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Genetics Otago
University of Otago Research Centre

Avian Ancient DNA with Alex Verry

Alex Verry’s PhD research field has just broken the one-million-year barrier. Having said that, though, it’s also an area that’s so young that Alex himself wasn’t aware of it before starting at university.

Alex holding a Takahe

We’re talking ancient DNA here, and the hot-off-the-press news of the oldest aDNA yet to be sequenced – that from million-year-old mammoth teeth preserved in the Siberian permafrost. And while the study of ancient genes traces back to the work of renowned Kiwi scientist (and Otago alumni) Allan Wilson in the 1980s, the subject itself has really taken off in the past few years. It’s only within the last decade or so that researchers have been able to extract aDNA from extinct species ranging from mammoths to cave bears to our own near-relatives, the Neanderthals.

Tragically, it’s also only decades since one species at the heart of Alex’s doctoral study – the New Zealand bush wren – itself disappeared, with the last recorded sighting of this tiny native bird on Kaimohu Island, off Stewart Island, in 1972. Like so many of our treasured endemic species, this endearing creature fell prey to introduced predators like rats and stoats.

Alex’s work, however, allows him to travel back to the time when these wrens were found throughout New Zealand. Indeed, his aDNA detective work allows him to look through the last 20,000 years or so, and especially at the effects of past climate change on populations of New Zealand’s endemic wildlife.

“There’s a strong signal of population structure caused by glaciation,” Alex says. In fact, the genetic evidence suggests the little wren’s evolution was similar to that of our national emblem, the kiwi, with populations contracting and diversifying due to fluctuations in climatic conditions.

And it’s the chance to make an important original contribution to our understanding of New Zealand’s past that has provided excitement, motivation and personal satisfaction.

“No-one had looked at bush wrens before at such a fine scale,” Alex says.

Alex working in the ancient DNA lab

Yet he’s far from a ‘one species researcher, having also worked on other native birds, such as the iconic moa – including taking part in archaeological digs. His willingness to “get involved in things” has seen him out in the field with living taonga, such as takahē, as well as with the preserved remains of their long-departed relatives. For instance, some of his ancient DNA work has resolved a long-standing puzzle on the origins of North Island and South Island varieties of takahē.

“Don’t be afraid to ask – and volunteer” is Alex’s straightforward advice for budding geneticists.

As for his own journey to the soon-to-be-completed PhD, it’ll come as no surprise to learn Alex originally wanted to be a palaeontologist (well, at least when he was a dinosaur-fixated 5-year-old). But his enduring “interest in the natural world” led him to take biology at university, where he stumbled across ancient DNA for the first time.

“What really drew me was listening to a lecturer describing [DNA in] ancient penguin bones,” he recalls. “I thought, ‘This is crazy – can you really do that?’”

As for the future, he’s ready to spread his wings (well, as a bird specialist, why not?!) – possibly with post-doctoral aDNA research in Europe.

Eventually, though, he’d like to end up back home in New Zealand, working in museums or in conservation.

“Or even running my own laboratory.”

 

Written by Mick Whittle

Images supplied by Alex Verry

Bacterial Biomes, Colorectal Cancer and Different Diets – Rachel Purcell

“I think you would be hard-pressed to find any disease that microbiome is not linked to at the moment.” Rachel Purcell commented when I joined her for a discussion about her research. Our microbiome is the genetic material from all the microbes that live in the human body, including bacteria, fungi, protozoa and fungi. The gut microbiome focuses on just those organisms found in the gastrointestinal tract. This is where Rachel’s research sits. She is interested in how the microbiome affects various disorders. This is mainly colorectal cancer, but also includes diseases such as diverticulitis, appendicitis, and IBD. Her specific area of interest at the moment is how the tumour microbiome, or the gut microbiome, influence the bodies responses. The microbiome may have an effect on the progression of the disease, or influence treatment methods.

Rachel explained that the gut microbiome is well characterised, and we have a good idea of what microbes are present. Rachel uses a technique called RNA-Seq, which allows her team to catalogue what is present, with the added benefit of providing information about the functions that microbes might perform. Rachel explained “microbiomes are very unique, and simply counting what is there is not giving us a good idea of what they are doing. Our approach is to look for functional links and then form our computational data, then we can pull things out, and then design experiments that we can carry out in the lab to see whether any of those actually reflect what we see in the sequencing data.” Rachel also explained “there is quite a lot of redundancy of function. Two people can have completely different microbiomes, but they can both function the same. We are trying to not just look at the ‘bugs’ but look at the function. We do try to resolve it down to the species level sometimes because you need to do that for lab work, but there is such a crossover.”

Characterising different microbiomes in all types of patients and getting an idea of what functions they might perform, is paving the way to understanding how our gut microbiome might affect our susceptibility to disease, and possibly treatment. Rachel explained that although this research is in its infancy, there are certainly possible treatments that can arise from the research. “With microbiome, there is always the possibility of manipulating it, which is a lot easier than trying to change our host genomes or our host responses. Even looking at what has been done so far, there is definitely a lot of potential for the therapies, I think.”

