Bay journal club recap

Some cool papers were discussed today in the BJC (similar to podcast, but without a mic, and with more baybes) that I want to bring to your attention:

-The chemokine growth-regulated oncogene 1 (Gro-1) links RAS signaling to the senescence of stromal fibroblasts and ovarian tumorigenesis: Epithelial-stromal interactions is the new hot thing in cancer. A lot of people are starting to believe that stroma plays an important and sometimes dominant role in carcinogenesis. One of the hypotheses is that epithelial cancer need the underlying stroma to transform into "tumour-supporting" cells for the heterologous tumour to grow. These transformed epithelial cells may control the stroma via the chemokine gro-1, and render them senescent. The senescent cells in turn direct/allow the epithelial cells to form tumours. Surprisingly the p53 -dependent senescence is required for tumour growth, since immortalizing the stromal cells actually completely inhibits tumorigenesis. So do we accumulate these senescent tumour-prone environments as we age? Is targeting p53 in the stroma a viable approach? What is special about senescent cells that makes them more tumour-supporting.



-Targeting and tracing antigens in live cells with fluorescent nanobodies: Everything nano has sex appeal. Very very small sex appeal. these nanobodies are basically single chain antibodies from the camel that are fused with gfp. You can infect/transfect the contruct expressing them to get live imaging of stuff within the cell without having to worry about fusing your gene of choice to gfp, and wether that alters it's expression/function/localization. the monoclonals are screened using phage display. The movies showing PCNA throughout S-phase are amazing.

A male contraception pill: This is cool. Most male contraceptive pills are too toxic. The reason is that anything that seems to affect testes seems to also affect the brain somehow. Perhaps because both regions are immune-priviledged, or perhaps because they both serve man's intellect. To get around this researchers have fused a drug that disconnects sertoli cells Adjudin to FSH, a male hormone that regulates sertoli cells and spermatogenesis and is only taken up by seroli cells. A nice trojan horse delivery to reduce toxicity. Yet I'm still worried about the side effects...

Finally
Perk-dependent translational regulation promotes tumor cell adaptation and angiogenesis in response to hypoxic stress. Where our very own Rob is a co-author, showing why PERKY tumours have more angiogenesis...

Word of the week

nu‧ta‧tion  /nuˈteɪʃən, nyu-/ Pronunciation Key - Show Spelled Pronunciation[noo-tey-shuhn, nyoo-] –noun

1.	an act or instance of nodding one's head, esp. involuntarily or spasmodically.

2.	Botany. spontaneous movements of plant parts during growth.

3.	Astronomy. the periodic oscillation observed in the precession of the earth's axis and the precession of the equinoxes.

4.	Mechanics. the variation of the inclination of the axis of a gyroscope to the vertical.

Check-out these fant-nastic videos of dancing plants to back this up...

Jack O'Autoclave

Yeah, I carved a jack o'latern and autoclaved it. I thought it would be safer for children if the pumpkin was sterilized.
Before & After
It kinda stinks now and I think I'm going to have to keep it in the fridge so it doesn't rot. Although rotting jack o'laterns are extra SCARY.

Podcast feed now live on iTunes

So I finally caved-in and got us some real commercial hosting with libsyn, to accomodate all the new listener we'll get from the publicity on the next CMM/BMI biweekly. Sorry open source folks but it just wasn't working out with ourmedia/openarchive. Since putting the show on iTunes the listeners are trickling in, and we have finally crossed the hundred download treshold and continue our steady increase. The next show will be up shortly, and not to spoil it, but we'll have a mystery guest... If you liked the shows you can vote for us at popcurrent, podcastalley, and iTunes...

Bacteria on Mars

I think I ran into this article on digg.com about renewed questioning of the data sent back from the Viking landers that concluded there was no life on earth. Indeed one of the experiments apparently indicated that there was life and another test, looking for organic molecules came up negative. However, the same organic molecule test also came up negative in the Antarctic where there is such molecules and has been shown to have poor sensitivity. It seems that the discovery of some very strange bacteria adapted to crazy environments on earth inspired this renewed questioning of the "Life on Mars" question. Especially now that they have found a bacteria living far beneath the earth's surface that survives on energy supplied by radioactive isotopes underground. They also grow very slow. Like 45 to 300 years between cell divisions.

