The 30th Anniversary of the Culture of Helicobacter pylori

On Easter Thursday 1982, which was the 8th of April, we performed endoscopy on a man in his 60's who I recall had a recurrent bleeding duodenal ulcer.  This was a major problem for him because he also had a heart valve problem and therefore was required to take anticoagulants (making him more likely to bleed from the ulcer).  Dr Warren and I were in the third week of a study of 100 consecutive endoscopy patients and we had already entered more than 30 patients in the study.  I took two gastric biopsies to the pathology lab and one to the micro lab (for Dr Pearman).
I have no idea what I did that Easter but I suspect that I was on-call as registrar in haematology with many very sick patients to attend to.  Luckily I lived only 15 minutes from Royal Perth Hospital.
In Perth, the Easter Break is four days (Good Friday to Easter Monday incl.) so the bacterial cultures which had been set up on the Thursday morning were not examined until Tuesday morning, at which time the typical "water spray" appearance of Helicobacter colonies were visible.
The next day, an excited John Pearman called me to come and see the bacteria they had grown from a patient cultured the previous Thursday.  He showed me the culture plates and we peered at the Gram stained smear of the bacteria through the lab microscope.  The bacteria were Gram-negative - pink (at least that part was correct) but were not obviously spiral - they were all shapes and sizes!  After 6 months of disappointment, I was not going to break out the champagne on such borderline evidence of success.  After all, why should we suddenly be able to grow the bacteria when all other attempts had failed?  What were we doing differently?  In the next week John's lab was able to culture Helicobacter (which we called Campylobacter in those days) from several more patients.  Reflecting on this, we realised that in the previous attempts, lab staff had been examining the plates after 48 hours then discarding them if nothing new was visible.  After all, biopsies covered in saliva and dragged up from the stomach through the channel of an endoscope would be severely contaminated with commensal organisms.  These irrelevant "commensal organisms" (fungus, oral streptococcus, bacillus and hundreds of other species) would be expected to completely cover the plates after 48 hours and obscure any new kind of bacteria.
But biopsy specimens taken from the human stomach for Helicobacter were a little different.  The wall of the stomach is exposed to a puddle of acid which kills most of the bacteria being swallowed from the mouth.  So the biopsy samples were sometimes almost sterile (except for Helicobacter pylori which lives under the protective mucus gel layer); and even non-selective blood agar plates could be incubated for 3-5 days with quite a few areas of clean agar visible upon which Helicobacter could slowly grow.
Normally, after two days, the lab technician would have discarded the cultures after seeing nothing worth keeping at the 48 hour inspection (Easter Saturday).  However, that Easter may have been particularly busy so that urgent cases took precedence over our clinical research; which was regarded more as a hobby than as science.  I recall that there was a MRSA (methicillin resistant staph-aureus) control program in the hospital that month so maybe the microbiology staff were overloaded.  In any case, on Easter Saturday, the technologist did not examine the research cultures and left them to sit for three more days until the Tuesday morning examination.  The first culture plate probably looked like this:

That first culture became the "type strain" of Helicobacter pylori, ATCC #11637.  This bacterial strain has been studied by thousands of research labs and costs £150 to obtain from the NCTC.  You can read about the type strain of Helicobacter pylori here: pdf file of NCTC citation copied on 2012-04-04

Are Aircraft Cancellations Really Necessary for Ash Clouds from Volcanoes Thousands of Miles Away?

There are four well described cases of flameouts caused by volcanic ash clouds which have been extensively studied and recorded. The article linked here by Marianne Guffanti discusses all these episodes and reviews the issue of volcanic ash in detail. One concludes from the article that there is actually very little data available on the subject.

The most famous near-crashes are:

1982, BA 9, Boeing 747, London to KUALA-LUMPUR to PERTH, Mount Galunggung volcano, Indonesia. Distance from Volcano = 100-200 km.

1982, SQ, Boeing 747, probable international flight, Mount Galunggung volcano, Indonesia. Distance from Volcano = Uncertain - but nearby.

1989, KLM, Boeing 747, Near Redoubt volcano Alaska, about 135 km from Anchorage.

