Bubble, bubble, toil and trouble…

When I’m starting off with a new class, and encouraging them to “have a go, because, after all, what’s the worst thing that can happen?”, I like to tell them about when I myself was in Year 10. My best subject of that year was History, and we had been studying the Renaissance and the Voyages of Discovery. As the end of topic test approached, I was vying with my best friend, Chris Mortimore, for top spot in the class (this was back in the days when class results were pinned to the classroom door for all to see). Lots of the available marks were for key dates, who did what to whom, or when did how to what, and so on…. I learned them all. Or nearly all.

When the final results were read out, Chris had beaten me to first place by one mark, because he had learned one date that I had not – 1517, the year when Martin Luther nailed his theses to the church door in Wittenberg and kicked off the Reformation. Nearly 40 years later, the only date I can remember from that year is the one I got wrong.

So my message is that getting things wrong is a really powerful way of learning. Don’t be scared of making a mistake – it will help you remember, it will help you learn.

It can also be a barrel load of fun, as my Year 10s found last week.

The context was Respiration, exploring this idea that living things need to release energy from food, and that while the reaction is chemically identical to combustion, the actual process must be slower and more controlled and take place at remarkably low temperatures, something made possible by the wonderful enzymes they learned all about in Year 9. I show them some yeast in a warm water bath, bubbling merrily away after the addition of some sugar. Look, I say happily, here’s an example of a living organism respiring sugar, using enzymes to do so, and producing carbon dioxide as a waste product.

They nod with varying degrees of enthusiasm and understanding.

But hang on, I say, how do you know that any of that is true?

They stop nodding and look puzzled. What do I mean?

Why take my word for it? I’ve just told you a whole load of stuff about what’s going on in that boiling tube – you’re just going to accept it on faith? What kind of scientists do you think you are?!?!?

They continue to look puzzled. Where is this going?

Go on, I say, design some experiments and test at least 3 of the statements I’ve made about respiration in yeast.

Both of my classes, Set 1 and Set 2, found this wonderfully difficult. Firstly, they struggled to grasp what I actually meant. I tell them to go back to the statement:

here’s an example of a living organism respiring sugar, using enzymes to do so, and producing carbon dioxide as a waste product

and think about how they could test the veracity of otherwise of what it says.

OK, they say, we could test the gas to see if it really is carbon dioxide….

Right! That’s the idea! Off you go!

Even on this easy starter for ten, there are some hilarious moments. The demo I showed them had a delivery tube passing bubbles through a test tube of tap water. Many of the groups let the gas bubble through the tap water and then attempted to collect the gas with a syringe, and then squirt the contents of the syringe through some lime water. When I suggest that they just move the delivery tube to a test tube full of lime water, they look at each other, and then laugh in mutual recognition of their own inability to see the simple and obvious. No matter – they won’t forget this experimental detail ever again.

I was also hugely amused by the group who tried to establish optimum temperatures of 37’C by heating the tube directly in the bunsen….

And then they really struggled. What else could they do? I tell them not to over-complicate. They have a very simple experimental set up – they only need to tweak the contents of the tube to test the other assumptions.

But what other assumptions????

And then, slowly, group by group, they started to see it.

What if we left out the sugar? What indeed! Try it!

They try it and, lo and behold, there is no bubbling. Seems that sugar is, indeed, vital for whatever is taking place in the boiling tube.

What next?

Well, there were, of course, some clues in the apparatus and reagents I had provided. Why the HCl and NaOH? Well, what effect would those chemicals have on conditions inside your boiling tube? Oh, pH change. Oh, enzymes. Oh…. oh!

Bingo, now they’re re-running the experiment but at high and/or low pH. And waddayaknow, the bubbling stops, or slows significantly. It seems reasonable to infer that some enzymes have been denatured.

The groups who had earlier tried to establish 37’C conditions in the blue flame of a roaring bunsen now realise that it gives another test – boiled yeast will be dead yeast. And dead yeast, it turns out, doesn’t bubble either.