 

Background

Rachel grew up in Ireland and has done her fair share of globe-trotting. Her travels have left her fluent in English and French, she also speaks a little Italian and Spanish, and a little Te Reo. Growing up in Ireland, Rachel reflected on her education in convent schools “studying science in a school where a lot of the text was redacted, definitely piqued my interest. I had a nun teaching me science and it was the strangest experience. A lot of things we glossed over, I thought ‘l want to know what this is about’. For a long time, I wanted to be a scientist, from a very early age.” In line with this plan, Rachel completed a Medical Laboratory Science and then a Biomed honours degree from University College Cork.

An opportunity presented itself for Rachel to attend the Pasteur Institution, an internationally renowned biomedical research institution in France. She completed her masters in bacterial genomics here, joking about the time “way back when it took two years to sequence the bacterial genome.” This research is where Rachels interest in bacterial genomics began. Following her master, however, she followed her interest in cancer research and went on to work in diagnostic cancer labs. “But I was always keeping an eye on what was going on in the bacterial genomics field and it was cool to be able to put the two things together—micro and cancer genomics. I guess I have a background in both because when I went back to work in diagnostics it was always in histopathology, and always looking at cancers.”

Seeking a change of location, and wanting to emigrate somewhere that spoke English, Rachel and her husband opted for New Zealand over Canada. She has been here for over sixteen years and raised her children here. She now resides in Arthur’s pass, enjoying the scenery and the calls of Kiwi in the night.

 

Colorectal Cancer

When I quizzed Rachel on which burning question she would most like answered, she responded “It would have to be about cancer prevention. Can we actually prevent a lot of the cancers that we are seeing? Here and everywhere, I do not think we are putting enough effort and research into prevention. We are targeting the wrong end of cancer, trying to treat people and come up with different solutions. If I could do anything, it would be in the preventative space. For example, trying to predict who is going to get these cancers, particularly sporadic cancers, and some way that we can prevent them. Whether it is by targeting the microbiome with faecal microbiome transplants, or even food interventions. I would love to think that that was going to be the way of the future.”

Rachel suggested that screening from a young age would be a beneficial step. “Because we are seeing quite an increase, particularly in colorectal cancers, in younger people now, under the age of 40-50, which we did not see many of before—it used to be a disease of old people. I mean, it has got to be something lifestyle-related. It is not going to be hereditary with the way things are changing so quickly, and I think the most obvious thing is what we are taking into our bodies, our food, and our diet, in general, has changed so much over the last 30-40 years.

Rachel also explained that simply screening people and informing them of a cancer risk would be inadequate, particularly if diet changes are a part of treatment.” When it comes to diet, a lot of it is social as well, and down to education. It is not just about trying to put interventions in place, it is a whole package.”

 

Education

Education was a theme that came up in my discussion with Rachel. Although her research does not involve genetic engineering, many people associate genetics research with genetic modification. I asked Rachel how well educated the public is on these matters. “In New Zealand, we are lagging behind, and there is a hangover of fear about genetic engineering…I think some of it is probably political. People do not understand that much of what we eat, use, and grow is genetically engineered. The idea that it is three-headed fish and stuff, it is an issue around education for sure. We are not doing that very well… we are very far behind.”

In regard to how we might go about instilling confidence in genetics research in the public, Rachel suggested “we need more education, right from kids in school, about how to assess where they are getting their information from. With the internet, you type something in and take the first hit. You do not know how to tell if your information is correct, or whether it is an imbalanced source, that is such an issue these days. Many people get their information from social media, which is scary. As scientists, we used to have public trust, and we were the voice of reason and truth, but that is all changed with social media platforms. Scientists are not present enough in that space, fighting the mystery. Part of our job now is to fill the void, because if we do not fill the void, it is filled with rubbish. A lot of us probably thought, in a sense, we were above that. We actually have to get down and dirty with the public. We have got to start from a young age. Kids need to learn how to actually evaluate the information that is out there, and I do not think that is happening.”

With the possible implications of her research, and the possibility of preventing cancer, it is understandably frustrating that the public is still lagging behind in their understandings of what genetics research is, how it works, and the benefits it could provide. In Rachel’s words, “I think it is time for change.”

 

Written by Don Sinclair 

Images Supplied by Rachel Purcell

Vanessa Lattimore—Unwinding the Genetics of Breast Cancer

Vanessa’s Work

BRCA-1 and BRCA-2 are the names given to two genes, which everybody contains a copy of in their DNA. Some individuals contain an epigenetic variant (a mutation) in these genes, which we know is associated with an increased risk of breast cancer. Interestingly though, two individuals may have an identical genetic mutation, and display breast cancer in different ways, at different stages of life, and one may never develop cancer at all. Vanessa Lattimore is investigating why.