2000, Unknown airline, Boeing 737-800, Mijake-jima volcano, Distance from Volcano = about 130 km (near Narita airport).

In all cases the plane was practically in sight of the volcano and flew into a dense cloud.

Mt Redoubt is 135 km from Anchorage so that ash cloud was very fresh. Actually, the KLM pilot described it as a "black" cloud.

The British Airways flight 9 to Perth was 100 km from the active volcano Mt Galunggung volcano and experienced a total flameout. The other episode occurred a few weeks later in the same area and that plane landed on two remaining engines somewhere in Indonesia.

There is only one likely report of engine damage after a faint ash cloud was penetrated by a jet. In the detailed report linked here, Thomas J. Grindle describes the case of a research DC-8 NASA jetplane which flew into a cloud of ash coming from Mt Hecla in Iceland. The cloud was not noticed by the crew but instruments recorded the event and they did not the absence of stars for 7 minutes. Aerosol of 20,000 particles per cm^3 were detected for seven minutes, as well as sulphur. The flight path was 800 miles north of the volcano and supposedly 200 km away from the cloud. The plane flew normally for another 47 hours then was inspected. There was internal abrasive engine damage probably caused by the ash cloud, although it is admitted that it had flown through a sandstorm a few days earlier after which no damage was discovered on internal inspection. This event is taken as evidence that even an invisible ash cloud can damage a plane. However, it is possible that the cloud was much denser than they thought since it was nighttime. Also, it was surprising that the windshield was not abraded, just the engine, which would support the sandstorm hypothesis since "sand blasting" was only seen in the engines. If the inspection after the sandstorm was deficient, would they have questioned it in the official report when at the time, it had little relevance?

Based on these data, should Australian travellers be grounded? The idea that an ash cloud could circumnavigate the globe and then, even though it appears to be a transparent brown stain on a satellite image, could noticeably affect a plane, has been accepted without question by Australian airlines. This is clearly a situation far beyond the actual recorded cases.

Presently, ash from Chilean volcano Puyehue must cross the Atlantic and Southern Oceans, a shortest distance of about 11,000 km and a "cloud path" distance of 19,000 km. The "ash cloud" is visible in thin streaks of light brown transparent air by satellite images. There is no apparent data as to how much ash is actually present. However, it logically would be extremely diluted. Its transparency must indicate a very small amount indeed.

An animated image of the ash cloud is shown below.

Like many things airlines do, cancelling Australian flights because of a Chilean volcanic eruption, has very little basis in fact. It might have about the same safety benefit as preventing people reading their Kindle during landing. The current cancellations of flights in Australia have affected more than 100,000 travellers but no-one has looked again at the evidence base for cancelling flights. Meantime it costs aviation, and the public, tens of millions of dollars (in Australia) and probably hundreds of millions in Europe and the USA (but there they are at least much closer to the volcano - typically planes are flying close to iceland and parallel to the ash cloud).

It would make sense to have research planes fly through the transparent ash cloud and take measurements so that we know how much ash is actually present when a cloud is visible. After that, the engine effects could be correlated with the air sample measurements. These could be posted on the web as ash concentration charts. Then we would know. There are other dissenting voices on the web, read the pilots forums.

June 21st 2011

My Latest Genome SNP report from DeCodeMe

This post is an update on my SNP genome scan report in which there has been a few developments. It came about because my dad (Bob Marshall) had his 80th birthday last week and we made a detailed report on his ancestry based on DeCodeMe. By the Y-chromosome he was related to Somerled the Viking-Scottish 12th century king (as are millions of other caucasians). However, I noted the high risk he has for macular degeneration (5x, 46%). This rang a bell because his grandmother (Jessie Boneham) went blind after "she had her cataracts removed but the operation didn't work" suggesting retinal disease after age 85 years. Anyway I looked again at my age related macular degeneration risk and see a lesser but elevated risk (2.88x, 23%). Last month my eye exam was normal except for early arcus senilis and slight refraction problems. I'll continue with a two yearly check. This year I decided to seriously attend to my blood pressure (erratic and about 20mm above ideal levels if not treated) and also my cholesterol. My SNP risks reflect a 50% risk of hypertension, as well as diabetes, obesity and heart attack (although modestly elevated). Good news is that my risk of muscle damage from my statin is low so I can take these with impunity. My recent blood pressure readings are graphed in one of the documents on the web site. An episode of angioedema caused me to change my ACE inhibitor to an ACE receptor blocker and so far I have not had any more side effects.