Genzyme office space

Ever wonder what it would be like to have an office? Well if you ever graduate and sell your soul to Genzyme, it might look like this. State of the art green building, with crazy natural light diffusing technology and german style interior. These days it pays to be green: 34 percent water savings, 42 percent electricity cost savings, Over half of all materials used in construction contain recycled content, More than 90 percent of construction waste was recycled.

Another fine collection of IA updates

Just when I thought the Street Samurai was dead or something, an excellent collection of IA updates are in the hizouse.

Blue jean dye kills cancer cells.

The common dye found in blue jeans and ballpoint pens is called phthalocyanine and is a light-activated, or photosensitive, agent with cell-destroying properties. But it is not water soluble and so don't take off those pants just yet, you're safe. So how do you kill cancer cells with it? Well using gold nano particles coated with the dye as a trojan horse for delivery and then shinning a laser at the right spot to activate the dye. Seems to work in HeLa cells anyways. Bonus: I got to use laser, nanoparticle, and blue jeans in the same paragraph...

Plant-Guys Stiffed for RNAi Nobel?

Of course you heard the debate here on the bayblab first (see posts, and podcast epi #1). Some plant researchers got together and wrote a letter to nature, where they point out that the discovery of RNAi, for which this year's Nobel in Physiology or Medicine was awarded, was actually made in plants before it was made in C. elegans by this year's laureates. They object that no one in the plant field was recognized for this work and suggest that David Baulcombe would have been a suitable 3rd laureate.

Differentillielio

I always find it difficult to explain scientific things in languages other than english, because all the litterature you read ends up being in english. This makes it difficult for me to give science talks in french schools for things like LTS. I found this really practical english-french science lexicon. Hopefully this can be useful for you frenchies out there, or to the confused anglos (ahemm Rob).

Mice like to travel too

I am not making this up: apparently mice find shipping pleasurable. At least that's the conclusion of this paper, where mice grew fond of the food's artificial flavoring that it received during shipping. Yet I still don't like air canada food...

Coffee and my Liver

Seems that drinking coffee protects you from cirrhosis of the liver. It's just some correlative study of coarse and is not really proof but it just makes sense to me because I like coffee and beer and I don't like cirrhosis of the liver.

Bayblab podcast episode 2

Here's the latest podcast, episode 2. We talk in this one about dog testicles, russian sociopaths, bigfoot's fossil, Craig Venter's ego, and why Rob doesn't like aliens. The rss feed seems to be down most of the time, so until the people at ourmedia resolve their problems or we migrate our files to a commercial server you may have to download manually. I apologize for the lenght, we'll try to keep it down next time but Kamel wouldn't shut up. Seriously who invited this guy.

Interpretive Dancing

Ran accross this beauty of an abstract describing how your creative dance abilities are genetically determined. (don't ask how I ran into this.) The article describing this genetic study has such phrases such as "the dancing phenotype." Wow, I had no idea people did research like this.
Of course the genes responsible relate to serotonin transport, so it's all in your head and nothing to do with rythm in your muscles or someting. Related in a way is an article I found that summerizes some data suggesting that dancing helps retain cognitive abilities as you age.

Constructive Criticism

It's always fun to get feedback on a talk. There's always lots of useful feedback, and I also find a lot of it quite funny. Here are a few entertaining comments on my presentation in a recent class:

• "I also felt that you were knowledgable about the topic but completely uninterested."

• "For future presentations, try to stand straight and not move you arms all over the place."

• "I feel like you missed setting the mood for you audience."

Next time I'm bringing candles, jazz and coignac.

Systems Biology Word of the Week

hys‧ter‧e‧sis  /ˌhɪstəˈrisɪs/ Pronunciation Key - Show Spelled Pronunciation[his-tuh-ree-sis]
–noun Physics.

