Tuesday, September 30, 2008

To study bacteria without growing bacteria

It is a well known fact: Bacteria are very diverse and adapted to a very specific niche. If that niche disappears some bacteria will adapt and a new niche will be found and exploited. There are only so many bacteria that can be studied in the lab and often these studies can be flawed because one cannot replicate the conditions under which the bacteria normally strive....and then comes metagenomics.

Metagenomics is the study of gene expression and genome organization in a specific environmental condition. This is quite useful when studying microorganisms that live in extreme conditions impossible to fully replicate in a lab setting. I found this article at the Science Daily site. It is about an article published in Nature by Philip Hugenholtz and MIT researcher Gene Tyson.

“By employing the techniques of metagenomics we can go beyond the identification of specific players to creating an inventory of the genes in that environment.”

“We find that genes occurring more frequently in a particular community seem to confer attributes beneficial for maintenance of the function of that particular ecological niche.”
I really think bacteria hold the secret of our long term survival on this planet, studying these wonderful cells will allow us to identify specific solutions to very complex problems....if we can only survive long enough as a species.

Monday, September 29, 2008

Dressing up for disease....

I have been saying that for a long time to my students including nursing and medical students. This article was publised on the New York Times website

"In 2004, a study from the New York Hospital Medical Center of Queens compared the ties of 40 doctors and medical students with those of 10 security guards. It found that about half the ties worn by medical personnel were a reservoir for germs, compared with just 1 in 10 of the ties taken from the security guards. The doctors’ ties harbored several pathogens, including those that can lead to staph infections or pneumonia.

Another study at a Connecticut hospital sought to gauge the role that clothing plays in the spread of methicillin-resistant Staphylococcus aureus, or MRSA. The study found that if a worker entered a room where the patient had MRSA, the bacteria would end up on the worker’s clothes about 70 percent of the time, even if the person never actually touched the patient."

Sunday, September 28, 2008

And I am working so hard!

On October 12th I will be running the half-Marathon in Victoria (Royal Victoria Marathon. I would like to reach a new milestone...a new personal best but I am afraid it will be impossible and it seems my VO2 Max is to blame for this. What is VO2 Max? In a nutshell it is the amount of oxygen my body can use and it is measured in ml/kg/min. Right now, my VO2 max is estimated at 56-58. Not bad at all but not enough....far from enough! I would like to achieve 1h 30 minutes...but my VO2 Max would need to be at least 62....I am almost there!

Last year, during the Island Race Series, I raced every other week. I had a lot of practice, a lot of speed work and also I was 8-10 pounds lighter (I am now 172 pounds). During one of those races, the Comox Half Marathon, I ran 21.1 km in a time of 1h 34 minutes 10 seconds. I tried to do this two weeks ago at the Lands End Half Marathon only to find out that I am not running fast enough, not because I am not trying but because my body cannot. I need more training, more speed work in order to increase that important VO2 Max value!

By the way, a new record was set today for the marathon distance....42.2 km in 2h 03minutes 59 seconds....that's 2minutes 56 seconds per kilometer....for 42.2 km. Haile Gebrselassie is a running machine, a biological machine with a VO2 max of about 82.....but he is way lighter than me (that's my excuse) ;-)

Friday, September 26, 2008

I will not complain again!

Everybody has to read THAT STORY

Thursday, September 25, 2008

Genetic diversity can have an ugly side (I guess)

Sweaty T-Shirts and Immunity

A corny question to ask a prospective mate might be: So...what is your zodiac sign? A better question could be: So, what's in your HLA? A few studies suggest that people tend to choose their mates based on MHC dissimilarity. A paper by Chaix et al. published in PLOS Genetics demonstrates that European American couples are really dissimilar when MHC loci are compared....way more different than what is expected by pure randomness. Although this selection could be a semi-counscious choice as stated by the following:

"In a less direct way, other studies have focused on odor preferences: in “sweaty T-shirts experiments”, in which females were asked to smell T-shirts worn by different males, it was shown that females significantly prefer the odor of T-shirts worn by MHC-dissimilar males, although such preference was not found among females taking the contraceptive pill. However, in another sweaty T-shirts experiment, in which males where chosen from a different ethnicity from the females and females were not aware of the nature of the smell (contrary to the two previous studies), females significantly preferred the odor of males having a small number of HLA alleles matching their paternal inherited alleles than the odor of males having fewer matches."
The authors also mention that this selection could be totally up to the egg to "choose" the right sperm cell....