What seems obvious to an experience scientist, or experienced teacher, was a really difficult thinking exercise for some very bright Year 10 students. But hard thinking is memorable thinking and without doing a single second of revision, or copied a single note from the board, the vast majority will have understood and remembered all the important points of the lesson.

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Meet Smokey Pumba, the Forces Pig…

Visiting my mother in Cornwall over half term, she asked me to clear out some of the paperwork I had left filed in my old bedroom. I dutifully obliged and unearthed a treasure trove of documents, including letters from old girlfriends, my notes from undergraduate lectures with the incomparable Nick Davies, and my PGCE project work, including Section 1B (Subject Teaching), where I had to submit two essays based on my classroom work at one of my placement schools.

Here is the first one, submitted on Friday 4th June 1999 – blimey, where does the time go? –  titled: Teaching Forces: a critical evaluation of the use of a cartoon pig to enhance motivation and learning in a mixed ability Year 7 group. It’s not very profound or revolutionary, but it gives an insight into how I’ve always approached teaching.

nb: I’ve cut it fairly heavily….

Anyway, see what you think…

Introduction

Traditional Forces teaching is characterised by line drawings of wheelbarrows and seesaws, stick-men and car braking distances, embellished with directional arrows to which are attached numbers, all suffixed with the letter N. Although some attempts have been made to make the concepts more immediately relevant and the illustrative examples more colourful, the subject, at a conceptual level, is inescapably dull. Children, especially Year 7 pupils, manifestly enjoy the practical work, playing with Newton meters, constructing pulley systems, and so on, but there is a discernible drop in enthusiasm when the making of paper ships stops, and the drawing of a wheelbarrow begins. It was during just such a lesson that I decided to introduce The Pig…

The Pig

(long section giving background describing girls disengagement from Science at secondary school).

The Pig and its use in the Module

I used a cartoon drawing of a Pig to replace the traditional abstract diagrams of weights. This proved immediately popular. Being a Year 7 class, our first priority was clearly the Pig’s name. Debate was fierce and ultimately resolved by a ballot of class suggestions that saw Smokey Bacon, Pumba and Pugsley emerge as the favourites. I rather liked the idea of the Pig being called after the Swahili word for “fart”, and the vote produced a tie between Smokey Bacon and Pumba, so we compromised and called it “Smokey Pumba”, a result, presumably, of eating too many bacon sandwiches. This important point established, the children effectively appropriated the Pig. It was their Pig and they cared about it.

The children liked drawing the Pig. They liked discussing what was happening to the Pig in certain situations (floating in a bath, standing on a diving board, stuck in a hole requiring a lever to extract him) and whenever I started a lesson with the words, “To explain this next idea, I need to draw the Pig…” the class would give a loud and spontaneous cheer.

pigs at the pool

The girls were concerned for its well-being. When I first drew a Pig to demonstrate the use of a Newton meter, I drew the supporting hook through the Pig’s back and a cry of dismay went around the class. When I subsequently marked the books, every single girl had very carefully drawn a little harness around the Pig’s tummy to which they could safely attach the hook. It was extremely touching.

newton pig

This involvement with the subject was also apparent during the lesson on Floating and Sinking. I merely sketched two Pigs in a swimming pool on the board, one with a greater downward Force than upward thrust (it was sinking), and one where the downward Force was balanced by the upward Thrust (it was floating). Again, the girls elaborated on the theme. Sinking pigs had unhappy expressions and were emitting a stream of bubbles as they sank. Floating pigs were cheerfully buoyant. In every case, the appropriate arrows and Forces were correctly drawn…

At the end of the Module, I set a homework which asked them to do a big drawing of a Pig (or Pigs) illustrating a scientific concept that they had learned that term. Cheerful pigs pushed supermarket trolleys to illustrate friction. Apprehensive pigs watched as the stopping distance of their car increased in wet conditions. Suitably attired astronaut pigs prepared for take-off in their rockets. And so on. If the enthusiasm and energy that went into this task was representative of their feeling for the course as a whole, then the Pig had done its job.

