Tuesday, 26 May 2015

Australian Wine Research Institute

Yesterday, I flew down to Adelaide for the day and visited our collaborators at the Australian Wine Research Institute (AWRI). AWRI are our partners in the Australian node of the Yeast 2.0 synthetic biology project. While I was down there I gave a seminar and we had fun discussions over the progress of our collaborative project. The photos below show a couple of interesting scenes from labs at AWRI. Of course, a trip to AWRI wouldn't be complete without some wine consumption, so we ended the visit with a wine and cheese tasting.

It was a bit jarring to walk through labs and see wine bottles sitting around on lab benches

This was cool though- this is a GC-MS for detecting different metabolites in wine, on the very right hand side is a sniffer where you stick your nose, so you correlate specific wine aromas with the detected chemicals. One of the latest discoveries from AWRI is identifying the chemical that gives a peppery smell to wine, which turns out to be the same compound that gives a peppery smell to pepper!

Saturday, 23 May 2015

Death by Grant Review

This year I am serving on an NHMRC grant review panel, which means I will once again get to spend my birthday in wintery Canberra for the panel meeting. For some reason (more grants submitted? less panel members?) this year the mostly unpaid workload is much higher. I have 23 grants to review within the next week, which means I will spend pretty much every waking moment looking at grants. I do have a feline advisor in my lap at the moment to give her recommendation on each grant.

Not an actual view of my grants to review, since I do it all electronically

Friday, 22 May 2015

Kittybiome Update

The power of successful whining! Thanks to the efforts of Holly Ganz over at Kittybiome, they have worked out the required paperwork for international shipping of kitty poop from Australia to the USA, so Australian cats can now partake in the Kittybiome project. Of course now I'm trapped into having to increase my pledge support to allow sequencing of my cats microbiomes :)

Tuesday, 19 May 2015


A couple of years back I blogged about crowdfunding of science (and games). Yesterday, I came across a scientific project on kickstarter which I felt I had to support- Kittybiome! The microbiome is the collection of bacteria, fungi and other microorganisms that live in us and on us, and there is increasing evidence that these microbial communities play important roles in our health. Thus, Kittybiome aims to use modern DNA sequencing technologies to characterise the microbial communities that live on and in cats.

The combination of silly and serious questions Kittybiome seeks to address include-
  • How do grumpy cats compare to happy cats?
  • How do athletic cats compare to couch potato cats?
  • Does it matter if you feed your cat a paleo-mouse diet?
  • How do indoor and outdoor cats compare? 
  • What happens when your cat goes on antibiotics? 
  • How does the microbiome change during your cat's nine lives?

I would like to add the question- how do different cat breeds compare in terms of their microbiome?

I would have been happy to support at a level that allowed sequencing of the microbiomes of my cats Lyra and Chihiro, but sadly that was only an option if you live in the US or Europe. Since I live in the scientific third world, I can only support the sequencing of the microbiome of a shelter cat. Still it looks like Kittybiome is a kickstarter success as it is already over-subscribed with 22 days still to go. Go Kittybiome!

(Full disclosure- Kittybiome is co-founded by my friend and colleague Jonathan Eisen)

Lyra and Chihiro want to know why Australian cats are discriminated against by Kittybiome

Thursday, 14 May 2015

Serious technology needs a serious crane

In my copious spare time I serve on the Management Committee for the Ramaciotti Centre for Genomics. The Ramaciotti Centre provides technology and services for genomic research, particularly in the area of next-gen DNA sequencing. The Centre is based at the University of New South Wales, but is supported by a consortium of universities and research institutes around the Sydney area (including Macquarie).

Last year I was part of a team led by Marc Wilkins that attracted funding from the Australian Research Council for a new PacBioRSII sequencer. This sequncing instrument will extend our technical capabilities enabling the generation of very long DNA sequence reads compared with other technologies, as well as enabling the detection of methylated and other modified bases in DNA.

After purchasing the instrument, one technical hurdle that had to be overcome was actually getting it into the building, as the Pac Bio sequencer was too big to fit through the doors. The solution- get a big ass crane. Here's photos of the sequencing instrument being installed (Thanks to Marc Wilkins for the photos).