2.the phenomenon exhibited by a system, often a ferromagnetic or imperfectly elastic material, in which the reaction of the system to changes is dependent upon its past reactions to change.

ie Lactose utilization switching in E. coli is hysteretic due to the regulatory architecture of the Lac operon.

So amazingly obvious, yet so confusing.

Gairdner award lecture

Every year we look forward to the Gairdner award lectures, since the laureates are usually top notch scientists, and it's a preview to the Nobels. Ronald Evans was no exception, and he came to talk to us about "Nuclear Receptors: Metabolic Engineering and the Dawn of Synthetic Physiology". Basically his research involved PPAR receptors, and their importance in fat metabolism. In it he suggested it might be possible by gene transfer or pharmacological means to change the muscle physiology and metabolism to fight the obesity epidemic. If the lecture is coming in your neck of the woods, here's the bayblab rating as a preview:

• Appeal of the topic: 10/10. Who doesn't enjoy discussing how fat americans are.
• Analogies: 6/10. Definately pop-sci level analogies. Something about musical chairs. Usage of very bad puns. Somehow included pictures of his african safari into the talk.
  
• Powerpoint: 9/10. I was disapointed by the lack of animation, but he makes up for it by including videos of mice running on treadmills. Mystery western blot pops-out in the end.
  
• Delivery: 8/10. Mannaged a couple of jokes. His voice was soothing but he was animated enough to keep us interested. Purple stripped tie focused our attention on him.
• Cookies: 0/10. No coffee or cookies. Big mistake in the afternoon.

Arbitrary rating: 82.37%

Big biceps, small testes?

In the last edition of PNAS, an article discusses the evolutionary tradeoff in a horned beetle between developping weapons vs large testes. If the horns are prevented from developing, the beetle invests more into testes growth. So in this classical sexual competition, you have to choose between outcompeting by force or by sexual prowess. This could mean only one thing Kim Jong Il: sooo small, so small.

PHD comic

A little plug for a really great site.

Vaccines Will Not Work for AIDS

Speaking of the ever-elusive AIDS vaccine, one of the most compelling statements I've heard in a long time on the subject came from none other than David Baltimore, Nobel-winning retrovirologist who discovered reverse transcriptase and the outgoing President of Caltech. Once the US "nation's leader in the effort to create an AIDS vaccine", Baltimore said in a talk at Synthetic Biology 2.0 "having spent myself many years thinking about and working with people on the development of an HIV vaccine, I came to the feeling that we need new and better approaches. The standard approaches were not going to work....the reason that HIV is a killer is because the immune system is unable to control it. And so when you try to make a vaccine which is dependent on the immune system for its function, the immune system has already failed that test. It doesn't know how to control HIV." His solution? He's calling it "synthetic immunology", engineering the body's immune system to do what it cannot on its own do, recognize and clear HIV.

On the Origin of Species

I guess Google Print was beat to the punch on this one, but the complete works of Charles Darwin are now available online, including research journals and field notes from his voyages on the HMS Beagle (and of course the famous Origin of Species). Many of the books are available in both text and images of scanned pages (and some audio versions as well). There is a huge wealth of stuff here and some pretty cool reading.

Chicken counting

An AIDS vaccine is heading for clinical trials in South Korea. It was developed at the University of Western Ontario. Dr. Yong Kang heads the group and of course he also does work on VSV. Of course, as this article in The National Post quoting our very own Dr. Earl Brown says "Don't count your chickens." In regards to his hopes for this vaccine. Apparently the quote ends there. The question remains, I guess, are we allowed to count them after they have hatched? The timeline suggests using the vaccine in uninfected people within 6 years.

Wikiality

Here comes the new authority in all matters : Stephen Colbert's Wikiality. In fact 100% of the references in my latest paper are from the site. here are some entries:
Scientists:
Scientists are evil spawn of Satan dedicated to encroaching on God's holy territory with their airplanes and cloning. They condone homosexual behavior and believe that it doesn't cause any harm.
Scientists are often liberal. They are almost always found in foundations and universities. Scientists are very logical beings, this is their weakness, use it! Scientists are behind liberal's magical machines.

