Thursday, April 05, 2012
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
Tuesday, June 21, 2011
Wednesday, January 12, 2011
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.
Thursday, September 02, 2010
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:
Sunday, May 23, 2010
- 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.
- Make certain that all you computer backups are be up-to-date.
- 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.
- 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).
- 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.
- Delegate academic tasks requiring deadlines to trusted colleagues.
- Pay cellphone bills and top up credit cards in advance so that your telephone doesn't go off-the-air before you return.
- Carry a secure thumb drive with your recent work on it.
- Check that you have done the ISTAR USA visa form on-line (this is even necessary for Aussies. We are descended from convicts remember!).
- 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.
- 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.
Sunday, April 25, 2010
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.
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 – .
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.
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.
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.
Friday, November 13, 2009
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).
- The plush cotton towel weighs 21g dry and 55 grams wet.
- It is 12 inches by 9 inches and has the SA logo in the top left corner (see picture)
- The required amount of water is added to the towels.
- The towels are microwaved to reach a temerature of not more than 50C
- Before distribution, the temperature of the towels is tested with the back of the hand to make sure they are safe to use.