Congratulations Macquarie iGEM team!

Well I'm a couple of weeks behind on this news, so much for the immediacy of blogging. Anyway, great news from the Macquarie iGEM student team, who have been in Boston to compete at the 2015 International Genetically Engineered Machine (iGEM) Jamboree. This is an international synthetic biology competition with student teams from 280 universities around the world. Last year I went along with our team as an advisor and watched them win a gold medal.

The 2015 Macquarie iGEM team has done even better than last year's team. They won a gold medal for their project "Solar Synthesisers", plus they were runner up for the Best Energy Project and were finalists for the Best Basic New Part and Best Model. Fantastic job! Congratulations to all of the medal and prize winners at the 2015 iGEM Jamboree, full results here. Great to see other Australian teams competing, with UNSW, University of Sydney and ANU also successful at IGEM.

The 2015 Macquarie IGEM team with their poster in Boston

On the Channel 7 news

Last week I was interviewed by Dr Andrew Rochford for the Channel 7 nightly news. It was an interesting experience being interviewed for 20-30 minutes and then seeing which ten words they decided to show on the TV. The news piece went to air Monday night on the 6 pm news, and was about NutriKane D, a medical food derived from sugarcane. As part of the ARC-funded Training Centre for Molecular Technology in the Food Industry, we have been undertaking research on the effects of NutriKane D on the human gut microbiome (the collection of microorganisms that live in our digestive tracts).

Turns out the 10 words they did include from me on the 7 News had nothing to do with any of our actual research here, but at least the microbiome work got a mention latter in the news item. There's also film of my PhD student Hasinaka and myself in the lab.

NutriKane D- I've actually been taking myself for the last few weeks, combining half a packet with yoghurt each night. Anecdotally, it seems to be doing good things for my digestive system.

So You Think You can Synthesize Season 2 Finale

The final episode of So You Think You can Synthesize Season 2 is now available on YouTube. I think our iGEM students did a great job, and it provided a fun opportunity for me to exercise my painful overacting skills (honed from a misspent youth playing roleplaying games).

Eureka Awards

Last night I had the pleasure of attending the Eureka Awards at the Sydney Town Hall. Sometimes described as the Oscars of Australian Science, the Eureka Awards are presented each year by the Australian Museum. I wasn't nominated for an award, but I was invited to one of the Macquarie University tables for the event (I think the Uni likes to roll out its Laureate Fellows for special occasions). Congratulations to all the winners. Macquarie did pretty well, taking home two Eureka prizes (congrats to Dave Raftos and Jin Dayong). For me the highlights are always the Sleek Geek awards for the best science movies made by primary and secondary school students. Interestingly, Paige Beebe, who won the secondary school prize for her movie "the Secret of the Appendix" is actually the grand daughter of Nobel Prize winner Barry Marshall.

Since the Eureka Awards are a glamorous scientific gala, I had to dust off my tux and bowtie (thanks Phyllis for tying my bowtie!)

Food Science #2

While on the theme of food, I gave a talk earlier this month at the Annual Convention of the Australian Institute of Food Science and Technology. This was a first for me, I've never before attended a food science conference, and I've never been to Luna Park in Sydney, though I did visit Luna Park in Melbourne when I was about five years old. I enjoyed the omics session I spoke in, interesting talks on Aspergillus aflatoxins (Hi Dave), the genetic basis of taste differences in humans, and applying "Big Data" to food safety. Lunch was a bit disappointing for a food science conference, but there were excellent muffins at morning tea.

Luna Park seemed an unusual venue for a scientific conference

Kittybiome Update #2

I am now in possession of an attractive Kittybiome T-shirt, a sampling kit to let me collect my cat's faecal material, and a mountain of paperwork to allow me to ship kitty poop to the US. Now, I just need to get my cat to cooperate.

my T-shirt and kitty poop sampling kit

Food Science #1

A couple of weeks back, we had the official launch event for our ARC Industrial Transformation Training Centre. This was originally named the Food Omics Research Centre (FORC), however the Australian Research Council didn't like our name and instead told us that we would be called the ARC Training Centre for Molecular Technology in the Food Industry. Go ahead and see if you can make a good acronym out of that!

