I was privileged to speak at the Aspiring Women in Science conference in Brisbane, Australia last month. I think this is a fantastic initiative, which gives senior school girls an insight into working in various fields of Science (including Engineering and Medical specialties). Girls from years 10, 11 and 12 from all over Queensland were invited (mostly aged 15-17). Why girls? I attended a few of the talks myself and it reinforced my own view that there are experiences and conditions specific to women in Science. In talks on Science-as-a-career, information and advice from a woman’s perspective wouldn’t normally come up. It’s only fair to be as informed as possible when making a life choice. Both research and non-research careers were featured in the conference program.

We heard a lot of inspirational stories from Scientists in many different fields. Professor Ian Frazer – inventor of the Human Papilloma Virus vaccine Gardasil – was the keynote speaker. He spoke of his exciting adventures of discovery, from his childhood in Scotland to fulfilling his dream of building the Translational Research Institute in Brisbane. His dream will allow local scientific discoveries to be developed to commercialisation in Australia, instead of being sold to overseas companies. The virus (HPV) is a major cause of female cancer deaths in developing countries, and Prof Frazer is still battling to spread this message.

In the other sessions many women spoke of their work, of what excites and challenges all Scientists, and the challenges that women in Science in face because they’re women. Although we like to think that parents have equal roles nowadays,  a woman in research will likely have to decide whether she puts her children in childcare from a young age or give up research. Grandparents and other extended family are often not around to help because research fields are so specialised that researchers are likely to live far from their home town. These are stories that are familiar to me and were reinforced as I spoke to and listened to other women.

Several researchers, including Prof Frazer, spoke of the frustration of grant writing, the pressure of finding research funds, and the difficulty of sustaining a research career through short-term employment cycles. But more than one researcher also mentioned a published research study showing that a female name on an application for a (US) University Science position means the applicant is less likely to win the job, and the starting salary will probably be lower. Women also compete for grants, publication, promotion and leadership roles. And they drop out faster than men.

I don’t want to sound too negative, but students should be informed when they’re planning their future. I also believe things are slowly improving and if we keep on challenging the system it will keep on getting better. Being aware of the problem is part of working for a solution.

I can speak for scientific research and the thrill of discovery – if it excites you and you’re willing to give it a go – then go for it. Determination is part of the secret of success. I’m inspired by Jim Carrey’s lesson from his father: “You can fail at what you don’t want, so you might as well take a chance on doing what you love.”

But I do think that if you’re taking a risk it will be a bolder and better one if you have a safety net – such as family support, or a professional qualification as a backup plan.

I can’t pass up the opportunity to present these words from one inspirational woman about another, Maya Angelou (nothing to do with Science).

The Aspiring Women in Science conference was co-ordinated by Ela Martin and St Aidan’s Anglican Girls’ School in Brisbane. Part of the reason I was invited to speak is my history as a past student. I admire the school for making this conference and the school’s facilities and resources available to ALL girls in Queensland. Queensland’s a big place and some girls travelled a long way to make it. So, to Ela Martin and St Aidan’s, to Queensland University who supported the conference, and to all the Scientists who gave their time, a big thank-you for your initiative. I hope this idea has wings – per volar sunata.

 

Mitosis has to be one of the more beautiful things in nature. It’s a choreographed dance of the chromosomes. It’s so small that we can’t see it without a microscope, but it goes on in our bodies billions of times a day.

DNA is a very long molecule made up of the genetic alphabet (which has four letters: A, C, G, T). A gene is made of a certain sequence of DNA letters (or bases) and spells out an instruction for a step in the complex workings of our bodies (such as the structure of insulin). The genes are strung together along the chromosome, and each cell has a set of chromosomes. For our bodies to grow, these cells need to make copies of themselves. The problem of how to distribute the copied chromosomes evenly to the two “daughter cells” is handled very elegantly.

 

Chromosomes arrested at mitosis and stained with Giemsa (unbanded).

Human metaphase chromosomes stained with Giemsa (unbanded). The two halves of each chromosome are copies of each other.

