Archive for May, 2010

My first posting for the Stem Cell Network is up! Woohoo…

Please check it out!!!!

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Earlier this month, I wrote about a recent paper which looked at creating a “pain scale” based on the facial expressions of mice. I finally got around to reading the actual published paper.

Here’s the reference: Langford, DJ et al. Nature (2010). Some interesting things I noted:

“Causing headaches in mice”
This one made me blink when I read it in a news release. How can you claim to cause headaches in mice when your study is looking at how to classify pain in mice? Well, apparently, some of the mice used were transgenics which carried a gene linked to familial hemiplegic migraine in humans. These mice seemed to exhibit a baseline level of pain, presumably due to the transgenic gene they carry. I wouldn’t say that’s equivalent to “causing mice headaches” but hey, I don’t write for newspapers.

They measured what?!
When I read the news releases, I was under the impression that lots of fancy imaging software was being used, that microscopic twitches and fine-detail facial expressions were being mapped, and in general, crazy stuff was going on. How wrong I was! The original article included representative images used to rate different levels of mouse pain. For each trait, there were three images. Images set to a scale of 1 to 3 – 1 being “normal” and 3 being “severe pain”. After looking at the pictures, I had a “And this needed to be a scientific study… why?” moment. For example, under “orbital tightening”, there was a normal mouse, a slightly squinty mouse, and a mouse whose eyes were dry and narrowed to slits. Any animal technician would (or at least, should) be able to tell you that the mice in the #3 category were in pain and that the animals in the #2 category were not doing well.

But, to be fair, it is true that recognizing and using something daily is not the same as having a defined, well-studied scale to refer to. If making an official scale helps animal care, I’m all for it. To be honest, I’m a little surprised that a scale as not been officially developed (studied and peer reviewed) before, considering that the majority of animal facilities use some sort of point-scale for rating animal health.

Looking forward to hearing more from this group. Hopefully they’ll go into some more applications next time.

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Saturday was the first of five preview openings for UBC’s Beaty Biodiversity Museum. All five events run 10am to 3pm or 4pm and are free to the public and feature activities for the entire family.

One of the first things I noticed was that UBC has finally figured out that it is damn hard to find anything on campus if you’re not a regular student. (Even today, I encountered a very lost Asian man looking for a building whose name started with “L”. Hmm…) From the bus loop, there were maps and numerous signs directing people to the museum.

The museum is located within the Beaty Biodiversity Centre, a multidisciplinary research institution situated between the Aquatic Ecosystems Research Laboratories (AERL) and the Food, Nutrition and Health (FNH) buildings. From the road, the whale skeleton is visible – it is a mammoth 25m long and hangs suspended in a giant glass atrium.

Inside, there was a long line up of amateur photographers, families and science enthusiasts jostling for the best view. The whale is visible from a full 360 degrees, thanks to a cleverly designed descending ramp.

25m long blue whale skeleton hanging in the Beaty Biodiversity Museum at UBC

At the bottom of the atrium were displays of selected specimens from the various collections housed in the museum, including mounted and unmounted birds (Wilsonia species, flightless cormorant), small mammals (weasels, chinchillas), skulls from various antlered species, an incredibly well preserved turtle, and some GIANT bugs. While impressive, I was a little disappointed at the relatively few items on display. I hope the finished museum will feature more specimens – I saw no pelts (the Vertebrate collection has a beautiful tiger pelt which was donated privately, for example), and very few plant, fish and invertebrate representatives.

Aside from the displays, visitors also had the opportunity to view a movie detailing the journey of the Blue Whale from the East Coast to UBC. One interesting factoid: The whale skeleton actually broke into over 1000 pieces while in transit. When it arrived at the university, museum staff had to reassemble the broken bones!

Outside on the grounds surrounding the museum, tents were set up with family-friendly activities such as bone assembly games, microscope stations, and arts and crafts. All of the stations were staffed by enthusiastic red-shirted volunteers. It was a welcoming atmosphere, with lots of people wandering around, watching, listening and learning.

