Hot tub rash

After the pinkeye outbreak of 2007 the lab now has a hot tub rash outbreak. The Pseudomonas folliculitis happens when the pseudomona bacteria infects hair follicles, and it usually resolves itself within 2 weeks. For some reason it seems to have only affected some individuals and not others. All of them were female. Any idea why?

At least no-one had a prostate infection, unlike this poor sap:
"A previously healthy 38-year-old white male presented to the emergency room with a 10-hour history of fevers, chills, and significant suprapubic pain. He also complained of dysuria and feelings of incomplete emptying after voiding. He denied any history of sexually transmitted diseases, recent urinary tract infections, or genitourinary trauma. He did mention having sexual relations with his wife three times the previous week in a newly purchased hot tub. His wife was asymptomatic."

"P. aeruginosa can survive in a variety of moist environments due to its minimal nutritional requirements and growth temperature range (4 to 42°C) (1). Although inhibited by chlorine levels in water of 2 to 3 ppm, P. aeruginosa can multiply to densities of 10⁴ to 10⁶ organisms/ml when levels drop to <1>4). These characteristics allow it to multiply in hot tubs, where chlorine levels are rapidly dissipated by the warm temperatures (39 to 40°C) and aeration (4). Hot tub use has been linked to P. aeruginosa folliculitis and more-serious infections, including pneumonia and those involving the urinary tract (cystitis, prostatitis, and urosepsis) (2, 3, 5-7)."

Rapamycin update

Since some of us in the bay are interested in the translational inhibition activity of rapamycin I thought I would point out an excellent piece at not exactly rocket science reflecting on some new data on rapamycin's effects on aging in mice. Very interesting. The original article at Nature. There are also some great links in the article.

Cancer Carnival #23

Welcome to the 23rd edition of the Cancer Research Blog Carnival! Most of our readers are probably either recovering from Canada Day or gearing up for Independence Day, but there's always time for some science in between.

Kicking things off this month, we have PalMD following up on his Cancer 101 posts (some of which were featured previously in the Cancer Carnival) with Cancer 202 - Radiation Therapy. In it he briefly discusses the basics of radiation treatment including its effects on normal tissue and how to target a tumour.

Radiation is a powerful tool in medicine, but like any tool, whether it be a knife or a pill, it must be wielded properly and ethically. The best medicine combines good science, compassion, and ethical behavior to help people. Radiation therapy is one of medicine's most sophisticated techniques, and must be used only by certain experts. It's also really cool.

PalMD does a great job of explaining the basics in an easy to understand way. If you missed any of the other posts in this series, check them out here.

Next up, MolBio Research Highlights sends us some blogging on peer reviewed research. The topic? Cancer Stem Cells. Francisco Barriga is inspired by three recent papers and tries to make sense of it all with a nice review of current thinking and controversy.

[D]uring the last years there has been a lot of controversy regarding the existence, function and clinical implications of cancer stem cells. This confusion stems (no pun intended) from the lack of clarity in the field nowadays, arising mainly from misconceptions regarding the origin and function of these cells. On top of all of this is the confusion derived from media-hype and some not-so knowledgeable scientific journalists.

Francisco clears up some of this confusion with a summary of the cancer stem cell hypothesis and discussion of unresolved issues in the field.

Cancer stem cells are always a hot topic, and Alexey at Hematopoiesis discusses some ways that existing drugs can affect CSC populations.

Recently, anti-cancer activity of some well known drugs was discovered, which was shown to rely on targeting of cancer stem cells (CSC). Explanations for some very effective anti-leukemic drug combination were recently found in the laboratories. I’ll give you some examples of “from-bed-to-the-bench” translation coming from leukemia clinic.

Three drugs, and their possible uses, are examined.

Over at Scienceblogs, there has been some discussion about NIH funding strategies, and whether they're too conservative. Mike the Mad Biologist draws our attention to a New York Times article that laments the lack of progress in cancer cures and wonders if more money should be put into high-risk, high-reward projects. Orac comments on the same article, asking "Are we playing it too safe in cancer research?" and the Mad Biologist continues his analysis of the culture of caution at the NIH.

Finally, there were celebrity deaths in the news last week with one, Farrah Fawcett, losing her battle with cancer at the age of 62. While it was overshadowed by other events, she did get some attention with some raising awareness about anal cancer, some retrospective and discussions with her oncologist.