 

Mitosis is the solution. Mitosis is broken up into a series of phases: interphase, prophase, metaphase, anaphase, telophase. You could break prophase up further by adding prometaphase: the part of prophase between the nuclear membrane breaking down and metaphase (where the chromosomes line up at the metaphase plate).

Now follow the captions under the pictures.

The interphase nucleus - the DNA from all the chromosomes intertwined with each other is represented by grey modelling clay. (Actually it seems that the chromosomes stay in relatively distinct domains - but under the microscope they appear as one entity.)

The interphase nucleus.   The DNA from all the chromosomes, intermingled with each other, is represented by grey modelling clay. (Actually it seems that the chromosomes stay in relatively distinct domains – but under the microscope they appear as one entity.) The DNA in the interphase nucleus copies itself as the cell grows.

 

The DNA in the nucleus starts to package and take shape as prophase chromosomes.

The DNA in the nucleus starts to coil up in a pre-determined order and take shape as prophase chromosomes.

 

The DNA folds up in a pre-determined order to make recognisable chromosomes. When the cell is ready to divide each chromosome has two chromatids or identical halves, joined at the centromere.

The DNA folds up further to make recognisable chromosomes. When the cell is ready to divide each chromosome has two chromatids or identical halves, joined at the centromere.

 

At metaphase the chromosomes meet in the middle of the cell at the metaphase plate. Then as the cell divides to become two daughter cells, the two halves of the centromere split and travel along the microtubules in opposite directions, pulling the two halves of the chromosome behind them.

Metaphase - the chromosomes line up in the centre of the cell at the metaphase plate. They are attached by their centromeres to microtubules which stretch across the cell.

Metaphase – the chromosomes line up in the centre of the cell at the metaphase plate. They are attached by their centromeres to microtubules which stretch across the cell.

 

At anaphase the two chromatids (half chromosomes) become the new chromosomes as they separate and move in opposite directions along the microtubules.

At anaphase the two chromatids (half chromosomes) become the new chromosomes as they separate and move in opposite directions along the microtubules.

 

The chromosomes start to unravel to form the two new daughter interphase nuclei. The cell membrane (the outer covering) pinches at the centre and the one cell finally becomes two (cytokinesis).

The chromosomes start to uncoil to form the two new daughter nuclei – telophase. The cell membrane (the outer covering) pinches at the centre (cytokinesis).

 

The cell membrane pinches at the centre (cytokinesis) so the cell finally becomes two cells.

Cytokinesis finishes and we have two new cells in interphase.

 

If a chemical that destroys the microtubules is added to a laboratory culture, the chromosomes are stopped at metaphase. Cytogeneticists (chromosome scientists) use this technique to get enough metaphase chromosomes for analysis. Chromosome banding helps us recognise the chromosomes and identify any changes when an abnormality is suspected. Of course, the cell is also full of other organelles that have to be shared between the new cells.

The modelling clay images above are from my claymation showing mitosis. Modelling clay is a great medium for demonstrating and thinking about how things work, move and change. For the claymation I used a phone camera resting face down on a glass coffee table over the models.

(Cross-posted from Fireside Science at SciFund Challenge.)

Today is Rare Disease Day. Its main aim is to raise awareness among policy makers and the general public. There are over 6,000 rare diseases and 80% of these have a genetic cause.

We have over 20,000 genes coded by over 3,000,000,000 letters of genetic code. Genetic diseases are caused by mistakes in one or more of these genes. These are like typos or spelling mistakes. Not all genetic changes cause disease. But some debilitating genetic diseases are caused by simple one-letter mistakes.

There are also longer mistakes – sections of chromosome can be taken out (deleted) or added in. People with chromosomal syndromes are likely to have several unrelated symptoms, because a cluster of different genes is affected.

