Welcome to Winter

Welcome to the blog for EEMB40 - the Ecology of Disease - for Winter quarter 2009. It will also serve as a class website and you will find links to lectures etc. in a box at the top right imaginatively called 'links'.

You are all welcome, and encouraged to post here. To do that all you need to do is to send me an e-mail saying just that. I will then add your address and google will send you an invitation to be an author. Just follow the simple instructions and away you go.

Postings should be relevant to the class but the blog is specifically designed to be a place where you don't need to worry about how relevant your post is. (I give you 'Basket full of puppies' as an example). I will be posting lots of things that I take out of lecture (for time purposes) but that some of you may find interesting. By putting it here you can look at it at your leisure and you know it won't be on the exam.

I try to post every day when the class is running and, where possible, the postings are relevant to the current topics we are covering in class. You can access older postings (there are over 160 of them from the two previous times I have taught this class) either by scrolling down the page and repeatedly hitting the 'Older posts' button at the bottom right or by using the 'Labels' (scroll down and they'll be on the right hand side) to pull up posts on particular topics.

Final words

Well I told you summer was fast.
We will grade the final as quickly as possible and the results will be entered before the end of the week - probably by Thursday. As far as I know they should be available to you shortly after they are entered.
If you have questions about the final exam, the course or infectious diseases generally then e-mail is the best way to reach me. I may take a few days off before the next quarter starts but then I'll be having regular office hours on Weds and Thurs 12-1 if you want to catch me (or other times by appointment of course).

I have been musing over developing a similar course on the ecology of non-infectious disease (diabetes, heart disease, cancer etc for beginners) - although some of that is already covered by other courses here eg. MCDB23 Biology of Cancer and MCDB24 Genetics and Human Disease both taught by David Kohl. Or maybe a much more general course - How and why we die (including infectious disease, non-infectious disease and 'accidental' death, homicide and suicide). That would be fun, if a little morbid. I think I'd also need to enlist some help with that one. If anyone has any suggestions I'd really appreciate your comments.

Final exam review

Just a reminder: there's a link to a final exam review guide below. Please take a look before you come to the review session at Woodstocks, 2 pm today.

Why should you come to the review session?
1. I'll be answering questions from lecture, quizzes, and the review sheet.
2. I'll give you your total grade up to now, along with Quiz 4.
3. I'll go over some more review questions that aren't on the review sheet.
4. You can eat pizza the whole time.

Pandemic flu

Sometimes it's easy to overlook the obvious sources. The CDC maintains a very nice Pandemic flu webpage ('One stop access to US Government avian and pandemic flu infomation.')

I was just looking at this before putting a link to it on the blog when I noticed it had exactly the figure I tried to find yesterday - an up to date and clear map of the distribution of H5N1 in both birds and humans.
Relevant material previously on the blog:
Flu season (I briefly mentioned this today)
Spanish flu
Malaria control for the 21st century (the star wars mosquito defence system)
Morbidity and mortality

Measles vaccine (again)

TV stations, Radio Stations and Newspapers are all in the business of attracting customers. Whilst they all present the news they do so in a way that they hope will grab your attention and keep you watching, listening or reading.

For many subjects this doesn't matter and for some it enhances the experience - 'Coming next: you won't believe what happened in the Red Sox game.'

But when it comes to health I think the news media has an obligation to ensure that the headlines, crawl lines or whatever they call them, do not distort the message.

This week there was news of yet another study that found no link between the measles vaccine and autism. eg. the AP news report:

New research further debunks any link between measles vaccine and autism, work that comes as the nation is experiencing a surge in measles cases fueled by children left unvaccinated.

This science story was picked up by most news outlets as an item that would be of interest to their readership. A quick google news search suggests over 300 articles in the last couple of days. But, bearing in mind that many more people scan the headline than will read the article, let's look at some of the headlines.

The good
Autism and measles vaccine: no link found -- again
Study Dispels Link Between Autism and Measles Vaccine

The Bad
As Seen on TV: MMR Vaccine and Autism
MMR and autism again

and the Ugly
Do Measles Vaccines Put Children At Risk For Autism?
Measles vaccine linked to autism?

All these articles are reporting the same story.

Modern perils

In poor countries inadequate sanitation and garbage disposal, combined with poor resources at a local level mean there are numerous habitats for mosquitoes to breed in. From abandoned drainage ditches to discarded tires, buckets and bottles the problem is immense. In the absence of environment blanketing DDT the focus has turned to bednets - keeping mosquitoes (at least the nocturnal ones) from biting people.

In the developed world a new problem is arising - abandoned swimming pools. This problem has increased with the recent sharp rise in foreclosed and abandoned homes. In America the concern is not Malaria but West Nile virus. Fortunately such mosquito magnets can be detected remotely (although somewhat expensively) by the use of aerial surveys. Abandoned pools are generally green with algae. This is a regular tool in mosquito abatement in the Bay Area. For example, see this article today in the San Jose Mercury News:

The Santa Clara County Vector Control District will conduct an aerial search Monday for mosquito breeding sources that could potentially carry West Nile virus.

The district has made two previous aerial surveys this year, in early May and early August, which have led to more than 860 inspections and 135 treatments or fish plantings on local properties.

There's a longer article here about the problem in San Bernadino County. Remember the bottom line from this class - whenever anything changes in society there are new possibilities for disease transmission, potentially leading to outbreaks of new diseases or resurgences of old diseases.

HIV and Malaria

Coinfection, a term we introduced last week, that describes the simultaneous infection with two or more diseases is big news these days. In Africa the big coinfections are HIV and Tuberculosis, which we briefly mentioned, and HIV and Malaria.

The interaction between AIDS and Malaria is complex and only just being unraveled. One conclusion though is that coinfection has helped fuel the spread of both diseases in sub-Saharan Africa. (eg this 2006 paper and this 2007 paper).

A student, Randa, sent me this great link to a symposium on HIV and Malaria held at Caltech this year. There are videos of all the talks and the split screen with presenter and slides makes the talks very watchable. You can see:

David Baltimore, Ph.D., Nobel prize-winning discoverer of the molecule that HIV uses to copy itself into our DNA, discusses the origins of HIV, the failure to find a cure, and his own approach toward treatment.

