This poster is on the wall by my desk. It was drawn by my young friend Nicholas. Nicholas is really keen on all things science and came with his mum to have a look at a science lab. He had done his research on leukaemia and brought me this cool picture. Thank-you Nicholas.

Stop Leukemia – by Nicholas

This is a nice summary of the Research Bazaar conference held in Melbourne last week. We learnt various programming languages and did other researchy-type things. This was the first ResBaz but I think it was so successful there’ll be more. Read more about it here!

Rosanna's Research

ResBaz, or Research Bazaar, was hosted this year for the first time at the University of Melbourne and I got to attend this awesome conference (so did a couple of other QAECOlogists, check Saras Windecker’s blogpst for an impression). ResBaz is all about open science, sharing, collaborating and getting the message out there. To make this happen, the attending researchers were trained in digital tools such as R, MATLAB, Phython, mapping software and version control.

I only attended two streams, R and SQL (databases), but because of all the mingling with fellow researchers under the big bazaar tent (as well as twittering, lots of twittering!), I also got a good impression of all the other great stuff that’s out there. I have to say, it’s good to know what all the options are when doing your research. If you missed the conference, here’s a list of all the cool…

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In the 21st century we have an amazing amount of knowledge at our fingertips. This includes the human genome sequence – (most of) the 3,381,944,086 letters of DNA code for a human, known as the human genome sequence. It’s publicly available and you can look it up or download it if you have a computer with internet. Maybe some of us in the developed world are even starting to take it for granted.

The downloadable sequence is just a reference – each one of us has our own unique variation of this standard. Many of us now have reason to find out the sequence of one of our own genes, for example to see if we have inherited a higher than average risk of cancer, or if we carry a gene for a genetic disease. It’s even possible to get your own whole, unique, genome sequenced (at a cost).

In the 1980s the human genome sequence was a dream. Using the technologies available at the time we’d still be sequencing by hand. The Human Genome Project led to a lot of automated sequencing methods being developed – and they’re still being improved, which is still bringing the cost of DNA sequencing down.

This huge project was undertaken by many laboratories across the world. It was intended to be, and has been, a resource for improving health care. It’s not the only sequenced genome. Simpler organisms like viruses and yeasts, which have much smaller genomes, were sequenced before the human genome, and as time goes on we’re getting genome sequences for more and more living things.

So how was the human genome sequenced? There are a range of basic techniques and tools that allow DNA to be manipulated and  read. I’ve put together a Prezi which gives a visual overview of these tools.

Prezi: Tools for DNA discovery and innovation

DNA tools

To see this Prezi with more detailed explanations click on the link above.

DNA can be thought of as a long string of “letters” (nucleotide molecules) strung together. This makes up the code of life and it’s translated into a different language that can make any of the huge variety of proteins, like collagen, haemoglobin, insulin or botox. DNA can be cut, rearranged and joined back together. This makes it very versatile – it can be manipulated. It can be cut up and pasted into different organisms and the host organism will treat it like its own DNA – because the code of life is universal.

Another useful feature of the DNA molecule is that it’s made of two strands which pair together and each one can be made anew from its partner. Thus we can make new DNA in the test tube. One DNA strand can also find its partner so we can find or pick up a whole piece of DNA if we have a  just a small section of its partner.

So these tools for DNA analysis can also be used for our own purposes – for example. to make proteins such as human insulin in massive amounts. You can even make a gene from scratch if you know the code of the protein you want to make. But you’ll still need a live organism to process it into protein for you. Amazing! Diabetics used to rely on pig and cattle insulin, but the human version is better for us!

Cross posted from Fireside Science at SciFund Challenge

Further reading:

https://chromosomesandcancer.com/2013/06/18/the-human-genome-project-and-cancer/

https://chromosomesandcancer.com/2013/07/07/the-last-frontier-of-the-human-genome-sequence-repetitive-dna/

http://www.genome.gov/12011238

The Wellcome Trust’s Sanger Centre has a lot of information, videos and interactive tools that help explain DNA analysis and how the Human Genome was broken down into sections and sequenced. http://www.sanger.ac.uk/about/engagement/yourgenome.html

The WordPress.com stats helper monkeys prepared a 2014 annual report for this blog.