The more common genetic diseases are more likely to be researched. There were several labs working to discover the genes for some of the more well-known diseases at the same time – such as cystic fibrosis, Duchenne muscular dystrophy and fragile X syndrome. This competition created a sense of urgency that helped speed up the discovery of these genes. Finding out what gene causes a disease can go a long way to understanding the disease. Sometimes very effective treatments are found by knowing the cause of a disease. The more common genetic diseases that still aren’t fully explained are usually caused by the combined effect of multiple genes. It’s a lot harder to track these down. But there are probably still a lot of rare diseases that could be simply explained but aren’t being researched.

A lack of awareness of rare diseases often means there is misdiagnosis or difficulty getting a diagnosis. People with rare diseases have shared their stories on the Rare Disease Day websites. This is Judit’s story (Judit stars in this video).

This is the opening title of Paper Thin. Yesterday was the last day of filming and I got a look at some of the Director/Producer Elizabeth Duong‘s work. It’s exciting – this will be a touching but beautiful film. It’s based on a true story of a girl called Sadako who developed leukaemia after exposure to radiation in Hiroshima.

One of the hallmarks of leukaemia that’s caused by radiation or toxic chemicals is very rearranged chromosomes. I’m working on unravelling the patterns and causes of the very disorganised genetics of this type of leukaemia (known as therapy-related acute myeloid leukaemia).

Sadako hoped for a cure. My hope is that with the help of this film this research can continue and realise her dream for future leukaemia patients. A big thank-you to Elizabeth and all her helpers, who have given their time freely. A special mention also to Daniel Hernandez who composed the original soundtrack. It’s awesome. Here we have Essendon Symphony playing the opening theme and I think that’s Daniel playing over the stings.

(This is cross-posted from the Fireside Science blog at SciFund Challenge.)

We care about our health and the health of our loved ones. If only we had explanations and cures for all of humanity’s illnesses. But there are still many diseases that aren’t being researched, even though they cause real and obvious suffering.

Medical research is paid for in a number of ways. The obvious one is the drug companies, where there’s a cost-benefit consideration. I’ll discuss the other options, and how it works in Australia.

The biggest pool of money comes from the government. We have the National Health and Medical Research Council (NHMRC), which runs several grant funding schemes each year. There are also some Fellowships that provide researchers with a secure salary for up to five years. Research grants typically last three years, and they usually include salaries for scientists working on the project. Only 16.9% of Project Grant applications were funded for this year. And the competition gets stiffer every year. So this is clearly not a reliable source of funding for most research wish lists. In the words of the crowdfunding site microryza, “Our system for funding science is broken. Our planet’s biggest funders are so conservative that they fund … only the most obvious ideas. Discoveries that matter are languishing.”

Charitable giving picks up a lot of research that the government doesn’t fund. Besides the work they do supporting patients and their families, some patient advocate groups raise funds for research. There are also private citizens who set up research trusts, and many many more who donate to research. Most of these charities and trusts pull less weight than the government grants, but there are some very large ones based overseas, such as the Wellcome Trust and the Bill & Melinda Gates Foundation.

There’s also a new movement known as crowdfunding. You may have heard of Kickstarter. There are other crowdfunding sites specifically for scientific research. Examples are microryza (now renamed experiment), Petridish, and SciFund Challenge. There have been some remarkable successes like the microbiome project but most projects ask for a modest amount. Researchers are turning to crowdfunding more and more as other sources of funding become harder to get.

So there’s a limited pot of money for research. Who decides what it’s used for? Government grants are hotly contested. One of the tasks of the grant writer is to convince the reviewers that theirs is an important problem and the team has the expertise to solve it. Some charitable trusts have a similar review system, but it can also vary quite a lot and can depend on the wishes of the donors. Crowdfunding cuts out the middle man and it’s the donor who must be convinced that the project is worthwhile.

So, why isn’t there more research into your disease and what can you do about it?

You will need researchers who have an interest in your disease and some funding. Which brings us to awareness. Greater awareness by governments, policy makers, researchers, and doctors who make diagnoses will help your case. Under-recognition of rare diseases is a huge problem which can also be addressed by awareness.