Vanessa manages the familial breast cancer study in New Zealand. In her own words, “essentially we are trying to enrol families who carry high-risk variants of BRCA-1 and BRCA-2. The reason for this is that we want to understand why individuals with the same genetic change (that increases the risk of breast cancer), display breast cancer in different ways.” The genomes of those that carry variants in the BRCA-1 and BRCA-2 genes can be studied for various factors, such as whether there are additional genetic changes present, that could be responsible for how breast cancer presents differently in different patients. Part of this study involved comparing the genes of 300,000 individuals with the breast cancer variant genes and comparing them to approximately 150,000 people in a control group who have no breast cancer variant genes. This work has, unfortunately, been postponed due to COVID-19 but is well underway.

Another project of Vanessa’s involved collecting tissue samples of 367 women with breast cancer. These women donated tissue to the Christchurch tissue bank, which Vanessa’s team could use to extract DNA from, and test whether any of the women carried high-risk gene variants. Vanessa explained “we found that 13 women (of 367) carried high-risk breast cancer genetic variants. Of those 13, around half were not referred for genetic screening. This is really important as, if you know you carry a high-risk variant, you can manage the risk. For example, you can get a mastectomy, or you can have extra surveillance to detect the disease earlier if it does develop, which is a good option because if you get it early, you get better outcomes. But these women were not being referred for various reasons, because they did not fit within the current guidelines for referral. This adds evidence towards a screening of all breast cancer patients, which will allow everyone [carrying a high-risk variant] to be identified, and then they get an opportunity to manage their risk accordingly. It is really important not only for those individuals but also for their family members. Being a genetic disease, many of their family members will carry the same variants, and many of those will not have developed the disease yet. If they know that they are high risk as well, they can potentially prevent themselves from developing it.” This work is part of a recently published study.

Vanessa is now working on a project using oligonucleotides (short DNA or RNA molecules) to target BRCA-1 and BRCA-2 in certain regions. The goal is to repair the gene in men and women who carry the high-risk variant, in order to lower their risk of getting breast cancer. Vanessa explains the possible implications of this “if you have got a high-risk variant, then the biggest thing that you can do to lower your risk is a double mastectomy. That is hugely invasive and has side effects. However, if we are able to, for example, give someone an injection that lowers their risk as much, then that would be a lot better.” Oligonucleotide research, and its applications, is still in its’ infancy and Vanessa’s research is in its early stages.

Vanessa at Graduation, assuming the essential taekwondo pose.

To be clear, this process is not a form of genetic engineering and does not involve the manipulation of genes themselves. When our DNA is required to create a protein, a copy of the relevant gene is made, containing only the relevant information for forming that specific protein. This copy is called RNA. The process of copying the gene contained within the DNA, to form the RNA copy, is known as splicing.

As I mentioned earlier, everyone contains a copy of the BRCA-1 and BRCA-2 genes in their DNA. Those that contain epigenetic variants (mutations) in their genes are not able to produce functional proteins from their BRCA-1 and BRCA-2 genes, because the mutation causes the splicing step to be cut short. The idea is to use oligonucleotides to ‘fix’ the splicing step in people carrying genetic variants, with the hope that the RNA copy of the gene becomes functional and can go on to produce a fully functional protein.

 

Breast Cancer in Aotearoa

Vanessa explained the approximate frequency of variants in the BRCA-1 and BRCA-2 genes. “One in nine women will get breast cancer at some stage in their lifetime, and of those, I think around 3- 5%, sometimes up to 10% depending on the study you look at, will carry a high-risk variant. The majority of people do not have the genetic variant, but there are still a significant number that do. In the general population, men have one in 1000 chance of developing breast cancer. It changes for men, to about one and 100 if they have the variant, whereas in women it can increase up to roughly 70%. Men still have a much lower risk, even if they have the variant, but it is still much higher than what they had otherwise. But they also have less breast tissue, which is probably a big factor behind it.”

Vanessa, in one of the bake-off competitions run at the Otago School of Medicine in Christchurch.

I asked Vanessa how we might go about implementing the findings of her research into clinical practice in New Zealand. The issue that is often raised when proposing a genetic screen of a population for a specific genetic mutation, is that other mutations can be found, where we do not know what they mean or what their associated risks are. These are called incidental findings, and if every unknown incidental finding that was discovered was referred to the public health system for treatment, the public health system could not cope. The way around this is to offer a genetic screen but to look specifically at the BRCA-1 and BRCA-2 genes, as we know that there are actionable outcomes if a mutation is discovered. Vanessa explained “I think it would be hugely beneficial to offer everyone the opportunity to have a genetic screening that looks at specific genes (in some cases specific changes in certain genes), which if present, you can actually do something about, or at least have that awareness going forward. Even having awareness is great because, for instance with BRCA-1 and BRCA-2, we would know every family that carries it, and they will all have the opportunity manage that risk, and that will lower the incidence of breast cancer. This will save lives. I know that. That would be great.”