You can read my full SNP report plus other health reports here: http://www.bajama.mine.nu/~barry/decodeme/ . I also include an AVI file showing a movie of my coronary calcium CT scan and you can go into the directory below to see my actual raw SNP data in case you want to research it. I don't know what use this information is but I do want to hold true to my idea of a public health record. More and more people care less and less about this type of data - its becoming so common.

What else is new? Well, I am saving up to have my total genome done. I would also like to do my whole family, but the Western Australian DNA bank refuses to store the DNA at present. They are so precious that they only do storage for bona-fide research projects, not for people like me who are just exploring their own family. So I may just keep it frozen in the back of my -80C refrigerator at the H.pylori Research Lab.

So much data privacy - so much wasted value - I opted out and put my genome on the web here

Time and time again my research has been slowed down by difficulties accessing research data. Some groups are determined to make it more and more difficult to access data for research. Data mining - I don't care as long as there is no malicious intent. Congratulations to the USA government for introducing the non discrimination for genetic data act. This means that US citizens need not worry about higher premiums on the basis of their genetic code. In Australia where we have free universal health care, and private medicine if you want a premium convenient service, we should have no serious concerns about health insurance discrimination.
In the meantime, I am sharing my genetic code profile. This was quite an expensive effort but the number of disease related information items increases by about 6 per year. Over the next 20 years I expect to see 120 diseases and risks laid out for me in the report.
You can look at my genetic report here:
Have fun!

make a Conference Trip from Australia to the USA - Without Killing Yourself!

In April this year I might have found the best combination for a trip to the USA from Australia incorporating an important international conference and several lectures. Try this schedule if you can.

1. Allow for a low activity week prior to departure. You will likely have visa and travel arrangements, family visits and last minute supplies to organise.
2. Make certain that all you computer backups are be up-to-date.
3. Test that all your essential files are accessible via the internet while you are away. With "cloud computing" you can now have a shared folder to use from anywhere. I use "dropbox" and have a 50 Gb space there. Just watch out if you go to China, you might be blocked by the big firewall. With DropBox you can use a folder you have already created, but cannot access the web interface.
4. Subscribe to a "hotspot" wireless network so that you can check email in the airports and coffee shops without incurring Telstra roaming fees (I find Boingo is the best).
5. For non-electronic communications, set up paper mail forwarding, letterbox checking and junk-mail removal by the your neighbours. Also notify neighbours you will be away.
6. Delegate academic tasks requiring deadlines to trusted colleagues.
7. Pay cellphone bills and top up credit cards in advance so that your telephone doesn't go off-the-air before you return.
8. Carry a secure thumb drive with your recent work on it.
9. Check that you have done the ISTAR USA visa form on-line (this is even necessary for Aussies. We are descended from convicts remember!).
10. Don't drive yourself to the airport. You will be too rushed. If the taxi service is not 100% reliable, have a backup plan. Preferably, pay the extra $50 to have a private car service take you to the airport.

In the USA, address the issue of Jet Lag by arranging a schedule as follows:

