iGEM 2012 University of Calgary

Thursday, 4 October, 2012

My friend Iain recently completed his undergraduate degree in Cellular, Molecular and Microbial Biology at the University of Calgary. I learned from his Facebook page that he is a member of cool UC iGEM 2012 team. Check out more info on their Wiki page, http://2012.igem.org/Team:Calgary

iGEM: “A team of undergraduates competing in the International Genetically Engineered Machine competition held by MIT. We build microbes to solve complex real world problems.”

Interview with Dr. Naweed Syed, Hotchkiss Brain Institute, Neurochip co-lead researcher

Friday, 17 August, 2012

Interview with Dr. Naweed Syed, Hotchkiss Brain Institute, Neurochip co-lead researcher

Earlier this month I had a fascinating interview with Dr. Naweed Syed, Hotchkiss Brain Institute, head of University of Calgary Department of Cell Biology and Anatomy. Dr. Syed is one of the lead researchers behind neurochip − “a microchip with the ability to monitor several functions of the brain.Neurochip is “a novel lab-on-a-chip technology that, through an ultra-sensitive component built directly on the microchip, also enables direct imaging of activity in brain cells.”

In one fascinating part of the interview, Dr. Syed talked about Parkinson’s patients who have really bad tremors and don’t respond to drugs anymore. Currently, surgeons insert a deep brain stimulation electrode to allow the patients to stimulate the electrode themselves which release dopamine to stop the tremors. Unfortunately, the electrode can continue to stimulate the brain cells beyond the limit. Resulting in what is known as excitotoxicity. (Too much dopamine constantly being produced and brain cells being over excited.) In essence, nobody is there to tell the electrode when the stimulation is enough and can be stopped to avoid damage because there is no loop going back to tell it. Dr. Syed suggests implanting a two-way link where machines (capacitors and transistors) and the brain cells can talk to each other to better control the stimulation loop and avoid/reduce the problem of excitotoxicity.

Have a watch of my extensive interview with Dr. Syed to hear of his explanations and the background info in his own words for the latest advancement in research in neurochip.

As an alumnus of University of Calgary, it makes me really proud to see cool research done in Calgary, Alberta. At the same time, near the end of the interview, I asked Dr. Syed about the challenges of getting the required funding for the research program to succeed and to keep doing cutting edge researches right here in Calgary. Given the achievements his team has made so far, I would hate to see any of these world class scientists leaving Canada to go to United States/China, etc because our three level of governments and private industry partners are not putting in the needed funding to keep doing these ground-breaking researches that can lead to better medical devices, better drugs, etc right in Calgary, Alberta, Canada.

On a personal note, a very close friend has Parkinson’s and I hope the device Dr. Syed talked about can be developed, tested, and approved soon so that my friend and other Parkinson’s patients can benefit.

News references:

University of Calgary, UToday “New advances for neurochip

CTV News (with video), “U of C researchers achieve major milestone

Calgary Herald, “New microchip helps take detailed images of brain – University of Calgary researchers achieve new milestone

Millions of cancer-free stem cells cultivated in days using new U of Calgary discovered method

Friday, 25 May, 2012

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As a University of Calgary alumnus, it is exciting to see ground breaking research coming out of my alma mater. Quoting CBC News, “‘Safe’ stem cell discovery unveiled in Calgary – U of C researchers say they can create cancer-free cells quickly by the millions” (links and emphasis added)

“The findings by Derrick Rancourt and Roman Krawetz were published in the May issue of Nature Methods.

Rancourt said the discovery of a plentiful and reliable source of stem cells represents a great alternative to embryonic cells, the use of which is hotly debated.

With current methods, it takes one million adult cells to create one stem cell.

“In this new, finely tuned bioreactor, we are able to make 10 million ‘safe’ stem cells from 800,000 adult cells in 12 days,” said professor Rancourt, who is also deputy director of the McCaig Institute for Bone and Joint Health.

The researchers create the low risk stem cells by cultivating adult cells without the cancer gene ‘cMyc’, they said in a release.

