Sunday, February 28, 2010

Prion evolution

One of the big unanswered questions in biology is what is life? Some philosophers of science have pointed out that a science (biology) where the topic of study (life) cannot be defined is unacceptable. Drawing the boundary between life and non-life is hard because of a number of discoveries that appear to exist in the gray area - from viruses, to viroids, to satellites, to prions.

Prions are just proteins and do not show metabolism or contain any nucleic acid or genetic code but they have recently been shown to undergo Darwinian selection in the same way as living organisms. Check out the Science paper from last month, Darwinian Evolution of Prions in Cell Culture, or the BBC report on the research, 'Lifeless' prion proteins are 'capable of evolution'.

"Now we know that the abnormal prions replicate, and create variants, perhaps at a low level initially.

"But once they are transferred to a new host, natural selection will eventually choose the more virulent and aggressive variants."

Saturday, February 27, 2010

Rare Disease Day

Over in India it's National Science Day on Sunday and if you are Jewish then it's Purim. The last day of February is also Rare Disease Day.

Whilst we have had a slight explosion of 'days' 'weeks' and months' of celebration or awareness lately (February also sees National Weatherman's Day, Ferris Wheel Day and Plumb Pudding Day) Rare Disease Day sounds like a good idea. There is a lot of interesting information at the website and more at the sponsoring organization NORD - the National Organization for Rare Disorders.

Why is Rare Disease Day important?

Rare Disease Day is the perfect occasion to inform or remind people that rare diseases need to be paid special attention to, because:

  • Rare diseases are life-threatening or chronically debilitating diseases with a low prevalence and a high level of complexity. Patients with very rare diseases and their families are particularly isolated and vulnerable. The life expectancy of rare disease patients is significantly reduced and many have disabilities that become a source of discrimination and reduce or destroy educational, professional or social opportunities.
  • The rare disease patient is the orphan of health systems, often without diagnosis, without treatment, without research, therefore without reason to hope.
  • The lack of specific health policies and the scarcity of expertise translate into delayed appropriate diagnosis and difficulty of access to care. The national healthcare services for diagnosis, treatment and care of rare disease patients differ significantly in terms of their availability and quality. European citizens have unequal access to healthcare services and to orphan drugs.
  • Research on rare diseases is scarce

Plants have pathogens too

Not a wildlife disease, but just as scary. Stem rust, a fungal disease that effects wheat, caused many a famine before scientists bred resistant wheat, leading to a revolution in agriculture. Now, a new strain of stem rust, Ug99, is threatening a crop that provides a third of the worlds calories.

Its Going to Happen...

...In roughly 30 years when the prions are no longer laying dormant.

Friday, February 26, 2010

Veggie Libel Laws


A technician from Ethiopia's National Veterinary Institute vaccinates cattle against rinderpest (1987).

Scientific American had an article at the end of last year about the elimination of Rinderpest - Cattle plague: An extinction worth celebrating

In the 1980s, billions of dollars worth of livestock were lost in several major outbreaks in South Asia, the Middle East and Africa.

Flash forward to 1994, when the FAO formed the Global Rinderpest Eradication Program (GREP). Working with government agencies and organizations around the world, GREP charted the geographic distribution of rinderpest, worked to understand the disease better, and took local action to fight it.

Local actions included training veterinarians and farmers to recognize and report the rinderpest, establishing emergency response plans, setting biosecurity protocols, and working with countries to create programs for monitoring and controlling the disease.

The efforts paid off. In the past 15 years, 170 countries and territories have been certified as rinderpest-free by the World Organization for Animal Health, the international certification body for animal diseases. The last major outbreak was in Kenya in 2001, and the disease's final stronghold was in a small, overlapping area of Somalia, Ethiopia and Kenya that the FAO now says appears to have been cleared.

It now looks like rinderpest has been essentially eliminated but formal declaration of victory is on hold whilst surveillance continues to ensure it is really extinct. An international statement about Global Rinderpest Freedom is expected to be made within the year 2010. This would be the second time that a disease has been eradicated worldwide after smallpox in humans. FAO have a Status report on progress made to date in eradication of rinderpest: highlighting success story and action required till global declaration in 2010 (links to pdf document). I think this document illustrates the difficulty of working on a global scale.

Correlation and Causation

from xkcd.

How Serious is the Threat of Mad Cow Disease?

The link above is for a video in which:

"Three UC Davis agricultural experts debate the seriousness of mad cow disease in a discussion sponsored by the Institute of Governmental Affairs. The speakers include Dean Cliver, a national expert on mad cow disease and a professor of veterinary medicine, Food and Safety; Daniel Sumner, an agricultural economist who directs the UC Agricultural Issues Center and an expert on the international beef trade and potential effects of embargoes; and José Bervejillo, an agricultural economist at the Agricultural Issues Center with expertise in the policies and economics of cattle diseases and the international beef market."

Thursday, February 25, 2010

Re-invent the Syringe

    So far I've only posted computer-game related material (I wish I could do more, but their arn't that many great disease oriented games), but i thought I should share a video about the spread of HIV in third-world countries.

   While this is a great idea, I think it will be difficult to prevewnt existing syringes from being reused. Once the substitution begins, reusable syringes will be more prized and used more often to get their moneys worth. It'll take time for this substitute to be used because while it is the same price, it's still more expensive because it cannot be reused. I love this idea of non-reusable syringes, and think that it's great because even factories that make syringes would endorse the product because it forces hospitals to buy more syringes (bad for hospitals though). But the medical factories (is that what they are?) would have to sell or convert existing syringes, but a demand for reusable syringes would lead to demand-fueled inflation.
I hope this works out for the best.

Autism Debate continued

An article in Time magazine about Jenny McCarthy, former Playboy model turned anti-vaccine crusader.

Fatal Familial Insomnia

Prion diseases are all, fortunately, rare. Unless we throw some cannibalism (actual or hi-tec) into the mix - then they can increase dramatically in prevalence. It seems likely that most, if not all, prion diseases occur as rare genetic mutations. I very briefly mentioned Fatal Familial Insomnia in class. This is an extremely rare prion disease caused by an inherited genetic mutation. The mutation responsible has been found in just 50 families worldwide. Although patients frequently do not show symptoms until middle age or later the subsequent progression into complete sleeplessness is untreatable, and ultimately fatal.