Forces pig

Case Study

Jessica was one of the most able pupils in the class. She consistently scored highly in homework and class-work and had done well in End of Module tests. Her contributions in class were alaso good. There was, however, an impression that she found it too easy and that she was under-performing relative to her ability…. She seized on the Pig as an opportunity to extend herself. She used her considerable skills as a cartoonist to create colourful and accurate Forces diagrams, and at the end of the course she produced a cartoon strip, that she had done in her own time, of Smokey Pumba stealing apples from an orchard (and its dire consequences!). The quality of her class-work and homework increased. She completed the End of Module test (and its extension) in 19 minutes flat and still came top of the class.

Analysis

Analysing test results is a joyless task. The huge number of uncontrolled variables and the impossibility of doing matched pair comparisons render results largely meaningless, and besides, it is a depressingly narrow view of the purpose of education. I have therefore limited myself to asking two questions. Did the girls score higher than the boys in the test? And, more importantly, did the girls show a general improvement in their test scores relative to their previous results in other tests?

There was not a significant difference between the percentage scores of boys and girls (Mann Whitney test, N=13 boys, 13 girls, Z= -3.09, p>0.7). Girls did, however, score significantly better on their Forces test than they had on the previous two tests in the course (contingency table, 2DF, total chi-squared = 6.0734, p<0.05). In other words, girls showed a significant improvement in their relative score compared to boys….

 

 

 

 

Give me a beer…

Sometimes I just like to be silly.

Let me qualify that.

There are times, particularly when immersed in the complexities of metabolic pathways, that it really pays to do something different, to lighten the mood and provide another way of looking at something. Of course, you also want to provide something that helps the students understand a tricky concept, and if what you do is unusual and memorable, then it will also help them retain that understanding.

Here are my dramatis personae:

glycolysis elephant 1

Yes, you got that right. A purple cuddly elephant (a Xmas present from a tutor pupil), 2 juggling balls, an apple, a top hat and 3 dissection pins. Let’s see if the Biologists among you can figure out what I’m trying to illustrate. My students did!

So, first, I arranged the props as follows…

Glycolysis elephant 2

The elephant, lying on its back, with both juggling balls and one dissection pin, safely tucked between its legs. To one side and a little ahead, the apple with 2 dissection pins jabbed into it; on the other, also a little ahead, the top hat, brim up.

What am I trying to show?

At this point, of course, they haven’t a clue. But they’re already giggling. If nothing else, I have avoided that cardinal sin of teaching, being DULL.

I then slide the elephant along the table, making little dooby doo noises. More giggling. But I’ve got their attention! They really want to know what this is about.

When the elephant arrives between the apple and the hat, it becomes agitated! I switch from dooby doo noises to zips and zaps…

Glycolysis elephant 3

…things start to change! I take the dissection pin off the elephant and plunge it, with a pleasing “thunk”, into the apple. And I take one of the juggling balls off the elephant and put it in the hat. Note that the apple now has THREE dissection pins in it, which is the clue that enables them to guess the first clue…

Ah! Is that ATP???

Indeed it is. The molecule that acts as energy currency in cells, adenosine TRI-phosphate, with each dissection pin being a phosphate group. The apple with just two pins was ADP, adenosine DI-phosphate. By making a molecule of ATP, by transferring a phosphate from the elephant to the apple, we’ve manufactured some useful energy for the cell to use.

And making ATP this way is called…?

Substrate level phosphorylation…

Testing them without testing them, they get all the benefits of retrieval and application and usage, without the stress of doing something that scores them out of 10…

But what do the other things represent?

Let’s start with the elephant. It’s clearly (ahem) a…?

sugar phosphate

exactly, with how many carbons?

3

yes, the 3 carbon fragment that you get from splitting?

fructose bisphosphate

right, after the glucose has been?

phosphorylated

well done, at the start of?

glycolysis…

And the molecule we end up with? The elephant deprived of its dissection pin and juggling ball is?