 

The Road to GO

Vanessa grew up on a farm near Methven, well accustomed to the outdoors. Vanessa has some great stories from the farm. One time while out roughing, she and her sister came across a set of antlers stuck to a water trough. When they got closer, it turned out to be a live wild stag! Another endearing story was raising a baby Thar, called Forest. “Honestly, Thar are incredible. If you think lambs can run around all day, Thar are insane. We used to run around yelling “Run, Forest, run!” and he would chase after us. One day he was walking along the second-floor veranda, less than a week old, and he trotted off the edge. My sister said, “oh my god!” But looked over, and he kept walking, like it was nothing! Honestly Thar are incredible.”

Vanessa competing in taekwondo .

Vanessa is also well adept in martial arts and has competed internationally. “I started Taekwondo when I was eleven, but actually quit three months after and started karate, which I have been doing for about 21 years. I went to worlds last year, and I went overseas and did a few tournaments before COVID. It was good timing. After that, I did not have anything to aim for, and I started from scratch. Now I am a white belt in karate.”

Not knowing what she wanted to do after high school, Vanessa attended university for the sake of doing something. She explained “I did a Bachelor of Science in Conservation and Ecology because I love animals and I decided I wanted to work in a zoo. I figured if animals are going to be stuck in a zoo, they should have a good life. I was going to ‘save the animals’. But I worked out pretty soon that you could not actually get a zookeeper qualification at university, you had to do a specific course in Auckland.” She then went on to do honours, sequencing the genome of the spider species Dolomedes aquaticus. She then took some time off to work and explained “it was during that one and a half years I had off, working over that time, I realised that genetics was a career you could have because I did not realise that before that point. I also learned that I really enjoyed research and decided that I wanted to do research and a PhD. I decided to start looking at options. My two choices were either going to be the genetics of something to do with farming to improve farming in some way. Or human health, because I wanted it to be relevant and make a difference in the world. I developed the project that I came up with, with Logan [Walker], genetics of breast cancer splicing. Which is exactly what I am doing still. It fit me perfectly. I started that, and have been here ever since, it has been eight years now. I love it.”

 

Oligonucleotides

University of Otago advertisement, featuring Vanessa.

I asked Vanessa what question relating to her research she would most like answered, in her own words, “it would probably be something to do with… whether there is a genetic target that we could go after that would help us to stop breast cancer occurring, or cancer in general. Something to stop cancer from happening. Prevention is better than cure. If we can prevent breast cancer, then that would be ideal.” Vanessa used an example of similar research for spinal muscular atrophy, to explain how this method could work. The SMA-1 gene is responsible for producing a protein that goes on to develop muscle tissue. Those containing a mutation in the SMA-1 gene, cannot produce the protein, and end up having muscle degeneration. This occurs from childhood, and usually, those with spinal muscular atrophy will never be able to walk. However, we also have another copy of the gene, called SMA-2, which Is identical to SMA-1, apart from four single nucleotides (of approximately 500,000 base pairs) different. Researchers have used oligonucleotides to attempt to alter the splicing of SMA-2, such that it produces a functional protein, identical to the type SMA-1 should produce. Vanessa explained “that way the whole gene is made into a protein and produces functional protein. And these children walk. It is incredible. It is actually incredible.”

Vanessa then explained that some animals like elephants and blue whales, have multiple copies of the BRCA-1 and BRCA-2 genes in their DNA, and are not prone to breast cancer. The effect of this is that even if the original copies of the BRCA genes develop a mutation, they can still produce functional protein from the copies of the genes. This is a naturally occurring example of the process described above involving the SMA genes. These animals naturally have redundant copies of genes built into their DNA. For cases where we have similar, but not identical copies of a gene, like SMA-1 and SMA-2, there is the potential to use oligonucleotides to intervene, and create a functional copy of the non-functional gene.

Christchurch Tissue bank

Vanessa holding a sample of extracted DNA, the cloudy polymer in the tube is DNA!

Vanessa praised the Christchurch Tissue bank and it’s overseer, Helen Morrin, for being an absolutely invaluable resource for her research. “Trying to collect samples as they come in takes a while. For the study involving 367 women, samples were collected by the tissue bank between 2013 and 2017. I was able to access and get given them all on a day. I do not have to wait that four-year period to collect the samples. The amount of work that would go into collecting those samples over that time is a lot. It is a great thing; the tissue bank is absolutely invaluable…Depending on what tissue they are getting, they may get tumours and they will break them up into little pieces that they can divvy out. Thus, they can be used for multiple projects. For my project, I was looking at germline rather than somatic changes, I was not interested in the tumour, but the blood. They had four blood spots about [this big]. I was able to get up to six, three-millimetre punches from one of those blood spots to get DNA from it. They have still got plenty left for other projects in the future, or if we need to go back and get more. It is a really good resource. because it not only saves researchers a lot of time, it can also be used for multiple projects, with the same amount of effort to collect it.”