Kimberly Shriner, M.D. , leader of the Phil Simon Clinic Tanzania project, discusses the difficulties and rewards of ministering to HIV positive patients in Africa.

Joel Breman, M.D., D.T.P.H., Senior Scientific Advisor at the Fogarty International Center of the NIH, discusses the battle against Malaria

Bruce Hay, Ph.D., Caltech Associate Professor of Biology, explains a new way to spread genetically-engineered malaria-resistance throughout the African mosquito population.

Martha Sedegah, Ph.D., Senior Scientist at the NMRC's Malaria program, discusses two promising new malaria vaccines.

Specicide

I hope that you found something in Wednesday's lecture to make you think a little. How far can we infringe on human rights if the ends justify the means? (and who decides?)

Are there species that we should deliberately drive to extinction?

Before you say no, try reading Olivia Judson's controversial article in the New York Times entitled 'A bug's Death: Should we send the malaria mosquito the way of the dodo?' . In this article she advocates the extinction, or "specicide", of thirty mosquito species through the introduction of recessive knockout genes".

Would this be the first step on a very slippery slope (a lot of people hate snakes, many people dislike spiders etc. etc.) or would the ends justify the means - eliminating the mosquitoes that vector malaria would save at least one million human lives every year?

Presidents Malaria Initiative

Workers trained in Indoor Residual Spraying (IRS) march on World Malaria Day in Agoro Sare, Kenya.
Source: James Kei/The Standard

"Americans are a compassionate people who care deeply about the plight of others and the future of our world, and we can all be proud of the work our Nation is doing to fight disease and despair. By standing with the people of Africa in the fight against malaria, we can help lift a burden of unnecessary suffering, provide hope and health, and forge lasting friendships."

-- President George W. Bush in a Malaria Awareness Day Proclamation on April 24, 2007 .

For more about the President's Malaria Initiative check out their webpage.

Relevant material previously on the blog:
Smallpox 2002 (Don't click on this one unless you've got 90 minutes to spare)
Gates foundation
Heroes and Villains
Polio eradication

Sciencedebate 2008

An organization called Science Debate 2008 has been working to restore science and innovation to America’s political dialogue. As part of this process they came up with a list of 14 science related questions for the candidates to answer. Barack Obama has submitted answers which you can see here. John McCain has said he will also answer the questions.

Of particular interest for this class is question 6:

Pandemics and Biosecurity. Some estimates suggest that if H5N1 Avian Flu becomes a pandemic it could kill more than 300 million people. In an era of constant and rapid international travel, what steps should the United States take to protect our population from global pandemics or deliberate biological attacks?

Here is Senator Obama's answer (in white) with my comments interspersed in black. This is a non-partisan blog, if Senator McCain submits answers before the class ends I'll comment on that too.

It’s time for a comprehensive effort to tackle bio-terror. We know that the successful deployment of a biological weapon—whether it is sprayed into our cities or spread through our food supply—could kill tens of thousands of Americans and deal a crushing blow to our economy.

Overseas, I will launch a Shared Security Partnership that invests $5 billion over 3 years to forge an international intelligence and law enforcement infrastructure to take down terrorist networks. I will also strengthen U.S. intelligence collection overseas to identify and interdict would-be bioterrorists before they strike and expand the U.S. government’s bioforensics program for tracking the source of any biological weapon. I will work with the international community to make any use of disease as a weapon declared a crime against humanity.

Hmm, I rather wish that they had left the last four words out of the question. I'm going to be disappointed if the answer is solely about bioterror when the intent of the question was about pandemics more generally. There's nothing here that is very interesting from a disease perspective except perhaps the mention of bioforensics. We now have the capability to trace strains of bacteria and viruses to particular source strains and often particular labs.

And to ensure our country is prepared should such an event occur, we must provide our public health system across the country with the surge capacity to confront a crisis and improve our ability to cope with infectious diseases.

This is a bit more interesting. Hospitals have been losing 'surge capacity' (aka empty beds) for years - either in search of greater efficiency or greater profits. There's no mention how this will be done, but the acknowledgment that we need it is a good sign.

I will invest in new vaccines and technology to detect attacks and to trace them to their origin, so that we can react in a timely fashion. I have pledged to invest $10 billion per year over the next 5 years in electronic health information systems to not only improve routine health care, but also ensure that these systems will give health officials the crucial information they need to deploy resources and save lives in an emergency.

This is getting more interesting. Funding for health information systems is a great idea. This will allow us to catch an epidemic in the early stages AND even when there isn't an epidemic we will still help improve people's health by tracking any long term changes in endemic diseases and making causal connections.

I will help hospitals form collaborative networks to deal with sudden surges in patients and will ensure that the U.S. has adequate supplies of medicines, vaccines, and diagnostic tests and can get these vital products into the hands of those who need them.

Ah, interesting, but what does it mean when a presidential hopeful promises to 'help hospitals form collaborative networks'? Does he mean there will be funds available or incentives or he will push for new legislation?

We also have to expand local and state programs to ensure that they have the resources to respond to these disasters. I will work to strengthen the federal government’s partnership with local and state governments on these issues by improving the mechanisms for clear communication, eliminating redundant programs, and building on the key strengths possessed by each level of government. I introduced legislation which would have provided funding for programs in order to enhance emergency care systems throughout the country.

Sounds like some obligatory politician phrasing.

I will build on America’s unparalleled talent and advantage in STEM fields and the powerful insights into biological systems that are emerging to create new drugs, vaccines, and diagnostic tests and to manufacture these vital products much more quickly and efficiently than is now possible. Unfortunately, the Bush administration has failed to take full advantage of the Bioshield initiative. Because of the unpredictability of the mode of biological attack, I will stress the need for broad-gauged vaccines and drugs and for more agile and responsive drug development and production systems. This effort will strengthen the U.S. biotech and pharmaceutical industry and create high-wage jobs.

Whilst no-one will be surprised that Senator Obama got a shot in at President Bush I would have advised him to take the high road and to praise President Bush's commitment to both malaria and HIV programs in Africa. He could have pledged to match or increase funding.

US can block mad cow testing

I almost missed this. An appeals court ruling coming out right before the holiday weekend. AP had the story but I didn't notice it on Friday.

The Bush administration can prohibit meat packers from testing their animals for mad cow disease, a federal appeals court said Friday.

