This sticky end is a clue to cancer’s causes

How do healthy cells turn cancerous? Their  DNA gradually accumulates errors. Most of these errors aren’t important, but occasionally they stop the cell from working properly. They might cause a cell to grow out of control – and this can lead to cancer.

Myelodysplastic syndromes, or MDS, are a range of blood disorders caused by such errors in the genes. Some types of MDS are relatively mild, but about a third go on to become acute myeloid leukaemia (AML). Thanks to research on MDS we understand its causes a lot better than we did ten or fifteen years ago.

My lab recently published a paper describing three cases of poor prognosis MDS and one case of AML with unusual but remarkably similar changes to the DNA. This complicated structure could not have been predicted by the standard methods of analysing cancer DNA or chromosomes. These features showed us the likely steps that led to these diseases.

Each long string of DNA is folded up neatly to make a chromosome. This is a Claymation that shows how Barbara McClintock’s classic breakage-fusion-bridge cycle causes chromosome abnormalities. The video shows one way that chromosomes (packages of DNA) can become disorganised.

The  telomeres (that cap and protect the ends of the chromosomes) are shown falling off, making sticky chromosome ends which join together (see NOTE 2). It’s well accepted that these changes greatly increase the chance of cancerous gene changes. This process has reproduced many, many times in the lab. The problem is that it’s not often been demonstrated in actual cancers. But we did that.

Sometimes only part of the telomere erodes away – enough is lost that it no longer protects the chromosomes from sticking together. But there can be enough telomere DNA left to be a molecular signature of the telomere.

The arrow points to green dots in the middle of a chromosome. This is the left-over telomere signature that tells us that this abnormal chromosome was made by the joining together of sticky chromosome ends that had their telomeres eroded away. The other green dots are at the chromosome ends. The left and right photos show the same cell but in the right one the abnormal chromosome is identified by its red and blue label.

The arrow points to green dots in the middle of a chromosome. This is the left-over telomere signature that tells us that this abnormal chromosome was made by the joining together of sticky chromosome ends that had their telomeres eroded away. The other green dots are at the chromosome ends. The left and right photos show the same cell but in the right one the abnormal chromosome is identified by its red and blue label.

In our four cases we found that there was a small but non-functional piece of telomere DNA left behind where the two chromosomes joined. Because the telomeres didn’t function, the two chromosome ends could stick together. These caused breakage-fusion-bridge events that caused a protective tumour suppressor gene to be lost, and may have also caused cancer-causing genes to multiply.

MDS and AML have similar genetic causes, so if we learn about the causes of one of them it can help us understand the other. This is often the case with cancer research in a broader sense – if we understand the basic mechanisms in one cancer it can help us understand the mechanisms at work in other cancers better. Telomere fusion could potentially play a role in any cancer, so our MDS research is relevant to cancer research in general.

 

 

NOTES
The paper: The dicentric chromosome dic(20;22) is a recurrent abnormality in myelodysplastic syndromes and is a product of telomere fusion. Ruth MacKinnon, Hendrika Duivenvoorden, Lynda Campbell and Meaghan Wall, 2016. Cytogenetic and Genome Research 150(3-4):262-272
The gene errors discussed here usually occur in the body cells rather than the reproductive cells, so they’re not inherited.
For simplicity the Claymation shows telomere fusion in chromosomes that are dividing.  In fact it probably occurs when the DNA is unravelled in the interphase nucleus.

This is cross-posted from ChromosomesandCancer.com.

Bedtime Science: Why do seeds travel?

A lot of plants have seeds that are made to travel to new places. Why is this?

Plants get their energy from the sun. They need this energy to grow. What happens if a seed falls from a lovely leafy tree? The new plant is in the shade. The sunlight falls on the leaves above it and the seedling won’t get as much.

Not only that, but it’s trying to grow in space that’s taken up by the big tree’s roots. It’s not going to grow big very fast.