The next preview session is May 29th, which is also UBC’s Alumni Weekend. It’s free, it’s hands-on, and it’s science celebrating the diversity of life. I would encourage everyone to check it out!

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In the latest in Frankenstein-ian science, researchers at the J. Craig Venter Institute in Rockville, Maryland have reported the creation of the world’s first cell containing a synthetic genome. Already the discovery is being marketed as the creation of “synthetic life” in some popular media.

On the heels of such spectacular headlines come the fears of the wary, the paranoid, and the misled. Already on Facebook, there is a Stop Synthetic Life group.

I wasn’t able to find the paper yet – today’s announcement seems to be a pre-paper announcement, correct me if I’m wrong – but looking through various sources here’s what I’ve found:

The genome was created, yes, in the sense that the bits of DNA was made in a test tube rather than an organism. But it wasn’t a novel genome by any means. It was a replica of an existing genome from an existing strain of Mycoplasma with a few non essential genes removed and a few marker genes added (so the genome could be distinguished from the “natural” version). Science already creates mice with jellyfish genes and plants that resist pesticides, among many other examples… A few marker genes is hardly novel.

This edited genome was then sequenced into chemical fragments, stitched together with some clever biochemistry, and inserted into an “empty” Mycoplasma recipient. The recipient was able to use this artificial genome and propagate naturally, thus producing “synthetic cells”.

Pretty cool, yes. Certainly an interesting achievement. But synthetic life? Hardly. And at a cost of $30-40 million USD, I can’t help but think that there would have been better uses for this money.

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In a collaboration between UBC and McGill researchers, a study was very recently published in Nature Methods which looks to quantify pain based on facial expressions in mice. The study has since been popularly named the “Mouse Grimace Study” in popular media, such as the local Vancouver Sun and online at Science Daily.

I can’t seem to get access to the full journal article at the moment, but from what I’ve read, the study investigators injected mice with solutions containing varying levels of irritant. They suggest that the pain level is somewhat similar to a headache. I’m a bit skeptical at that assertion – how can you claim to cause a headache in a mouse, when your study is trying to measure pain response in the first place?

I would guess that the injections are actually more similar in discomfort level to a human receiving a vaccination. As most people probably have observed, some vaccinations are more painful than others, depending on the salinity and contents. (Side note – received a new vaccination of MMR a few months ago at the insistence of my employer… MMR = liquid pain)

After injecting the mice, the authors used some fancy imaging to record things like, ear position, whisker twitches and eye movement. The results of these images are compiled into a scale based on the pain intensity of the injected solution. So, theoretically, the “mouse grimace scale” could be used to determine how much pain a mouse is in.

It’s important to note that the authors are looking at mild pain stimuli, not moderate (eg. fight wound, superficial surgery, etc.) or high (eg. invasive surgery, broken limb, etc.) levels of pain.

Granted, I haven’t read the entire paper yet, but as someone who’s worked with animals, I’m a little skeptical about measuring mouse facial expressions as a response to mild pain stimuli. Ear twitches could be in response to sound, perhaps at a frequency the authors do not detect. Blinking could be a result dryness in the eyes after being whisked out of a cage and then dropped back in, perhaps too quickly.

It should be interesting to read the actual article. Can’t trust popular media any more than you can trust scientists! I’m heading out to the university in a bit, so perhaps I’ll be able to download a copy there.

[Photo by Dale Tidy]

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The President’s Cancer Panel took a surprisingly strong stand against chemicals and toxins in our everyday life by recommending organic foods and filtered water in their latest report.

It’s an unsurprisingly bleak look at the chemical wasteland we find ourselves in today. It is difficult to navigate food, make-up and other every products without encountering something of questionable health value. Indeed, as NY Times columnist Nicholas Kristoff noted in his latest opinion piece, even newborn babies enter the world “pre-polluted” with an average of over 300 unnatural contaminants.