Wednesday, February 24, 2010

Ethical Questions in the Handling of BSE in The US- Olivia Cvitanic

As Professor Latto discussed in class today, the compensation for farmers whose flock of sheep or cattle are killed because they have tested positive for BSE (Scarpie for sheep) or are suspected of being infected is about 50%. Not only is this compensation simply not enough financially, but many farmers who own their own, smaller livestock farms suggest that it’s emotionally difficult too. These farmers claim they share a “special stewardship relationship” with their animals. While that particular argument is not so convincing for me, the lack of compensation for farmers is a real problem. If the government wants to seriously stop the spread of BSE then they must help farmers who have invested all their time in raising these animals only to see them killed at a loss to their pocketbooks. This situation has led many farmers in the U.K. and the U.S. to resort to some questionable ethics in terms of allowing possibly unhealthy cows to be killed for human consumption.

In March 2001, farmers in the United States became particularly agitated over a case in Vermont where many cows and sheep were slaughtered on suspicion of disease, but were not tested first. Farmers claimed this seizure of livestock on the part of the USDA was “an abuse of government power” for which they should be “ashamed of themselves.” The farmers claim that there was “no convincing evidence was ever put forward” that scientifically suggested that these animals were indeed infected. However, the USDA had the authority to and did kill the livestock instead of testing them first. Perhaps simply killing the animals and paying the farmers “compensation” is more effective? Definitely not for the farmers, and I would assume it’s less expensive for the government to slaughter all the suspected animals rather than test them, which is, in my opinion, wrong and most definitely an abuse of power. The article from which I’m citing, entitled “Slaughter on suspicion: Vermont” asks why the government could not simply use the new and highly accurate Prionics tests. Though the tests take 3-4 hours to run, United States farmers argue that France does 20,000 tests a week on its livestock. Why can’t the United States assume similar costs and, more importantly, similar responsibility?

Mmmm...squirrel brains

Sorry to disappoint all you squirrel eaters, but I stumbled across an article in the Lancet that associates consumption of squirrel brains with Creutzfeldt-Jakob disease. They suggest that "caution might be exercised in the ingestion of this arboreal rodent". Can't argue with that.

Creekstone Farms

In politics these days there is a lot of fake outrage. It's a bipartisan game and democrats and republicans are equally guilty. What worries me is that all this fake outrage seems to distract people from cases where they should be outraged

In the Creekstone Farm case even USA Today, not renowned for their radical politics, seem to be a bit shocked. The response from politicians? Deafening silence.

"In a nation dedicated to free market competition," says John Stewart, CEO of Creekstone, which is suing USDA, "a company that wants to do more than is required to ensure the quality of its product and to satisfy customer demand should be allowed to do so."

When regulators disagree with reasoning like that, you know the game is rigged.

Tuesday, February 23, 2010

Stanley Prusiner

If you win a Nobel prize you get not only a nice medal, a posh banquet in Sweden, over a million bucks and the adulation of your peers but you also get to write your own biography for publication. These are actually quite interesting and are all available at the Nobel Foundation website.

Here are some excerpts from Stanley Prusiner's biography.

In July 1972, I began a residency at the University of California San Francisco in the Department of Neurology. Two months later, I admitted a female patient who was exhibiting progressive loss of memory and difficulty performing some routine tasks. I was surprised to learn that she was dying of a "slow virus" infection called Creutzfeldt-Jakob disease (CJD) which evoked no response from the body's defenses. Next, I learned that scientists were unsure if a virus was really the cause of CJD since the causative infectious agent had some unusual properties. The amazing properties of the presumed causative "slow virus" captivated my imagination and I began to think that defining the molecular structure of this elusive agent might be a wonderful research project. The more that I read about CJD and the seemingly related diseases - kuru of the Fore people of New Guinea and scrapie of sheep - the more captivated I became.
I had anticipated that the purified scrapie agent would turn out to be a small virus and was puzzled when the data kept telling me that our preparations contained protein but not nucleic acid. About this time, I was informed by the Howard Hughes Medical Institute (HHMI) that they would not renew their support and by UCSF that I would not be promoted to tenure. When everything seemed to be going wrong, including the conclusions of my research studies, it was the unwavering, enthusiastic support of a few of my closest colleagues that carried me through this very trying and difficult period.
As the data for a protein and the absence of a nucleic acid in the scrapie agent accumulated, I grew more confident that my findings were not artifacts and decided to summarize that work in an article that was eventually published in the spring of 1982. Publication of this manuscript, in which I introduced the term "prion", set off a firestorm. Virologists were generally incredulous and some investigators working on scrapie and CJD were irate.

Monday, February 22, 2010

Embrace Life

We can often have a significant impact on disease prevalence in people simply by changing human behavior. We have seen examples of this with both AIDS and Lyme disease. But the big question is how do you change human behavior? One common method is the Public Service Announcement. With the rise of cable TV and the deregulation of the broadcasting industry in the 1980's the power of such ads to reach people has been diminished. However, the rise of the internet has now made it possible for locally produced Public Service Announcement to go viral and, for virtually no cost, reach an audience of millions overnight. What is interesting is that all the Cable news networks are now showing the video above, for free, and not as part of a public service announcement but because it is 'news' because everyone is watching it on the internet!

Although the video is not disease related (except for the potential Toxoplasmosis link) I would remind you that although your age group has a relatively low risk of death the number one cause of death (by a huge margin) is road traffic accidents.