Wednesday, September 24, 2008

A little advice can go a long way!

Here is something I found on LifeHack.org. They post a list of important things that can help students get ahead after college. A very important one is the 4th one....Craft your own personna.
Here's what they write:

"In today’s world, one of the worst ways students damage their future careers is by sharing too much of the wrong kind of information online. Assume that everything you post online is going to be available to prospective employers, clients, or investors, all of whom increasingly turn to the Internet to research potential employees or partners. Keep the drunken stories either anonymous/pseudonymous, or marked as “private”, and be sure to build out public-ready profiles, under your own name if at all possible."
So always be very careful about what you decide to post on Facebook and other social websites.

Picture from: http://www.flickr.com/photos/87704480@N00/192719734/

May the best of ideas win

Google if offering up to 10M$ for an idea or ideas that will have an impact on the world....can you think of something? Click HERE to be redirected to their site!

Tuesday, September 23, 2008

A true inspiration

I do not consider myself as a religious person at all but Sister Madonna Buder inspire me, what a character and a warrior!

Science tattoos

I know a few students that have, somewhere on their body and I do not care, a tattoo of a molecule. For instance a known carcinogen or the famous double helix....anyway...if you are thinking of getting one or if you already have a science tattoo, THIS SITE might be of interest to you.

Picture source: http://www.flickr.com/photos/_tim/149500684/

Monday, September 22, 2008

What's in your feces?

There is a very interesting theory in immunology: the hygiene hypothesis. Basically, if you are too clean and not exposed to enough dirt, scum and bacteria...you will suffer eventually. Our immune system has evolved to detect, recognize and eliminate millions of different molecular structures found among other things, on viruses and bacteria. Early exposure seems to be a key to a healthy immune system and a allergy-free life. This is, once more, confirmed by a new study published today (Sept 22nd, 2008) Clinical and Molecular Allergy. Fecal samples collected from 21 infants showed that a poorly diverse gut microbiota is associated with eczema development early in life.

"We found a significant inverse association between fecal bacterial diversity and eczema in early life. In addition, we found a significant increment in fecal bacterial diversity from ages 1 to 4 months in healthy children, but not in children who developed eczema by age 6 months."

To understand these findings, it is important to realize that our immune system is often "educated" through the gut, in fact more than 70% of the immune system is gut-associated. Experimental mice models show that a sterile gut leads to an abnormal immune system geared towards the development of allergies. In their article, the authors mention a reduced microbial diversity has also been implicated in various diseases including Crohn's disease and coeliac disease.

Click HERE to find a .pdf version of this very interesting article

Saturday, September 20, 2008

How we learn

I am fascinated by this simple fact...our brain changes daily and when we go to bed at night the connections are not quite the same as they were when the alarm clock buzzed too early in the morning. Just imagine learning again EVERYTHING we know, having to use a fork again, riding a bike etc...Of course there are conditions that will steal away from your knowledge and abilities but children, of course, have to learn everything. Just using this little game where you have to place a cube in the square opening of a container seems to be quite a challenge...and it is!

I found this on one of my favorite blogs, Cognitive Daily. I think if you are into cognition, learning and behaviour...you will like this posting!

Here is the link:

Friday, September 19, 2008

Une similitude?

If you are from Québec, chances are that the picture on the left is embedded in your brain! Yes, it is the little house in Chicoutimi that stood up to torrential rains and a crazy river....When I compare this picture with the one on the right, a house that survived hurricane Ike, I can only imagine what the people of the Saguenay went through in July of 1996!

Want to know more about the Saguenay floods? Click here (From Radio-Canada Archives)

First PICTURE of an exoplanet...pure beauty!

