few of our Genetics Alumni.

We would love to extend this series to all corners of the world so if you would like to contribute to this series as an author or are doing something interesting and would like to be featured let us know!

The first post in this series will feature PhD Student Bryony Leeke based at the Francis Crick Institute in the heart of London. Tune in here Friday 1pm to find out more.

Studying cancer biology to help our taonga species

Growing up in Bavaria, Germany, Lara Urban loved being out getting dirty while spending time in nature—and she also had a thing for all sorts of off-beat animals.

“And sharks,” she recalls, laughing. “I especially liked sharks.”

So it’s little wonder that, as an adult, Lara’s now “having an amazing time in New Zealand” working with two of the world’s most endangered species, the kākāpō and the takahē. (True, they’re a bit cuter than sharks, but still … )

What is surprising, though, is the academic route that Lara’s taken to become a post-doctoral researcher (and Humboldt Research Fellow) at the University of Otago.

As a self-professed “nature child”, always wanting “to do something for nature conservation”, it was obvious she’d take ecology at university. She then jumped at the chance to travel the world studying exotic wildlife.

Then Lara made an abrupt-seeming career change—a PhD on the genetics of human cancer at the European Bioinformatics Institute and the University of Cambridge.

Yet for Lara, it all made perfect sense. Her conservation field experience had made her aware of the huge potential of genetic and genomic technology, and the mass of useful information made available by these modern techniques.

“I realised I had to become really good at analysing these sorts of data,” she explains.

To get more proficient in bioinformatics and analysing complex biological information, she therefore searched for “the most statistical PhD position” she could find. Working on the molecular biology of cancer ticked this box perfectly, she says. And this, in turn, eventually gave her the opportunity to bring together “the molecular experience in the lab” with her original love of nature and conservation.

“I’m definitely more of a biologist than a statistician,” she says, “and I wanted to combine them both. It’s super-exciting, taking things used in one field to a different one.”

And Otago seemed an ideal place to begin her post-doctoral research.

“New Zealand researchers are pioneers in using genomic techniques in the conservation of endangered species and ecosystems,” Lara says.

Now she’s applying the same models and methods she used to study human health to help save two of this country’s iconic endangered birds—for instance, by looking at “the genetic pathways of disease susceptibility” in kākāpō or “the genomic diversity of wild takahē populations” compared to those in sanctuaries.

Illustration by Poppy Ollerenshaw Whittle

She’s also really keen to further employ genomic technology for conservation purposes; for example, by using environmental DNA analysis of soil and water samples to monitor species remotely and non-invasively, while “interfering as little as possible” in fragile ecosystems. (At Cambridge, Lara co-founded a real-time DNA sequencing organisation, PuntSeq, that monitors biodiversity in the River Cam.)

Having been at Otago for a year, she’s still enjoying the Kiwi experience and, especially, spending plenty of time in this country’s unique natural environment.

“I find New Zealand’s remote nature exciting, it’s an amazing experience to see what nature is really like,” Lara says. “It’s one of the most amazing places in the world and has come up to all my expectations, including really nice and open people.”

And another major boost is the opportunity to collaborate with a hugely diverse group of ecologists, conservationists and Māori iwi, “the kaitiaki (guardians) of these taonga (treasured) species”.

“It’s the perfect set-up of how science should be conducted,” Lara says.

 

Written by Mick Whittle

Images provided by Lara Urban, thanks to the Takahē and Kākāpō Recovery Teams

 

Distinguished Award for Distinguished Professor

Time is a precious thing for Distinguished Professor Neil Gemmell—little wonder, given the breathtaking scope of his academic achievements and endeavours. Yet he still believes that just a few minutes a day could make all the difference to wider public appreciation of science and technology.

The renowned evolutionary and reproductive biologist has recently been awarded the Royal Society Te Apārangi’s Hutton Medal for a career’s worth of groundbreaking research. And while Neil’s openly “humbled” to be so recognised, he’s quick to point out that the “ongoing push for new discovery” has been a group effort not a solo pursuit. Indeed, he reckons that the “stunningly good work” New Zealand’s scientists undertake now “needs to go more mainstream”.

“Science and knowledge need to be valued as highly as we value sports,” he says. “Wouldn’t it be cool if there was a five-minute run down of science and technology each night on the news as there was for sports?”

And talking of time, it’s a mark of Neil’s heartfelt desire to communicate about science that he’s given up more than five minutes of this valuable commodity to talk to the GO Blog about his life and his work. (Thanks Neil! It’s much appreciated, especially in the busy build up to Christmas and the New Year.)

We began by asking him how he keeps up with such an ever-changing subject as modern evolutionary biology. His answer was prompt and refreshingly honest: “It is not easy!”

As well as a heap of reading and “a ton of email alerts”, plus conferences and webinars when he can, Neil also receives constant new information “from students and colleagues working in the [various] fields”. Social media, too, is put to good, productive use.

“My Twitter network often lets me know about upcoming work weeks in advance of publication, sometimes months in the case of pre-prints.”

At the same time, however, he’s aware of the downside of such a full-on approach to work, in particular that “you almost never turn off—there is always something you are planning, working on or desperately trying to finish”.