A federal judge ruled last year that Creekstone must be allowed to conduct the test because the Agriculture Department can only regulate disease "treatment." Since there is no cure for mad cow disease and the test is performed on dead animals, the judge ruled, the test is not a treatment.

The U.S. Court of Appeals for the District of Columbia Circuit overturned that ruling, saying diagnosis can be considered part of treatment.

Gut-boosting molecule could fight off stubborn bugs

From this week's New Scientist magazine, a report on how to deal with a particular drug resistant bacteria:

Taking antibiotics can make us vulnerable to attack by tougher, antibiotic-resistant invaders, leading to nasty stomach bugs and the spread of dangerous infections in hospitals. Now a molecule has been found that could be mixed with antibiotics to thwart these harmful invasions.

The gut bacterium vancomycin-resistant enterococcus (VRE) has trouble taking root in a healthy intestine, but after a course of antibiotics it can multiply a thousand-fold and spread to the blood. The reason for this was thought to be that antibiotics kill not only their target bacteria but also harmless gut microbes, freeing up nutrients and niches that allow VRE to thrive.

But when Katharina Brandl of the Sloan-Kettering Institute in New York and colleagues treated mice with antibiotics, they found that levels of Reg3g, a protein made by "friendly" bacteria that kill VRE, dropped by 80 per cent. This suggests that a lack of Reg3g is partly to blame for the VRE increase that follows antibiotic treatment.

To see if boosting Reg3g levels could help, Brandl's team gave mice doses of lipopolysaccharide along with antibiotics. LPS is a molecule found on the surface of some bacteria that stimulates the gut to make Reg3g. These mice ended up with higher levels of Reg3g than mice that just took antibiotics, and they also had fewer VRE colonies - about the same number as mice that had taken no antibiotics. Brandl suggests giving LPS orally to humans taking antibiotics.

Accident, homicide, suicide

I think everyone should be aware of the leading causes of mortality for people in their age group. It helps to put risks in perspective and helps you see the reality behind various media scares. The CDC compiles this data so it is readily available. Take a look at the data from your age group (I'm presuming most of you are in the 15-24 age group). What is very conspicuous to me is that none of the leading causes of death are disease related - infectious or otherwise. Road traffic carnage dwarfs everything else, and homicide (and 'legal intervention') and suicide round out the top three. But notice that the overall death rate is low (90 per 100,000).

As you move into the next age group (25-44) notice that the overall mortality rate almost doubles (178 per 100,000) but that's still quite low. The carnage on the roads continues but AIDS, Cancer and heart diseases are moving up.

As we move into the 45-64 age group the death rate starts to rise sharply, up to 700 per 100,000. Mainly due to rising rates of heart disease and cancer. If you look at the final category of 65+ you'll see Pneumonia and Influenza crack the top 5.

I was thinking about this today because of the sad news that a 66 year old Santa Barbara woman, out running, was hit by a drunken driver early yesterday morning. I assume this will go down in the statistics as a motor vehicle 'accident'.

So please drive, walk and bike safe this labor day. And every other day for that matter. Even in our quiet paradise town by the sea there are drunks on the road at 7.30 in the morning.

This has been your labor day public service announcement.

Mentally and emotionally stable

"Individuals will be mentally alert, mentally and emotionally stable, trustworthy, physically competent....."

This is part of the US army regulation covering scientists working on bioweapons. (Actually bioweapon 'defence' since the US doesn't work on bioweapons).

Unfortunately it appears that this modest list of conditions - which, let's face it, isn't that different to the characteristics you might look for in a date - is too much for the workers at the US Army Medical Research Institute of Infectious Diseases (USAMRIID). In 2007 the deputy commander for safety wrote:
'The possibility of losing talented and well-trained researchers to other facilities.... with less stringent programs.... may impact the ability of the Defense Threat Reduction Agency to provide research personnel to combat biological agent use.'

This is all coming to light now because of the case of Bruce Ivins, accused of killing five people in the anthrax attacks of October 2001. Regardless of how fishy you think the whole thing smells a big question needs to be answered - how can we prevent our own bioweapon 'defence' labs from being the source of bioweapon attacks? There have been a few articles along this line but we need a much bigger debate on this and whether the huge expansion in 'biodefence' facilities will cause a greater risk than the risk of a terrorist or other bioweapon attack they seek to prevent.

Diagram

Or, if you prefer your learning to be in 'scribbled on index card' form then you should check out the 'Indexed' blog. A fresh one every day.

There are several disease related ones:
Hands to yourself
And pick up some ointment
Epidemic
Sickening

Maps

If you like your data in map form then here are a couple of sites you might want to explore over the holiday weekend.

First up is the Global Atlas of Infectious Disease, I did get quite a few broken links there but there's still some nice maps in the infectious disease section.

The Worldmapper website takes an interesting approach to mapping geographic data. It uses an algorithm that distorts the size of the country to represent the value of interest. The example shown below is HIV prevalence (proportion of people 15-49 with HIV). They have a number of such maps for diseases (eg TB, Cholera, Rabies, Influenza etc) and a whole range of other categories.

National Bio- and Agro-Defense Facility

One of the new BSL-4 labs in the USA will be associated with a proposed federal animal disease research laboratory. The proposed National Bio and Agro-Defense Facility (NBAF) would research high-consequence biological threats involving zoonotic and foreign animal diseases. There are six sites that are still in the running:

Athens, Georgia
Manhattan, Kansas
Flora, Mississippi
Plum Island, New York
Butner, North Carolina
San Antonio, Texas

The new lab will essentially replace the current Plum Island animal disease center, which does not have a BSL-4 lab. One option is to build it on the Plum Island site but the cost of this is much higher.

Choosing the location for the facility is creating some tension between the local residents, who don't want the lab and local politicians, businesses and universities who do want the lab, either for the research possibilities it would provide or the money and jobs it would provide, or both. The average cost for the six finalists is $721 million. Residents in Athens, Georgia who don't want the lab there have a very active website, as do opponents of the lab in North Carolina and Kansas. What do you think? Is this just nimbyism? FYI, the University of California submitted an 'expression of interest' in hosting the lab but was not invited to submit a full proposal by the Department of Homeland Security. UC's plan was to build the lab at the Lawrence Livermore National Laboratory.

