This PCR is extremely Wittwer

Posted by John on 28 January 2015 | 6 Comments

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OK, confession time. I used to work some crazy hours in order to fit some library screening into a part time job while finishing my degree. No, that's not the confession - more, when I put the PCR on I would sometimes look out the window and note the wind direction. Occasionally, very occasionally (*cough*) if the wind was blowing in the right direction and looked right, I would walk home  - paraglider in the car- drive out to the Otago Peinsula and if I was lucky soar above a beautiful beach for a couple of hours. Land, back it the car and 20 minutes later I'd be back in the lab to run the gel. Three to three and a half hours from putting on the PCR to running the gel.

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qPCR inventor and his NZ connection

Posted by John on 11 May 2014 | 3 Comments

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So you might have read the previous entry about the visit to see the first thermalcycler "Mr Cycle" at the Smithsonian. You haven't? No problem, I'll wait while you jump over to have a read . . . .
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I mentioned to Mallory (who kindly showed me the items) about the invention of qPCR and the original apparatus. Upon leaving, I contacted the person involved in those early days (including the photo of myself with Mr Cycle) and he replied back about how Mr Cycle had been on the bench next to him when he joined Cetus. Unfortunately the original qPCR apparatus had been disbanded - as he wrote "It was really just a light stand, a camera, a thermocycler, a light source and a PCR brought together"

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Visiting the original PCR

Posted by John on 23 February 2014 | 4 Comments

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A trip to the USA last year was a a chance to mix business with pleasure. Usually these are two separate entities but one that combined both occurred on a trip to the Smithsonian Institute (American History Museum) in Washington. While Belinda headed off to see the First Ladies' dresses, I was lucky enough to head behind the scenes to a particular storeroom in the Smithsonian. This in itself is not particularly exciting since the Smithsonian only has a fraction of its items on display at any one time so must have more storerooms than display rooms!

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PCR turns 30

Posted by John on 2 November 2013 | 6 Comments

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A revelation comes in different forms. "Eureka!" called Archimedes and ran through the street naked.
"Holy shit" said Kary Mullis in 1983 and pulled over to the side of the road he was driving on (although the word 'naked' does appear in the title of his autobiography). Mullis had just conceived the concept of the polymerase chain reaction or as better known to us all as PCR.

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Come in spinner

Posted by John on 14 April 2013 | 2 Comments

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That last little job before running your qPCR - no, not trying to remember which random sample you loaded in the wells; rather, centrifuging down the reactions to the bottom of the wells. This removes air bubbles and ensures all reaction components are combined.

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two better than one

Posted by John on 10 September 2012 | 6 Comments

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Working with RNA viruses (and multiple isolate strains), sometimes it can be hard enough to get sufficiently conserved sequence for primers (and harder if designing a TaqMan or probe-based assay). However a recent example in our lab showed the benefit of designing multiple assays for the same target and comparing the performance across template dilutions.

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Posted by John on 24 January 2012 | 5 Comments

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Happy 2012 to everyone. Of course I relate most things to PCR stuff (well, this is a PCR blog) and this year marks 20 years since I first did a reaction. Which means it's 20 years since my first blank gel and 20 years since I amplified strange bands, wrong-sized bands - before hitting the conditions and getting it right.
Or at least for the positive control. . .

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New Zealand scientist "on a par with Galileo"

Posted by John on 1 August 2011 | 1 Comments

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An interesting article on Allan Wilson (with the words used in this subject line) in the latest issue of NZ Listener  - promoting the upcoming lecture tour by the PhD student who, with Wilson, published on "mitochondrial Eve" - our common female ancestor from Africa.

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room temp stable

Posted by John on 6 February 2011 | 0 Comments

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Well, not wishing to brag as the temperature heads over 30 degrees again but the warm weather here in Gisborne made me think of the question we're often asked about the PCR reagents we sell from our European manufacturer Solis BioDyne. Yes, all their reagents (dNTPs, ladders, PCR masters etc) are stable at room temperature for up to a month and we're often asked 'how stable are they really?)
Solis regularly demonstrates the stability of their enzymes and the hot weather here made me think of a recent demonstration they showed - and kindly let me reproduce here. As they say, a picture speaks. . .

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making one band from many

Posted by John on 11 October 2010 | 0 Comments

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This article was originally published at BitesizeBio here
It’s the molecular biologist’s version of ‘I have good news. . and bad news’.
The good news is that I amplified the DNA band of interest. The bad news is that I amplified these other bands as well! Oh, and this smear. What to do?
Typically you might try and cut out the band of interest and gel-purify – an issue if it’s a lower intensity product and most of the DNA is lost in the subsequent purification. Or the products are more closely spaced than your dexterity allows.

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