Pyruvate.

Bingo.

So that’s the context and the pathway. They know all this, they’ve just not seen it represented with cuddly animals and edible fruit.

But now to the key bit…

What’s the juggling ball and what’s the top hat?

Again, they’re on top of this, now that the context is clear. The juggling ball represents hydrogen, stripped from the sugar phosphate by dehydrogenase enzymes, and the top hat represents NAD, the hydrogen carrier that is reduced when it receives the hydrogen from the sugar phosphate via the enzymes.

It’s worth stressing the importance of this. In order to convert sugar phosphate into pyruvate and make essential ATP, you also have to have an empty top hat.

But how do we empty the top hat so that we can keep doing this, and keep making ATP?

No problems here – they are all confident that the top hat delivers the juggling ball to the electron transfer chain in the mitochondrion, enabling it to come back and accept another juggling ball from the next elephant to pass by.

Trouble is, this only works in the presence of oxygen. What happens if there’s no oxygen? What happens if the top hat cannot pass on the juggling ball in this way?

Short answer, the whole thing stops. No more elephant conversion, no more triple pinned apples, no more energy for cell, in a word, death.

Unless….

How else could we empty the hat? What else might be prepared to accept the juggling ball from the hat, freeing it up to go and help convert another elephant?

This takes them a little longer, but with a few nudges and winks and helpful joggling of the relevant prop, they get it…

The elephant!

Glycolysis elephant 4

Notice what we have here. We still have the triple pinned apple (the essential ATP), but we also have an empty hat because the juggling ball has been returned to the elephant.

(nb: what I really need here is another elephant to demonstrate that the process can continue…. note to self – buy more purple elephants)

But we don’t have pyruvate anymore. A purple elephant with one juggling ball (pyruvate) that accepts a juggling ball (hydrogen) from a top hat (NAD) has become a different molecule – a purple elephant with two juggling balls – or as biochemists like to call it, lactic acid.

The mystery of anaerobic respiration revealed, emphasizing the importance of oxidising NADH.

They liked this. They also liked this….

Hope you do too.

Whipping the Worm

Last November, I burbled on the IRIS project about curating the Human Whipworm Genome. A lot of genes have flowed across our screens since then, and as the project enters its second year I still have over 50 students from Years 10, 11, 12 and 13 enthusiastically learning about genome curation and putting it in to practice.

But this year I also want to start explore its potential for A-level teaching. See what you think…

Take a look at this screenshot from the Apollo genome editing software.

screenshot Apollo pic

Ooops. I work across 2 screens and I always forget that screenshots grab both of them.

OK, ignore the photo on the left, which shows my youngest son George in the process of diving into his snow burrow last winter. We need to focus on the image on the right. Let me try some judicial cropping…

screenshot Apollo pic

Ah! That’s more like it. So, what to look for?

First, notice how it’s divided into two vertical sections – the thinner one on the right with the heading “tracks” – we’ll come back to that. For now, concentrate on the left hand division. It has a few bars at the top, with zoom in/out icons and left right arrows, below that a yellow area with a long thing in it, and below that a thick white area with lots of horizontal parallel bars of  various colours and lengths.

First thing to notice, check out the numbers at the top of this left hand section.

5,000,000…… 10,000,000……15,000,000…. all the way up to 30,000,000…

These refer to the number of base pairs on the bit of whipworm genome we’re looking at. 30 million base pairs long!!!! This is a serious chunk of DNA! And if you look in the middle top, TTRE,chr2, it tells you we’re looking at the entire length of Chromosome 2 of the Whipworm. It’s there, on the screen, right in front of you, sequenced and accessible and real. Mind blowing.

I think this is an extraordinarily powerful image for conveying exactly what a genome is. But what makes it even more powerful is what you can then do with it.