Now that we have an official name, we realised that we hadn't had a formal launch event for our Centre (which has now been up and running for over a year). We went ahead and had a very successful launch event with various dignitaries including Senator Arthur Sinodinos, and Professor Aiden Byrne, CEO of the Australian Research Council.

One of the central purposes of this funding scheme is to train PhD students and postdoctoral researchers in collaborative research with industry. We were funded in the first round of this scheme, and arguably, we are one of the most successful of these Centres as we have our full allotment of 10 PhD students working on collaborative projects with our industry partners.

Students and staff of the ARC Training Centre for Molecular Technology in the Food Industry

Single Molecule Imaging

We recently hosted a visit from Antoine van Oijen from Wollongong University. Antoine is a fellow ARC Laureate Fellow (not often one can use the word fellow three time in one sentence), who is doing very cool single molecule imaging work. Antoine was a faculty member at Harvard and Groningen before he moved out to Australia, so it's a great coup for Wollongong to recruit him. 
We had some fun discussions about possible collaborative projects and he gave a great seminar while visiting MQ. Hopefully, I'll get the opportunity soon to visit his labs down in Wollongong.

I'm not sure what this is, but it has pretty colours and I got the image from Antoine's web page.

So You Think You can Synthesise Season 2

Last year you may recall the gold medal-winning Macquarie University iGEM team ran an online synthetic biology-themed reality series called So You Think You can Synthesise. This years Macquarie University iGEM team is busy beavering away on their synthetic biology project Solar Synthesisers. As part of the "human practises" (I would translate this iGEM-ism as "Outreach") segment of their project, they are creating So You Think You can Synthesise Season 2.

I'm blogging about this not just to give them a gratuitous advertisement, but also because I was involved in filming the final episode yesterday. While only episodes 1 and 2 are currently up on Youtube at the moment, the final episode has now been filmed, and I know who won, bwahahahaha. However, my lips are sealed. One spoiler I can reveal is that the final episode has a Japanese Iron Chef theme. The reason I know is that I was brought in to play the role of Chairman Kaga, the host of the Iron Chef TV show.

I should mention that I was a big fan of the Japanese Iron Chef, and one of the culinary highlights of my life was attending a dinner function where Hiroki Sakai (Iron Chef French) and Chen Kenichi (Iron Chef Chinese) each cooked a course.

Placeholder Iron Chef photo until I locate the photo of me with Hiroki Sakai and Chen Kenichi

If its my birthday, this must be Canberra

Yesterday was my birthday, and for the third year out of four, I've spent it in Canberra, serving on an NHMRC grant review panel. I've been in Canberra all week, reviewing 75 microbiology grants. I feel a little depressed about it, as grant success rates may drop as low as 10% this year, which means an awful lot of very good grants will not be funded. On the bright side, my panel arranged a birthday cake for me!

Its my birthday and I have a cake, thanks to my grant review panel

Catching up #2- Centre of Excellence

The main reason I've been missing in action on the blogging front is I've been working on a large grant application for an ARC Centre of Excellence. We've put together a bid for a Centre of Excellence in Synthetic Biology led by Macquarie. Thanks to the heroic efforts of our team across six universities we managed to get a good looking application submitted last Wednesday, now we need to wait and cross our fingers (toes, eyes, and whatever is crossable).

Centres of Excellence always make me think of Bill and Ted's Excellent Adventure. Hopefully, we won't have a heinous outcome.

Catching Up #1- Exams

It's been over a month since my last post. It's been pretty crazy over that time. It started with hiding at home for a week to mark 100 exams papers for my unit Molecular Biology and Genomics. I was entertained by a number of artistic efforts, the highlight of which is the answer to question 14 below. There was also a large number of cat drawings, I particularly liked the answer from one student where they used drawings of a cat with/without a tail to discuss the potential phenotypic effects of gene knockouts.

An interesting response from one of my students to exam question 14- How does TATA binding protein interact with type II eukaryotic promoters that lack a TATA box?