Also worth checking are:Global warming, and Evolution.

Ultra-thin Rob

Coming this January, and just in time to shed off the extra turkey weight from Christmas, is a new calorie burning Coke product . Knowing Rob's love of Coca-Cola products, does this mean we're going to watch him waste away in the new year?
The funny thing is Wired magazine predicted this soft-drink development a few months ago in their Found: Aritifacts from the Future column.

The main active ingredient in the weight-loss drink is epigallocatechin gallate (EGCG), a green tea extract that, according to Coke, increases metabolism and by extension burns calories. I don't know about weight-loss activities, but EGCG has been shown to have neuroprotective effects in ALS, have anti-cancer effects and be anti-diabetic (possibly by acting as an insulin mimetic) -- among other effects. It makes you wonder at what point these 'natural' compounds will begin being regulated as drugs, especially when they have such wide-ranging and varied effects and are being used as additives in products that will almost certainly be abused.

As an aside, here's an interesting list of weight-loss drugs and their side effects.

Milking Snakes

I saw a great doco on TVO recently. It was about novel drugs derived from studying venoms of poisonous animals. It looks as if most of them have a mode of action that relates to neural transmission. Nature from PBS has some links on the subject of venom derived drugs. It looks as if the field is also quite busy since there has been an FDA approved drug based on the cone snail for calcium channel therapeutics. Check out you tube for a vid of a cone snail eating a fish. What is also pretty cool about this research is that work in the field involves cone snail colleting on the great barrier reef. From the PBS article about the doco: "Bryan Fry has milked thousands of snakes during his career." no comment.

A bad case of dumbed-down science

We were recently discussing the perils of analogies in science. This is an extreme example, where the work involves from what I can infer, a reshuffling and/or substitution of protein domains to make new peptide antibiotics. "You have a string of letters and that string of letters reminds you immediately of a sentence, a kind of incomprehensible sentence, and you wonder in that sentence, 'Is that meaning hidden?'" asked Stephanopoulos. He used the example of a sentence: "Dave asks a question." What Stephanopoulos did was the equivalent of substitute different names for Dave and found that the peptide often still beat the bacteria.

Harvard evolutionary biologist Marc Hauser said that using grammar rules to decode genetics and medicine is growing more popular. But he said he worries that too many people are calling grammar what is really just simple code, not nearly as complicated as human language. Berwick said the bacteria-fighting grammar rules are equivalent to the extremely basic spelling rule, "i before e except after c." The grammar rules Stephanopoulos developed are about what 2-year-olds learn on their own by listening to adults speak, he said." WHATTTTT?

How to win a Nobel

PLOS this week has a review of the book "how to win a Nobel" by Peter Doherty. Here's a few pearls:
(1) Learn to write clearly and concisely. The problem with much of science is that the scientists hurt their own efforts by being unintelligible.
(2) Be generous and culturally aware. Acknowledge the achievements of others. Every young scientist needs frequent reminders that it is important to have as few enemies as possible.
(3) Time is precious. Women in particular are vulnerable to “death by committees,” and their representation is sorely needed.
(4) Avoid prestigious administrative roles. This is a major source of destruction, particularly to those from clinical backgrounds. Now a sometimes beleaguered vice chancellor, I can only underscore the importance of this point.
(5) Live a long time. It may take 50 years for the Nobel recognition of a discovery!
Also I warmly recommend Santiago Ramon y Cajal's classic from 1898, Advice to a Young Investigator.

Carl Sagan Center of Astrobiology

For those of us hoping that there will be a spot for a biologist on a future Mars mission, rejoice. While NASA is cutting funds in astrobiology, SETI picking up the slack: " [today] a distinguished panel of institute trustees and staff will announce the formation of the Carl Sagan Center for the Study of Life in the Universe. The center's activities will focus on astrobiology and be dedicated to the memory of planetary scientist and astronomer Carl Sagan." Hopefully this will help restore some credibility to the whole enterprize, that some people dismiss as more faith than science.