Meet the Clostridiums

In this class I try quite hard not to present an overwhelming variety of different diseases and microbes. But here on the blog anything goes. So for those of you who want to learn about more microbes, meet the Clostridiums.

First up, we've already mentioned. Clostridium perfringens as the causative agent of gas gangrene - a major cause of death in World War 1.

You might also have heard of Clostridium botulinum, or at least of the disease it causes - botulism. Botulism is a paralytic food poisoning that is fortunately rare. The bacteria grow on food and cause harm in people as we digest a toxin produced by the bacteria. The neurotoxin is one of the most powerful toxins known to man, a single microgram is lethal. It is also used (in minute doses!) in the cosmetic treatment known as Botox.

Clostridium tetani is the causative agent of tetanus. The symptoms, muscle spasms and difficulty swallowing are caused by a neurotoxin produced by the bacteria. Infection generally occurs through wound contamination, and often involves a cut or deep puncture wound. Infection can be prevented by immunization, and this is often successful even if given after the wound occurs. Which is why it's a good idea to get a tetanus shot after a deep cut or puncture wound. If you wait to see if an infection develops it is too late for immunization to be much use.

The final member of our happy little Clostridium family is Clostridium difficile. C. difficile, or just C. diff. is the latest, greatest threat in nosocomial infections and there have been numerous outbreaks lately. Try a google news search on Clostridium difficile to see where the latest outbreak is (Canada apparently). C. diff is an interesting bacteria because it is found as a natural part of the gut flora in a small fraction of people, usually with no problems. But if the usual gut flora is eradicated with broad spectrum antibiotics C.diff can greatly increase in numbers and release toxins that cause severe diarrhoea and death in some cases. Some new strains appear to be producing much more toxin. Hospitals are very good places to find people taking broad spectrum antibiotics and, apparently, are good at spreading C.diff around as well. There was an MSNBC article with the subhead ‘C. diff’ rivals MRSA as the next deadly bacteria threat, experts say' in May of this year.

Correction

I was just checking that something I said today was correct when I found out that something else I said was incorrect....

First, the correct bit. Yes, in answer to the question, HIV and other retroviruses contain genes that code for the reverse transcriptase they need to replicate.

However I think I then said that reverse transcriptase would not normally be found in human cells. (After all it's called reverse transcriptase for a reason - transcription usually goes from DNA to RNA).

But I was totally forgetting about transposons, in particular, a type of transposon called a retrotransposon. You might have heard of transposons referred to as 'jumping genes' for their ability to move about within the genome. Retrotransposons achieve this trick by being transcribed to RNA and then back to DNA in their new position. This transcription from RNA back to DNA occurs via, you guessed it, a type of reverse transcriptase. Since their discovery in the 1980's it has been found that retrotranspons are common in the genomes of animals and, in particular, plants.

Targeting reverse transcriptase is still a viable strategy for HIV drugs though and HIV drugs such as Retrovir, Epivir, Viread and Viramune are all reverse transcriptase inhibitors.

In a link to earlier lectures, transposons in bacteria can carry genes for antibiotic resistance and are capable of moving these genes from chromosomal DNA to plasmid DNA and back again. This is an important mechanism in the acquisition of multi-drug resistance.

This might be a bit much biology for some of you but I thought it was interesting.

Relevant material previously on the blog:
Endogenous retroviruses (read the New Yorker article on endogenous retroviruses, it's excellent)
The Lost Children of Rockdale County (links to the PBS program I referred to in class)
STD versus STI

Science Roundup

Here are a couple of infectious disease related stories that caught my attention on Science Daily today.

Malaria Researchers Identify New Mosquito Virus
Researchers at the Johns Hopkins Bloomberg School of Public Health's Malaria Research Institute have identified a previously unknown virus that is infectious to Anopheles gambiae—the mosquito primarily responsible for transmitting malaria.

Although the virus does not appear to harm the mosquitoes, the researchers determined it is highly infectious to mosquito larvae and is easily passed on to the adults.

In theory, we could use this virus to produce a lethal toxin in the mosquito or instruct the mosquito to die after 10 days, which is before it can transmit the malaria parasite to humans. However, these concepts are many years away.

Some Cells Self-destruct For The Greater Common Good.
'(R)andom molecular processes during cell division allow some cells to engage in a self-destructive act to generate a greater common good, thereby improving the situation of the surviving siblings.'

Normally, salmonellae grow poorly in the intestine because they are not competitive with other bacteria of the gut. However, this dynamic changes if salmonellae induce an inflammatory response, namely diarrhoea, which suppresses the other bacteria. The inflammation is triggered by salmonellae penetrating into the intestinal tissues. Once inside, salmonellae is killed by the immune system. This in turn creates a conflict: salmonellae are either suppressed by the other bacteria in the gut, or die while trying to eliminate these competitors.

As Ackermann, Hardt and Doebeli report, salmonellae have found a surprising solution to this conflict. Inside the gut, the samonella bacteria forms two groups that engage in job-sharing. A first group invades the tissue, triggers an inflammation, then dies. A second group waits inside the gut until the inactivation of the normal intestinal flora gives them an opportunity to strike. This second group then multiplies unhindered.

(Barely) Relevant material previously on the blog:
Book recommendations
Dengue fever
Zoonoses as Biological Weapons

More Measles

The measles story is taking off in the media and, in contrast to the first stories, some of these reporters are getting it right. I haven't read them all, a google news search lists 524 articles on this topic, but I did look at a few and saw some good reporting. The MSNBC report was good: Vaccine-wary parents spark public health worry - Informative and accurate without sensationalism. Even the figure is useful and interesting.

On a totally unrelated note, did anyone else watch the Olympic men's marathon? 75 degrees at the start, 85 degrees at the end, 50% humidity and the winner simply outlasts everyone else at an insane pace to finish in 2:06:32, only a couple of minutes outside the world record, on a hot and sticky course, and then says:
"I had to push the pace because my body gets tired when I slow down."

Okay, that's my problem right there, I tend to get tired when I speed up. I knew I was doing something wrong.

Stick a needle in me

After yesterdays post I was musing on the nature of vaccination. What if we could separate the public and private benefits? Imagine there was a 'vaccine' for a serious illness, and it's hard not to think of AIDS, BUT it only conferred herd immunity not individual immunity. That is, there would be no individual benefit to taking it, but, if sufficient people were vaccinated, the disease would have a growth rate less than one and be eliminated.