Is it a prop out of a sci fi movie?

So I posted a few weeks about Serious Equipment needing a Serious Crane. While the PacBioRSII is a cool piece of equipment, it basically looks like a big box. Nowhere near as cool looking as this crazy thing:

I think we got this from a Star Trek movie set

Or maybe its a steampunk thingie from Girl Genius

It seems to be looking at me

OK so these are pictures of the Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) instrument that has just been installed at UNSW. I was part of a team led by Mike Manefield and Federico Lauro that attracted funding for this instrument from the Australian Research Council. I'd never seen pictures of one until Federico showed me these, its truly a crazy looking thing. What this thing does is fire a pulsed beam of ions at a sample, and then it can identify the compounds present by collecting secondary ions produced by running them through a mass spec. It can thus produce a image map with a sub-micron resolution showing what chemicals are present. We hope to use it to analyze the metabolic activities of different bacteria within complex communities.

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!

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

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 :)

Kittybiome!

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

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

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).

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.

Greetings from Tuscany!

I am currently in Tuscany for the Gordon Research Conference on Multidrug Efflux Systems. This is the first time I've been able to attend this meeting since the very first one in 2003. There are actually a few hundred different Gordon Research Conferences (GRC), each on a different scientific topic. I'll be at another GRC in August in Hong Kong. GRCs are typically smallish meetings (100-150 scientists) held in relatively remote locations, so attendees are "trapped" at the meeting. I've always liked this format, as you eat all meals together and stay at the same location, so it provides a great opportunity to meet people and chat about science.

GRCs encourage speakers to present unpublished data, but this has the consequence that all presentations at the conference are confidential so I can't blog about any of the cool science being discussed. I guess I can at least chat about presentations from my own group. I gave a talk and Karl had a poster on our work on the new family of drug efflux pumps that we have discovered. My talk seemed to generate alot of interest as I had about fifteen people ask questions at the end of my talk. The good thing about talking early in the meeting is I don't have to stress over my talk, and I can relax and enjoy the rest of the GRC.

This GRC meeting is held at the the Il Ciocco Resort which is near Lucca in Tuscany. It is a very attractive location, though currently somewhat foggy and rainy.

View from my window this morning

Thanks to Karl Hassan for finding this cartoon. It's not quite this bad.

Syn Bio and twitter

Well I've so far avoided getting on twitter (or facebook) as I have enough time sinks already. This probably makes me a fossil. I recently hosted a planning meeting to start organizing a bid for a Synthetic Biology Centre. My colleague Louise Brown is very active on twitter, and commemorated the occasion with this tweet.  

In case you don't want to follow the link, here's the photo of us

JAMS turns 4, Blog turns 3

Well, I'm a month or so late, but JAMS (Joint Academic Microbial Seminars) had its 4th birthday, and celebrated in its usual fashion by holding an afternoon symposium, followed by dinner at the Australian Museum.Excellent speakers as usual, the highlight for me was Kat Holt's talk on using genomics to understand the epidemiology and evolution of bacterial pathogens causing diseases such as typhoid and dysentery.

A talk on typhoid and dysentery is of course a perfect lead in to dinner, which was in the dinosaur room. A great chance to catch up with colleagues and friends, except for the second year the band was so loud, it was hard to converse with anyone (yes I've become an old fuddy-duddy, plus I'm also somewhat deaf).

I know when JAMS has its birthday, it is also the birthday for this blog as one of my first blog posts was about the first JAMS symposium. So happy birthday all round!

Yay! Biggest ever attendance for a JAMS meeting. Who is that thoughtful looking fellow there in the front row?

Grants and My friend the Chocolate Cake

I'm miles behind on my blogging, but in the meantime we've written an ARC Discovery Grant and three National Health and Medical Research Grants. The  last of those were submitted to Canberra today. As I was walking home from University today I was listening to some old 1990s music on my headphones, and happened to be listening to "I've got a plan" by My Friend the Chocolate Cake.