• When arriving in the USA from Australia, try not to do anything critical for at least 4 days. If you immediately attend a conference you will sleep through it and learn nothing so your whole expensive trip will be wasted. Therefore, one strategy is to enter via Los Angeles on Monday or Tuesday, then continue straight through to Las Vegas for 4 days rest (Wed-Sat).
• Day 1-4: Sleep as much as possible, swim and walk around the streets for exercise and experience the sunny climate which helps you change your sleep/wake cycle. You don't have to gamble but Vegas never sleeps so at 3 am you can go out to eat. The Hotels are excellent with world class variety shows. Also, there are great outdoors attractions such as the day trip to the Hoover dam. All the top US technology stores are available and fast internet is the norm if you need to work.
• Airlines in and out of Las Vegas might be less reliable as they are the cheap flights. Also they have luggage limits sometimes.
• Day 5-9, (Sat-Wed): Travel to your final conference destination.
• Maximise your conference value by staying in the actual conference hotel because you can take a nap in the middle of the day so as to be fresh for the afternoon sessions. You also save bus travel time and/or cab fares. When looking at the actual extra cost, $150 per day extra is probably money well spent.
• Day 9-12, (Thur-Sun): Take a second break incorporating the weekend. This might involve a travel day and a rest period in a city where you can visit relatives or friends.
• Day 13-17 (Mon-Fri): These are more work days travelling to visit colleagues, conduct business, give seminars etc.
• Day 18-21 (Fri-Sun): These are final wind-up, consolidation and recovery days in preparation to travel back to Australia. In my case this involves one day of travel back to Los Angeles. Then during this weekend I recommend staying in Burbank - actually the Residence Inn - where you can have a hotel suite, free internet and free breakfast. While organising for travel back to Perth, do some final shopping, see a movie, enjoy the climate and throw away anything you don't need (especially conference materials). On the Sunday morning, my "must see attraction" is the Page Museum in central LA which incorporates the La Brea Tarpits which have trapped hundreds of prehistoric mammals. The LA Museum of Art is next door with a nice restaurant. Finally, allow two hours for a visit to Fry's Electronics, the world's largest electronics and computer gadget shop (it has 68 checkouts).
• Day 21-22 (Sun-Tues): Fly back to Australia. Realistically, four hours of low intensity laptop work, reviewing manuscripts etc. might be done during the trip. However, dry eyes and poor posture often limit this to less. Don't start something you cannot finish in the time available - you may not get back to it for several weeks. If you plan laptop work make sure you charge the PC before leaving. Sometimes the older planes do not have a compatible power connection, even on business class.
• Day 23-25 (Wed-Fri): Only essential work duties are possible. Don't expect to safely perform high level patient care or intensive administrative activities. My typical day starts at 4-6 am with 2-3 hours of email and document work, then 4 hours at the University from 9 am -1 pm, then a 2 hour nap after lunch and then an evening event from 6-9 pm.
• Day 26-27 (Sat-Sun): Perform activities necessary to follow-up from the international trip and revert to normality.
• Day 27-30 (Mon-Wed): Allow for a gradual return to normality. I notice that a depressed mood can continue until 12 days past the day I left East Coast USA. Thus, on the above trip, which allows for three final recovery days in Los Angeles, I am completely normal one week after arriving back in Perth.

There is often a temptation to extend a USA trip with academic activities at the end. My experience is that I am looking forward to going home by three weeks and I always regret the fourth week away. So in reality, a conference in the USA requires at least 14 days of related activity and 7 days of recovery time. If extra lectures are planned then allow a 50-50 split between R&R and work or you will burn out. Tomorrow I leave for a three week USA - Europe - UK - Asia international trip with just a carry-on cabin bag. My best record for this is 5 countries on three continents in three weeks but it was gruelling and my follow-up afterwards was very inefficient.

Words to avoid in presentations and in speech

This month I have decided to go public with my list of “meaningless words” which should no longer be used in public, especially not in meetings or presentations and never on TV or radio. Here are the ones I recall today.