How would such a thing be possible you ask? Simple, the vaccine would prevent you from transmitting the disease but would not prevent you from getting it. Assuming the vaccine had some level of side effects - say 1 in a million actually get AIDS from the vaccine - what do you think the rate of uptake would be?

Sad to say, I'm guessing it would be very low (<1%). People, they ain't no good. In fact I'm guessing that even with NO side effects the rate of uptake would be low. I'm not sure what the R0 for HIV is, but let's imagine that there needs to be 75% coverage to establish herd immunity. IF such a vaccine were possible should the government introduce legislation to make vaccination mandatory? Or would it be sufficient just to offer an incentive? How much? $10, $100, $1000? Should individuals who contract AIDS from the vaccine be compensated or did they accept this risk when they agreed to be compensated? Do you think we could realistically ever achieve a 75% vaccination rate?

And then just to make this more complicated, imagine this was a decision you were making not for yourself but for your children.....

Mad Cow

If I could be bothered I would have a t-shirt made that says 'Ask me anything about mad cow disease.' But I'll probably never get around to it so let's just pretend I have one. We didn't have much time to cover mad cow disease but I'm glad I was able to squeeze it into 20 minutes of summer's hectic schedule. If you have any questions about it please catch me in office hours or before or after lecture or by e-mail. As part of that generation that could have been killed it is a topic that has been of great interest to me. I'm also reminded of the subject every time they have a blood drive on campus (eg this week). There's something about knowing that your blood is considered too risky to be collected that brings the whole issue home. Even my wife who only spent a couple of years in England is not allowed to give blood.

As I think I wrote on an earlier post I'm not a vegetarian and don't have any particular agenda here. On the other hand, in the interests of full disclosure, I should say that since first doing some research about this issue in the mid-1990's I haven't actually felt like eating red meat....

Measles outbreaks

A news report was out today on the main CNN homepage about measles cases in the U.S. being at the highest level in more than a decade.

If this had been a few days earlier I would have considered using it as a exam question: 'Rewrite this article as if you had some basic understanding of herd immunity.'

There will always be some fraction of the population that cannot be immunized. However if a sufficient proportion of the rest are vaccinated those who cannot be vaccinated (who probably have more serious problems to worry about) are protected. So, not getting children vaccinated is not just a (probably misguided) attempt by parents to reduce their child's overall risk - it is also a selfish act that should be labeled as such.

(Of course I'd probably feel totally different if I actually had children myself. But I don't. I have a dog though and he's vaccinated.)

Midterm

Someone asked me when the midterm would be returned and without thinking I said it would be returned in section next week. Now that I think about it we will be grading it tomorrow, and maybe Friday depending how quick we are, so there's no reason we can't return it after class on Monday. If you have feedback on the format then please let me know, otherwise the Final is likely to be similar.

TUESDAY SECTION - Role play assignment for next week

Wednesday section, you can disregard this post because I'll hand out your parts in section today.

For the Tuesday section, I'm posting the parts for the role play for next week in the links section on the blog. The role play is called An Outbreak in Zentonia. The panel members are: a medical doctor, a disease ecologist, a newspaper reporter, a US congress member, a citizen in Zentonia, and an environmentalist. Please select a part that you would like to play for next week. Additionally, you may choose to be an audience member ONLY IF YOU WERE A PANEL MEMBER LAST ROLE PLAY. If you were in the audience last time, you must choose a panel part this time.

To print your part, open the Word document from the link provided, and scroll down. The first page is the introduction and moderator part (that's me). The next few pages are the audience part. After that you will find one page for each part as you scroll down: the role is listed about halfway down each page under the heading "Your role."

My goal for this week is for everyone to really stay in their role. Try selecting a role that you don't necessarily agree with, and play Devil's Advocate. It's fun, and it'll make the discussion more interesting, since many of us may actually have similar opinions.

Mad Cow USA

The New York Times had an article on Mad Cow disease and the fate of the US beef industry in June this year. It's a nice update of the current state of affairs in the US.

Relevant material previously on the blog:
Mad Cow USA
Sexually transmitted Lyme Disease ?
World's worst mouse plague

Good luck

One more, in honor of the Olympics.

Disease and culture

This week in section we will be discussing the interplay between disease and culture. We've already talked in lecture about several instances of culture/behavior impacting disease transmission. For example, boarding up windows in nineteenth century London kept the "miasma" out and the Tuberculosis bacteria in. Likewise, as mentioned today, people who like to hike around and live in rural, wooded areas in the Northeast are at greater risk for Lyme disease.

Sexually-transmitted diseases like HIV/AIDS are ripe with potential for both cultural differences in transmission and disease impacts on culture. Some reports (from research done mostly in Kenya and Uganda) have shown that circumcised men are around 50% less likely to contract HIV from heterosexual sex. In these countries, where circumcision in infancy is not the norm, the clinical trials involved circumcising adult men in a safe medical procedure. Many people may not know that in western countries, the female-to-male sexual transmission rate of HIV is very low (as shown in studies like this one). In a sense, western (American and European) females are essentially a dead-end host for HIV, since they can get the virus sexually from men but do not pass it on. Most of infected men contract HIV either by having sex with men or through intravenous drug use. On the other hand, women in Africa seem to be a more competent host, and African men contract HIV from heterosexual sex much more readily there. Though the scientific community does not yet know why, some reports suggest that this may be related to circumcision rates and concurrent STIs.

Finally, another huge source of new HIV cases in the US is from intravenous drug users (IVDUs, in the public health lingo). Australia has addressed this problem by creating needle-exchange programs that allow intravenous drug addicts to get clean needles. The US has thus far refused to adopt this strategy, which Australian National Affairs Editor Mike Steketee argues is a case of "ideology sometimes get[ting] in the way of saving lives." Is giving out clean needles as a public service antithetical to the "War on Drugs"? Does it promote drug use, or save lives? A similar ethical issue surrounds the question of whether or not to give school kids access to condoms in conjunction with sexual education. These are all direct ways in which our own culture may facilitate or inhibit disease transmission.