That's it for this month. Next month is our the Cancer Research Blog Carnival's 2nd anniversary, so start writing those cancer posts, and submit them here. We always need hosts as well, so if you're sick of seeing the carnival here on the Bayblab, email us to sign up for a future carnival. For older editions, visit the Carnival Homepage.

And don't forget, the Cancer Research Blog Carnival now has subscription options; you can follow by email or RSS feed. An aggregated feed of credible, rotating health and medicine blog carnivals is also available.

Preeclampsia and oral sex

So I'm teaching cardiovascular anatomy and physiology right now, which is funny because Rob is teaching the drugs for that system in pharmacology at the same time. I was reading up on preeclampsia, which is a type of hypertension that can develop during pregnancy, looking for hypotheses for causes. I'm doubly interested because I've recently stumbled upon a potential regulatory protein which could be associated with the disease. To make a long story short there is definitely a strong immune involvement, and a problem in the placental interface although the details are surprisingly not well fleshed out (to an outsider anyways). I was also somewhat amused to find out that there is a putative protective role of oral sex and swallowing of seminal fluids for preeclampsia. The idea being that HLA and HLA-derived peptides may tolerize the mother to the foreign antigens of the fetus in the same way that we tolerize other food-related antigens passing through the gut. While this paper certainly isn't definitive, a correlation at best, the treatment has few side effects, so might as well err on the safe side:

"we investigated whether sHLA antigens are present in seminal plasma. Using a specific ELISA we detected sHLA class I molecules in seminal plasma. The level varied between individuals and was related to the level in plasma. Further studies showed that these sHLA class I molecules included classical HLA class I alleles, such as sHLA-A2, -B7, -B51, -B35 and sHLA-A9. Preliminary data show lower levels of sHLA in seminal plasma in the preeclampsia group, although not significantly different from the control group."

Geothermal energy induced earthquakes

A really quick movie about a new geothermal energy project that raises concerns that it may trigger large earthquakes is available at the new york times.
I found a couple of interesting points in the video. I did not realize that there was any large geothermal projects in North America, but the largest group of plants is in California. Also I was extremely skeptical that drilling into the ground could possibly do anything that would cause an earthquake. An existing geothermal project however already does.
I would have liked to have heard more from the company about why the new project will not cause earthquakes.

Which language has the most words?

I heard an interesting factoid at lunch yesterday. There are apparently one million words in the English language which supposedly puts it far ahead of any other language. This came as a surprise to me, while I've grown to enjoy English for its precision, this would mean it contains over ten times the amount of words of the french language (80k). It is no surprise to me however that French is stagnating, simply because the language is regulated by committee, and we all know how efficient those are. And so when we need a new word say to convey the meaning of "email", a group of people in France have to get together and pick one (courriel). Hardly a natural and vibrant process. But does the English language truly have a million words? Wolfram alpha will quickly tell you that the Oxford dictionary has 600k words, putting it ahead of say Spanish with a mere 225k. English is growing very quickly because it incorporates other languages readily, perhaps because most English speakers are not native. In fact China has the largest population of anglophones in the world. The original claim that there are 1 million words comes from the university of Texas which has an algorithm caching and crawling social networking sites all along identifying any expression used over 25 000 times as a word. Of course many people have problems with this, since it is not an accepted definition of a word. It incorporates any deformation or misspelling of common words, commercial trademarks, onomatopoeia which would include for example: "what", "wat", "waht", "wh4t", "whaaaaat", "whassssssssssssup" etc ... Many people have critisized the methodology itself, since the "Global Language Monitor" claimed the millionth word in 2006, 2007, 2008 and 2009.
So does this mean English really has the most words: not likely. Agglutinative languages such as Finnish most certainly have more words and more readily create new words to adapt to changing time by fusing existing words creating an almost infinite number of combination. Yet English remains dominant perhaps not in the number of words, but in the reach and power of the language.

Ununbium - a "new" element

Some may have noticed a little article on the right of the front page of the Ottawa Citizen... "Hey, science fans, there’s a new element in town". In it, Tom Spears implies that the discovery of element number 112, known as Ununbium, is a novel thing.