To have a better chance at life this seed needs to get away from its parent. That’s why nature has come up with all sorts of different ways for seeds to travel. We’ve looked at helicopters, hooks and darts (prickles). Can you think of any more? Go and have a look outside. Maybe you can discover more some for yourself.

Blown dandelions (Viggo Venneløs løvetann)

Do you know what these are?

EXTRAS

Image attribution: By Erlend Schei (http://www.flickr.com/photos/nerdegutt/3585220976/) [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons

Hint: Taraxacum

Majority of island flying foxes are on the brink

Once upon a time, there was a tiny piece of paradise on Earth, where unique animals and plants were living their day by day mostly peaceful. As, nothing is perfect, not even the paradise, sometimes, there were some trouble, like long droughts. Many animals would die, but species would survive. Quite often, like once a year, there was some pretty strong winds with rain (aka cyclones).  But still, it was a paradise surrounded by blue and calm lagoons full of a kaleidoscope of marine wildlife. The number of unique species on this land was above average per its land mass. The place was steaming with some amazing creatures like oversized pigeon that walked on the ground, colourful geckos or giant tortoises of different shapes. These animals, and many others, depended on the many unique plants of their land, and of course, the plants depended on them for pollination and for moving their seeds around. This paradise was created and perfected over millions of years.

 

One day, not to long ago, the paradise was discovered by a species that believes that it is the one superior to all others. And this day marked the beginning of the end of the paradise. Unfortunately, this is not a story but it is history. True history. The paradise was not fictional, but real. It is a tiny island in the western Indian Ocean. After the species that calls itself ‘wise man’ (Homo sapiens) appear in the history of this paradise, it took a blink of a second (compared to the geological time of the island) to destroy most of its forest and lead many unique species to extinction.

 

But the wise man never learns from his mistakes. This narrative of Mauritius is like many other small isolate islands around the world (and some island continent as Madagascar or Australia). Worst, adding salt to the injury the trail of destruction continues. A few days ago, we learnt that majority of island flying foxes are threatened with extinction, while others are already extinct. Flying foxes are stigmatise just because they are bats although they survive mostly only on fruits and never drink blood. Even their cute eyes and bright and fluffy fur are not enough to go against the bashing they suffer. Most people do not realise that the flying foxes are very important for the maintenance and survival of the tropical forest, especially of isolated islands of the Pacific and the Indian Ocean. Instead, we hunt them for fun, sport or meat.

 

Mauritius flying fox resting during the day

A cute Mauritius flying fox resting during the day

Like for climate change, we all need to act to save biodiversity for the ensure that many species can survive and for our own survival. For the flying foxes, we need to be aware if the tropical fruits we are eating are not endangering them. This will be a good starting point.

 

References:

F. Rijsdijk et al. 2011. Mid-Holocene (4200 kyr BP) mass mortalities in Mauritius (Mascarenes): Insular vertebrates resilient to climatic extremes but vulnerable to human impact. The Holocene 21 (8): 1179-1194.

E. Vincenot, F.B.V. Florens, T. Kingston (2017) Can we protect island flying foxes? Science 355 (6332): 1368-1370.

The smallest orchid of Mauritius

The Mauritian flora is well-known as it started to be described in late 1760s by Philibert Commerson. Nearly half century later, Thouars published the first major study about Mauritian orchids. Today nearly 100 native species of orchids have been recorded for Mauritius (Roberts & Wilcock 2003, Pailler & Baider 2012, Baider et al 2012; Fournel et al 2015).

The vast majority of the original forest cover that once existed on Mauritius has been destroyed. Today no more than 1.6% of good quality forest exist in isolated fragments. So, as expected part of the Mauritian orchids are extinct (~ 30%), and most of the still extant species are threatened with extinction. One can imagine that the many orchids disappeared before they could be collected.

Nevertheless, in 2000, a new orchid was recorded in Mauritius. It call Taeniophyllum coxii (Summerh.) Summerh.. Other orchids were added to the list later, but this one had something very special. The tiny T. coxii is the smallest known orchid in the Mascarenes. It rises to less than 1 cm in height, with roots that can span up to 6 cm laterally, but they are usually much smaller. Its flowers are less than 1 mm in diameter! More, the orchid is aphyllous, or it has no leaves. The young plants look like tiny sharp blades.