Shrimp Running on a Treadmill

science definately needs more videos : run my pretty apetizer run... "A shrimp encountering a bacterial infection has mechanisms to fight this infection, but, like humans fighting an infection, the shrimp may not be as physically fit. In response to the movement of the belt of a treadmill submerged in water, shrimp will walk at slow treadmill speeds and swim at higher speeds. We have used this treadmill system to stimulate shrimp to high levels of activity after they have been injected with a dose of a common shrimp bacterial pathogen, Vibrio campbellii. "

MC Hawking Drops His Music Video Debut

Wow, this is the greatest animated video I've ever seen. MC Hawking, the undisputed king of theoretical gansta astrophysics, just put out his first video for the hit track "What We Need More of Is Science". A must-watch! Also awesome is the trailer for the album, "A Brief History of Rhyme".

From the smallest to the largest genome project

Clocking at a little under 160Kb, the carsonella rudii genome encodes 182 protein. Talk about streamlined. In fact this insect symbiont may be on the way to becoming an organelle. Still this is not as interresting as a free living organism in our quest to find the "minimum genome". Craig Venter (of the human genome fame) is interrested in finding this minimal genome to develop the new field of synthetic biology... "The Synthetic Biology Group is also interested in understanding and thus engineering new pathways ... Most genomes contain hundreds to thousand of genes necessary for adaptive living in complex environments. By synthesizing minimal genomes the team believes it is possible to construct simple cellular life with desirable synthetic properties... the team is dedicated to developing only synthetic organisms that completely lack the ability to survive outside the lab." Craig also recently announced the 10M$ X-prize genomics challenge (the same prize that was awarded for sub-orbital flights last year), to map 100 human genomes in 10 days. All you need is a few thousand summer students and lots of gels.

Organelle-sized fossils?

As we sipped bubble-tea the other night we were discussing how incredible it was to find a 550M years old single cell fossil. When we think about fossils we usually picture bones, which over time are permineralized, meaning the organic matter is replaced by minerals. Recently there has been accounts of soft body fossilization of the bone marrow. But that's still a long ways from intracellular fossilization. Even bacterial fossils are not single-cell fossils, they are usually remnant colony structures such as stomatolites of cyanobacteria or ferromagnetite deposits from magnetobacteria, or evidence of bacterial decomposition or "tunnels" (endoliths) left behind. So how can somthing like a flowing lipid-based membrane of a cell mineralize? Well it turns out the process is called diagenetic phophatization "Early diagenetic phosphatization of the remains probably occurs following shallow burial and in proximity to decomposing phosphate-rich macroaggregates. Depending on phosphate availability, the resulting phosphate layers are deposited on the outside, inside, or enveloping the acritarch organic walls from both sides...under local conditions where pH and activities of P and HCO₃- turn phosphatization on and off"

Cellular Randomness

I vaguely recall a discussion with Bayman about cells being different due to just random fluxuations. A paper in PLOS addresses just that with analysis of mRNA and protein abundance in individual clonal cells. It looks like there indeed is alot of randomness especially when it comes to mRNA abundance (figure suggesting chromatin structure effects above) but it seems (on first glance of the paper) that lots of this effect is buffered and protein abundance is less random. I wonder how OPEN PLoS is and if posting the figure like this is OK?
Summary in Nature Methods (need subscription).

lan-egeddon

The gamer nature of the average bayblab reader should welcome one of their own into the fold.

Pure Pwnage is a made-for-internet TV series about a pr0 gamer named Jeremy whose sole drive is to pwn n00bs.

This is another example of how anyone cna acheive stardom on the internet. Episode 12 is about to be released, you can download it on the site or see it's silverscreen premier in Toronto.

Highlights:
-Doug's (Jeremy's friend) comment about RL (real life): "It's basically like FPS but better graphics"
-Jeremy - You can train a n00b, but he'll just be a trained n00b...

Bayblab podcast episode 1

You can download or stream the first episode of bayblab podcast here until i setup a proper rss feed for you ipod lovers...