Here's the problem. As an avid science fan, and chemist, my first reaction was "wasn't 112 there last time I looked at the periodic table?". And, sure enough, all the PTs in the lab (none of which were printed in the last 12 hours) all indicate element 112 there, smiling at me below mercury and just raising the question about what prompted the article... and its front page position.

So, here's the wikipedia scoop. Ununbium was first discovered in 1996, in Darmstadt, Germany. Like most of it's heavy brothers, 112 is synthesised by smashing things together, in this case, its lead and zinc. So what is new? Well, the IUPAC overseers of these things have re-confirmed that the discovery was real, and have credited those German discoverers with the first atom of Ununbium... meaning they can now name it.

So, is this a case of a journalist getting it all wrong in science? Am I being too pedantic by getting annoyed at how it's taken 12 years for this discovery to be reported by the Ottawa Citizen... and even then that they haven't really told the story.

What are some of the worst examples of science reporting that you can think of?

Hypercolor T-shirts

I'm not really sure what our reader demographics are like here at the Bayblab, but I'm sure some of you remember Hypercolor T-shirts - the shirts that changed colour with heat. If you ever wondered how that worked, Wikipedia comes to the rescue:

The color change of Hypercolor shirts is based on combination of two colors: the color of the dyed fabric, which remained constant, and the color of the thermochromic dye. The dye is enclosed in microcapsules, tiny (few micrometers in diameter) drops of liquid sealed in a transparent shell, bound to the fibers of the fabric. The liquid is a leuco form of a dye (in this case crystal violet lactone), a weak acid (1,2,3-benzotriazole), and a quaternary ammonium salt of a fatty acid (myristylammonium oleate) dissolved in a solvent (1-dodecanol). At low temperatures, the weak acid forms a colored complex with the leuco dye, interrupting the lactone ring. At high temperatures, above 24-27 °C, the solvent melts and the salt dissociates, reversibly reacts with the weak acid and increases the pH. The pH change leads to closing of the lactone ring of the dye, which then regains its colorless (leuco) form.

Low temperatures allow a weak acid to react with the dye, converting it to its coloured form.

Whatever happened to those shirts anyhow? That they were easily ruined by washing them at higher than recommended temperatures didn't help, but I'm sure it had more to do with people not needing any more attention drawn to overactive armpits.

Cancer Carnival #22

Welcome to the June edition of the Cancer Research Blog Carnival - your monthly stop for cancer-related news and breakthroughs. I've been a bad keeper this month, both in soliciting hosts/posts and in timely delivery, so let's jump right in to the good stuff.

Omics! Omics!
Dr. Keith Robison ponders tumor supressors as he moves back into the cancer field, likening cancer researchers to the seven blind men who hasn't yet figured out the elephant in front of them

A great mystery for many such genes is why the tissue specificity of the tumor syndrome? In each of the genes mentioned above, the tumor syndrome appears to be very specific to a tissue type, yet in each of these cases the genes involved have been shown to be parts of cellular machinery used by every cell. Why does a failure of a general part manifest itself so specifically?

The Spittoon
Erin Cline Davis sends us a couple of links from the 23andMe blog's SNPwatch feature.

SNPwatch gives you the latest news about research linking various traits and conditions to individual genetic variations. These studies are exciting because they offer a glimpse into how genetics may affect our bodies and health; but in most cases, more work is needed before this research can provide information of value to individuals.

The first discusses new SNPs associated with testicular cancer, including one that may explain why the disease is more common among caucasians. The second involves a recent study that identifies genetic differences between benign and malignant neuroblastoma, including several SNPs in the BARD1 gene, also mentioned in Dr. Robison's post, above. 23andMe customers can browse their own data for these SNPs, which of course doesn't substitute for professional advice.

Bayblab
Here at the Bayblab, Bayman talks about new systems biology approaches to predicting anti-tumor activity of immune cells.

They fed the info into some sort of machine learning algorithim, which came up with some pretty clear-cut boolean style predictive rules that a mere organic being (aka tumor immunologist) could never have possibly concieved of with a million years of deductive reasoning and experimental testing.

As Bayman puts it: "It's Big Blue beats Kasparov all over again!"

Respectful Insolence
Orac at Respectful Insolence has a post up, Cancer research explained briefly, that explains why we'll never have "a cure for cancer". It's a simple explanation, and one that's important to be aware of. While there, be sure to click through to see the full comic in the post.