1. Basically
a. This word has become a favourite of scientific people especially when they are answering questions. I am also guilty. Example as follows - Question: If the DNA is copied until the primer just falls off, how is it that all the pieces of DNA end up exactly the same length? Answer: Well, basically, you are almost correct however, only the first copy gives a random length. After that, basically, the primer in the next cycle has to start 637 base pairs from the start point of the first copy. So, basically, all except the first copy are the same length, basically 637.
2. I mean
a. This seems to be used as a spacer between sentences, where the speaker continually likes to embellish details and add ideas. I mean, just as one would normally give the listener person a chance to talk by leaving a short gap in the conversation, by using “I mean” the gap is stolen back so that the normal person might not get a word in edgeways. I mean, let’s say that it was you being the listener, and you are a nice polite person; I mean, like Marj in the Simpsons. Then you never have a chance to speak because ...
3. Sort of
a. A vague term implying that the speaker has not put any thought into the discussion and is sort of making stuff up as he goes along. This seams to be common in presentations from young artists.
4. Yeah
a. Australians have become adept at placing this word in the middle of sentences as some kind of emphasis. I think it is very common in interviews with surfers; yeah – .
5. Absolutely
a. Television personalities, especially on gardening shows, continually say absolutely. Then the show “Absolutely Fabulous” started up perhaps as a send up of this trend. Recently it has been used more and more by almost everyone. By adding this word, a very vague concept suddenly becomes absolutely correct and proven beyond all doubt. Also, other words can be added to it, especially “fabulous” to make something rather mundane and boring into something apparently exciting. Take the concept of picking up handfuls of animal poo. We don’t have smellovision yet, and the warm temperature of a putrefying heap is hard to transmit to the gardening audience. But I can call it compost and say how this material is absolutely the best thing for your garden. How absolutely fabulous it is to feel the warmth as you thrust your hands into the pile in order to experience nature as the good bacteria convert biodegradeable organic material into absolutely perfect plant nutrients. Actually, it sounds rather attractive as I write this.
6. Umm
a. A non word, also used as a spacer to stop other people butting in. Luckily there is no need to use this on TV interviews because a smart editor will cut out all the wasted time anyway, so as to add more content, or another “non umming” person to the time allocated for the story.
7. Like
a. This word is more often used by teenagers – or even myself actually – as emphasis in a story. But it is used rather informally, among friends, with alcohol on board usually, and often as a preamble to an acted out part of the story telling. I am having trouble explaining it but here goes. Just say that I am telling you about a scene from the movie Avatar. So the main actor Sam Worthington is just a dumb marine so he’s like, “I need to walk again so I will do anything to pay for an operation”; but Sigourney weaver, she’s like some kind of genius professor so she’s like “don’t break the machinery you dumbass!” etc.
8. You know
a. Everyone uses this Phrase, again a spacer to show that you probably don’t know all the facts but what you say is probably about right. Of course, as the brainy listener, you probably have more information or already have heard this story, but if you do know it you would not be so rude as to correct the speaker or embellish his own story. You know.

I think it might be fun to add a few more of these and give funny examples. It would be good practice for a screen writer in a sitcom. My son reminded me of a program we used to have which converted normal speech to “Jive” which was a kind of black American street gang speech which most Australians would hardly ever hear but probably rappers and people from Los Angeles might be familiar with. Time is up – I can’t spend my life just doing a blog. Back to real life.

Singapore Airlines wins Hand Towel Stakes: Secret Technology Revealed

Nobel Laureate's Travel Log: Hot Towels! Who would have thought they were so difficult to get right. The best hand towels are from Singapore Airlines. The luxurious cotton towels arrive hot but not scalding, damp but not dripping wet and are very lightly scented. In comparison, Qantas towels are tiny scraps of material with no pile on the towel, usually dripping wet, and often too hot or too cold because they don't have enough substance to retain any heat during distribution. Emirates towels are a little better but no-where near the SA standard. Cathay Pacific are close but not quite as nice as the SA towels.
So that I could spend the remaining years fo my life sometimes using decent hand towels, I obtained the secret hand towel formula from SA. Here is how they do it (this could be a draft S.O.P. for the rest of the airlines).

1. The plush cotton towel weighs 21g dry and 55 grams wet.
2. It is 12 inches by 9 inches and has the SA logo in the top left corner (see picture)
3. The required amount of water is added to the towels.
4. The towels are microwaved to reach a temerature of not more than 50C
5. Before distribution, the temperature of the towels is tested with the back of the hand to make sure they are safe to use.

The sad thing is that Qantas staff probably never fly on other airlines, or apparently have no way of providing input into the proceedures they use every day. The low quality hand towels have persisted for several years already so maybe they can try to match the world best. I have other suggestions for Australian travel industry which I will put here from time to time under "Travel Log" subheadings. Watch out for next week's entry which will be "Security".