The Stench of Rendering Plants

Residents who live near the Los Angeles River have complained for years about the constant, lingering smell of death. They don’t live near a cemetery or a mortuary; they live near Darling International, the rendering plant that disposes of Southern California’s dead horses, cows, and zoo animals. Residents have complained that the stench of the rotting carcasses is so abominable that it can induce vomiting. One resident who lives over ½ a mile away from the Darling Rendering Plant, must constantly spray air freshener in her home to keep it from smelling like a rotting corpse. While citizens complained about the almost unbearable odor, Darling International made $488 million last year alone. After hundreds of complaints over the past few decades about Darling’s intolerable reek, the company agreed to not take the bodies of animals that had been dead for over 24 hours. But what actually occurs inside of rendering plants to cause such a nauseating smell? When carcasses are delivered, they are minced and boiled in large vats that reach temperatures over 250 degrees. The animals fat is then stripped and made into tallow, which is in everything from lipstick to candies. The animals bone matter is dried and used as animal feed. While Darling renders the bodies of livestock, one of Los Angeles’s other rendering plants disposed of 1,354 tons of euthanized cats and dogs last year. While Darling International is said to expel the worst smell of any of the rendering plants, the plant that disposes of nearly 1,400 dead pets each year cannot smell much better. To read more about Los Angele’s four rendering plants, visit

Sunday, February 21, 2010

Men dumb, women sexy

The personality changes in humans caused by latent toxoplasmosis are subtle and only revealed by relatively large psychological surveys. However when the results were published at least one newspaper reported them as:
Parasite makes men dumb, women sexy

"Infected men have lower IQs, achieve a lower level of education and have shorter attention spans. They are also more likely to break rules and take risks, be more independent, more anti-social, suspicious, jealous and morose, and are deemed less attractive to women.

"On the other hand, infected women tend to be more outgoing, friendly, more promiscuous, and are considered more attractive to men compared with non-infected controls.

"In short, it can make men behave like alley cats and women behave like sex kittens".

Saturday, February 20, 2010

Parasite Rex

Carl Zimmer, a journalist, write and prolific blogger has long been fascinated by parasites, especially those that change our behavior. If you'd like to read more aboutr these amazing organisms then his book, Parasite Rex, is well worth a read and his blog, the Loom, is well worth a visit.

Fight HIV with HIV!?

What do you think?

Diseases are Fun!: Infectonator : World Dominator


It's a game about zombies.

A very simple game, in fact. Point on the screen near a group of people, and those nearby will become zombies (most of the time). Helpful hint: try to infect stronger enemies like police, soldiers, gangsters, terrorists, or Eskimos.

   Upgrade them to make them stronger, faster, and more infectious. Also included are "special" zombies like undead Ronald McDonald and Colonel Sanders.

   Starting in Africa, Spread your Infection across the globe to places like Tokyo, New York( where you can attempt to Infect Spider-Man), and the North Poll (where you can unlock Zombie Santa).


Disease in Haiti

Unfortunately, it was just a matter of time before stories like this started emerging from Haiti. With so many displaced people without access to proper sanitation facilities and clean water, it's likely that things will get worse before they get better.

Friday, February 19, 2010

More on Guinea Worm

Gathering drinking water at Guinea worm infested pond.

Guinea Worm disease, also known as dracunculiasis is contracted when a person drinks water that is contaminated with microscopic water fleas carrying infective larvae. Like Cholera the presence of Guinea worm disease is an indicator of extreme poverty, including the absence of safe drinking water, in a community. Victims are totally incapacitated as a worm emerges from their body and this leads to further poverty as, for example, farmers cannot farm.

There is no vaccine or medicine to treat or prevent Guinea worm disease. Infected people won't even realize they have it until a year after drinking contaminated water, when they will develop blisters as the worm begins to emerge. Extracting the worm safely is a tedious and painful procedure.

Amazingly the fight against Guinea worm has occurred using the simplest of all tools - education and changing people's behavior.
The most effective way to prevent it is to filter the tiny water fleas out of drinking water using fine-mesh filter cloths.

Because humans are an essential host in the life cycle if all human cases can be prevented then the disease can be eliminated. Guinea worm is now in a race with Polio to be the second disease that humans eliminate from the planet. You can read more about the efforts to eliminate Guinea worm at the Carter Center Guinea Worm eradication page.

"Hopefully Guinea worm will be the first parasitic disease ever eradicated. If and when that happens, we will have done it without a drug and without a vaccine to treat or prevent the disease. If we can do that, it will be one of the greatest achievements in public health."

The Possible Link Between Cats and Schizophrenia

While cats were loyal companions to pharaohs during ancient Egyptian times, they were not domesticated and were free to roam the land. Prior to the 18th century, schizophrenia was a rare disease. However, when cats become more domesticated in the late 18th century, there was a sharp increase in the incidence rate of schizophrenia. Recently, 2 separate studies have established a link between schizophrenia and having a pet cat. In one study, of the 165 schizophrenics screened, 51% said they had a cat as a child. In a different study, 52% of schizophrenics reported having a childhood cat. While researchers do not know if the cats of these schizophrenics were the host of toxoplasmosis, the connection between owning a cat and developing schizophrenia cannot be ignored. Additionally, researchers found that toxoplasmosis and schizophrenia are highly uncommon in areas with no felines. While researchers are still investigating the link between cats infected with toxoplasmosis and schizophrenia, more data is continually being published linking the two. To read more about the relationship between infected cats and schizophrenia, visit Link 1 and Link 2.

Thursday, February 18, 2010

Toxoplasmosis in Cats and Humans

Since the question “Why don’t we just vaccinate cats?” was asked in class. I decided to do some research with this particular question in mind. It turns out that, currently, there is no vaccine to prevent toxoplasmosis in cats or humans. However, there is treatment. Cats are usually treated with a course of antibiotics called Clindamycin. Like humans, healthy cats who become infected with the parasite are usually asymptomatic and unless they contract feline immunodeficiency virus (FIV) or feline leukemia (FELV). Thus, cats do not need treatment unless their immune systems are compromised. I did find it curious that toxoplasmosis is treated with antibiotics, which, to my understanding, treat bacterial infections, and I would not think antibiotic drugs would prove effective against a parasite, which falls under the eukaryote family. Treatment of toxoplasmosis in humans is usually Pyrimethamine, an anti-malarial drug, taken in tandem with the antibiotic Sulfadiazine. Like cats, humans can also be treated with Clindamycin. Due to the nature of the disease and it’s close genetic make up of humans, especially when compared to viruses and bacteria, it is difficult to target the toxoplasmosis gondhii and the effects of the treatment can be hard on the body. In humans, treatment with Pyrimethamine can prevent the body from absorbing B vitamin folate as well as cause bone marrow suppression and liver toxicity. However cats are not spared the brunt of treatment, Clindamycin can cause severe diarrhea in both cats and humans.