“We are the first team to prove that we can use the bioreactor to efficiently make stem cells that then become mice without cancer,” said Krawetz.

The next stage will be to use the discovery to put human cells into the new bioreactors to design treatments for arthritis, Rancourt said.

Also have a watch of CTV News report, “Researchers mass produce super cells

Derrick Rancourt, PhD & Roman Krawetz, PhD: Bioreactor & Pluripotent Stem Cells

Interested readers can find a good literature review from Dr. Mehdi Shafa’s (one of the paper’s contributors) April 2012 PhD thesis Reprogramming of Mouse Fibroblasts to iPS Cells in Stirred Suspension Bioreactors using Physical and Genetic Methods” (PDF file).

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U of Calgary biosensor project takes students to competition at MIT

Friday, 4 November, 2011

This looks pretty cool. University of Calgary biosensor project takes students to competition at MIT (emphasis added)

A group of undergraduate students has developed a process that uses genetically modified bacteria to help monitor the levels of toxins in oil sands tailings ponds. The project has earned them a spot at the International Genetically Engineered Machines (iGEM) World Championship Jamboree at the Massachusetts Institute of Technology Nov. 5 – 7.

Eleven students from the faculties of medicine, science and engineering created a biosensor–a sensor that is biologically based–to detect levels of naphthenic acids (NAs), which can be toxic in certain quantities. The students spent months growing bacteria in a laboratory and adding a mini genome to enable the detection of NAs.

From Edmonton Journal, “Bacteria used to find oilsands toxins” (emphasis added)

“We decided early on we wanted to do an oilsands project because it’s so relevant to Alberta, it would be easier to get funding, and it was interesting to us,” said Emily Hicks, 21, a fourth-year biomedical sciences student and team captain.

The group created a bio-sensor to detect levels of naphthenic acids (NAs), which can be toxic.

The researchers grew bacteria in a laboratory, then added a mini genome to help detect the NAs. If NA gas is present, it causes a change in the bacteria which is then recorded on a computer hooked up to take readings.

“It will essentially start to form something that gives us a charge,” Hicks said.

We can see that on the graph.” The process takes just a few minutes.

Energy companies conduct regular sampling to monitor tailings pond toxins.

The students’ process “presumably will be a lot lower cost,” and could one day be used in Alberta’s oilsands, said Lisa Gieg, U of C assistant professor in biological sciences and faculty facilitator of the project.

“We still have a lot of ways to go to develop and standardize, but that’s the vision, to eventually use it as a screening tool, to try to detect, in particular, naphthenic acids.”

“The University of Calgary iGem team will be tweeting from the finals. Follow them on twitter @iGemCalgary and follow the conversation #igem2011


iGem Calgary – Last Project Night – TGIF Parody – iGEM Calgary 2011

University of Calgary drops Access Copyright Licence

Tuesday, 12 July, 2011

At this point, I’ve written way more about recent Canadian copyright law than I ever wished or planned to. But as a Canadian who cares about our digital future, I see I don’t have any choice but to make my voice heard and to keep an eye on things!

With a Harper majority government, judging from what the government tried to do previously, I expect to find it will kowtow to the US government and the lobbyists represented industrial giants and again try to ignore the loud complains by Canadians in the various copyright consultations.

Here is some information on what the University of Calgary decided to do.

* IMPORTANT ANNOUNCEMENT, JULY 6, 2011 – The University of Calgary has notified Access Copyright, the Copyright Collective, that as of September 1, 2011, the university will no longer operate under the Interim Tariff as presented by the Copyright Board in December 2010. Read the rest of this entry »

Scott MacIsaac – Portrait of a Young Award-Winning Classical Pianist

Saturday, 11 June, 2011

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If you spend some time with Scott MacIsaac, the first thing you will notice is that he is an easy going & sweet young man. And if you are lucky to hear him play the piano in a concert, you will discover he is a talented classical pianist and has also won many awards.