Vanessa has a deep-rooted passion for her research that shines through in her explanations. She has a clear vision of where her research might lead while being entirely open to her findings and results. Her research could have far-reaching results and in my opinion, is likely to become a routine part of our healthcare system. Vanessa’s interests extend far beyond the laboratory of course, and she has retained a love for farming and farm life and continues to excel in martial arts. I asked Vanessa what she would most like to be remembered for, to which she responded “I would like to make a positive impact in some way. Exactly what for would either be in my research or saving the planet. Or at least helping raise awareness of the situation, and making positive changes to correcting it in some way.”

 

Written by Don Sinclair 

Images Supplied by Vanessa Lattimore

Genes, Medication and Mental Health Frustrations—With Simran Maggo

Pharmacogenetics

We are all aware that our genetics play a part in our likelihood of contracting certain diseases. The combination of genes we inherit from our parents determines what diseases we are susceptible to. Are you aware that our genetics also determine our reactions to drug treatments as well? This fascinating field of medicine is called pharmacogenetics, and it looks at how our genes affect our responses to medication and the associated side-effects of medication.

Simran in the lab with research technician Allison Miller

Research Fellow Dr Simran Magoo has been interested in pharmacogenetics for the last 10-15 years and has a strong interest in drug-induced adverse drug reactions. Simran explained, “I just find drugs interesting—How you could take a medication, and how I could take the same medication, and even if the dose was tailored towards our respective body weights, you could have a side effect, and I could not.” Simran’s current research is focused specifically on mental health medications and the reasons why there is such variability in which medications have efficacy for each individual. Simran explained, “a lot of people are prescribed antidepressants…and a lot of people report, either that it does not work for them, or that they get some horrible side effects.” In this case, usually the best (and only) option for the patient is to try successive prescription medications until they settle on one with some efficacy for their condition, and minimal side effects. The issue with this is that the process of changing medications can often compound mental health conditions. There is a drug called Venlafaxine for example, (an SSNRI used to treat depression among other things), which has great efficacy for some, but not for others. For those that report low efficacy, the withdrawal process involved in coming off the medication can be traumatic, making it difficult to stop and move onto the next medication, and thus make recovery a lot more difficult for the patient.

Simran explained how his research is attempting to improve on this process. “We have been looking at recruiting people (who take prescription medications for mental health conditions) into our various studies and seeing: is a person’s genetic makeup associated with specific side effects they get, or, associated with whether the antidepressants work or not?”

Simran noted that while medication is a great option for those suffering from mental health conditions, it should not necessarily be the first option. Simran explained “I think antidepressants should probably not be your first line of thought. I think there are various other therapies, cognitive therapy, or group therapy, or just talking to someone. It may sound bizarre coming from someone who has studied pharmacology, and usually, would probably be pro-drugs. But I think for mental health, drugs help. They definitely help, but I think they should probably be one of the last resorts.”

 

Journey to Genetics

A young Simran in Africa.

Simran has traversed a fascinating path to conducting his research with Genetics Otago. Simran was born in India and moved to Africa with his family at about six months old. His father, a mechanical engineer, was an expatriate in Zimbabwe. Simran and his family spent seven years in Zimbabwe, before moving on to Botswana. As a result, Simran speaks Hindi and Punjabi, and some Setswana, the language of Botswana. Recalling much more of his time in Botswana than Zimbabwe, this is where Simran completed the majority of his schooling and remembers it as a great place to grow up, but commented it would be very hard to compare to New Zealand. During this time, Southern Africa was a great place to be as the economy was thriving, and as his father was an overseas employee, they enjoyed some perks such as entrance to the best schools. Although he commented that after attending an international school for two years, he “actually did not like it much,” explaining “I preferred the local public schools. I suppose I found the international schools pretty snooty, and full of rich kids. Our family, we are not super rich, and I suppose I just did not fit in. I just found going to regular school was more my kind of thing.”

Recalling one experience with a particular teacher that stuck with him, Simran says “I suppose back in those days there used to be a bit of segregation or racism, so to speak. This may sound really wrong, but it actually happened. They put all the white kids in one class and put all the non-white kids in another one. I was obviously put in the other one. But the teacher said to me “look, you may see a big difference between that class and our class,” but I think she said something about God’s brain, like “your brain is no different than theirs. Do not let that get you down. What they are going to learn, is exactly what you are going to learn, so there is going to be no difference.” So yeah, I suppose that was an interesting time.”

As Simran approached high school graduation, his family was looking at possible countries to migrate to next and had applied for residency in a few countries, including Australia and New Zealand. He recalls the New Zealand residency came through and his dad one day asking “Simran, do you want to go to New Zealand? Because we have applied for residency and it just came through, and you have almost finished year 12.” Simran explained “And that is basically how I ended up in New Zealand. He gave me my passport, gave me a bit of money and he was like, “go check it out!”” After being accepted into Auckland University, Simran visited Dunedin and decided the small city was much more his kind of pace, and subsequently began studying health sciences there. Simran joked “I think, not everyone, but most people want to be a doctor at some point in their life. I think I wanted to, or maybe my parents wanted me to, but I was not sure. But, I did not get into medicine. However, I came across the Department of Pharmacology, which seemed really interesting.” He went on to complete a bachelor’s degree in pharmacology, followed by a postgraduate diploma, masters and PhD. Simran’s family soon joined him in Dunedin. He explained “Basically, Dad said, ‘this is the day that we are going to pack up, and we are also going to come,’ he said, ‘Just look at a few houses.’ I had a few houses picked out, and when they came, we decided on one. We have been living in that house since then.”