An adult plant of Taeniophyllum coxii

An adult plant of Taeniophyllum coxii

and a baby (yes, there is an orchid in this photo!)

and a baby (yes, there is an orchid in this photo!)

 

The species is known to occur in few mainland Africa countries (Ghana, Malawi, and Zimbabwe). Therefore, its discovery in Mauritius represents a large extension of its range. Not surprising, its first collection on Mauritius happened to be the 8th to be made in the whole world.

Dave Roberts, saw a single plant growing on a native coffee plant (Coffea macrocarpa), when he was doing his PhD field work. Three years later, Vincent Florens and me found nine plants in poor shape. Later, we found single individuals or thriving colonies of the species in other places (Roberts et al. 2004).

The current conservation status of T. coxii is not fully known, but on Mauritius the species would be classified as Critically Endangered using the IUCN Red List criteria. For this, and other orchid species to survive, there is need for a long-term conservation of their habitat, including restoration the Mauritian native forests.

 

References

Baider, C.; Florens, F. B. V.; Rakotoarivelo, F.; Bosser, J.; Pailler, T. 2012. Two new records of Jumellea (Orchidaceae) for Mauritius (Mascarene Islands) and its conservation status. Phytotaxa 52: 21-28. DOI: http://dx.doi.org/10.11646/phytotaxa.52.1.3

Fournel, J.; Micheneau, C.; Baider, C. 2015. A new critically endangered species of Angraecum (Orchidaceae), endemic to the island of Mauritius, Indian Ocean. Phytotaxa 222 (3): 211-220. DOI: http://dx.doi.org/10.11646/phytotaxa.222.3.4

Roberts, D. L.; Wilcock, C. C. 2003. Orchid flora of Mauritius. in J. Hermans and P. Cribb. Proceedings of the European Orchid Conference and Show. London. p. 294-303.

Roberts, D. L.; Florens, F. B. V.; Baider, C.; Bosser, J. 2004. Taeniophyllum coxii (Summerh.) Summerh. (Orchidaceae): a new record for Mauritius, Indian Ocean. Kew Bulletin 23 (4): 493-494.

Pailler, T., Baider, C. 2012. Polystachya jubaltii Pailler (Orchidaceae), une espèce nouvelle endémique de Mascareignes. L’Orchidophile 195: 285-289.

 

What’s the point of prickles?

Have you ever stood on a prickle? Going barefoot in summer often meant a foot full of bindii prickles where I grew up.

These prickles that are even more painful to stand on.

5376444-PPT

Three-corner jacks are very painful if you stand on them.

What good are prickles anyway?

A prickle is attached to a seed which is catching a ride somewhere. The sharp (ouch) pointy bit attaches it to something, usually an animal. If you take a dog for a walk through long grass you might discover a few prickles and other seeds that stick well to dogs and socks.

I found all these different seeds sticking to my socks after a walk in long grass. They’re  full of hooks, darts and bristles.

burr

This is a burr magnified ten times. It’s about the size of a little fingernail. Look at all those tiny hooks. Did you know that velcro was invented by copying the little hooks on burrs? I never knew that before!

And these…

arrowhead seed

These little arrowheads aren’t so sharp, but look at all those little bristles that can get stuck on socks and fur. This is taken with a 10x microscope – the arrowhead is about 7 mm or 5/12 inch long.

And this…

photo (88)

…this photo is life-size.

I’ll bet where you live there are different types of prickles and other things that can stick to your clothes.

PHOTO ATTRIBUTIONS

Three corner jack (Emex australis): Julia Scher, Federal Noxious Weeds Disseminules, USDA APHIS ITP, Bugwood.org
Creative Commons License   licensed under a Creative Commons Attribution-Noncommercial 3.0 License.