In defense of cats everywhere, people, especially Americans, are not usually infected with toxoplasmosis from their precious Mr. Whiskers. Instead, most Americans contract toxoplasmosis through ingestion of raw/undercooked meat or unwashed produce that has contaminated soil on it. So, the best way to avoid getting toxoplasmosis in developed countries is to thoroughly cook or clean your food. So, some of this has been reiteration of what was covered in class, but I thought the treatment plans as well as the immune system similarities between cats and humans were noteworthy or at the very least, interesting. If you would like to read more or view the sites where I got my information, here are the links:

A Man's Best Friend

Everyone has heard the term "a dog is a man's best friend." However, these furry friends are a little too loyal when it comes to Toxoplasmosis. Studies show that "50% of stray dogs and cats carry T.gondii antibodies, which means that they have been infected and may transmit the parasite to you. Reports show that dogs in shelters, dogs living in close contact with wild birds and rodents in rural areas, and dogs fed raw meat are at mich higher risk for being infected by T.gondii. Since 2000 there have been identified incidents of dermatitis (a general term for a skin rash) in a dog associated with an unidentified Toxoplasma gondii-like parasite." Next time you let your dog jump into bed with may want to reconsider.


It is a little surprising to me how little follow up there has been to Jaroslav Flegr's 2002 paper describing a relationship (although not necessarily a causal relationship) between latent Toxoplasmosis infection and road traffic accident rate. The original paper Increased risk of traffic accidents in subjects with latent toxoplasmosis: a retrospective case-control study has only been cited 24 times since then. Whilst that's quite respectable for a science paper it hardly suggests the large scale interest this paper deserves.

Using Web of Knowledge (available through the library website, or use the off-campus login) you can easily find the papers that cite Felgr and see which of them perform similar studies. Of the 24 citations the majority are either reviews, concern Toxoplasmosis in animals, or look at psychological effects in humans. A few of the papers look at behavioral effects in humans but only 3 investigate the road traffic accident angle.

Flegr's group found the same relationship in a totally different data set in the Czech republic:
Increased incidence of traffic accidents in Toxoplasma-infected military drivers and protective effect RhD molecule revealed by a large-scale prospective cohort study

and two studies in Turkey find similar results to Flegr:
Higher prevalence of toxoplasmosis in victims of traffic accidents suggest increased risk of traffic accident in Toxoplasma-infected inhabitants of Istanbul and its suburbs
Is Toxoplasma gondii a potential risk for traffic accidents in Turkey?

Wednesday, February 17, 2010

Diseases are Fun!: Phage Wars 2

Another sequel! I played this game quite laboriously, causing me to procrastinate on an important paper, but whatever. In this game, you are a virus, and you must infect other cells on the 'map' whilst competing with other viruses for control of the entire map. It's rather tricky at first, but once you start sequencing your experimental virus with better and better upgrades, it becomes easier. But it can be a little too easy, and the lack of some options can make the game a little boring late game. Smarter AI, more options for upgrades, and possible multiplayer would make any future Phage Wars game a huge improvement. I really enjoyed the simple computer interface in-between rounds: very 80's retro Macintosh feel to it. If you discover a unstoppable strategy, try switching it up. The game loses it's charm if it's too easy.

Brain slugs and other parasites

The recently resurrected show Futurama has always contained a lot of science jokes and, basically, nerd humor. As well as the brain slugs, which show up in a number of episodes, there is whole episode about parasites - 'Parasites Lost' -that I have blogged about before. It raises a lot of interesting issues about parasites and their effect on their host.

The brain slugs in Futurama do not make very good parasites (which makes them funnier) because they are so visible, they make their hosts speak in a very obvious monotone, and their influence on their host is a little crude -

: (monotonous) I suggest we all go to the Brain Slug planet.
Fry: What do we do there?
Hermes: (monotonous) Just walk around, not wearing a helmet.

There are several patterns for knitted or crocheted brain slugs on the internet. The one on the cat above is at Etsy. I rather like the baby hat here, or you can find a free pattern here. Of course you could buy the officially licensed brain slug action figure but where's the fun in that?

Tour a BSL-4 lab

As I was searching the web on biosafety labs, I found this site that shows the different security measures, precautions, and equipment used in a BSL-4 lab. Click here to see everything at BSL-4 labs.

Tuesday, February 16, 2010


Okay, one last post on last week's topic - biosafety.

Popular Mechanics magazine had an article about Biosafety labs in May last year. In particular they got a look at the new $105 million BSL-4 facility at Fort Detrick.

The first rule in any fight is to know the enemy—and that places this outwardly normal office building on the front line of a war against invisible foes that can mutate into more powerful strains. Jahrling, one of the nation’s most seasoned virus hunters, has no illusions as to which organisms have the upper hand: “The bugs are always one step ahead.”

There is no mention in the article of the fact that Fort Detrick was the source of the anthrax used in the 2001 anthrax attacks. It didn't 'escape' from the building, it was deliberately removed by a scientist who worked there. I presume that there are now new procedures in place to prevent this happening again. At least I hope so.

Malaria killed King Tut?

Exactly what killed the boy king has been much disputed over the years, but an article in the New York Times cites new genetic evidence that malaria may be the culprit.

More historical background here.

Monday, February 15, 2010

Hospital Survival Guide

I said in class that there wasn't much you could do to prevent nosocomial infection in hospital but the Daily Mail, a British Newspaper, had an interesting article today that comes up with a variety of obvious, and not so obvious, ways you can help reduce the chances of infection if you do have to have an operation.
Your hospital survival guide: The ingenious tricks that can save you from superbugs and other hospital disasters

  • Swallowing 300mg of aspirin daily for three days prior to surgery can halve your risk of developing a deadly infection, according to research from Dartmouth College in the U.S.
  • Keep visitors off your bed. If they truly wish you a speedy recovery, your visitors should take a seat in a chair, not on your sheets. In a study published in the British Medical Journal, researchers found that a combination of infection-control strategies that included eliminating visitor contact with a patient's bed was able to stop the spread of MRSA and reduce the number of infections by 70 per cent.
and of course:
  • Don't touch the toys!. Any children coming to visit need to be kept away from toys littering the waiting room. When University of Nottingham researchers swabbed the surfaces of 12 toys in an intensive-care unit, they found half of them swarming with various strains of bacteria, including Staphylococcus aureus.