“It can feel like a bit of a treadmill and the trick, not yet mastered, is to know how to get on and off without losing momentum. That said, my lifelong passion is spending time on or near the ocean—I love to fish, sail and generally muck about in boats.”

Just as important, he says, is spending time with family who, while “not quite as aquatically-focused” as he is, are always “a lot fun to just hang out with, whether at home or on holidays”.

Given this love of the sea, though, it’s no surprise to learn that Neil originally wanted to study marine biology while still at school.

“However, genetics was the hot area as I entered university, it was something I was good at, and I became intrigued by the idea of linking the two areas—if you look at my research there has been a strong focus on things marine.”

Indeed, in bringing together marine and genetic science, Neil recently made world headlines with an environmental DNA (eDNA) study of Scotland’s famed Loch Ness. While the loch’s celebrated monster was not recorded, the project drew the attention of a huge global audience to eDNA and its ability to monitor biodiversity in novel environments. Again, it’s about public awareness of the power and potential of science.

Yet even as a youngster, Neil knew that his own “passion and aptitude for learning” was the exception and not the rule.

“Let’s just say that academic achievement was not widely appreciated by classmates (sadly this continues) so I tended to keep a low profile,” he says. It’s an experience that perhaps explains why popularising science is now such a focus, with genetic literacy a “top priority”.

“Helping people to understand, prepare for and influence the many ways genetics is already impacting our lives in health, in food, and in our environment needs to be to the fore, because the new genetic technologies now emerging are going to affect us in myriad ways.”

And this is especially true for New Zealand, Neil says.

“I do think we need to focus more on understanding and protecting our environment—Aotearoa New Zealand is a unique treasure that we have responsibility to care for and doing so will generate many benefits.”

Educating and enthusing the next generation about science and technology is therefore vital “as we navigate a genetic future that is already changing our world”.

“We can either follow passively or choose to lead,” Neil says.

The first step, therefore, is to tackle our present-day challenges.

“Obviously right now climate change and multiple other factors place us on the brink of massive ecological collapse,” he says. “I think in 20 years things will be worse, but that we will have generated the technologies, some of these genetic, needed to avert the worst of the current climate scenarios. Perhaps in 50 years we will begin to see things improving on that front.”

And while that may seem far off today, Neil’s hope for the future “is for a better tomorrow”, for people and for the natural world.

“Our healthcare will be better than it ever has been, likely with tailored genetic editing (DNA and RNA) being used in multiple therapeutic areas, perhaps even leading to individual enhancements,” Neil suggests. “And primary production will reach efficiencies unheard of—likely using a variety of synthetic biology approaches to literally manufacture food from simple compounds with minimal environmental impact.

On the environmental front, “we will have documented almost all known life using sequencing,” Neil believes.

“We will better understand these living components of our biosphere and perhaps have some understanding of their complex interactions in simple ecosystems and communities. Perhaps we will even have reconstructed species once extinct, but in doing so likely learn through that process to value more the species and natural systems that we have so recklessly destroyed at unprecedented rates over the Anthropocene.”

It’s a future vision that’s as inspiring and as broad as Neil Gemmell’s own research career to date.

Written by Mick Whittle

To read more about Neil’s latest award, the Hutton Medal, and the groundbreaking research that led to it, follow these links:

https://www.royalsociety.org.nz/what-we-do/medals-and-awards/research-honours/2020-research-honours-aotearoa/2020-hutton-medal/

https://www.royalsociety.org.nz/what-we-do/medals-and-awards/research-honours/2020-research-honours-aotearoa/2020-hutton-medal/2020-hutton-medal-acceptance-speech/

https://www.otago.ac.nz/news/news/releases/otago747810.html

 

Genetics Teaching Programme Prize Winners 2020

Congratulations to the winners of the teaching programme awards for 2020!

In 1972 the first Genetics course was started here at Otago by Associate Professors Ann Wylie and Russell Poulter, consisting of a single third-year paper. Now, almost 50 years later, this has grown to become a degree program drawing expertise from eight departments across the University.

Associate Professor Wylie began teaching at the university in the Department of Botany during her honours year in 1945. After leaving to complete her PhD at the University of London she returned to Otago in 1961 taking on a position teaching cytology and genetics within the Department of Botany.

Despite her background in Botany she, together with Associate Professor Poulter, developed a course that covered the rapidly expanding breadth of Genetics including the recently described rII bacteriophage, the lac operon, Aspergillus, Drosophila, and human cytogenetics, many of which remain important components of the degree programme to this day. Associate Professor Poulter recalls “Lectures were in the Benham Theatre in Zoology which had steeply tiered desks. No white-boards, no projectors, no photocopiers (handouts were printed). Lectures began by cleaning the board, and writing on the board also involved turning your back to the class. As a result amongst the students, the art of making paper darts out of handouts was highly developed.” Associate Professor Wylie took this in her stride and was well known for the rigorous standards to which she held her students.

In honour of her contribution, in 2005 the Board of Studies for Genetics established the Ann Wylie Prizes in Genetics to encourage excellence amongst students majoring in Genetics. These are awarded to the top achieving students in 300 and 400 level genetics papers,