The importance of science: from an invasive to an endemic species

Science is about always about making new questions, cleverly doubting the status quo. This is what makes it moves forward and improves everyone’s knowledge. Most of the time it is done in small steps, rarely as major inventions or breakthroughs.

Mauritius, a small island in the Western Indian Ocean, was once the home of the world famous dodo. Although small, because it is quite isolated, the flora and fauna evolved mostly in isolation, resulting in proportionally high levels of endemism.

Although Mauritius has one of the last places in the world where human set foot, it took no time for this rich endemic biodiversity to vanish or too become very rare and so, threatened with extinction. We know this because Mauritius flora and flora has been well-documented.

In an offshore volcanic islet 4 km north of Mauritius, named Gunner’s Quoin or Coin de Mire (Mauritius was colonised by both the French and the British, so name of many places have an English and a French version). This islets cover only 76 ha but it has some remnants of the native vegetation, and it is a stronghold of some now rare endemic species.

During a short expedition to Gunner’s Quoin, we came across a liana without leaves, having thick stem with constrictions at more or less regular intervals, which makes it resembles a line of sausages. Nearly all individuals were growing together creeping down a steep slope, looking like a green waterfall. Samples taken showed that there was no other known plant like this on Mauritius, or in the world. So it was described as a new species.

Cynanchum scopulosum, a Mauritian endemic leafless liana

Cynanchum scopulosum, a Mauritian endemic leafless liana

 

A green waterfall formed by this very rare species

A green waterfall formed by this very rare species

However, it seems that this ‘green waterfall’ was known before. Previous surveys in the 1980s and 1990s, however, saying that it was formed by an invasive species was growing there. A few years later, we also found a map from 1930s with the same information (and it also shown other places were the species was growing on the islet). This said invasive species is of the same family and superficially resembles the new endemic species.

The lesson is simple: if samples were collected and preserved in herbarium collections, the wrong field identification could have been corrected. This could have to helped to avoid this endemic species, which is restricted to this islet only, to have today a more healthy population and be less be threatened with extinction, or not threatened at all.

 

Reference cited

Florens, F. B. V.; Baider, C. 2006. On the discovery of a new endemic Cynanchum (Apocynaceae) on Mauritius with a description of its habitat and conservation status. Phelsuma 14: 7-12

Putting poison in the pantry: Plastic microfibres

All sorts of plastic get into waterways, pollute the ocean and poison sealife. There is growing awareness about the damage caused by plastic bag pollution and microbead pollution, but scientists have shown that much of the plastic in the ocean is actually plastic microfibres. In some waterways they make up close to three quarters of the plastic pollution.

Plastic “is like a little sponge for … chemicals”. Poisons stick to the outside of plastic. The smaller the pieces of plastic the more chemicals can stick to them. This is because the more bits a piece of plastic is broken into, the more outside surface there is for chemicals to stick to. Dr Chelsea Rochman found a chemical that was banned in the USA in the 1970s (DDT) on every piece of plastic she took out of the ocean. (DDT is still used in certain circumstances, but much less than before its hazards were known.)

Shellfish eats plastic, little fish eats shellfish and big fish eats little fish. The toxins of concern that stick to plastic don’t break down easily. Each time these poisons go up the food chain they get more concentrated.

Where do these microfibres in the ocean come from? They come from washing synthetic clothes. Addressing this problem will be a mammoth task, because synthetic clothes are so common.

About 0.7 grams of plastic microfibre end up in rivers, lakes and oceans when a polar fleece jacket is washed (there are about 30 grams in an ounce). People eat seafood that has eaten microfibres. These and other research findings are summarised in Microfiber Pollution and the Apparel Industry from the University of California Santa Barbera.

What can be done? Natural fibres were used for thousands of years before synthetic fibres were invented, but according to the Catalyst video, around 2/3 of our clothes are now synthetic. Plastic microfibres would be much harder to phase out than microbeads. Some solutions have been suggested, such as adding filters to washing machines, waterless washing machines, gadgets that catch the fibres in the wash, and new types of synthetic fibre.