1918 flu

We won't talk about influenza for another couple of weeks but there were some news reports this weekend based around a paper to be published in Nature this week that shows that survivors of the 1918 flu pandemic are still producing antibodies to the virus 90 years later. It is not known how unusual this is or whether this is typical of immunity to influenza strains.

Relevant material previously on the blog:
Lyme Disease and President Bush
Now THAT'S what I call an ecosystem service.
Attack of the Lone Star
The Lyme Disease Controversy

Your Sunday public service announcement

Fluoroquinolones are a family of antibiotics with a wide range of action against both gram-positive and gram-negative bacteria. Because they are easily taken up by human cells, fluoroquinolones are commonly used against bacteria that inhabit host cells.

Unfortunately it appears that these very useful and widely used drugs may have a number of serious side effects. Just last month the FDA ordered their strongest "black box" label warning to alert patients to the danger of possible tendon ruptures and tendonitis.

The FDA is not releasing numbers but apparently there have been 'hundreds' of cases of Achilles tendon ruptures. Obviously there is an interaction with lifestyle here, and those that are physically fit, and put pressure on the Achilles tendon are most likely to be injured.

'Sometimes patients have no symptoms before they experience a rupture in their tendon -- commonly their Achilles tendon. Sometimes it's been reported on the first day of taking a fluoroquinolone ... a sudden snap or popping sound that is tendon rupture with no preceding warning.'

So, if you have to take an antibiotic for any reason, do your homework. Look up the side effects. If it seems you are at extra risk for those side effects (like you run or play a sport) then you might want to ask your doctor if there are alternatives. Quinolone antibiotics associated with tendonitis and tendon rupture include Cipro and generic ciprofloxacin, Factive (gemifloxacin), Levaquin (levofloxacin), Avelox (moxifloxacin), Noroxin (norfloxacin), and Floxin and generic ofloxacin.

Procrastination

When you are in college you get to spend long hours procrastinating when you should be studying for exams. When you get older and leave college all that changes. Unless you never actually leave college - then you can spend long hours procrastinating instead of writing exams. Inspired by this analysis of the Obama and McCain websites I ran the Disease Ecology blog through the Wordle website giving the picture you see above. The size of the word indicates how frequently it has appeared on the blog. I'm not quite sure how to interpret it (apart from the fact that I say and use the word 'interesting' too much), but it does look pretty

Back to the midterm.....

Oh, and there are some sample questions up. Check the link box at the top right.

XDR-Tb in California

This story literally hits close to home. The study finds that there have been 18 XDR and 77 pre-XDR cases in California in the last fifteen years. Most of them have been the result of improper Tb treatment (lack of medical supervision, misprescription of second-line drugs, etc) or HIV infection.

There's also an extensive article in the New Yorker about "Superbugs" that summarizes a lot of what we've learned about MRSA and other antibiotic resistant bacterial strains, especially those found in hospital ICUs. The amount of work and care required to sanitize a ward of Tisch Hospital at NYU infected by a completely resistant Klebsiella pneumoniae strain is impressive.

Gerbils and coffee

If you are reading this (someone is, right?) then you've probably noticed I try to post daily. Sometimes I have something in mind for the post, something I've found while preparing the lecture or something I didn't have time to mention. Sometimes I won't have anything particular in mind so I take a look at some websites to see what disease related stories I might have missed lately that are nice and topical. A good source for science stories, of all types, is Science Daily. They nearly always have some great articles and, conveniently, you can select stories by topic. For example here are their current Infectious Disease stories. Here's an item I missed a couple of weeks back. It has both gerbils and coffee - what's not to like? (I particularly like the way that although the coffee link is really rather tenuous the computer generated 'Related Stories' suggests a whole bunch of coffee related stories).

By moving through the coffee via the empty spaces between the ground coffee particles, the water picks up the flavour of the coffee. Stephen Davis and colleagues at the Faculty of Veterinary Medicine, Utrecht University, report in Nature their discovery that the spread of the bubonic plague bacteria in Central Asia by gerbils, works much the same way.

Plague bacteria percolate through the landscape transmitted by fleas from one great gerbil family to the next, from burrow system to burrow system. It’s the first time percolation theory is used to accurately describe the natural dynamics of an infectious disease. The discovery might be helpful to understand how outbreaks of disease occur in other populations. It may, for example, shed new light on spread of bovine tuberculosis in badgers, and spread of viral diseases in populations of African lions.

The only thing that bugs me about Science Daily is that they don't seem to provide direct citations to the source articles - just a couple of hints like the authors name and journal. It usually isn't hard to track down but I don't know why they don't give the full citation. Here's a link to the original paper - The abundance threshold for plague as a critical percolation phenomenon. It has a lot fewer references to coffee but it does have a very cool satellite photograph of gerbil burrows.

HPV and Cervical Cancer

I didn't have time to say much about the Human Papillomavirus vaccine but I did want to mention the issue. PBS have a very nice site from a show on the subject
You can watch the whole show at the site, or download it as an mp3 file to listen to, and also read an interview with a 'vaccine expert' that raises interesting issues and find out the basic facts about HPV and the vaccine. If you can't see what all the fuss is about take a deep breath and read some of the posted comments.

Also, over the next couple of days I will be writing the midterm and will post some sample questions here. I'll also put up a cumulative list of the terms we have covered to date (ie a subset of the larger glossary) which might be useful.

Relevant material previously on the blog:

Well, this post actually but I wanted to draw particular attention to it.
Solver for the SIR Model of the Spread of Disease
Vaccine safety
The height of reckless irresponsibility

Disease and human culture: next week's discussion section

Just to clarify, you will only be assigned to read ONE of the two papers for next week (either the Lafferty paper or the Fincher et al. paper)--Wednesday people, you will understand this tomorrow. I posted both papers on the blog in case you lost your copy I handed out or in case you were interested in reading both.

I realize that these papers might be a bit challenging (especially the methods section) for some of you who aren't very familiar with reading scientific papers. In my opinion that is part of the value of the exercise! However, if you're having trouble understanding part or all of your paper, please feel free to email me at mordecai@lifesci.ucsb.edu in the next week with questions. I want this to be a rewarding (not frustrating!) experience.

Also, to enhance our discussion, be thinking over the next week about examples of how cultural practice impact disease transmission, and how disease prevalence may in turn impact the development of human culture. Religious food and clothing taboos are interesting, for instance...