The lyrics "I've got another plan, this time it will work" seemed appropriate given the grant writing we've been doing to try to attract funding for our on-going research to investigate mechanisms of virulence in the pathogen Acinetobacter baumannii, to understand how bacteria control drug efflux pumps that make their resistant to antibiotics, and to see if we can use "friendly" plant root bacteria to protect against agricultural crops against plant pathogens. Now we just have to wait eight months or so to see if any of these projects get funded.

This totally looks like the chocolate mud cakes from cafes in Glebe that I used to live on when I was a PhD student

Fitbits!

How do you motivate me to do something I don't want to? Turn it into a game or competition!

For Valentine's Day, I bought Fitbit flexs for Phyllis and myself. A somewhat courageous choice of present that seems to have worked out well. Fitbits are wearable devices that can track your activity (exercise, sleep patterns, etc).

So, I now know that walking  from my home to Macquarie University in the morning through the Lane Cove National Park is 4.8 km and takes 5,700 steps (which puts me along way towards the daily goal of 10,000 steps).

The odd thing is that even though I have not work a watch for over twenty years, I find myself trying to check the time on my Fitbit flex many times a day.

Warning- scary closeup of my arm

Mind those sausage-stealing kookaburras

I was out at the Sydney Institute of Marine Sciences (SIMS) last Friday. I gave a guest lecture to finish up the SIMS-CMB Summer Course on Marine Microbial Ecology. Suhelen Egan at UNSW has been organizing this course for the last few years, this has been the first time I've actually been able to make it. It was a fun day, Martin from my group was able to get a portable flow sorter setup and the students were able to sort cyanobacterial cells from Sydney Harbour water they had collected that morning.

I gave the final presentation of the workshop, which had the added advantage that I was there for the celebratory BBQ at the end of the workshop. The only danger were the local sausage-stealing kookaburras. One of the students was a favourite target of the kookaburras, losing several BBQ-ed sausages to them. Next year we might had to add an extra lecture to the course on how to defend your food from kookaburras.

Kookaburra at SIMS. Actually food-stealing kookaburras are a problem at Macquarie Univerity as well- I once lost a lemon poppyseed muffin to a kookaburra

Welcome Lisa!

We're very pleased to welcome Professor Lisa Moore from the University of Southern Maine, who is visiting us on sabbatical for four months. Lisa's visit is supported by a prestigious Endeavour Foundation Fellowship. Lisa is an expert on the physiology of Prochlorococcus, a photosynthetic marine cyanobacterium that is one of the key primary producers underlying the entire marine food web.
Fun fact- there are an estimated 1,000,000,000,000,000,000,000,000,000 Prochlorococcus cells in the world's oceans.
We will be collaborating with Lisa on sequencing and bioinformatic analyses of marine cyanobacterial samples from around the world's oceans.

Lisa

Creating a new society

I was in Melbourne last week meeting with synthetic biologists from all around Australia. We have  decided to form a new society or association representing synthetic biologists. Claudia Vickers from the University of Queensland is the driving force behind this new body and our meeting decided this she should be our chairperson or president (still working on the terminology). I was volunteered into being deputy president? vice chairperson? something like that anyway. As well as needing to finalize titles, we're still working on the name of our new learned society, because its important to have a good acronym. The Australian Society for Synthetic Biology (ASSB) clearly is not a good option.

For those of you who want to know more about synthetic biology please see some of my previous posts-
Yeast 2.0 at Macquarie
Greetings from Boston

That reminds me, while we don't yet have a website up for our new synthetic biology organization, we do now have a live website for Synthetic Biology at Macquarie.

Synthetic Biology Image taken from http://www.genspace.org/blog/wp-content/uploads/2011/08/Harry-Campbell-Illustration.jpg

Congratulations Dr. Farrugia!

Congratulations to Daniel Farrugia, who has been awarded a PhD for his work in my group on the bacterial pathogen Acinetobacter baumannii. Daniel has published a couple papers examining the differences between hospital and community strains of this pathogen, and when I manage to find time to finalize them, has two more manuscripts still to come. Daniel is now currently taking a well deserved break in Malta, and I believe will soon be looking for a postdoctoral position in Europe.
 

You are stuck with this until I find a more appropriate photo