Sunday, February 14, 2010

Valentines Day repeat - Dengue Fever

Okay, so it's a repeat but I felt like listening to it. In contrast to most bands with disease related names (eg Anthrax, Cholera, Bubonic Plague and Ebola) Dengue Fever are not only not a heavy metal band but play 'Southeast Asian pop, Vietnam-war-era lounge music, klezmer, ska, surf rock, and Ethiopian jazz'. One of the band apparently caught Dengue Fever which is where the band got their name. I suspect Anthrax, Cholera, Bubonic Plague and Ebola can't say that. Dengue Fever (the band) are based in LA.

Dengue fever (the disease) is a hemorrhagic fever caused by a virus found primarily in the tropics and Africa, with a geographical spread similar to malaria. Dengue is transmitted to humans by mosquitos. Although it is a hemorrhagic fever the mortality rate, especially with medical care, is much lower than other hemorrhagic fevers such as Ebola hemorrhagic fever.

The video isn't actually a video but I like this track - One Thousand Tears Of A Tarantula.

Happy Valentine's Day

Saturday, February 13, 2010

I'm not sure how reputable the New York Post is, it always seems a bit tabloidy to me, but they had a pretty interesting column on the Lancet's retraction of the Wakefield paper (that originally suggested a link between autism and the MMR vaccine.) Not mincing words it is called: Junk Science Kills: Who'll apologize to dead kids. The last sentence is something I was trying to say in class on Friday, albeit less succinctly.

Even with the retraction, the widespread rumors of a vaccine-autism link will prevail: The broader anti-vaccine movement is alive and well, albeit without a shred of evidence to support their case. As the chief of Infectious Disease at Philadelphia Children's Hospital, Dr. Paul Offit, reflected sadly, "This retraction by Lancet came far too late. It's very easy to scare people; it's very hard to unscare them."

Friday, February 12, 2010

Diseases are Fun!: Pandemic 2

 (this probably has already been posted, but it's a good start for my disease computer game series. Pandemic 1 is fine, but P2 is a far superior game)
A great disease simulation game, and one of many. In Pandemic II, you create a disease in which to infect and kill every human on the planet. Your disease can be a adaptable parasite, a well-rounded bacteria, or a rapidly-evolving virus. As you infect the world, you gain evolution points to upgrade or downgrade your disease.
   If you play, name the disease after yourself, and it you can get top ten on the leader-boards, you'll get some extra-credit!*
   Here is a hint. Try to infect all the countries before they shut down their borders, otherwise it will be IMPOSSIBLE to win the game.
   I'll post new games with descriptions, but feel free to look for them yourselves.

*disclaimer/joke: I have no authorization for giving any extra-credit. But if extra-credit was given for high-scores, I suggest a modest 0.1 point(s) for high-score per rank; that is, 1 point for first place, .9 for second, .8 for third, and so on. 10th place would be a whopping 0.1 extra-credit points.

Unguarded mini fridge and Denialism

I've posted the first one before but it's still funny. Enjoy the weekend.

The Daily Show With Jon StewartMon - Thurs 11p / 10c
Michael Specter
Daily Show
Full Episodes
Political HumorHealth Care Crisis

Nosocomial Infections and Antibiotic Resistance, Olivia Cvitanic

As Professor Latto discussed in class, the death toll in the United States due to Nosocomial Infections is appalling. As was also demonstrated in lecture, the U.S. doesn’t look good when compared to other European countries who not only have much lower infant mortality, but also much lower rates of Nosocomial Infections while spending much less in the process. Certain Asian and Latin American countries actually have lower rates of Nosocomial Infections as well, which seems ironic because the U.S. and its physicians pioneered many areas of the medical field in the 20th century, not to mention originally stressed the importance of cleanliness in hospitals.

The U.S. Nosocomial Infection situation is especially bad considering that the three main infections acquired are MRSA (methicillin resistant S. aureus), vancomycin-resistant enterococci,, and gram negative enteric bacilli. So, not only are patients becoming infected during their stay at the hospital, but they are actually acquiring infections that cannot be treated effectively without second line antibiotics which are expensive and a painful. Even if you endure the strain on your wallet and body, MRSA currently has a 20-40% mortality rate regardless of treatment. To add to this “perfect storm,” most patients that come into the hospital are seriously ill and tend to be very young or very old. Thus, their immune systems are already compromised by their illness and age. These patients serve as the perfect breeding ground for bacteria as well as for development of antibiotic resistant strains. Unfortunately, there does not seem to be a clear answer to these problems facing our Health Care and Hospital System. However, I think that some changes must come about because at the rate we are going we will lose our precious weapon against bacteria: antibiotics as well as go completely broke in the process. Not to be too despondent, but it’s important to realize the consequences of our decisions. If you would like to view the Nosocomial Infection rates country by country or read the article that links the Nosocomial Infections and antibiotics, here are the links respectively:

Thursday, February 11, 2010

Animal antibiotic use

Over the last two nights Katie Couric on CBS News had a two part series on the use of antibiotics on farm animals. You can watch the videos here or read the transcripts.

Part 1: Animal Antibiotics a Threat? (video) and transcript
Public health officials are worried that the widespread use of antibiotics on healthy animals may be putting people at risk. Katie Couric investigates this potential health threat.

Part 2: Antibiotic-free animals (video) and transcript
American farmers use more growth-promoting-antibiotics than any other place in the world. Katie Couric reports on a possible alternative in Denmark, which bans antibiotic use in livestock.