Framing Science
Have you ever wondered how accurate some of the information on medical dramas is? What about using a show like House to teach medical ethics? Matt Nisbet writes about misleading medical programs and the balance between raising issue awareness and getting medical facts right, citing the recent cancer-related Gray's Anatomy finale as an example.

"Many people view the cancer problem as much simpler than it actually is," Brawley says. "That's because they get their medical information from television shows. But television shows are by and large fictional, and much of the medical information there is also going to be fictional."

Hematopoiesis
Finally, our friend Alex at Hematopoiesis has written about stem cell derived cancer killing NK cells.

Dan Kaufman’s lab from University of Minnesota demonstrate for the first time efficient cancer killing activity in vivo, mediated by immune cells derived from hESC. They generated natural killer (NK) cells using previously published protocol and investigated their anti-cancer activity on the range of tumors in vitro and in mouse leukemia model.

He goes on to the results and the advantages of such an approach. For a Hematopoiesis bonus, check out this post about the cancer stem cell hypothesis complexity/controversy and how it's changed over the years.

That's it for this installment of the Cancer Research Blog Carnival. We always need hosts and posts so email the Bayblab to sign up, and get your posts in here. Visit the Carnival Homepage for previous editions.

And don't forget, the Cancer Research Blog Carnival now has subscription options; you can follow by email or RSS feed. An aggregated feed of credible, rotating health and medicine blog carnivals is also available.

Burger H&E

I imagine it played out like this:

An internist, a surgeon and a pathologist walk into a fast food joint and each order a burger. The internist says, "I wonder if there is any meat in there", the surgeon takes a bite, turns the pathologist and says: "can you tell me if there was meat in there tomorow?"...

So I guess after a bunch of H&E later and a manuscript sent to the annals of diagnostic pathology, we find out that the meat content on average barely breaks 15%. On the other hand you'll find connective tissues, blood vessels, bone, plant and intracellular parasites and lots of water. Thankfully, no neurons...

So the moral of the story is never bring a pathologist to a fast food joint if you want to be able to enjoy your burger.

Cow's milk allergy & recombinant proteins

A quick post about stuff I don't understand:
A friend of mine has an infant that is allergic to cow's milk. This is common and, who cares, since the infant is being breast fed. EXCEPT for the fact that the infant is allergic to the dairy products that the mother is consuming. This is somewhat uncommon but certainly not unheard of. My interpretation of this is that a protein antigen not only passes relatively intact from the GI tract of the mother into her blood, but is then incorporated into her breast milk without being completely broken down to amino acids and/or incorporated into human milk proteins. I always thought that proteins were almost completely broken down into, at most, a few amino acids long before absorption. The previous link suggests that relatively intact dietary protein is present in our blood.
Does this lend credibility to those who fear the biological activity from ingested proteins that are introduced into our food artificially as in the case of bovine growth hormone in cow's milk or Bt toxin in GE crops?
Anybody with some helpful information?

Wolfram|Alpha

A new search engine has recently gone online, though Wolfram|Alpha seems more a competitor to Wikipedia than to Google. The idea is to serve as a data search and computational engine.

Wolfram|Alpha's long-term goal is to make all systematic knowledge immediately computable and accessible to everyone. We aim to collect and curate all objective data; implement every known model, method, and algorithm; and make it possible to compute whatever can be computed about anything. Our goal is to build on the achievements of science and other systematizations of knowledge to provide a single source that can be relied on by everyone for definitive answers to factual queries.

It can solve equations for you, tell you notable events for a given date, or give you the current sky position of Pioneer 11. Try typing in your favourite gene, or even your first name. It's a cool little resource. I had fun playing around with inputs to see what it could do.

Extreme Mammals at AMNH

I was in New York City (and environs) this past weekend, and was fortunate enough to get an invite to a blogger preview of a new exhibit at the American Museum of Natural History. Unfortunately, my camera battery crapped out on me in the early going but luckily the press kit included in the blogger gift bag had some photos to share, so you won't have to suffer pics taken on a camera phone.

Extreme size: Indricotherium, the largest land mammal known, greets you at the exhibit's entrance

The exhibit is Extreme Mammals and is put on in collaboration with the California Academy of Sciences, San Francisco; Cleveland Museum of Natural History; and our own Canadian Museum of Nature here in Ottawa.