Governments and industry have started to phase out microbeads, but they will have to become more aware of microfibre pollution if the plastic pollution problem is going to be solved. Consumers can play a role too, in the choices they make and in spreading awareness. Two advocacy groups, Plastic Soup Foundation and Parley for the Oceans, have started a campaign to raise awareness. In the clothing industry, Patagonia is supporting research by scientists at University of California Santa Barbera into the problem.

It’s not just seafood. Microfibres are also found on land. What’s in your food?

Published research:

Chelsea Rochman et al., University of California Davis 2015. Anthropogenic debris in seafood: Plastic debris and fibers from textiles in fish and bivalves sold for human consumption. Nature Scientific Reports 5, Article number 14340. http://www.nature.com/articles/srep14340 

Mark Browne et al., University of New South Wales 2011. Accumulation of Microplastic on Shorelines Woldwide: Sources and Sinks. Environ. Sci. Technol., 2011, 45 (21), pp 9175–9179 http://pubs.acs.org/doi/abs/10.1021/es201811s

Niko Hartline et al., University of California Santa Barbera 2016. Microfiber Masses Recovered from Conventional Machine Washing of New or Aged Garments. Environ. Sci. Technol., 2016, 5021 pp 11532–11538 http://pubs.acs.org/doi/abs/10.1021/acs.est.6b03045

Other links:

Microfiber pollution and the apparel industryresearch summary (research. http://brenmicroplastics.weebly.com/project-findings.html) and a literature review (http://brenmicroplastics.weebly.com/microplastics-pollution.html) of other

 

The bad green is threatening unique species to oblivion

In my last post, I shown that not all green is good. That some plant species are a threat and can even make other plant species disappear. The bad guys plants are what is called invasive alien plants, non-native plants or exotics plants.

Most people would know the problem that invasive alien animals can cause. For example, only one species of mosquito, the tiger mosquito, is responsible increasing cases of dengue, chikungunya and zika in the last decades.

aedes-albopictus-cdc-gathanysmall

A small non-native animal that causes a lot of trouble

 

But the impact of invasive alien plants is less known as fewer species can disrupt human life as quick as non-native animals. The famine weed, Parthenium hysterophorus, it is a small herb that is disrupting lives in Africa – it decreases crop yields, make meat unfit for consumption, causes health problems like asthma, among other problems.

Small herb with pretty flowers that behave like an evil outside its native environment

Small herb with pretty flowers that behave like an evil outside its native environment

 

But many invasive alien species are a slower trouble-maker. Well, slower just on our on perception of time. Large trees can survive for decades and centuries, so competition with invasive alien plants needs to be measure on larger time scales.

In the island of Mauritius, in the Western Indian Ocean, this process the very few best preserved and protected native forests are today dominated by alien species! In average, nearly 80% of the stems of these best preserved forest are of non-native species.

The main problem is that the levels of invasion is set to get worst. The invasion is progressing, slowly but surely. When comparing todays number of species, number of stems and basal area of forest on forest areas where surveys were done in 1930s and in 1980s, we see a clear tendency of the invasion getting worst making the native forest, little by little, be submerged under this tsunami of alien species.

Some endemic species have disappeared from these forests because of the invasion. The number of trees in one of these forests have more than halved in near 70 years. Also the biomass of native trees in this forest is less than half of it was in 1930s.

Once the commonest shurb in one of the studied sites, this Mauritian endemic plant, has vanished from that forest in less than 50 years

Once the commonest shrub in one of the studied sites, this Mauritian endemic plant, has vanished from that forest in less than 50 years

 

This high invasion is also seen in other forest on tropical oceanic islands around the world. The invasion is putting the planet on the way to lose many unique species, many unique interactions, many unique ecosystems. All these without even considering the effects that global warming (that is a fact and not a hoax) is and will cause.