Nosocomial Related Deaths

Despite the efforts of Florence Nightingale, Holmes, and Semmelweis to help prevent the spread of deadly infections, 100,000 people in the US die from nosocomial infections annually. Although the rate of acquiring a nosocomial infection has remained stagnant for the past few decades, the rate of nosocomial infections per 1,000 patients has increased over 2% due to shorter inpatient stays. To decrease nosocomial infection rates by 1/3, hospitals and health care facilities would only need to have an effective hospital epidemiologist, one infection control practitioner for every 250 beds, active surveillance mechanisms, and ongoing control efforts. That’s it. To read the rest of the CDC’s findings, visit

Wednesday, February 10, 2010

Progress in finding a cure for HIV/AIDS

In collaboration with our British counterparts across the pond, scientists in London and the US have solved a crucial piece of the puzzle in finding a cure for AIDS. After 20 years of research, scientists have grown a crystal that allows them to see the enzyme integrase. When someone is infected with HIV or another retrovirus, the integrase enzyme is used to copy its genetic information in to their DNA. Although current HIV and retrovirus drugs are used to target integrase, scientists were never fully sure how the drugs prevented the spread of HIV. With this high-quality crystal, scientists can clearly see how integrase inhibing drugs work, how to improve them, and how to prevent integrase from becoming resistant. As scientists gain a better understanding of how various HIV/AIDS treatment drugs operate, they can begin to work on a drug that will effectively cure someone of HIV. To read more about this remarkable crystal and how scientist discovered it, visit:

Bathroom/Laundy Fomites: Mmmm....

For this blog post I decided on a topic that will undoubtedly gross a lot of you out, and certainly make you far more aware of pathogens.
When professor Latto mentioned fomites such as doorknobs, teddy bears, and more, I started thinking about everyday objects that could be fomites. As it turns out, almost every thing could be a fomite, but most you do not have to worry about. What i did want to explore, however, is fomites in the bathroom, specifically the toilet and its seat.
I began doing my research and quickly ran across a phenomenon that some of you may know about without realizing it, the toilet plume. It is a simple, but utterly nasty, side effect of flushing the toilet that is defined by a plume of toilet water droplets being shot into the air, and spreading throughout the bathroom. According to university if Arizona professor Charles Gerba, who conducted a study on this in the 70's, bacteria and viruses where shot into the air at a height of up to six feet, and remained airborne for up to 2 hours after each flush, before finally settling on surfaces, including your toothbrush. The average number of visible water droplets per flush ranged from 27-104, and covered an average area of 6 square meters, or ~20 square feet.

Some may suggest closing the lid before flushing, but Dr. Gerba found this had no effect on the amount of bacteria released, just slowed the time span, giving you time to wash your hands and get out before it reached the sink, in many cases. Since this is not fun to think about, I tracked down a nice video and put it:


And while this may freak you out to no end, take heart in the fact that the bathroom, and the top of the toilet seat specifically, are among the less bacteria rife objects in your house/dorm. Take for instance, a sponge used to clean pots and pans, it is rife with bacteria because it presents the prefect breeding ground for them, warm moist, and often dark. Oh, and your wet laundry? Even worse. Because there are trace amounts of fecal matter in underwear, when that underwear gets washed, the fecal matter gets tossed around in a warm dark place and spreads to your other clothes. Say you wash the undies separately, well the bacteria remains in the washer even after several non-infected washes. God forbid you let your wet laundry chill in the washer for a long time before throwing it in the dryer, because the bacteria only multiply in that perfect breeding environment. Studies also found that the heat from the dryer is not enough to kill off all the bacteria that has freshly infected your clothes.
So be wary of that laundry, and placing your hands or other objects on surfaces in bathrooms, especially communal/dorm bathrooms.


The Nosocomial Colonization of T. Bear

The Nosocomial Colonization of T. Bear
Walter T. Hughes, Bonnie Williams, Bobby Williams and Ted Pearson Infection Control, Vol. 7, No. 10 (Oct., 1986), pp. 95-500

It's worth a quick read. The bear's (and yes, technically they are known as T.Bear) were already being used in a program in the hospital to encourage handwashing!

In view of the potential hazard, we suggest that this item not be used in hospitals or day care centers as recommended by the NIH and T. Bear Foundation. It must be emphasized that our criticism is not of the T. Bear Handwashing program, but rather of this one item utilized by the program. Nevertheless, although extensive development and promotion of the T. Bear Program are well under way at the national level, we are not aware of any objective experimental studies that have been reported. The program caused excitement at our hospital. Patients, parents, nurses, doctors, housekeepers, and technicians begged for a lovable T. Bear and the colorful lapel badge. But the objective is not fun with teddy bears, but rather washing hands to prevent infection. Will the T. Bear concept influence the busy surgeon, pediatrician, nurse, anxious parent, or sick child to perceive hand- washing to be "kid stuff' or an effective modality for preventive medicine? It would seem that objective motivational studies are warranted.

Malaria and Watermelon

I came across this blog post about malaria as depicted in Little House on the Prairie. A nice reminder that malaria was once common in parts of North America, and people had no idea that it was caused by mosquitoes.

Tuesday, February 9, 2010

Natural Immunity to Ebola- Olivia Cvitanic

A recent study conducted in rural Gabon has concluded that there may be some natural immunity people have acquired to combat Zaire ebolavirus (ZEBOV) in areas where the disease is especially prevalent. The researchers tested 4,349 people from 220 randomly selected villages in Gabon using the ELISA method. Out of the people tested, 15.3 % tested positive for ZEBOV. This figure increased to almost 20% in especially forested areas. Individuals were tested using the Western blot which determined whether an individual had anti-ZEBOV IgG. IgG is an immunoglobin. Immunoglobins are proteins that make up antibodies. Also, researchers studied individuals’ CD8 T cells and tested for an antibody response upon “ZEBOV stimulation.” The results indicate that a significant portion of the population living in very rural areas of Gabon “have both humoral and cellular immunity to ZEBOV.” One theory as to why people in these rural areas exhibit higher levels of immunity suggests that many of the tropical fruits growing in rural Gabon have been contaminated by bat saliva. Fruit bats have been known to spread the disease so this theory is possible. While Ebola is not a serious problem in the United States, there are serious outbreaks that occur in Africa. In order to prevent future outbreaks or even eradicate the disease completely in Africa, is it possible to use these ZEBOV immune people’s blood serum in the same way it was done with Lassa virus? In The Coming Plague, a missionary nurse, Ms. Pinneo, survived Lassa fever and anti- Lassa antibodies were present in her blood afterwards, though she suffered debilitating effects from the disease later on. Since, in the case of Ebola, there are only two strains Ebola-Zaire and Ebola-Sudan, I don’t see why a vaccine could not be developed to prevent future outbreaks or at least “a serum” to help treat infected persons as was used to treat a researcher infected with Lassa fever in The Coming Plague. To be honest, this article was a little difficult for me to understand because of all the medical and biological jargon; however, the presence of Ebola immunity was news to me and I thought deserved attention. Many of the terms such as seroprevalence and IgG I had to look up on my own. If you would like to read more, here’s the link:

The needle and the damage done

The retraction of the Wakefield article has provoked a number of editorial and Op-Ed pieces. I spotted this one in the LA Times a few days ago - The damage of the anti-vaccination movement.