Distractions

Thought the other members of the bayblab would appreciate this.
Found on Boingboing.

Bayblab #1 at predicting the IgNobels

We have a surge of traffic to the bayblab website today thanks to our successfull prediction of "Termination of Intractable Hiccups with Digital Rectal Massage" as a IgNobel 2006 laureate in medecine. We are currently the #6 hit on google for those particular search terms. It never felt so good to be experts in the science of assology. This is a testament to the superiority of bayblab to sites like thompson scientific. Our team of experts recognised back in June the potential of this reaserch based on the limited scope of this new field of assology and the lack of any references and citation to the work. Other winners include :
Maths: How many photos must be taken to almost ensure no-one in a group shot has their eyes closed, by Nic Svenson and Piers Barnes
Ornithology: Why woodpeckers do not get headaches, by Ivan Schwab and the late Philip RA May
Nutrition: Why dung beetles are fussy eaters, by Wasmia al-Houty and Faten al-Mussalam
Acoustics: Why the sound of fingernails scraping on blackboards is so annoying, by D Lynn Halpern, Randolph Blake and James Hillenbrand

Methuselah

Some info on the 'Methuselah' tree. Apparently it's the longest living thing alive. However I was wrong when I stated earlier that it is a species. Methuselah is the name of a specific bristlecone pine tree that is 4725 years old. There is also a somewhat interesting NOVA doco on Methuselah. Someone needs to update the wikipedia entry on Methuselah, because the biblical Methuselah doesn't hold a candle to this tree, he lived and died during the course of this trees life.
Lo-res pic included.

Taking the best friend thing to a whole new level...dogs will cure cancer

The case is made for dogs as a realistic cancer model for drug development in this month's Nature Biotechnology. The arguments are quite compelling, and given the clinical trial bottleneck currently limiting the development of new therapies, I wouldn't be surprised if the cure for cancer is discovered in someone's pet dog sometime soon.

Computational design of receptor and sensor proteins with novel functions

As cited on the bayblab podcast, a computational based method for engineering receptors that bind a pre-determined ligand of choice.

Synthetic Biology

A number of high-profile researchers and institutions across the US are jumping on to a movement they're calling synthetic biology. The problems are old (biofuel production, cancer therapy, small molecule production, etc.), but the philosophy is new. The aim is to develop a bottom-up approach to assembling, from simple and standardized parts, living organisms that perform defined tasks. Check out the latest in the field - most of the talks from the synthetic biology 2.0 conference are available as online webcasts.

Nobel Rejections

I came across a paper summarizing some of the hostilities and/or manuscript rejections associated with discoveries that were eventually awarded a Nobel prize. Obviously, innovative science is often not appreciated immediately. Here's a few notable examples:

• Hans Krebs, manuscipt on the citric acid cycle. Rejected by Nature. Published in Enzymologia
  
• Kary Mullis, manusciprt on the polymerase chain reaction. Rejected by Nature, Science. Published in Methods in Enzymology
• Hartmut Michel, manuscript on the determination of the three dimensional structure of a photosynthetic reaction center. Rejected by Nature.
• Pavel Cherenkov, manuscript on "Visible radiation produced by electrons moving in a medium with velocities exceeding that of the light". Rejected by Nature.
  
• Burnet could not find any journal to publish his work on the production of antibodies. The work appeared instead in an unrefereed monograph.
  

Nobel prize to Digg users

Of course you've all read about the nobel in med to RNAi. Probably it is deserved? Seems just a bit premature as the mechanism/function is not nailed down. However the discovery certainly is profound.
You've probably read about it on nature news or some other science source. You know that slashdot sucks when almost ALL the comments on this post were non scientific. I think this made me finally appreciate the clear superiority of digg.com. Digg actually has good user comments.
Of course Slashdot and Digg pale in comparison to bayblabs authority.

Home Science Crafts Project

From the "OMG I can't believe someone did that, barfffff" department: A lazy sunday afternoon crafts project for your kids that involves mouse taxidermy. Or do-it-yourself hemroidal surgery on your pet turtle! Warning, you may be scarred for life.