CCR5

If you are curious about how scientists go about working out whether Bubonic Plague could have been responsible for the increase in the mutant form of the CCR-5 gene (known as CCR5-Δ32) then take a look at this paper ' Evaluating plague and smallpox as historical selective pressures for the CCR5-Δ32 HIV-resistance allele' by Galvani and Slatkin. They suggest that smallpox might be a more likely cause than bubonic plague. I think the paper is quite accessible and you can see how they use simple genetic models to back up their argument.

'No single smallpox pandemic was as devastating as the Black Death, but the cumulative toll of human life caused by smallpox constituted an even stronger selection pressure than the episodic decimation of bubonic plague.'

Relevant material previously on the blog:

The Great Chinatown Fire
Flagellation in German rock video
Plague as a Biological Weapon

Cartoon fun

As I mentioned I'm a big fan of the work Richard Muller did in turning a non-majors physics course at Berkeley into a very popular and well respected course called called 'Physics for Future Presidents'. He has recently come out with a textbook with this title and, if you are interested in how an atomic bomb works, or in the future of solar power, you can check out his website and the lectures on Google Video.

However on one pedagogical issue I have to respectfully disagree. In the 'Contents, preface and pedagogy' section of the textbook he writes:
'I avoid cartoons and other images that suggest the student is "just a kid".'

Well as you've doubtless noticed I love cartoons. They aren't there to entertain the kid in you, they are there because they act as a sort of mirror that reflects back an exaggerated version of societies concerns, fears and opinions. A good political cartoon can skewer a politician much more effectively than much lengthier editorial columns. For the best in political cartooning check out Daryl Cagle's webpage where he collects all the daily editorial and political cartoons and indexes them by category.

Society is also reflected back in some of the strips in the funny pages. The ongoing, and usually interminable, soap-opera strips sometimes throw up surprising diseases stories. Months ago Rex Morgan M.D. started a tedious MRSA (Methicilin resistant Staphylococcus aureus) storyline that has only just wrapped up. I just checked and this storyline started sometime back in March. ..

I was reminded of all this because Mark Trail this weekend was reminding us to check our animals for fleas lest the Bubonic Plague visit us again.

Doctors without Borders

For some nice recent articles about TB and, particularly, about the development of drugs check out this webpage, the result of a symposium entitled No Time to Wait, supported by Médecins Sans Frontières (aka Doctors without Borders), in New York aimed at stimulating efforts to accelerate the development of effective new treatments for tuberculosis.

Olympic dream

What horse related fact links the 2008 summer Olympic games in Beijing to the 1956 summer Olympics held in Melbourne, Australia?

In both cases the equestrian events were held in a different IOC member states - but for opposite reasons. In 1956 the equestrian events were held in Stockholm because Australia's quarantine laws were so strict it would have seriously affected the ability of countries to bring horses into Australia. China was awarded the 2008 games, despite concerns about human rights, and about pollution but almost totally unreported by the press was the fact that the equestrian events would have to be held in Hong Kong because of concern about horse diseases in China.

Triclosan: Ubiquitious menace?

I mentioned the Triclosan issue today. Take a look at your cleaning products (both human, like soap and shampoo, and household) - I bet that several of them mention being 'antibacterial' and the product is probably Triclosan.

If you google the term you'll see this is quite a hot topic. A google news search throws up this article from a couple of weeks ago:
Environmental Group Calls Triclosan a Ubiquitous Menace

This presentation, Antibacterial Household Products: Cause for Concern by Stuart Levy, from the 2000 Emerging Infectious Diseases Conference in Atlanta, Georgia and on the CDC webpage is a good overview of the resistance issue.

Relevant material previously on the blog:
Minié balls and infection before penicillin
XDR-TB in South Africa
Pollution and Antibiotics

Old habits die hard

Douglas Manor, in Queens, New York, is known for its old-timers who swim in the salt water of the bay for their health. Many of these residents have been swimming in the bay for over fifty years, and locals claim that the neighborhood has had a tradition of swimming since the 1800s. Ironically, although the residents of Douglas Manor believe that swimming in the bay is good for their health, the bay actually has high levels of fecal contamination, and local health authorities often issue warnings against swimming in the bay after heavy rains. The stubborn old folks, known as the Floating Heads, often ignore these warnings and insist that "no one has ever gotten sick swimming in this bay" or that "the city posts the advisories for liability sake, so they can’t get sued if someone says they came down sick from swimming.” Other swimmers simply insist that they don't swallow the water while swimming. Is that sufficient to protect the body (especially an elderly body) against infection by fecal-borne microbes?

The Times article states that "Douglas Manor, an almost entirely residential area, is one of the few neighborhoods in the city without a sewer system. Opinions vary as to whether cesspools or sewers better contain sewage outflow to waterways during rainstorms." If only the Times could interview Joseph Bazalgette about the relative advantages of sewers versus cesspools.

Maggot therapy

Tomorrow we will talk about antibiotics, antibiotic development and antibiotic resistance. The widespread appearance of resistance and the presence of such problematic strains such as MRSA in hospitals has led to a variety of rather old techniques being reconsidered. One of these is maggot therapy and new work published last week suggests that maggots may lead to some new antibiotics.

Maggot therapy is an old idea where fly larvae are used to clean out wounds. This sounds gross but because most fly larvae only feed on dead tissue it is actually a surprisingly effective technique. Some of the most widely documented cases come from the US civil war where numerous cases were observed of soldiers left for days on the battlefield who actually fared better than those who had been in hospital - because fly larvae had debrided their wounds. Certain surgeons, most notably a confederate medical officer, Joseph Jones. started actively using maggots to clean wounds.

"Maggots.. in a single day would clean a wound much better than any agents we had at our command ... I am sure I saved many lives by their use. "

Because of the current problems with antibiotic resistance hundreds of healthcare centers are now investigating and using maggot therapy. UC Irvine is a US hotbed of maggot therapy and has a webpage with all the information, links and references you are likely to need.

Research by British workers published last week describes the isolation of compounds from the maggots that have antibacterial properties.

"Maggots are great little multi-taskers. They produce enzymes that clean wounds, they make a wound more alkaline which may slow bacterial growth and finally they produce a range of antibacterial chemicals that stop the bacteria growing.”