The articles offer a few pieces of advice:

  • Choose organic foods whenever possible
  • Drink filtered water
  • Avoid BPA-containing plastics when storing or heating food – ideally, use glass or ceramic

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Vacations have a way of derailing the best of intentions.  I even took my laptop with me to get some writing done!  Alas, failure.

While I was away, Carl Zimmer wrote an interesting piece on the evolution of herbicide resistance in weeds.

The article discusses “Roundup” plants – plants which have been modified to be resistant to glyphosate, a chemical used to kill weeds.  Glyphosate is commonly used to kill weeds while preserving glyphosate-resistant plants (provided courtesy of Monsanto).  Glyphosate was thought to strike at such a key aspect of plant biology (preventing the construction of certain amino acids) that weeds would never be able to evolve resistance. But evolution wins out in the end, as less than 50 years after Roundup was introduced, we are now seeing glyphosate resistant weeds appearing in farmers fields.

Articles like this always have a tinge of irony for me.  It reminds me of just how prevalent genetically modified foods are – corn and soy beans are a big example.  Unsurprisingly, these are two of the biggest crops in the business. Corn and soy products are found in almost all processed foods. Monsanto recently released a new corn, in fact – Genuity™ SmartStax™ Corn. Get ’em while they’re hot!

At the same time, the plant geneticist in me is supremely impressed at the engineering involved. SmartStax Corn has eight traits for herbicide tolerance and insect protection! Theoretically, a farmer could rotate between eight different chemicals, thus reducing both his overall chemical dependency and the selective pressures (caused by chemical overuse) which can lead to herbicide and pesticide resistance.

And if you are inclined to vote against genetically modified foods, it is supremely hard to avoid corn and soy products.

If I were Jamie Oliver, the answer would be easy – Grow your own food, avoid supermarkets and source all your own meat. But, I’m not. And sadly, he has not chosen to swoop down on my office and provide me with answers.

I do think though, that agriculture as a business has no choice but to support the merging of science and food. Society as a whole constantly pushes for more product at lower prices. And GMO foods are a direct result of that. The agriculture business has learned to grow cheap foods cheaply, and who can blame them. It is a business.

Place the blame on ourselves, as consumers, for refusing to pay more money for real food. It’s easy to make chicken nuggets that contain “10% meat protein” and gobs of corn and soy product as filler. It’s cheap, easy and fast. It’s harder to make a real chicken nugget. But, when we can rely less on corn and soy as filler, we reduce our dependency on the agriculture business, increase demand for food diversity, and reduce the need for GMO foods.

As an aside:
Real nuggets contain: chicken, egg, flour, bread crumbs, salt and seasonings, and oil for frying.

Processed nuggets contain:
Chicken, water, salt, modified corn starch, sodium phosphates, chicken broth powder (chicken broth, salt, and natural flavoring (chicken source)), seasoning (vegetable oil, extracts of rosemary, mono, di- and triglycerides, lecithin). Battered and breaded with water, enriched bleached wheat flour (niacin, iron, thiamine mononitrate, riboflavin, folic acid), yellow corn flour, bleached wheat flour, modified corn starch, salt, leavening (baking soda, sodium acid pyrophosphate, sodium aluminum phosphate, monocalcium phosphate, calcium lactate), spices, wheat starch, dried whey, corn starch. Batter set in vegetable shortening. Cooked in partially hydrogenated vegetable oils, (may contain partially hydrogenated soybean oil and/or partially hydrogenated corn oil and/or partially hydrogenated canola oil and/or cottonseed oil and/or sunflower oil and/or corn oil). TBHQ and citric acid added to help preserve freshness. Dimethylpolysiloxane added as an anti-foaming agent.

And I have to wonder – WTF does chicken need an anti-foaming agent for??? And since when have “triglycerides” been considered seasoning? Certainly not in my spice cabinet!

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