Friday, 18 July 2014

What the hell is the Anthropocene anyway?

When I was a kid, I used to drag my parents out gem/mineral/fossil hunting all the time. Possibly in revenge for all these field trips, much later my Dad threw out my mineral collection that had been stored in his garage for a decade or two while I was working overseas (Not that I'm bitter about that or anything).

Anyway, as a 12 year old I was an expert on geological eras, periods and epochs. Apparently, my childhood knowledge is now out of date (and probably mostly lost in forgotten recesses of my mind). Mike Gillings has made me aware that there is a growing scientific opinion that we are now living in a new geological epoch- the Anthropocene. As a 12 year old I would have said we were living in the Holocene Epoch, but humanity is now have such an impact on the earth, that it is likely that we would show a strong signal in the geological record from things like changes to atmospheric CO2, biodiversity loss which would show in the fossil record, changes in trace element distribution due to pollution, etc. Hence we are likely now in a new epoch- the Anthropocene (Age of Man).

When the beginning of the Anthropocene should date from is a controversial topic, but there are probably three distinct phases to the Anthropocene: the ‘paleoanthropocene’, corresponding to the widespread adoption of agriculture some 8 to 10 thousand years ago, when clearing of forests and the consequent release of greenhouse gases potentially started affecting earth systems. The second phase began in the Industrial Revolution, coinciding with significantly increased carbon emissions and the environmental degradation associated with industry. The final phase occurred post World War II, and is called “The Great Acceleration”, because it is associated with very rapid growth in human population, resource consumption, energy use and pollution.

Mike Gillings and I have just published an opinion piece (anyone who knows us knows that we're both pretty opinionated) in the journal "Anthropocene". As can be seen in Mike's beautiful figure below, we argue that the different phases of the Anthropocene has resulted in demonstrable impacts on the microbial population of the globe, including-
1. changes to the human microbiome (the community of microorganisms that live in and on the human body);
2. the evolution of bacterial metal ion and drug resistance genes (from exposure to industrial pollution and widespread clinical and agricultural use of antibiotics)
3. the dispersal of disease-causing bacterial pathogens around the globe, e.g., spread of Old World pathogens to the New World during the Age of Exploration
4. Microbiogeochemical changes on a global scale, microorganisms play a key role in the global nitrogen, carbon, phosphrous, sulfur, etc cycling, and human activities from agriculture to industry have undoubtedly affected composition of microbial communities and rates of microbial activity

Some human affects on the microbiological world

Wednesday, 16 July 2014

We're FORC-ed!

So now we have no end of FORC jokes here, as we have launched our new ARC Industrial Tranformation Training Centre: The Food Omics Research Centre (FORC). The aim of our Centre, led by Professor Paul Haynes is to develop a molecular technology platform enabling the next revolution in the food industry. One of my PhD students, Hasinaka, is working within this Centre to investigate whether a sugar cane fibre-based dietary supplement can improve your digestive health through the changing the microbial composition of your gut. Something, I'll probably talk further about at a later opportunity.

Using omics technologies to improve the process of taking food production from "field to fork"

Monday, 14 July 2014

Yeast 2.0 at Macquarie

I've blogged before on Synthetic Biology, particularly with respect to the success of Macquarie University's iGEM teams- for instance, here and here. Synthetic biology is a new scientific field that combines engineering principles with molecular biological approaches to design and construct biological devices and systems. The rational synthesis of “designer” organisms has the potential to revolutionise biotechnological applications in areas such as bioenergy and biomanufacturing. 

I'm a bit behind in blogging but we've recently-ish (alright more than a month ago) had exciting news that the NSW state government has provided significant funding for Macquarie University to lead Australia in the international Yeast 2.0 project. Yeast 2.0 is an international collaboration between six countries, with the aim of building a completely synthetic yeast by 2017. Each collaborating lab is responsible for the design and synthesis of one or more artificial yeast chromosomes. The project was instigated by Jef Boeke at NYU, whose team has recently published in Science the first synthesis of a functional complete eukaryotic chrosomome (yeast Chromosome 3). Our involvement in this project has been led by our Deputy Vice Chancellor (Research) Sakkie Pretorius, and I'll be supervising the actual research staff working on this project (expect some job postings very soon!). This is a fantastic opportunity for Macquarie University to lead synthetic biology in Australia, and to use Yeast 2.0 as a chassis for developing novel synthetic biology applications useful in an Australian context.

Apparently, we are now doing Chr 16 as well as 14 (India dropped out)

Tuesday, 10 June 2014

Art or Science?

Ooops, looks like its nearly two months without a blog post. Probably my longest dry spell. It's been a little crazy busy here. I've been meaning to post these images for a while. These are the colourful output of my Molecular Biology and Genomics class. In our qRT-PCR prac, we sent the students outside to collect random plant samples, then they got to snap freeze their samples in liquid nitrogen and ground them to a paste with a mortar and pestle, so they could then isolate RNA from the plant cells. As some of you may be aware, I have a history of playing with liquid nitrogen.

Collection of spices? Powdered Dyes? Nope- try plant tissues frozen in liquid nitrogen and ground to a homogenous paste

Tuesday, 15 April 2014

We have Minions!

A couple of years ago, Oxford Nanopore made a big scientific splash when they announced they had developed a new DNA sequencing technology that would revolutionize genomics. Their MinION devices were the size of a USB stick, but were supposedly capable of sequencing long reads from single DNA molecules. After two years of wondering whether these devices were mythical, I can now tell you they actually exist. Together with Mike Gillings, we received five Minions in the mail today as part of a worldwide Oxford Nanopore beta test program. The big question now is- do they actually work?

Not mythical! Of course, we don't know yet whether they actually work

It is the size of a large USB stick. Thanks Mike for providing the skull of one of his students for scale.

I constructed Minionhenge on Mike's desk
Assemble the Minions!

Thursday, 10 April 2014

Racing up the Best Seller's List

Currently #285,426 on Amazon's best seller list (how the hell did it get that high?) is our new book on Molecular Methods in Environmental Microbiology. Andy and I would like to thank all our contributors for their hard work and their patience, as this book took a long time to see the light of day. I now remember why it was over a decade since I last edited a book.

Monday, 31 March 2014

News from San Diego

Well, its the start of baseball season in the US, and my beloved San Diego Padres just beat the hated Los Angeles Dodgers in their first game of the season. Yay!

While trying to get a news article about this game from the San Diego Union Tribune, I coincidentally came cross the latest genomic news. Craig Venter (who is famous for many things- sequencing the first bacterial genome, creating the first synthetic bacterium, sequencing his genome as the human genome, sequencing his poodle's genome, sequencing the world's oceans from his yacht, etc) has just announced raising $70 million to form a new genomics company- Human Longevity Inc. This company will be sequencing a hundred thousand human genomes each year as well as sequencing microbial communities living in/on people.

This should bring us closer to personalized medicine, where healthcare decisions can be tailored according to a patients genetics (and potentially the makeup of their microbial communities).