Let’s change the view – we can do this by turning the various tracks in the right hand column on and off.

apollo screen grab

Now we’re looking at a chunk – a scaffold – of chromosome 1. Although chromosome 1 has been sequenced, the precise order of the sequenced sections has not yet been determined. So this is scaffold 1 of chromosome 1. Notice that it’s quite a bit shorter than chromosome 2, measuring just over 11,000,000 base pairs long.

I’ve zoomed in to create a view between 5,550,000 bp and 5,800,000 bp on the scaffold. I’ve selected tracks that just show the computer predictions of which parts of the genome look like genes. These are the things visible in the white area.

There is a huge amount of information about the nature of DNA in that image! When a student reaches the point where they fully understand it, they’re becoming reasonably fluent in the topic.

I’ve used lots of analogies down the years to try and help students understand the differences between DNA, genes, chromosomes and genomes. This picture illustrates all of this and more. So the 11,000,000 letters? That’s the DNA. A continuous strand, extraordinarily long, comprising an unbroken sequence of the 4 DNA letters. We can zoom in for a closer look…

genome zoomed in

Notice just how zoomed in we are… a span from 5,670,850 to 5,671,000, just 150 letters, and look!, you can see them! In the middle. That’s  DNA, sequenced, and on display, part of the genetic code that provides information for making Whipworms. The coloured bars above and below it, with their mysterious asterixes and highlighted letter Ms can wait for now, though I expect most of you can work out what they refer to…

Again, I just find this utterly amazing. The power of this software! And we’ll be using this zoomed in scale when we’re fine tuning our gene edits, but let’s go back to that other image.

apollo screen grab

Having established what DNA is, students can now readily see that a chromosome is just a very very long chunk of the stuff.

So what are the genes?

Well, again, there they are, the discreet horizontal line/bar combos in the white area (though it’s important to note at this stage that these are just the computer predictions as to which bits of the genome look like genes – sometimes the predictions are right, but all too often they’re wrong, to a greater or lesser degree, which is why the genome needs to be manually curated). But for now, let’s just take them at face value.

And let’s have a closer look at some…

apollo screen grab

Here are ten. Gene 1211 to Gene 1220. Notice that they correspond to the section of DNA directly above them on the genome – their position, or locus, on the chromosome. Notice that they vary in length – gene 1215 looks quite substantial, gene 1220 is diddy. Notice that they’re made up of coloured blobs connected by long, thin lines. Notice that there are overlaps between neighbouring genes. Notice that there are gaps. And notice that they each have an arrow at one end – for some, the arrow points to the right, for the others, the arrow points to the left.

This last observation illustrates another key point about DNA – being double stranded, the information, the code, the gene, could be on either strand. But the strands are anti-parallel, they run in opposite directions, so when curating the genes, you have to know whether they need to be read from left to right, or from right to left…

This year, I plan to get all of this in place with the Year 12s before we start looking at the actual structure of the molecule. How the students will then use the software to learn more about genes and what they do….

…. is a topic for another burble.

Watch this space!

Flippin’ obvious…

Year 13 and Respiration – as I’ve blogged before, this is a story best told backwards, but I feel I’ve become so engrossed in teaching the extraordinary theory, that the investigative practical work has been a bit neglected. I feel a bit embarrassed, however, that I didn’t spot this opportunity years ago. Flippin’ obvious? See what you think…

So, we’ve powered through ATP, Chemiosmosis and how the ETC maintains the necessary proton gradient. They’ve built a molymod glucose and then oxidised it without using oxygen, to highlight how it’s the hydrogen atoms derived from glucose that are the source of the vital electrons. They know about dehydrogenase enzymes and NAD, but we’ve yet to touch either glycolysis or Krebs – the details of how glucose is stripped bare can wait.

It’s compelling stuff, but lots to take in, so as a pleasingly colorful break from the hardcore theory, I have always used a variation of an old OCR practical exam…

Fuschia Fizz

or maybe

Pink Fizz with different substrates

… and my emphasis has always been on a) making the connection between TTC reduction and dehydrogenases, and b) thinking carefully about the experimental design.