The common and high profile diseases such as cancer get a lot of research dollars. Their severity and impact on the community are obvious. Rare diseases don’t have this advantage. Rare Disease Day is an annual event that advocates for people with diseases, syndromes and conditions that occur in fewer than one in 2,000 people. Rare Disease Day is coming up – most years it falls on the 28th February, but every fourth year or 1,461st day it falls on that rare date – 29th February.

Patient advocate groups that offer research grants can have some influence. They can offer grants that are targeted to a specific disease or question. This can help them find researchers with the appropriate expertise, and attract researchers who are looking for funding. They can use the funds that have been raised specifically to improve the lives of the people they support. Crowdfunding is also a great way to target donors who are keen to support the cause.

About 80% of rare diseases are caused by genetic errors. Humans have over 3,000,000,000 letters in their genetic makeup, and these spell out over 20,000 pairs of genes. Many genetic diseases are caused by a one letter error in one of these genes. The human DNA sequence is now mostly known, so it’s possible to read the DNA sequence of the patient and compare it to a standard to find a needle-in-a-haystack DNA error. Unfortunately not all genetic diseases are that straightforward – but it’s a start.

Recently there have been some heart-warming examples of very rare but debilitating diseases for which the causes have been found with the help of sequencing and a persistent parent, being in the right place at the right time, or scientists who were looking for a problem to solve. These are some of the good news stories of modern genetics that are starting to make an impact on rare diseases.

If you want to help make a difference my advice is to support your disease’s patient advocate group, fundraise and lobby for research. If there isn’t a support group for your disease, you could start one. If your disease is rare, Rare Disease Day is there to help. And anyone can help raise awareness about a disease. Better awareness brings better understanding.

LINKS TO PERSONAL GENOME STORIES

Cracking the code – transcript of the Australian Story episode on ABC TV. A father’s quest to find the gene mutation causing his son’s disease.

Genome maps solve medical mystery for Calif. twins – Shots – Health news from NPR.

We gained hope.” The story of Lilly Grossman’s genome – National Geographic’s Phenomena – Not Exactly Rocket Science

James Lupski’s Research into His Disease Paved Way Toward Personalized Medicine – Quest (MDA Magazine Online – Fighting Muscle Disease)

The Solution to Diagnostic Delay May Be Closer Than We Think – blog post by the National Organization for Rare Disorders arguing that a rare disease app may help doctors diagnose rare diseases: “…most… rare diseases are unfamiliar to doctors… When doctors are unable to explain patients’ symptoms — as they are for at least three years in the majority of rare disease cases — psychiatric diagnosis is made by default.”

Cancer has been described as the most common genetic disease. This doesn’t necessarily mean it’s hereditary – usually the genetic mistakes that cause cancer arise in the body’s organs or tissues and can’t be inherited. We’re continually learning of new cancer-causing genetic mistakes.

If we think of genes as words spelling out the instructions for our bodies to function, there are different types of mistakes or “typos” that can cause cancer. Some of these are like spelling mistakes – an incorrect letter or two. The mistakes I’ll be talking about here involve whole words (or lots of them). For example one or more copies of a word are added – ” very big” becomes “very very big” – extra copies of a cancer gene (we call them oncogenes) can cause or accelerate cancer growth. Or if a word is lost – “don’t grow” becomes “grow” – this illustrates loss of a tumour suppressor gene.

I described the breakage-fusion-bridge cycle a few weeks back. The BFB cycle was a theory developed from studies with maize, but it also applies to some cancers. This is an example of basic research,  inspired by curiosity but eventually being useful in ways we never imagined. If you look back at that post it shows how the BFB cycle can cause gain or loss of genes. If a cancer gene is  multiplied, or if a tumour suppressor gene is in the part that’s lost, the cell can gain a growth advantage over other cells, which is part of the process causing cancer.

Here’s an example.

Cancer cell lines are cancer cells that can be grown indefinitely in the laboratory. I’ve just published a paper on HEL, which is a leukaemia cell line. It’s popular for studying how cells make globin (molecules in red blood cells that help us process the air we breathe).

The chromosomes of HEL are very abnormal. I’ve used a combination of techniques to show how the chromosomes are reorganised as well as which parts have been lost, gained and amplified.  It’s very complicated.