Here’s an excerpt:

A San Francisco cable car holds 60 people. This blog was viewed about 2,000 times in 2014. If it were a cable car, it would take about 33 trips to carry that many people.

Click here to see the complete report.

On the 9th of December there was a large oil spill in the Sundarbans of Bangladesh. Most of the 350,000 litres of furnace oil in an oil tanker spilt into the water. Check out these images from the BBC.

The Sundarbans in Bangladesh is the world’s largest contiguous tidal mangrove forest. The mangrove ecosystem is ecologically valuable, filtering contaminants out of the water. Mangroves are already threatened around the world. The Sundarbans is noted for its exceptional biodiversity but the oil spill is threatening many unique species including the Bengal tiger and the Ganges river dolphin. And mangroves are particularly sensitive to oil spills.

 

There’s also a huge human cost. The locals are not in the lucky position of having a government with money and technology to help clean up the mess. They’re scooping the oil out of the water with their bare hands. This oil is toxic and cancerous. Its components cause severe (poor prognosis) leukaemia. Children are exposing themselves. They need our help.

I’ve found a bit of news coverage online, but little from Australia’s government sponsored news broadcasters. There’s nothing from SBS (our overseas-focussed broadcaster), and only the one story from our ABC. This environmental disaster affects us not only because of the damage to a UNESCO World Heritage Site and the threat to wildlife, but also because the water in the Sundarbans is everyone’s water – it reaches your country in a manner of days. If the media won’t cover the story you can help play a crucial role. Pester the news media. Spread the story on social media.

Here are some tips on how to do this:

From Water Defense:

“Share information about the oil spill on your social media page to keep it top of mind. For the latest information check on Twitter @Sundarbans_SOS for regular updates and remember to use the hashtag #SundarbansOilSpill.”

From the River Dolphin blog:

“If this post bothers you at all, then I suggest you 1) contact major forms of news media (see post one for how to if you are in the US) and work HARD to get them to cover this story (US still not covering for the most part). 2) Write to the leaders of your country and ask them to pressure the government of Bangladesh to change this clean up solution IMMEDIATELY.  3) SHARE (don’t like… only sharing moves this story along) this post, and help us get the word out.”

An international response team including oil spill experts has now been sent to the Sundarbans in response to a request to the UN from the government of Bangladesh.

There’s an indiegogo campaign to raise money to get extra help to the Sundarbans – the not-for-profit Water Defense organisation wants to send a team to help clean the water. Why donate if there’s a UN team? Besides the obvious statement that a faster cleanup is better, there’s some controversy about using chemical dispersants to clean up oil spills. These dispersants end up in the water. The Water Defense team has a specially developed water cleaning foam that soaks the oil out of the water.

 

Follow Jennifer Lewis’s River Dolphin blog. Jennifer is the Director of the Tropical Dolphin Research Foundation. She reports on the human impact of the oil spill.

http://theriverdolphin.blogspot.com.au/

http://theriverdolphin.blogspot.com.au/2014/12/side-track-off-dolphins-for-one-post.html

http://theriverdolphin.blogspot.com.au/2014/12/ecological-disasterto-say-least.html

http://theriverdolphin.blogspot.com.au/2014/12/assessing-damage.html

 

More information:

http://news.nationalgeographic.com/news/2014/12/141216-sundarbans-oil-spill-bangladesh-tigers-dolphins-conservation/

http://news.sciencemag.org/asiapacific/2014/12/officials-scramble-respond-bangladesh-oil-spill

http://www.theguardian.com/environment/2014/dec/11/bangladesh-oil-spill-threatens-rare-dolphins

http://thinkprogress.org/climate/2014/12/24/3606793/experts-to-help-children-clean-mangrove-oil-spill/

http://whc.unesco.org/en/news/1209

http://en.wikipedia.org/wiki/List_of_oil_spills

 

 

 

 

This is a post from Francis Collins, the Director of the National Institutes of Health, and a well-known geneticist. It explains how genome sequencing can help people with a rare and unexplained genetic disease. I think he explains it clearly, what do you think? Is there anything that’s too technical for the layperson?