Seems to be happening at night- maybe to minimise the chance of dropping it on students

Ok it is a pretty sizeable piece of hardware

Thursday, 7 May 2015

About time for a gaming post

It's been a while since I've had a gaming related post. My friend Fraser sent me this link- The Fifty Best Strategy Games Ever Made. Sadly, I have only played 14 of them, Fraser tells me he has played 30 of them, putting me to shame (I have played most of the top ten at least).

Saturday, 2 May 2015

Wine making

Continuing on with the theme of practical microbiology, the day after the tour of a traditional cheese making factory, we had a tour of a Tuscan winery at Tenute di Badia.

First step- grow some grapes. The front rows seen here are Chardonnay grapes. The grapes are handpicked each year.

Not the engine from the Millenium Falcon, this is the grape crusher, the liquid from the crushed grapes gets piped over into the fermentation facility, the residue of the crushed grapes gets magically distilled into grappa.

OK now we are into some serious microbiology. These are 750 hectolitre fermentation vessels. Sort of puts the 30 litre fermentor in our department to shame. The crushed grapes ferment here for some period of time that I don't remember now because I drank too much wine. 

To be offically classified as a DOCG (Denominazione di Origine Controllata e Garantita) wine, the alcohol content has to be carefully managed during fermentation. These fermentation vessels have an outer sheathe through which cold air circulates to keep the fermentation temperature from getting too high.

Lots and lots of fermentation vessels. After these, age in oak barrels for quite a while, and put into bottles (yay!)

And the end results-
Vivace "lively" is their sparkling wine (can't be called prosecco because it's not the right region). Goes down very easily.

Dry white-

 Chardonnay- not as dry

Rosso- made from the exact same red grape as Chianti, but the winery is located 23 km away from the Chianti region, so it can't be called a Chianti.

Dessert wine (late harvest) and the Grappa. Some of the dessert wine mysteriously made it into my luggage for the trip home.

Cheese Making

Gordon Research Conferences are fairly intense experiences, each day starts at 8.30 am in the morning and then ends around 11 pm with a late night poster session (fortunately the poster session has alcoholic beverages available to help fuel scientific discussions). There is typically some free time in the afternoon though for 3 hours or so.

In our free time yesterday there was a tour organized of a traditional cheese making factory in Tuscany. Since half of the conference attendees are microbiologists, there was alot of enthusiasm about seeing practical microbiology in action.

The first requirement was that we all dress up in embarrassing outfits.

The cheese making factory sources 4 types of milk- cow, sheep, goat and buffalo, from which it can make 480 types of cheese! Once the milk arrives it is refrigerated in its own specific storage tank. The following day it is pasteurized at 73 C in this apparatus here (OK so you can't really see it, but we do we have a good view of the back of Melissa Brown's head).


After the milk is pasteurized, it is pumped into this large vat, I think it can hold 500 litres. Rennin and a starter bacterial culture is added, and the vat is heated to 30-40 C for an hour. After this incubation the milk separates into curds (solid) and whey (liquid). The curds are formed from the casein protein coagulating, while the whey is the rest of the milk proteins.

These two instruments are not medieval torture implements, but instead are used to cut up the curds in the vat so that the curds sink to the bottom. One of them is called a guitar, no clue what the other is called, but it sort of looks like a screw.


The whey is then sucked out, leaving the curds behind (seen here in action).

The whey is sort of a waste product of the process, but it is still useful. The whey is heated up to 90 C so that it curdles, and the curdled whey is placed into containers (seen here), refrigerated and voila we have ricotta, which is ready to eat.

Back to the curds. The curds are removed from the vat and poured into cylindrical containers that have holes in the bottom (like a colander). Excess fluid drains through those holes.

The curds are upended a few times into empty containers to help the curds settle and remove the excess liquid. (the guy with the bushy beard is the master cheesemaker)

Close up of the curds.

After the curds have drained, they are covered in salt to prevent bacterial spoilage, chilled, and then allowed to mature (exact time/method depends on the type of cheese).

Thanks to Caseificio Bertagni for showing off their cheesemaking and putting up with all the thousands of questions from enquiring microbiologists, and mostly importantly for letting us taste their delicious cheeses.