And we thought we were so very special....

When it comes to emotions, humans think they are special. We think we are the only creatures capable of empathy....NOT! Chimps, our closest cousins, do that as well! After a bad day or a bad fight some chimps will hug the broken hearted to comfort and to relieve stress. See...."animals" have feelings too!

via: Times Online

Wednesday, September 17, 2008

The Elephant, the Donkey and stem cell research!

It's not always easy to predict who is going to vote for which candidate...even the polls tend to predict a trend that fails to materialize when the the big day comes. This special year where our close neighbours will decide on a new administration, it seems like reasearchers involved in embryonic stem cell science can only vote one way....the Donkey way! As mentionned by Obama himself, embryonic stem cell research could be funded again if he is elected. This is a different view from McCain's who (might have) changed his mind since the California primaries

Here is a sample of what they said recently according to the Science Debate 2008


"I strongly support expanding research on stem cells. I believe that the restrictions that President Bush has placed on funding of human embryonic stem cell research have handcuffed our scientists and hindered our ability to compete with other nations. As president, I will lift the current administration’s ban on federal funding of research on embryonic stem cell lines created after August 9, 2001 through executive order, and I will ensure that all research on stem cells is conducted ethically and with rigorous oversight"


"While I support federal funding for embryonic stem cell research, I believe clear lines should be drawn that reflect a refusal to sacrifice moral values and ethical principles for the sake of scientific progress. Moreover, I believe that recent scientific breakthroughs raise the hope that one day this debate will be rendered academic. I also support funding for other research programs, including amniotic fluid and adult stem cell research which hold much scientific promise and do not involve the use of embryos. I oppose the intentional creation of human embryos for research purposes and I voted to ban the practice of “fetal farming,” making it a federal crime for researchers to use cells or fetal tissue from an embryo created for research purposes."

Here is what McCain said during the California primaries

"I believe that we need to fund this. This is a tough issue for those of us in the pro-life community. I would remind you that these stem cells are either going to be discarded or perpetually frozen.

We need to do what we can to relieve human suffering. It's a tough issue. I support federal funding."

Via: BioTechniques newsletter


SIMPLY A-M-A-Z-I-N-G......a true role model, a true warrior!

Not too sure about the last one...

Water memory???...I thought this was bogus....and I still think it is, unless somebody can "educate" me about this....anyway, still an interesting site!

Via: http://curry.mevio.com/

Tuesday, September 16, 2008

Ballistics and Mother Nature

Spores are really neat and they can be ejected from a sporangia at amazing speeds. I found this article in PLOS One...scroll down and download the videos. I really appreciate the Pilobolus one....a spore ejected like a rocket at a distance of almost 3m!

"In this study, we have used ultra-high-speed video cameras running at maximum frame rates of 250,000 fps to analyze the entire launch process in four species of fungi that grow on the dung of herbivores. For the first time we have direct measurements of launch speeds and empirical estimates of acceleration in these fungi. Launch speeds ranged from 2 to 25 m s−1 and corresponding accelerations of 20,000 to 180,000 g propelled spores over distances of up to 2.5 meters."
To view the Pilobolus video you can also click HERE

Monday, September 15, 2008

They finally understood.....

The Anglican Church apologized for misunderstanding Darwin's theory of evolution! It is a start....others will follow and stop thinking the Bible is a science book! Way to go Rev. Brown!

Read the article from The Guardian HERE

Rev Malcolm Brown: Good Religion Needs Good Science

If you are interested...more to read HERE

Sunday, September 14, 2008

Win some, lose some! Unfortunately!

I ran at the Lands End Half Marathon today. I was looking for a new personal best, under 1h 34min 1o sec...the time I got at the Comox half marathon last march. I wanted it pretty bad, too much! My goal was actually 1h 30 minutes....to reach such a goal my pace had to be 4 minutes 16 seconds per km.