Some groups claim only to oppose mandatory vaccines, but this ignores the need for what's called "herd immunity." That means a certain level of the population must be vaccinated (generally around 85% to 90%) so those unvaccinated are still protected.

Lack of herd immunity is what killed Gabriella "Brie" Romaguera. The New Orleans baby died of pertussis, or whooping cough. At one time, this disease afflicted more than 250,000 American children yearly, killing 9,000. Vaccinations reduced that to just 1,000 new cases annually by 1976; but by 2008, cases had soared to more than 10,000 annually.

Brie contracted the disease when she was a month old, too young for her first pertussis vaccine. "I'm not laying blame," her mother, Danielle, told me. "But people need to know they can infect other people's babies. It kills. People think these diseases don't exist anymore, but that's only because children are being vaccinated."

Monday, February 8, 2010

Disease on the radio

A story from NPR's On the Media covering the recently retracted paper falsely linking autism and the MMR vaccine.

From the same program, a story about whether or not the World Health Organization dropped the ball on the H1N1 outbreak. Very relevant to the course, including a discussion on how to define a "pandemic".

Hot off the press

A broad-spectrum antiviral targeting entry of enveloped viruses in Proceedings of the National Academy of Sciences this week.

We describe an antiviral small molecule, LJ001, effective against numerous enveloped viruses including Influenza A, filoviruses, poxviruses, arenaviruses, bunyaviruses, paramyxoviruses, flaviviruses, and HIV-1. In sharp contrast, the compound had no effect on the infection of nonenveloped viruses. In vitro and in vivo assays showed no overt toxicity. LJ001 specifically intercalated into viral membranes, irreversibly inactivated virions while leaving functionally intact envelope proteins, and inhibited viral entry at a step after virus binding but before virus–cell fusion. LJ001 pretreatment also prevented virus-induced mortality from Ebola and Rift Valley fever viruses.

Although the compound does cause damage to host cell membranes whose composition is nearly identical with that of virus envelopes, it caused them no ill effects. The reason, according to the researchers: Cells can rapidly repair their membranes, but viruses can't fix their envelopes.

"At antiviral concentrations, any damage it does to the cell's membrane can be repaired, while damage done to static viral envelopes, which have no inherent regenerative capacity, is permanent and irreversible."

A more general description of the paper is available here but there hasn't been much media interest in this exciting development yet.

Sunday, February 7, 2010

Hans Rosling on AIDS

Hans Rosling unveils new data visuals that untangle the complex risk factors of one of the world's deadliest (and most misunderstood) diseases: HIV. He argues that preventing transmissions -- not drug treatments -- is the key to ending the epidemic.

If you think this is a pretty cool presentation (which it is) then check out his most famous presentation 'the best stats you've ever seen' where he debunks a number of myths about 'developing' countries.

Saturday, February 6, 2010

Sunday is National Black HIV/AIDS Awareness Day

National Black HIV/AIDS Awareness Day, February 7th of every year, is a national HIV testing and treatment community mobilization initiative.

Among all race/ethnic groups, HIV prevalence is highest among the Black community, who account for 46% of the population living with HIV despite comprising just 12% of the population.

Phillip Cohen at the Huffington Post has more shocking statistics.

Friday, February 5, 2010

Acquaintance Immunization

Image from inSPOT a nonprofit Internet notification service that allows you to send e-cards to your sex partners to break the bad news that they should get tested. Cards can be sent anonymously but they suggest, not unreasonably, that cards with a name are much more effective.

On a related note tell me that this isn't a good idea:

It is well established that random immunization requires immunizing a very large fraction of a computer network, or population, in order to arrest epidemics that spread upon contact between infected nodes (or individuals. Many diseases require 80%– - 100% immunization (for example, measles requires 95% of the population to be immunized). The same is correct for the Internet, where stopping computer viruses requires almost 100% immunization. On the other hand, targeted immunization of the most highly connected individuals, while effective, requires global information about the network in question, rendering it impractical in many cases. Here, we develop a mathematical model and propose an effective strategy, based on the immunization of a small fraction of random acquaintances of randomly selected nodes. In this way, the most highly connected nodes are immunized, and the process prevents epidemics with a small finite immunization threshold and without requiring speci fic knowledge of the network.

From a paper entitled 'Efficient Immunization Strategies for Computer Networks and Populations' in Physical Review Letters.

So, for example, for a sexually transmitted disease you would only need the identity of a single sexual partner from a large sample of people (unfortunately this should be a random selection from those available which may cause difficulties). You then collate this information and target your vaccination on those names that come up the most frequently (most likely the 'superspreaders' in this case). But you have identified them without constructing the whole partner network.

Thursday, February 4, 2010

Herbs: The Root of Possible AIDS Cure, posted by Olivia Cvitanic

As many adolescents of my generation are aware, AIDS is a very serious disease that affects people on a global level. However, HIV/AIDS has proved most serious and prevalent in Africa. Currently, Nigeria has the second highest number of AIDS cases in the world so, understandably, finding a cure or any type of remedy to at least alleviate some of the suffering caused by the disease is in high demand. Since many Africans are very poor, some living on less than one dollar a day, many Africans have begun to look to local medicine men for medical treatment including HIV/AIDS treatment. Nigerians are no exception to this trend and one Nigerian medicine man in particular named Baba Chukuri claims he can in fact cure AIDS. While there is no scientific evidence that his “recipes” of herbs, roots, and barks will cure AIDS, many ailing Africans have travelled great distances to seek his medical care. However, as Chukuri himself divulges, his medicines cost a lot less than a trip to the hospital which may be one reason for his blossoming practice.