When I first heard Scott performing in 2009 at 16, I knew that Scott was talented but I only knew him as a person through the eyes of his grandpa Lee Yee 李怡, a famous Hong Kong writer/editorialist. In order to write about Scott in an informed manner, I spent an afternoon plus an evening chatting with Scott and his parents Doug, Wendy and grandpa Lee Yee. And conducted two extensive over the phone followup interviews with Scott and Lee Yee. I appreciate their time very much especially since Scott is leaving Calgary soon (in August 2011) to enter Yale‘s Certificate in Performance program to study piano with Professor Boris Berman.

The Portrait

After some careful considerations, I decided the best way for me to share my insights about Scott is to divide this article into three sections: 1) Impressions2) Two Q&As, and 3) YouTube videos (my  “Portrait of a Young Classical Pianist” short video, Scott’s TSO Competition videos, and his Calgary performance) allowing you chances to see Scott plays the piano and to listen to him and his parents in their own words.


I am not a piano/classical music expert, but judging from the multiple awards Scott has received over the years, I can safely and objectively say he is very talented! :) And the two performances of Scott I attended in the last few years, I thought the music were played beautifully and many pieces were performed full of passion. In chatting about piano music with Scott, I often saw his eyes lit up and his face filled with a big smile. And in our chats, he, even at his young age, recognizes a perfect performance doesn’t really exist and there are always things to improve in every performance.

When I raised the observation/fact that the career of a concert pianist can be tough and classical piano music isn’t exactly rising in popularity, I sensed he truly sees piano as his calling and willing to work very hard to overcome the challenges faced by concert pianists everywhere. And he even aspires to try to reengage the younger/newer generations to love classical piano music more. Scott clearly knows this is not an easy task so I really admire him for wanting to try. Read the rest of this entry »

Health Canada approved iPhone/iPad app for stroke diagnosis

Monday, 9 May, 2011

Health Canada approved iPhone/iPad app for stroke diagnosis

CTV News has done a great report where you can see the app in action.

“”In a medical emergency, medical imaging plays a critical role in diagnosis and treatment, time is critical in acute stroke care, every minute counts.” said Dr. Mitchell who is from the University of Calgary’s Faculty of Medicine.”

CBC also has a report that is worth a watch.

“”Now a physician anywhere can get a call on their iPhone and can immediately take a look at the images in the remote community,” said Ross Mitchell, a professor of radiology at the university who helped develop the software. “They can do more than just look at them. They can cut into them, rotate it in 3D, they can do all kinds of advanced visualizations and analysis, which may be critical to make the diagnosis.“”

Feels great to see some cutting edge tool developed in Calgary. From the University of Calgary, Faculty of Medicine press release,

“New research from the University of Calgary’s Faculty of Medicine shows that doctors can make a stroke diagnosis using an iPhone application with the same accuracy as a diagnosis at a medical computer workstation. This technology can be particularly useful in rural medical settings. This allows for real-time access to specialists such as neurologists, regardless of where the physicians and patients are located”

Here is the original JMIR (Journal of Medical Internet Research) technical paper, “A Smartphone Client-Server Teleradiology System for Primary Diagnosis of Acute Stroke“.

Discussion & Note

Not to take away from the significance and importance of team’s achievement, there are limitations in using the system over 3G network due to data transfer rate issues as indicated in the technical paper.

“The system should provide practical frame rates over cellular or wireless networks. In our experience, a single visualization server can accommodate 10 or more simultaneous iOS device users and is capable of delivering and displaying up to 14 frames per second on an iOS device connected over a 802.11g Wi-Fi network. The frame rate was enough to provide sufficient interactivity for comfortable use. However, the frame rate on a 3G cellular network was 1 to 4 frames per second, which was insufficient for practical use. We know that fourth generation (4G) cellular networks are now installed in many metropolitan centers. We estimate that the higher bandwidth of these new cellular networks should allow 10 to 15 frames per second to be delivered to smartphones. However, currently only the iPhone 4 and a few Android-based smartphones are capable of utilizing greater network bandwidth.”

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