Simran in his neighbourhood growing up.

Simran recounted an amusing story from his first job in New Zealand, working as a computer software salesperson. When he applied for the job, he had thought it would be in a computer store, but it was a door-to-door salesman role. This was in the early 2000s when not many people had computers in their homes. His work had travelled to Gisborne to do selling there, and Simran was relatively new to New Zealand. He inadvertently got invited into a Mongrel Mob house (joking that he was lucky to be wearing red that day). The place was messy and cluttered, but they were interested in purchasing a computer setup. He ended up getting the sale and a decent commission, and only later did he come to realise what the mongrel mob was!

 

Routine Genetic Cancer Screening in New Zealand?

In discussing his research in more detail, Simran explained that pharmacogenomics or genetics should ideally be a crucial part of the New Zealand healthcare system. This would mean that prior to the prescription of any medication, a patient should have a basic pharmacogenetic screen. This could provide basic predictions such as whether the patient is likely to have an adverse reaction to the drug, and whether the drug will have any efficacy at all. The benefits of this could be huge, we would have significantly less wasted medication, faster recovery times, and less adverse drug reactions. Simran explained his frustrations that this concept has not been taken seriously, asking “why is it that a very basic test like this is being held back?”, or “what do I need to do to actually convince people that this should be in routine every day clinical care?”

There is very good research for certain drugs that says, “if you have these specific genetic variations, you are likely to get these adverse drug reactions”. There are some very clear-cut examples where, if you have a specific variation, you are almost 90% likely to have a physical reaction. There is currently one medication in New Zealand that, prior to prescribing it, doctors have to do a genetic screen in their patient. However, this drug is used in antiretroviral therapy in the treatment of HIV, and thus is not commonly prescribed in New Zealand. Coming back to prescription antidepressants, Simran feels that “if you were to test for variation in the genes prior to prescription, you could most likely prevent people experiencing side effects. I would say there is enough evidence out there in the literature, as well as in some of the studies we have done, to show that if you have certain genetic variations, you actually have a higher risk of getting side effects.”

Simran in the Lab with Allison Miller.

Simran gave another interesting example that nicely demonstrates the importance of pharmacogenetics. A proportion of the population contains a mutation in their CYP2D6 gene. This gene is responsible for producing the Cytochrome 2D6 enzyme, therefore those that have a mutation in the gene cannot produce the enzyme. The enzyme is used in the process of breaking codeine down into morphine, a vital step for the codeine to provide effective pain relief. As the enzyme that facilitates this process is not produced in certain people, any codeine they take will never be converted to morphine. You can be prescribed as much codeine as you want, it will not work for you. To put it bluntly, Simran explained “there are millions of doses of codeine that probably get dished out in New Zealand every year, and it is basically the same as just throwing them down the toilet because they are not doing anything for the patient!” Simran then explained “I am one of those people. I have no 2D6 enzyme activity. So, when I had knee surgery, I told the doctor, look, please do not give me codeine or Tramadol or anything like that because it is not going to work for me.” His doctor thankfully understood and accepted this and prescribed alternate pain relief options. Some doctors though are not even aware of this, Simran explained: “I have colleagues who have said similar things to the doctors and the doctors have denounced it or said no, it is not possible.” Simran believes it would not be an unrealistic task to provide genetic screening before prescribing drugs. “You can either do it from a blood sample, a saliva sample, or a buccal swab. Those are all possible ways of getting good quality DNA. If a clinical lab was to set up a test, it would probably take less than a day from getting a blood sample to getting a result. It’s very possible, and in my head, very easy to implement.”

 

The Nature of Research

Simran and I discussed these frustrations and the difficulty of effecting nationwide change in the healthcare system. Research is a career with no guaranteed results, answers, or gratification, but comfort can be found in the fact that the research being conducted could ultimately have positive impacts on the world. “At the end of the day, no one comes to work and just does stuff…Most researchers are passionate in what they do, they have this overarching goal in their mind, or an endpoint, where the reason I am doing the data gathering, is going to help. It will probably not be tomorrow, or not even in five years’ time. But in 10 years’ time, someone might use one aspect of my research to actually translate this into, either clinical or other commercial economic benefits. Whatever knowledge is gained through any kind of research, medical or whatever, it might not be used immediately, but at some stage along the process that that data is useful. Any data gathered is useful.”

Simran’s fire photography shot, from a photography club.