As you might guess, mammals were the order of the day, from the largest to the smallest and everything in between. And in between was key - the exhibit features fossils and models of some cool transitional forms as well as those of our stranger cousins such as the extinct Macrauchenia or the familiar platypus.

Macrauchenia is straight out of a Star Wars or fantasy movie

Among the fossils, taxidermy samples and models were the stars of the show: a colony of sugar gliders. Though they were napping while we were there (extreme laziness?), the sole live animal display definitely drew a crowd, particularly among the younger attendees. There were also a few simple interactive displays.

Ambulocetus, or "walking whale" is one of the transitional forms on display

The exhibit is unapologetic about evolution, which features heavily in both the displays and the educator guide as they discuss common ancestry, evolutionary trees and adaptation among other things including the requisite 'fun facts' and trivia. Did you know that a new species of striped rabbit was first discovered for sale in an Asian food market? (extreme deliciousness?)

Overall, Extreme Mammals is a cool exhibit, worth checking out if you're in the NYC area where it will be on display at the American Museum of Natural History until January of next year. After that, it will be on tour and if you're patient it's scheduled to arrive in Ottawa June 4 to November 6, 2011.

Local content: Puijila darwini, an early fin-footed mammal, was discovered in 2007 by a researcher from the Canadian Museum of Nature, Ottawa

Thanks to Brian from Laelaps who put me in touch with the museum for the blogger preview.

Images © AMNH

Rent-A-Bay?

Was looking at this article on the booming market for renting virtual office space for small business.

"I wanted to launch my company, but the cost of having a professional location was simply too high," says Mr. Gerochi. "This gave me the push to do it. I pay $300 a month and I can appear big-time to major clients.

"I use their reception staff -- they take all my calls -- office space, mailing service. The building address is advantageous. It's more professional than a home address and filters out unwanted solicitation. I can rent a cubicle for $15 an hour or a window office on the 57th floor at First Canadian Place in Toronto for $25 an hour instead of sitting in the food court with my laptop." He also uses the boardroom ($70/hour) to network with industry leaders."

Great way for entrepreneurs to overcome crippling infrastructure and basic staffing costs. It occurs to me that even higher infrastructure and start-up equipment costs pose a similar huge obstacle to the would-be biotech entrepreneur. Research space is like office space, except way more high-tech and costly. Rental lab space sounds like a great solution. Does your institute have any empty lab bays or equipment sitting unused? Let's see that shit up on Craigslist. Starving PhDs with great ideas are ready to put it to good use. You could even sell off those unused technical support staff people-hours. Like lunch.

Oh, cool. Apprently you can already do something like this. Like here. Not to be confused with here.

Kids! Sue your parents for defective genes!

This story is a bit old, and a bit odd. A 13-year-old girl born with Fragile X syndrome is suing a sperm bank after genetic tests showed the genetic condition was carried on the father's X chromosome. (Weirdness about a girl inheriting an X-linked condition from her father, and a Fragile X male as a sperm donor explained here. The short version is that it's a spectrum, repeat-expansion disease whose severity varies from generation to generation so a mildly affected father could have a more severely affected daughter, though it's rare)

The legal premise is based on product liability law that is usually applied to manufacturer defects such as faulty car brakes

Donovan does not have to show that Idant was negligent, only that the sperm it provided was unsafe and caused injury. "It doesn't matter how much care was taken," says Daniel Thistle, the lawyer representing Donovan, based in Philadelphia, Pennsylvania. Genetic tests have revealed that she inherited the disorder from her biological father.

The idea of sperm as a commodity subject to product liability laws raises some interesting questions. In this age of personal genomes and genetic testing, how much responsibility does a sperm bank have to screen for genetic disorders with every available test? If a child inherits Fragile X the old-fashioned way, could they sue their parents?

Should genetic disease even be considered 'injury' for the purposes of legal liability? This is quite different from suing a car manufacturer after suffering an injury caused by defective brakes. No defective brakes and you make it to your destination without a crash and a broken leg. No 'defective' sperm and you don't exist at all.

Either way, as more and more genetic tests come into existence and screening becomes more available there will be interesting legal issues to navigate. I should have gone to law school!