I started fast, way under 4:16, too fast....wayyyyyy too fast. By km 12 I realized I was going to run out of gas before the end....and I did. By km 17 there was no way to reach 1h30...not even my previous personal best. By then, little demons started to tell me I should slow down, I would not make it, why am I doing this etc etc...in these times the left part of he brain, the logical one, tells you many things.....not always nice things! Oh well, I did something like 1h38....I do not have the official time yet but I did not reach my goal...not today! The Royal Victoria half marathon is in a month...I will be more reasonable by then...I swear!

PS. I love my new runners....Asics Gel Nimbus 10 (pic above).....like running on pillows! The right amount of support, the right amount of cushionning.......

Friday, September 12, 2008

It's going to be such a nice semester!!!

I have GREAT students this term, everybody seems to be prepared, eager to learn and, it seems to me, enthusiastic about the wonderful world of invisible life! Hurray....it is going to be a GREAT semester! Vive les bactéries!

Thursday, September 11, 2008

Universal flu vaccine and human Guinea Pigs!

Human trials of universal flu vaccine begin from PhysOrg.com

Clinical trials of a new vaccine that could protect against multiple types of flu are beginning at Oxford University. If successful, the ‘universal’ flu injection would transform the way we vaccinate against influenza and could offer immunity to a bird flu pandemic.


The problem with the Influenza Virus (the Flu virus) is that it changes over time. Small changes lead to drift and normally cause epidemics while more substantial changes, also know as gene shift, may cause dreaded pandemics. The problem with the flu vaccine is that it targets special protein found at the surface of the virus and that shift and drift creates "new viruses" no longer recognized by our immune system. So there...you need a shot every year...AND YOU SHOULD GET IT!

The problem with yearly shots is that new vaccine production is mainly based on statistics and the probability to find such and such strain in any given year. This is normally based on the study of previous years. In a way, it can sometimes be a long shot. Having said that, even with the uncertainty these shots can prove to be useful.

Many people do not want to be inoculated with vaccines for various reasons including the fact that some vaccines contain Thimerosal, a mercury-containing preservative, even if Thimerosal has been proven to be eliminated very quickly by the organism even in infants.

The bird flu that, so far, has killed close to 200 people worldwide reminds us that a pandemic is more a question of "when" than of "if" and the scientific community is trying its best to come up with a solution. The main problem in the production of a new vaccine against a probable bird flu pandemic is that we need the virus before we can produce a vaccine...in other words, we need the pandemic to start before we can inoculate people. The other problem is that vaccine production takes a lot of effort and the industrial capacity worldwide is limited. We would NOT have enough vaccines for everyone on the planet!

A new vaccine seems promising and would likely address many problems related to yearly vaccine production. A universal vaccine targeting ALL strains of influenza. WOW! That is a real need! On September 8th, human clinical trials started with a limited cohort of brave human Guinea pigs. This study, done at the Oxford university, could lead the way to a new and much needed vaccine. Read more HERE

Image source: http://www.flickr.com/photos/gustavocarrijo/12181990/

Wednesday, September 10, 2008

We are still here....

The Large Hadron Collider in Geneva has been humming for quite a while now....we are still here, no giant black hole was created....YET! The particles will keep on going in circle, almost at the speed of light, for weeks. Eventually some particles will smash into each other and then.....we will still be there!

If you are into nuclear physics, you can read all about it at the WIRED Mag site.

Monday, September 08, 2008

Superbugs and weed!

"Hey man...this is good stuff" might soon mean: "Hey dude, I got a cure against this MRSA bug thing". A few substances found in Cannabis sativa (Marijuana) including THC (the psychoactive ingredient) have been proven to inhibit the growth of Methicillin-Resistant S. aureus (MRSA). Based on their highly hydrophobic structure it seems like these compounds have an affinity for lipids and might indeed disrupt the membrane.

The authors point out that the mechanism remains elusive....I might know why it remains elusive!

Reference: http://pubs.acs.org/cgi-bin/sample.cgi/jnprdf/2008/71/i08/pdf/np8002673.pdf

New Scientist website

Just wanted to tell you about the New Scientist magazine website. The news feature is really great, if you are interested in science you will become addicted to this high quality format.