NIH Director's Blog

Hanners FamilyCaption: Whole genome sequencing revealed that sisters Addison and Trinity Hanners, ages 7 and 10, shown here with their mother Hanna, have a rare syndrome caused by a mutation in the MAGEL2 gene.
Credit: Courtesy of the Hanners family

At the time that we completed a draft of the 3 billion letters of the human genome about a decade ago, it would have cost about $100 million to sequence a second human genome. Today, thanks to advances in DNA sequencing technology, it will soon be possible to sequence your genome or mine for  $1,000 or less. All of this progress has made genome sequencing a far more realistic clinical option to consider for people, especially children, who suffer from baffling disorders that can’t be precisely diagnosed by other medical tests.

While researchers are still in the process of evaluating genome sequencing for routine clinical use, and data analysis continues to…

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As we’ve seen in previous posts, cancer is caused by some sort of error in the DNA of the cancer. Human DNA comes in 46 long strings called chromosomes and it sometimes breaks, but luckily the break is usually repaired. However, sometimes the repair process gets it wrong – for example two DNA ends are joined together that aren’t meant to be together.

This post is about a fairly recent discovery called chromothripsis. I’m going to describe it in terms of language, because after all, DNA is a language, and I think it will help picture what’s going on.

Anagrams are made by rearranging all the letters of a phrase or word to make another phrase or word, and it’s best if the new has a similar meaning to the old. Some examples are:

astronomer —-> moon starer
the meaning of life —-> the fine game of nil.

The rule for “perfect” anagrams is that all the letters are re-used in the new sentence.

Setting up printing originally involved arranging individual letters in a particular order on a plate. If the letters were dropped it wouldn’t be easy to get the letters back in the right order. If you had to put them back together in a hurry they’d be jumbled up and you wouldn’t get a meaningful anagram. In fact you’d probably have some missing letters left on the floor in a corner somewhere. Ok it’s starting to get complicated, but something similar can happen to DNA!

A printer inspecting a large form of type on a cylinder press. Each of the islands of text represents a single page, the darker blocks are images. The whole bed of type is printed on a single sheet of paper, which is then folded and cut to form many individual pages of a book.

At the beginning of 2011 Joshua Stephens and his colleagues published a paper that got a lot of cancer biologists excited. They noticed that the DNA of some cancers was very messed up. They even said that they’d found this in 10% of the cancers where they looked for it. Not only that, but they thought this had happened all at once by shattering of the chromosomes and rejoining of the broken pieces in a random and totally incorrect order.

Scientists love to make complicated words out of Greek roots. The Stephens paper called this process, this shattering and stitching back together of the chromosomes, “chromothripsis“. (An aside: The chromo- in chromothripsis is short for chromosome, or coloured thing. The authors say that thripsis means shattering into pieces.)

I had a couple of nice examples of chromothripsis acute myeloid leukaemia, but as someone who’s interested in chromosomes I wanted to talk about the chromosomes that were made by this whole chromothripsis process. There was no word for these new chromosomes so I came up with the term “anachromosome“. I like it because it has connotations of “new”, “remade”, and my favourite, “anagrams”. Although the anagram rule says all the letters have to be reused, there are apparently imperfect” anagrams which can leave out some letters to make the anagram work. This is more like an anachromosome. Inevitably lots of bits of chromosome don’t make it into the anachromosome and so are lost. Such wholesale shuffling and loss of large sections of DNA will probably kill the cell in most cases, but just occasionally it will produce a cell that can outgrow its neighbours – and turn cancerous.

This shows how the chromosome shatters and rejoins in a random order. Note that the two ends of the chromosome and the centromere (represented by a circle) are preserved. These are essential features of a functioning linear chromosome. From MacKinnon and Campbell 2013. Cancer Genetics 206:238-251.

This shows how the chromosome shatters and rejoins in a random order. Note that the two ends of the chromosome and the centromere (represented by a circle) are preserved. These are essential features of a functioning linear chromosome. From MacKinnon and Campbell 2013. Cancer Genetics 206:238-251.

References:

MacKinnon RN and Campbell LJ 2013. Chromothripsis under the microscope: a cytogenetic perspective of two cases of AML with catastrophic chromosome rearrangement. Cancer Genetics 206:238-251

Stephens PJ et al. 2011. Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development. Cell 144:27-40