But it’s never really worked as a classroom activity, other than a fun challenge in how many ways they can describe variations of the color pink. It’s not challenging, it’s not engaging, and, to be frank, it’s not a whole lot more exciting than watching paint dry.  This is the problem with any exercise where they just have to follow a recipe; the students carry it out dutifully enough, but they inevitably end up gossiping about other things and don’t learn anything during the course of the lesson.

No more!

This year, I just presented them with the reagents and apparatus, introduced them to TTC as a Redox indicator, and then asked them to use the stuff provided to test the hypothesis that respiration:

  • involves reduction
  • of glucose
  • by living cells
  • requiring enzymes
  • and anything else that they can think of…
  • with close attention to their CONTROLS….

The difference to the lesson was, just, wow. The students were now forced to think about what they were doing and why they were doing it. Working in pairs, they spent 30 minutes planning and rationalising their strategy, before finally trying it out. They puzzled about how to record the rate of TTC reduction, they had to think very hard about why the different sugars showed different rates and why yeast could reduce TTC with no glucose added. They got things wrong and they missed things out, but they remained interested and engaged throughout, and learned far more in the process.

The final proof was half way through, with all their boiling tubes set up and slowly pinkening, when the fire alarm went off. They did not want to leave the lab – they were happy to risk a firey doom rather than miss out on the experimental results that they were personally invested in, that they had full ownership of. Reluctantly realising that this wasn’t an option, they tried to smuggle the tubes out of the lab during the evacuation, until I pointed out that this would play havoc with their careful control of temperature…

So out we went, with lots of anguished glances back at their tubes of pink yeastiness.

(Happily, there was plenty of time for them to get back into the lab and finish off their investigation).

So a resounding success – he says modestly – but note how easy it is. I changed nothing about the practical, nothing to the technician’s order form – I just saved a few pence on photocopying the recipe. Flipping at its purest and best. Give it a go!

Long time, no burble…

Yes, still here, still teaching Biology, still trying new things…

Here’s an idea that worked quite well, with both my Year 10 classes this year.

Each desk (of two students) has a little tray with four small beakers and two teaspoons. The four small beakers contain, respectively, water, sugar, salt, and a solution of red colored food dye.

Arranged around the outside of the lab are 20 large beakers, completely empty.

The game is this – each of the large beakers must receive a small amount (say, the amount you could get on the very end of a teaspoon) from each desk every 20 seconds. All clear? Good.

Go!

Pandemonium ensues, as students race back and forth across the lab, transporting small amounts of sugar/salt/water/red liquid from the small beakers on their desk to the large beakers around the lab.

It’s hilarious to watch, as they get increasingly frantic, especially as I’m shouting out the 20 second intervals, and pointing out large beakers that are conspicuously empty. But after 4 or 5 minutes, it’s time to yell…

“Stop!!!”

And gently admonish them for being so wastefully inefficient. There is, I assure them, a much much easier way of achieving the same thing. Can anyone suggest an improvement?

And in both classes, one bright spark said, “Why not just put the sugar and salt and water and red liquid together?”

Go on then, I say, do it.

The bright spark demonstrates by pouring everything into one small beaker, producing a vivid red liquid which is mainly water with the various solutes dissolved in it. They then walk slowly around the edge of the lab, putting a tiny drop from their beaker into each of the large beakers.

What, I ask, has this person just made? And what do the large beakers represent?

The colour provides a handy clue. Yes, it’s blood…. which means the beakers are…? Exactly – the cells/tissues.

…there follows a discussion on why water is such a great transport medium – dissolve stuff in it, and wherever the water goes, the dissolved stuff goes too – and then we can introduce the structure of plasma and the functions of blood.

More next week, on practical Genomics….

 

Tales of PCR

Ten long years ago, when I first started work at OHS, I was chatting with a father of a student at a 6th form parents’ evening. It turned out that he was in charge of a small Biotechnology company which was closing down. I’m often a bit slow on the uptake, but even I couldn’t miss this open goal.

“What happens to all the kit?” I said, casually.