Systems Tumor Immunology: It's Big Blue Beats Kasparov All Over Again

One innovative approach to cancer therapy involves isolating immune cells (tumor-infiltrating lymphocytes or TILs) from a tumor, and then trying to expand and activate them against tumor antigens in the lab. It can work, but in practice, not an efficient practice. TILs are a mixed bag of cells with all sorts of different personalities, some of which may or may or not be interested in attacking tumor cells. Some, recruited by the ever-devious tumor cells, can even work to supress the activity of the good guys. So sometimes you get a bunch of TILs that work, sometimes not.

A new paper describes a systems biology approach to tackling the complexity of TIL populations with the aim of predicting anti-tumor activity. They profiled the reactivity of a ton of TIL populations, and correlated this inforamtion with a battery of surface markers. They fed the info into some sort of machine learning algorithim, which came up with some pretty clear-cut boolean style predictive rules that a mere organic being (aka tumor immunologist) could never have possibly concieved of with a million years of deductive reasoning and experimental testing.

Check it out:
Rule 1) If the CD8⁺CD28^-CD152^- subpopulation constitutes less than 43% of the entire TIL population AND the CD94+constitutes less than 0.4% of the entire TIL population, then the TIL population is tumor-reactive.

Also, by manipulating the relative proportions of different TIL subpopulations, they could affect reactivity as predicted by their adding machine.

Wicked. Who knew an abacus could do immunology?

See: Predicting and controlling the reactivity of immune cell populations against cancer

Nature Editors Still Concerned About Swine Flu

To their credit, they lay down some numbers. Most compelling, on the surface, is the following statement:

"There is ample reason for concern: a new flu virus has emerged to which humans have no immunity, and it is spreading from person to person. That has happened only three times in the past century."

That sounds kinda scary. Is it accurate? Would we have recognized the current H1N1 epidemic in its current form 100 years ago? Pinpointing flu strains down to the molecular level in thousands of patients worldwide, and integrated monitoring on the internet in real-time? It doesn't really seem reasonable to conclude there have only been three epidemics of this sort in the past century. Is our picture of the current, largely non-lethal flu epidemic not based entirely on technological revolutions of the past several years? How many swine or bird flu "pandemics" have gone totally unrecognized because of technological limitations? I guess we'll never know. Just like we have no idea when or if the swine flu will turn into some sort of apocalypse as most of the mainstream media would have had you believe a couple weeks ago. Of course there's always a chance. Like getting struck by lighting. Does anyone have the balls to put some numbers on this shit? I certainly don't.

I'd be surprised if our ability to predict the time of occurrence of a deadly flu pandemic has changed appreciably since 1909. How about we all agree that vigilant monitoring (as we are clearly already seeing) and balanced communication with the public (as we are often lacking) are important and leave the predictions, doomsday or otherwise, to Nostradamus?

See: Between A Virus and Hard Place

exhaustion hunt

I've read before about how the human body is supposedly evolved for running and that the earliest form of hunting may have been running after the prey until it collapsed of exhaustion. I always found that hard to believe. Why invest so much energy into a big brain when your survival depends on your ability to sweat and your endurance. But this video is simply amazing. I never imagined humans could be so much physically superior to other large mammals. Bonus points for David Attenborough narration.

Swine Flu Quote of the Week

"In the United States, Illinois had the most confirmed cases on Wednesday, with 122, surpassing New York with 97. Dr. Besser said that might be because Illinois was testing more. He said that Mayor Michael R. Bloomberg, on a visit to the C.D.C. earlier, had been asked by a reporter why New York had been surpassed, and had answered:

“You want 200 more cases? We’ll test 200 more people.”

More swine flu retrospective:
Global Flu Cases Top the 2,000 Mark

On "The Australasian Journal of Bone and Joint Medicine" (aka "The Merck Journal of Advertising Propaganda and other Bullshit"

This is really pathetic. TheScientist reports (Merck published fake journal):

"Merck paid an undisclosed sum to Elsevier to produce several volumes of a publication that had the look of a peer-reviewed medical journal, but contained only reprinted or summarized articles--most of which presented data favorable to Merck products--that appeared to act solely as marketing tools with no disclosure of company sponsorship."

Elsevier has pulled the journal from its roster, but you can bet there are many more so-called peer-reviewed biomedical journals out there that fit this bill. The only reason we're hearing about this one is that Vioxx gave some Australian guy a heart attack and he's suing.