Simran reflected “Research is really difficult. It is not a guaranteed career. For your entire career, you have to continue to apply for funding.” He offered some advice that a former supervisor had once told him, “Everyone will tell you, do what makes you happy. But in today’s world, you have to do what puts food on the table and pays a mortgage for your family, that is often more important than your happiness. But if you can find a career where you can both put food on the table and be happy, that is awesome…Research is something I enjoy, it has its ups and downs, quite sharp ups and downs, but it is something I enjoy. At the moment it is putting food on the table, and paying the mortgage and the bills, and things like that.”

Reflecting on what he would most like to be remembered for, Simran said “I suppose at this stage in my life, probably as someone who helped introduce pharmacogenomics into routine clinical care in New Zealand. I think that if I could be remembered for that, at this stage of my life, that would be an achievement.”

 

Written by Don Sinclair 

Images Supplied by Simran Maggo

Reading Between the Genes—An Afternoon with Dr. Anna Pilbrow

Dr Anna Pilbrow

We live in a nation where you can turn up to your GP, be screened for a range of Cardiovascular risk factors, and your GP can determine whether there is, say a 5%, or 20% chance that you may go on to have a heart attack in the next five years. Your doctor might recommend some lifestyle changes, and prescribe a blood pressure lowering medication. This may reduce your chance of having a heart attack, but there is no way to know whether you will actually go on to have one.

Now imagine a world where your GP can test you for a certain molecule, or combination of molecules (perhaps genetic material in the blood, or a DNA marker in your cells), and the presence or lack of this ‘marker’ can accurately predict whether you are going to go on to have a heart attack or not. And if you have already had a heart attack, you could be screened for similar ‘markers’ that can better predict your long-term prognosis.

This is the goal of Dr. Anna Pilbrow of the Christchurch Heart Institute. More specifically, she is interested in inherited susceptibility to heart disease. Anna recalls having an interest in medicine, and particularly heart disease, from a young age. Three of her four grandparents passed away within the space of a couple of years, from heart-related issues. This, she recalls, perhaps created a subtle awareness of the presence of heart disease in her family. Anna was a budding young thinker, winning the National Science Fair Technology category in 1997. Her project was a continuous ready-to-serve hard-boiled egg—think a cylindrical device that lets you hard-boil eggs, such that there is the perfect amount of yolk-to-egg ratio in every slice!

Anna cycling in Peru, 2018

Anna recalls these early experiences leading her in the direction of research, triggering her to do a biochemistry degree at Lincoln. Biochemistry—because it combines chemistry and biology—but also provides the option to take a medical route, which had always interested her. In her third year, she transferred to Otago to complete her undergraduate degree. Anna then had her first exposure to the Christchurch Heart Institute when she did a summer studentship under the supervision of Professor Vicky Cameron.

Anna then went on to do an honours degree at Otago University. Anna recalls her supervisors from this time, Warren Tate and Joanna Williams being instrumental in her success.  She recalls her education as being surrounded by “wonderful projects and people”. By this time, she felt a break from study was necessary, and thought “time to earn some money!” She spent nine months working as a research technician, and eventually thought “maybe I would like to lead my own research” and “maybe I will need to do that PhD after all!” She ended up doing a PhD with the Christchurch heart institute, and did a couple of years as a post-doc there, as well as a couple of years in San Diego.

 

Research

Working with human heart tissue

Anna’s research is fascinating. Her passion for her work is evident in her explanations, and her expertise is clear in her ability to explain the content of her research. You are most likely aware that many things contribute to your heart disease risk: environmental factors, your age, whether or not you smoke, your diet, exercise, etc. On top of all of that are your genetics—what you inherit from your parents. These lifestyle and genetic factors interact to generate your overall risk, but Anna is really just focusing on the genetic side. The aim of her research is to discover new markers that help us predict either: who is about to have a heart attack, or, in patients with established heart disease, who goes on to do better or worse.

 

Anna’s Dream

The idea is that somebody can turn up to their GP, and the GP will screen them for a range of cardiovascular risk factors (age, gender smoking, diabetes, blood pressure, cholesterol—they will measure all of these). From this, they can predict whether or not someone’s got say a 5%, or 20% chance of having a heart attack in the next five years.

Anna in Laboratory with Colleagues. Copyright Neil Macbeth

Currently, this only works really well on a population level, so if the doctor sees a hundred patients, and a certain amount of them all have a similar risk profile, you can say there is a 10% chance of that group of individuals having a heart attack in the next five years. They will all be treated the same. For example, the doctor might recommend some lifestyle changes, and prescribe a blood pressure lowering medication. But what we find is that within each group of risk, there is a proportion (say 10%) that will still go on to have a heart attack. That means 90% do not, but they are all treated the same, regardless. So, Anna explains her dream is to find a molecule—whether it is some genetic material that floats around in the blood that we can measure, or whether it is a DNA marker that is just in our cells—the idea is to find something that can help tease apart who is going to actually go on to have that heart attack, and who is not. The idea is to add value on top of our current predictors, to predict better on an individual level what will happen to that individual. The parallel is once somebody has a heart attack; we can predict who is likely to do better or worse. Currently, we do not get that prediction right all the time, and we could improve it by adding some other markers.