“Oh it just gets chucked out,” he said, cheerfully.

“Um, if you don’t want it,” I said, “can I have it…?”

And so it came to pass that I borrowed a friend’s large estate and drove down to an industrial estate near Abingdon and filled the back with all kinds of biotech goodies. I made off with Gilson micro-pipettes, a massive stash of tips and micro-tubes that we’re still using, 10 years on, and, treasure of treasures, a thermal cycler….

thermal cycler

Oh how I loved it!!! It was sleek and chunky and alluring. It looked amazing, it felt amazing, it just shouted, “Serious Biology.”

Only problem was, I didn’t have a clue how to use it. And while it did come with an instruction manual, it was not written in a language I could understand…

So for the next 2 to 3 years, my lesson on PCR consisted of me bringing the thermal cycler out of the prep room, fondling it, opening and shutting the lid with a satisfying clunk, whilst explaining how it worked with a little bit on Kary Mullis thrown in for good measure.

And so things would have probably continued until…

…  I found myself chatting to another parent who was a Professor in the BioScience department at the university. Parents can be very useful…. Somehow, our PCR machine came up and my inability to use it, so she immediately offered to send one of her post-grad students over to explain how it all worked.

Which he did. He also commented that it was a far better machine than the one owned by his department. Hurrah! This moved things on a little bit – though programming the brute remained problematic as a) the screen was almost unreadable (you had to be in dim light and at an angle of 38′ to make out the text) and b)the memory function wasn’t working. It would take me 20 minutes to plug in all the details, but unless you ran the programme immediately, all the instructions would be lost.

Grrrrr.

While all this was going on, I had been investing heavily in biotech kit. Lots of Gilsen micro-pipettes with a range of volumes.

micropipettes

Powerpacks, micro-centrifuges, vortexers, gel tanks, visualisers…. we are now seriously well-equipped!

biotech stuff

And it gets used. We transform E.coli and separate proteins with electophoresis and have tried a whole variety of DNA analysis kits. But I was desperate to do PCR.

The problem was identifying a workable protocol from which the students could not only learn all the relevant skills, but also which reliably produced interesting and usable data….

None of them worked. We tried a kit that amplifed non-coding Alu insertions from cheek cell DNA…. would have been brilliant for all kinds of synoptic stuff, from interpreting the gel to evaluating Hardy Weinberg distribution, but we got not a sausage, just some faint primer dimers on the gel front.

We tried a kit that amplified alleles of the PTC taste receptor protein, also from cheek cells. This would have been glorious – linking phenotype to genotype in the most direct way imaginable and really testing understanding of all the key concepts. Again, nothing.

I even (briefly) looked into emulating my old school where they (amazingly) use PCR to carry out site-directed mutagenesis on bacterial plasmids, but I just don’t have the background or the experiences or the training to make this remotely viable. After all, if I can’t get a ready made kit to work….

It was incredibly frustrating! And expensive (these kits don’t come cheap). I consulted friends and colleagues and contacts and the suppliers, but all to no avail.

In frustration with our inherited thermal cycler, I bought a new one… would this solve our problems…?

new thermal cycler

This had major advantages over the original – you can read the display, it’s very easy to programme, it remembers the programme…. and it’s PURPLE!!!!

But could we get PCR product? Could we buffalo…

And then…

We finally cracked PCR this year. The NCBE produces a PCR kit

for amplifying non -coding regions of chloroplast DNA. It’s based on FTA cards where you squash a leaf of your chosen species between two bits of card. Leave it to dry and then punch out a disc which is used as the basis of the PCR. I trialled it with some Year 12s last summer and rolled it out in full for the Year 13s this year.

We’ve had 100% success. Which means that in addition to the satisfaction of actually getting observable bands on your gel, the students also get to interpret the results and use them to construct possible phylogenies of a whole range of plant species.

Here are some recent results….

gels

Along with an exercise in figuring out what’s going on…

Interpreting your Chloroplast DNA PCR results May 2018

Synoptictastic!