 

 

References cited

Florens et al in press. Long term declines of native trees in a oceanic island’s tropical forests invaded by alien plants. Applied Vegetation Science. DOI: 10.1111/avsc.12273

Florens et al 2016. Invasive alien plants progress to dominate protected and best-preserved wet forests of an oceanic island. Journal for Nature Conservation 34: 93–100

When green vegetation is bad…

Being close to nature is for most of us city dwellers a free health medicine. It makes you relax, decreases anxiety, make your blood circulate better and sharpens your mind.

A peaceful sunny day in a restored forest of Mauritius

A peaceful sunny day in a restored forest of Mauritius

 

But for some, a walk in the woods can be very stressful indeed. The reason? Some plants around shouldn’t be there. The so called invasive alien plants, non-native species or exotics. Plants that we humans transported to places where they did not grow before, sometimes purposefully, sometimes accidentally. The alien plants behave like deadly diseases – a cancer killing the resident plants of the place. In turn, it reduces the resilience of the native ecosystems, which little by little will spiral out of control and collapse, bring other native species and its interactions to become rarer and rarer or to disappear altogether.

 

In the island of Mauritius, in the Western Indian Ocean, this process is happening in from of our eyes. The very few best preserved and protected native forests are today dominated by…alien species! If you are a good observer, you will realise that in most of the native forest left on the island you are surrounded by a ‘sea’ of strawberry guava (a species from the Atlantic forest of Brazil). Well, you don’t need to be a great observer as, in average, nearly 80% of the stems are of non-native species. Worrisome is that it does not stop here: the invasion is progressing.

Invasion can be extreme. All reddish stem are strawberry guava

Invasion can be extreme. All reddish stem are strawberry guava

Fruits of strawberry guava are disperse into the native forests by birds, alien pigs and alien monkeys

Fruits of strawberry guava are disperse into the native forests by birds, alien pigs and alien monkeys

 

Strawberry guava is also a major problem in other tropical islands around the world. It is considered the worst invasive species of Hawaii. To avoid the full destruction of unique species and its ecosystems, it is necessary to control alien invasive plants. Both on Mauritius and Hawaii, manual removal of stems of these alien plants are done on regular basis. But such approach can only be effective on small areas. Biocontrol, a much used tool for agriculture, when conducted carefully and well-studied is arguably the only way to reverse the fate of today invaded forest and bring it back to a more pristine state and to avoid extinctions of unique species. Luckily, an effective and specific biocontrol has been found for strawberry guava. It was introduced in some selected areas of Hawaii in 2011.

The biocontrol of strawberry guava affects the leaves

The biocontrol of strawberry guava affects the leaves weaking the plant

 

Understanding the problem is the beginning of the solution to bring back a world where all green is good for all.

 

 

Reference cited

Florens et al 2016. Invasive alien plants progress to dominate protected and best-preserved wet forests of an oceanic island. Journal for Nature Conservation 34: 93–100

Can you tell if that product contains microbeads?

Maybe cosmetics with microbeads are easy to spot because it’s proudly written on the label. Like this one:

g--r_blurb

Why would you want to know? Microbeads are tiny plastics that are polluting the oceans and waterways. Once they’re in the ocean they don’t go away. Poisons stick to them, and these poisons get into the wildlife that eats them. There’s more detail in a previous post.

But they’re not always the company’s selling point.  On the face of it this one is all natural and wholesome.

Hmmm - its green and you can see little black bits of exfoliating kiwi fruit seed, right? Wrong.

back-kiwi-2

Hmmm – it’s green and you can see little black bits of exfoliating kiwi fruit seed, right? Wrong!

Check the ingredients list.

kiwi_ing

Polyethylene is plastic (i.e. microbeads) and it’s there, near the top of the ingredients list, and kiwifruit extract is much further down, a few before the chromium oxide greens. And where’s the aloe? (Ingredients are listed in order, from what it contains the largest amount of, to what is present in the smallest amount.)

What about those seedy bits?  I took a closer look with a simple low-powered microscope.

kiwi-black-microbeads-png

These were big dark microbeads and there lots more smaller clear ones.

Look out for polyethylene in your cosmetics. You can find out about other plastics that are used for microbeads in my last post or The Story of Stuff.

Putting poison in the pantry