There's a short National Geographic video about Maggot therapy available on YouTube if you want to see some maggots in action. It's not super-gross but be warned it does contain maggots, an open wound, and maggots in an open wound.

Vultures, drugs and rabies

Over the last few years you may have heard stories about the decline of vultures in India. Population declines of over 95% were observed and some species may go extinct. One reason the press picked up on this around 2004 was the implication for the Indian Zoroastrian Parsi community, who traditionally use vultures to dispose of human corpses in "sky burials".

Eventually it was worked out that the vultures were dying because of a drug, diclofenac, commonly used in livestock. Vultures fed on livestock, ingested the drug, and died.

Now a new study, published in Ecological Economics this week, suggests that this loss of vultures may have led to an additional 50,000 rabies deaths in India. As the vulture numbers declined so the number of feral dogs increased. India has one of the world's highest incidences of rabies. and some of these dogs would have been infected with rabies. Calculations suggest an additional 5.5 million feral dogs between 1992 and 2006 leading to an additional 38.5 million dog bites. In India 123 people die of rabies for every 100,000 dog bites. This suggests at least 47,300 people died of rabies as a result of the vulture die off. Rabies is a very nasty viral disease which has a very high fatality rate. In fact, once symptoms develop, death is practically inevitable. There are only six known cases of a person surviving rabies once symptoms have developed. The best chance of surviving rabies is a prompt post-exposure vaccination that may prevent the virus from progressing to the symptomatic stage.

There is some evidence that vulture numbers may, in some areas of India, be starting to increase after the widespread use of diclofenac was discontinued.

Snippets

Here's a few news articles that caught my attention today. Two relevant, one not so relevant except that it argues for a greater familiarity with biology.

#1 A new report by the Centers for Disease Control and Prevention (CDC) shows the number of new HIV infections in the US is actually higher than previously estimated. The agency recently adopted improved statistical techniques that indicate that 56,300 people in the US contracted AIDS in 2006, up from the estimate of 40,000 that the agency has commonly cited as the annual infection rate.

#2 The death rate due to AIDS is so high in Uganda that a Ugandan official has suggested to MPs that funerals should be limited to Saturday afternoons to stop people taking time off work to attend them.

#3 British celebrity chef Antony Worrall Thompson has apologised after accidentally recommending cooks use a potentially deadly plant in organic salads. Thompson said he had confused henbane with a different plant. Presumably one that does not cause vomiting, convulsions and death.

This 'n that.

Well the first week is done. 16.6% of the course is over. I told you summer session was quick. Remember if you want to post here just send me an e-mail. You know you want to.... Even if you don't post anyone can respond to any of the posts - just select 'anonymous'. It just looks like you need a Google account because that is the default option.

Lecture slides are posted as pdf files usually within about half an hour of the end of the lecture to the right of this page. The glossary is also there and the syllabus plus your democratically agreed upon section rules and expectations.

Next week we will talk more about antibiotics and antibiotic resistance before moving on the the ever popular Bubonic Plague and a brief discussion of how the model diseases.

A smaller flea....

'a Flea Hath smaller Fleas that on him prey, And these have smaller Fleas to bite 'em, And so proceed ad infinitum.'
1733 Swift Poems II. 651

In the latest illustration of Swift's rule scientists yesterday published the first description of a giant virus that falls ill through infection by another virus.

This is re-igniting a debate about whether viruses are 'alive' or not “The fact that it can get sick makes it more alive.”

The giant virus which serves as the host (known as mamavirus), is itself found within single celled amoebae. A study of ocean water has revealed an abundance of genetic sequences closely related to giant viruses, leading to a suspicion that they are a common parasite of plankton.

“I think ultimately we will find a huge number of novel viruses in the ocean and other places,” Suttle says — 70% of viral genes identified in ocean surveys have never been seen before. “It emphasizes how little is known about these organisms — and I use that term deliberately.”

This isn't directly relevant to what we've been discussing this week, but the blog is also a place for breaking news.

Granted, this has become a tangent, but...

Speaking of well-known sewer systems, there is an urban legend that alligators once inhabited the Manhattan sewer system. The story goes that short-sighted New Yorkers would vacation in Florida and bring back adorable baby alligators as pets. Unfortunately, when these pets grew beyond their owners' control, panicked parents would flush the alligators down the toilets, leading to colonies of subterranean alligators living in the sewer systems. These alligators somehow eventually lost their eyesight and became albino (or so did their progeny, in some feat of rapid and potentially Lamarckian evolution). They are also reputed to protect the stash of "New York white" albino marijuana, also rumored to grow in New York sewers. Thomas Pynchon gives credence to these rumors in V. by giving Benny Profane a job wrasslin' gators in the New York sewer system. None of these tall tales, however, are thought to be true.

Tuberculosis and AIDS

Voice of America had a report yesterday on the problem of Tuberculosis for AIDS patients.

Tuberculosis is one of the leading causes of death in people with HIV, resulting in an estimated13 percent of AIDS deaths worldwide. As Véronique LaCapra reports, doctors working with the World Health Organization stress the need to coordinate the response to these two catastrophic epidemics, and to integrate TB screening and treatment into HIV care.

The report is inspired by, and refers to, this paper in the Journal of the American Medical Association: Opportunities and Challenges for HIV Care in Overlapping HIV and TB Epidemics

Relevant material previously on the blog:
Tuberculosis and vampirism
More vampire

To boldly go...

I was looking for some pictures of Bazalgette's sewer system when I came across the Sub-Urban website. Several of their explorations nicely document some of Bazalgette's original sewers and the scale of the system is impressive. It almost makes you understand why someone would want to explore it....

International year of sanitation

The UN General Assembly declared the year 2008 the International Year of Sanitation. Check out their website.

Cholera in Iraq

Iraqis fish in the Tigris River next to a sewage pipe.

From an AP article in the Houston chronicle last week. Two-thirds of the raw sewage in the capital flows untreated into waterways and residents in parts of the city still get their drinking water from the river.

"Iraq is on the cusp of a serious water crisis that requires immediate attention and resources," said Thomas Naff, a Middle East water expert at the University of Pennsylvania.

The World Bank has estimated that it would take $14.4 billion to rebuild the Iraqi public works and water system.

Relevant material previously on the blog:
The ghost map
Expecting the unexpected