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@MackayIM

2 Jan

What is a PCR cycle? 🧵
We sciencey types throw in words that we use for a specific purpose, but which also have other everyday meanings among most of the people on the planet.
We don't see that we do this ALL. THE. TIME.
"Cycle" is one of these words.

Here we're using "cycle" as it relates to the PCR = Polymerase Chain Reaction - a small, enzyme-driven cyclical DNA amplification reaction that we use to detect virus & do other sciency things (longer story)

When we do PCR to detect an otherwise undetectably teensy amount of DNA, we run 40 to 50 cycles of PCR. These 40 to 50 cycles (precise number varies by lab & kit) = the whole experiment (or "PCR run"), all of it.

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@MackayIM

30 Dec 20

Anatomy of a real-time PCR or RT-PCR (PCR or RT-rPCR) curve.

Two things to highlight using these stylised rPCR curves.
First.
The yellow arrows highlight threshold cycles.
These are the "results". The number from the point at which each curve crosses that arbitrary horizontal threshold are recorded by the lab and reported as "detected"

Second.
These values are *not* the same numbers as the TOTAL number of cycles that the rPCR is run for (you can read about cycles here if of interest virologydownunder.com/the-mechanics-…)

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@MackayIM

21 Dec 20

This morning, my early 🎄 present was showing signs of life!
#AussieMushrooms

And tonight...I'm starting to feel in mildly alarmed

Far out!

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@MackayIM

9 Dec 20

That website opinion attack piece on the Corman/Drosten RT-rPCR tests has a few confused & sometimes very wrong comments.
I'll preface this thread with a *presumption* I'm making - these authors haven't worked on or with this test themselves. And that matters a lot if true.

I'm not going through everything but here's one from their "Top10 things I hate about this test" list.
From Number 5. "nor does it contain any other negative controls"
But Corman et al. are actually very clear that negative controls were included.

"all assays were tested 120 times in parallel with water and no other nucleic acid except the provided oligonucleotides. In none of these reactions was any positive signal detected"

But even better, they tested primer specificity on a lot of human viruses, including CoVs:

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@MackayIM

9 Dec 20

Lyssavirus infection confirmed in Far North Queensland as bat-related injuries rise
abc.net.au/news/2020-12-0…

"While ABLV is more likely to be found in a sick or injured bat, bats that appear healthy may also be infectious."
conditions.health.qld.gov.au/HealthConditio….

"In Australia, evidence of ABLV infection has been found in species of flying foxes/fruit bats and insect-eating microbats. It is assumed that any bat in Australia could potentially carry ABLV"
health.nsw.gov.au/Infectious/fac…

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@MackayIM

7 Dec 20

@figshare

Hey all, if you want a mug like this; a guide.
Check my pinned tweet thread. Near the bottom is a link to my @figshare page where there's an editable .svg (Other images there as well).
I use @inkscape to make & edit .svg files.
Install the font I used (Repirse Script) *first*,

or use your own.
Edit the image to remove the text in the bottom right. Or keep it. Also think about squashing the image a little vertically tighter so it stretches further around mug, horizontally.
Export in a relavent image format (I save as .png format for here & my blog)

@Vistaprint

Next, find your local mug-making site. I used @Vistaprint but closer to home means faster delivery. Pick a mug colour (find another site if you can't get mug colours!). Place your image as a wraparound using the site's tool. Pay.

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Try unrolling a thread yourself!

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ɪᴀɴ ᴍ. ᴍᴀᴄᴋᴀʏ, ᴘʜᴅ 🦠🤧🧬🥼🦟🧻

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