 

Not Junk After All

In the last ten years, we have realised that most of our inherited susceptibility to complex diseases like heart disease, cancer, and Alzheimer’s, is not where we thought it was. If you think about DNA as a big long string, our genes are spaced along the DNA, but there are also long gaps of genetic material between the genes. Up until recently, we did not have a good idea of what it did. It was originally termed ‘junk’ DNA. But there have been some big advances in technology that have enabled very large studies to be undertaken. These “genome-wide association studies” look at most of the common variations in our DNA, within an individual, in a single experiment. Most of our DNA is the same, however, there are certain specific points where we vary. In a single experiment, we could work out what those points were for you. We could do it for me as well. But if we do it in ten thousand people, half of whom have heart disease and half of whom do not, we can compare the frequency of those variants between the two groups. The variants that are more common in the disease group than the healthy control group, are the bits of our DNA that are contributing to our inherited susceptibility for those diseases.

Anna tramping in Fiordland, 2020

These types of studies have been done internationally over the last 10 years or so. We now have a good idea of the points of our DNA that are contributing to our inherited susceptibility to heart disease. “Where we had been looking for years was in the genes,” Anna explained, “but it’s not in the genes! It’s in these long spaces of junk DNA between the genes. So very quickly we’ve thrown out the word ‘junk DNA’! Because it’s clearly not junk! It’s clearly doing something.”

This DNA is not coding for protein, that is what the genes do. It turns out that these long gaps of non-coding DNA code for other molecules. They can code for RNA molecules for example. We traditionally thought: the genes are in the DNA, you make the working copy of the DNA out of RNA, and this then gets translated into the proteins. It turns out that there is another RNA that is made from these non-coding regions. It does not get made into protein, but it goes about and does other things. One of these things is regulating how the protein-coding genes are made.

I asked Anna if there is one question relating to her research, she would most like answered, she explained “what I would like to know is the mechanism by which the DNA variants of the non-coding parts of the DNA are working. What are they doing, that then goes on to increase our risk of heart disease? Or even Alzheimer’s or cancer. 95% of our inherited susceptibility lies in the ‘junk’, so what is it doing? That is what I want to know.”

 

Regulation, COVID19, and Science Distrust

We live in a society that looks to science for solutions to our complex issues, as the scientific method has arguably been the single most important tool in the evolution of human society. Yet, we also live in a time where science and scientists are met with mistrust and undue scepticism. While scepticism and peer review are vital components of the scientific method, it can often be difficult for laypersons to know how to go about identifying false information, and how to apply good scepticism. In discussing this with Anna, I asked what she thinks the most important thing to keep in mind when considering complex or even simple science-based issues, particularly in relation to COVID-19.

“To me, [COVID has] been the most amazing example of how the value of science has really been showcased. Here in New Zealand, we have Dr Ashley Bloomfield standing side-by-side with Jacinda. Here was a scientist, leading our national response, supported by a huge team of epidemiologists, computer modelers, infectious disease control experts, academics, government employees, etc. To me, that was a great example of how the value of all of those years of research and knowledge all came together and came up with a really powerful response to a potential health disaster. I do not know if that answers what the public needs to know. But when there is uncertainty it is helpful if scientists and the government can deliver a single clear message. That is what the public needs in order to get behind something.”

 

Mentors

Anna Working in the Lab as a PhD Student.

One of the themes of Anna’s academic and professional career has been good mentors. Anna explains that her career has been driven largely “by serendipity and people.” Throughout our interview, Anna mentioned many people who helped her in some way, get to where she is today. She remembers Mr. White from her first year of primary school, an absolutely gifted teacher who brought together kids from all walks of life. She also remembers her form one and two teacher, Mr. Fowler, who was incredibly strong in teaching mathematics (up to her twenty times tables, she recalls), but also poetry, and he had an amazing class cricket rounders team!

She credits her first supervisor from her summer studentship at the Christchurch heart institute, Professor Vicky Cameron. Her honours project looking at synapses in the brain, supervised by Warren Tate, and Joanna Williams was also instrumental in her professional development.

When I asked Anna if she recalls the best advice she has been given, she struggled to come up with a single best piece of advice but instead credited those who are always there to advise her. “What I will say is that I have been incredibly lucky to have good mentors all the way through. Vicky for example has been a real key mentor. Beyond her, there have been others at the Christchurch Heart Institute, others at the school of medicine, my former supervisors, and peers, who have been very supportive and helpful along the way. I think it is only through them that I have been able to find a good path. So, my best advice would be finding smart, intelligent, amazing, and dynamic people to surround yourself with.”

This is one of the great qualities of a scientist, to be able to learn from those more experienced than them. An equally good quality is intentionally taking the time to pass on your skills, experience, and expertise to aspiring researchers. This is one of Anna’s goals, when I asked her what she would most like to be remembered for she did not hesitate:

“I want to give back”

 

Written by Don Sinclair 

Images Supplied by Anna Pilbrow

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.