Before totally denouncing Chukuri as a charlatan, it should be mentioned that Nigeria’s Institute for Pharmaceutical Research (NIPR) has begun to study the effects of the recipes made by Chukuri and other medicine men. Dr. Uford Inyang, NIPR’s Director General says, "On HIV, we've screened over 100 medicinal plants, out of which 10, 12, have seen a great deal of activity as anti-viral agent," Often these plants serve to help physicians and researchers develop new drugs. The NIPR is currently developing treatments for Tuberculosis, malaria, and an “immune booster” for AIDS patients through the use of the modern lab in tandem with local herbal gardens. In sum, I think the prospect of developing any disease treatment within African is exciting and would help bolster the economy and probably the morale of African people. Since, according to popular theory, HIV/AIDS developed from SIV in Africa, why shouldn’t the remedy for the disease be in Africa as well? If you would like to read the CNN article I referred to for this post, here’s the link:

Zinc fingers

Finally some good news in the battle against HIV and AIDS. Following the dramatic news last year of the world's first 'cure' a gene therapy technique has been developed and is already at a stage where they are enrolling HIV postitive patients into a clinical trial. In contrast to the example I mentioned though, they will not receive bone marrow transplants but instead their own cells will be genetically modified to carry the CCR5-Δ32 trait and then reintroduced into their body.

This development is the combination of our increased knowledge of the CCR5-Δ32 trait and some dramatic advances in the techniques of gene therapy. This new 'zinc finger' technique is nicely described in the New York Times article: In New Way to Edit DNA, Hope for Treating Disease just a few weeks ago.

Read to the end for some amazing, and perhaps slightly troubling, possibilities of using the same techniques to alter the human germ line:

Since the germ lines of rats and zebra fish have already been altered with zinc finger scissors, “in principle there is no reason why a similar strategy could not be used to modify the human germ line,” Dr. Porteus said. The kind of disease that might be better treated in the germ line, if ethically acceptable, is cystic fibrosis, which affects many different tissues.

The disease could be corrected in unfertilized eggs, using the zinc finger technique, Dr. Porteus said. But he added, “I don’t think our society is ready for someone to propose this.”

Wednesday, February 3, 2010

Problems with curing HIV

Curing AIDS means riding the body of the HIV virus. As we learned in lecture, the HIV virus replicates itself inside of human T-cells and destroys the CD4 cells that are essential for our immune systems. Current anti-retroviral drugs are so effective at reducing the amount of HIV in a person’s body that if someone takes the viral load test (the test that determines if someone is infected with HIV) while on an anti-retroviral treatment, the test cannot detect the HIV virus and will come back negative. However, as we learned that bacteria can remain dormant for long periods of time, so can viruses. Similarly to cholera remaining dormant in Copepods, HIV viruses can do the same in CD4 cells. During this ‘resting’ or ‘dormant’ stage, HIV does not replicate itself and may remain undetected in the body. HIV can remain dormant in cells for many years, even decades, and antiretroviral treatments currently cannot combat ‘resting’ HIV. Additionally, if someone infected with dormant HIV stops taking antiretroviral treatment, HIV will begin to replicate again and can lead to AIDS.

If there is to be an effective cure for HIV, it needs to be able to detect and effectively remove all HIV infected cells.

To read more about possible HIV cures and treatments, see

Viral chatter

Virus hunter Nathan Wolfe is outwitting the next pandemic by staying two steps ahead: discovering deadly new viruses where they first emerge -- passing from animals to humans among poor subsistence hunters in Africa -- before they claim millions of lives.

I try to keep the blog new and fresh but sometimes a past post is simply so relevant and interesting that I can't resist a repeat.

Check out Nathan Wolfe's talk at the TED conference earlier this year. TED (Technology, Entertainment, Design) invite some of the world's most fascinating thinkers and doers, and challenge them to give the talk of their lives. The best talks and performances are available on their website. You should all check out this talk, it is very interesting, very well presented and hugely relevant to this class.

Tuesday, February 2, 2010

Reading for next week's section

Please read this article from Wired about dropping vaccination rates and come to section next week ready to discuss it.

Missed vaccinations

I was just going to post on the Lancet story but Tate beat me to it. Hot news today. There have been a number of recent stories in the press about the alarming decline in vaccination rates. Here's one from a couple of weeks ago in USA today:
Missed vaccines weaken 'herd immunity' in children
It is very sad that this rumor about the measles vaccine and autism persists.
Parents such as Rebecca Estepp of San Diego decided not to vaccinate her younger son after his older brother was diagnosed with autism. When measles broke out in Southern California in 2008, "I had to decide, 'Would I rather have him get the measles or risk having him get autism like his brother did?' " says Estepp, national policy manager for Talk About Curing Autism. "My husband and I decided we'd rather he get measles."

The story also, sadly, illustrates one of the advantages of herd immunity - it protects young children before they get their shots:
Danielle Romaguera's daughter, Gabrielle, was only 7 weeks old when she died from whooping cough — one week before she would have received her first shot.

Click the illustration at the top for an amusing illustration of herd immunity from Britain's National Health Service.

MMR and Autism

The link between the MMR (measles, mumps, rubella) vaccine and autism has always been highly dubious at best, and now it has even less support. The medical journal The Lancet has taken the highly unusual step of fully retracting a paper published by Dr Andrew Wakefield on the link between vaccines and autism. Dr. Wakefield was recently found to have violated research rules by the General Medical Council, who ruled that he had shown a "callous disregard" for children and acted "dishonestly" conducting his research.

This ties in directly to the reading we will be doing for section next week, which I'll post later today.

Monday, February 1, 2010


In countries like the US Bubonic Plague is still present because it has a reservoir in a number of animal species but only occasionally do people get affected and we no longer see epidemics in human populations.

Other countries do still suffer from epidemics of bubonic plague though. Most recently Madagascar has suffered through four annual epidemics infecting thousands of people.

A number of articles have reviewed these outbreaks and there are some interesting facts:

  • Madagascar has accounted for 45% of all the cases of plague in Africa in the last 15 years.
  • The case-fatality rate is just under 8%.
  • All the Y. pestis isolates remain sensitive to streptomycin.
  • Plague outbreaks occur during the dry and cool season.