One of the gene abnormalities in HEL is amplification of the JAK2 gene. JAK2 is a well-known cancer gene that is often abnormal in blood cancers. The normal gene can be mutated to become a cancer gene, for example by a “spelling mistake” in the DNA. By adding extra copies of this abnormal gene the effects can be magnified. This is known as gene amplification. There are a few cancer genes that are commonly amplified in cancers.

To cut a long story short, JAK2 is amplified in the HEL cell line. And a nearby tumour suppressor gene (CDKN2A) has been lost. But only by looking at the chromosomes does the reason become clear. Some detective work tells us that there were some breakage-fusion-bridge events. I won’t go into the detail – if you’re interested it’s in the paper. But we have chromosomes whose ancestors had two centromeres, and if we use a DNA tag for the region between the centromeres we can see “stripes”.

Here’s an example from HEL that shows DNA amplified by the BFB cycle – we can show where a gene is on the chromosomes by labelling it with a fluorescence tagged DNA “probe”. The striped pattern reminds us of the yellow dots in the modelling clay demonstration:

The red is DNA that's normally at one end of some of the chromosomes. The stripes tell us that the end of a chromosome (22) is in the middle of these chromosomes and there are extra copies. This helps us work out how these chromosomes were made. It's a strong clue that BFB cycles were involved and the ancestral chromosome had two centromeres.

The red is DNA that’s normally at one end of some of the chromosomes. The stripes tell us that the end of a chromosome (22) is in the middle of these chromosomes and there are extra copies. It’s a strong clue that BFB cycles were involved and the ancestral chromosome had two centromeres.

The new chromosome with four copies of the yellow gene courtesy of the breakage-fusion-bridge cycle.

The new chromosome with four copies of the yellow gene courtesy of the breakage-fusion-bridge cycle.

Recently JAK2 amplification was also reported in triple-negative breast cancer. Triple negative means that three well-known genetic causes of breast cancer are not present. So finding JAK2 amplification would help explain the cause of some triple-negative breast cancers, and could help work out an effective treatment. Perhaps this JAK2 amplification is sometimes caused by BFB cycles. Without looking at the layout of the abnormal chromosomes we may never know.

To end this story, here’s Bruce Mercer’s cartoon diagram showing the BFB cycle in HEL: http://emph.oxfordjournals.org/content/2013/1/225/F6.expansion.html

Chromosomes that cause cancer. Part 2. The Philadelphia Chromosome.

This is a link to my latest post on the Fireside Science Blog on the SciFund Challenge website.

It describes the first discovery of a cancer-causing chromosome and the exciting progress in treating chronic myeloid leukaemia that it made possible.

Barbara McClintock published a paper describing the breakage-fusion-bridge (BFB) cycle in 1939. Many of her ideas were well before their time. Like many such profound leaps in thinking, the BFB cycle took a long time to catch on. She wrote in 1973, “I stopped publishing detailed reports long ago when I realized, and acutely, the extent of disinterest and lack of confidence in the conclusions I was drawing …One must await the right time for conceptual change.” Her work was appreciated much later and she was awarded a Nobel Prize in 1983 for her discovery of “jumping genes“.

A few weeks back I introduced this post by describing normal chromosome division. This time we’ll look at the breakage-fusion-bridge cycle. This is one way chromosome division can go wrong. Very wrong, in the sense that it can cause the chromosomes to keep changing, and this can cause cancer.

A human chromosome with two centromeres is abnormal. Chromosomes with two centromeres are not unusual in cancer cells. In fact they’re probably a lot more common than we think, because in both research and diagnostic labs the centromeres are usually not looked at.

To recap, a normal chromosome has one centromere. Before the chromosome divides, the two identical halves (chromatids) are held together at the centromere. When the chromosome divides the centromere splits into two halves, the chromatids become the new chromosomes, and the centromeres take the two new chromosomes in different directions into the two new daughter cells.

So what happens if there are two centromeres? If they’re both aligned so that they head in the same direction it’s not a problem – together they take a complete new chromosome with them. The closer the centromeres are together the more likely this is.

Now follow the pictures and their captions. These describe chromosome division in an abnormal chromosome with two centromeres. Especially follow the yellow dots.

A twist between the two centromeres when the chromosomes align ready for chromosome division.

If the two centromeres on a chromosome go in the same direction there’s no problem. But if there’s a twist between the two centromeres when the chromosomes align ready for chromosome division….

....then, when the two halves of each centromere separate they head off in different directions.

….then, when the two halves of each centromere separate they go in opposite directions. We have a “bridge” spanning the gap between the two centromeres.

The bit of chromosome between them gets stretched and can break.

The bridge is stretched and can break.

The broken chromosomes in the new cell join together - the top daughter cell gets an extra copy of the yellow gene. The bottom cell loses this copy of yellow gene.

The broken chromosomes in the new cell join together – the top daughter cell gets an extra copy of the yellow gene. The bottom cell loses this copy of the yellow gene.

The new chromosome copies itself to make two equal halves.

The new chromosome copies itself to make two equal halves.

If this process repeats..

If this process repeats..

Fusion of the broken bits of chromosome in the top cell.

Fusion of the broken pieces creates a chromosome with four copies of the yellow gene.

After replication - the new chromosome with four copies of the yellow gene courtesy of the breakage-fusion-bridge cycle.

After replication.

If the yellow gene in the pictures is a cancer gene (“oncogene”) the cell with extra copies might grow and multiply faster than its neighbours. We call this natural selection – the cells that can grow faster than their neighbours become more common which means the genetic change causing that is undergoing “positive selection”. Yes, the cells in our body can evolve and we know this best as cancer.

All this change happens between the two centromeres where the bridge forms. So if we find a chromosome with this type of change on one side of the centromere only it’s a clue that this might have been caused by the breakage-fusion-bridge cycle.

These are modelling clay images from my breakage-fusion-bridge claymation. They’re a bit rough but I hope it helps you understand what happens. Many, perhaps most, images demonstrating the BFB cycle show a different version – where the abnormal chromosome is created by two chromatids of one chromosome breaking and joining together. Most examples don’t show the version I’ve presented – where two different chromosomes have joined together. Check this out on Google Images (search for breakage-fusion-bridge).

Here’s the answer to the quiz from the telomere post. The arrows point to the ring chromosomes. Being rings they have no ends, so no telomeres.

answer to ring chr

Further Reading:

B. McClintock 1939. The Behavior in Successive Nuclear Divisions of a Chromosome Broken at Meiosis. Proc Natl Acad Sci U S A. 1939 August; 25(8): 405–416.

M. Kinsella and V. Bafna 2012. Combinatorics of the Breakage-Fusion-Bridge Mechanism. J Comput Biol. 2012 June; 19(6): 662–678.

R. MacKinnon and L. Campbell 2011. The Role of Dicentric Chromosome Formation and Secondary Centromere Deletion in the Evolution of Myeloid Malignancy. Genetics Research InternationalVolume 2011 (2011), Article ID 643628.

Something completely different – Solar lighting – making a difference to the world’s poorest people.

Here’s my latest post in SciFund Challenge’s Fireside Science blog.

Check out the other posts too. This is a blog about anything and everything science.

Claymation update – nearly there!

The new Fireside Science blog at SciFund Challenge

I know, it’s been a long time between posts. I’m working on a breakage-fusion-bridge claymation to show how some cancer chromosomes are very changeable. It’s a steep learning curve but hopefully I’ll have it thoroughly mastered soon.

In the meantime here’s a post from Abby Buchwalter in the new group blog “Fireside Science” – SciFund Challenge’s Guide to Life, the Universe, and Everything. Abby and some of the other graduates of the first SciFund Challenge course (including myself) have started a group blog hosted by the SciFund Challenge website. Here we plan to bring the world of Science to readers in an easily digested form.

Abby describes a cell using only the 1,000 most common words in the English language.

Enjoy.