Community Genomes: using the example of Bauhinia Genome for genomics education. What is a genome project, and why are they important?

Lesson Overview

This genomics education lesson plan was formulated and tested on some year 6 students with the help of their teacher Michelle Pardini at the Hong Kong ICS School. Using the example of the ongoing citizen science Bahinia Genome project from Hong Kong it hopes to serve as a model to inspire and inform other national genome projects, and aid the development of crucial genomic literacy and skills across the globe. Inspiring and training a new generation of scientists to use these tools to tackle the biggest threats to mankind: climate change, disease, and food security. It is released under a CC-BY SA 4.0 license, and utilised the following slide deck and final quiz. Promoting open science, all of the data and resources produced from the project is immediately put into the public domain. Please feel free to utilise, adapt and build upon any of these as you wish. The open licence makes these open education resources usable just with attribution and posting of modified resources under a similar manner. Contact BauhiniaGenome if you have any questions or feedback.

Bauhinia Genome overview

For a slidedeck for the lesson plan laid out here you can use the set in slideshare here.

Lesson Preparation

Background Knowledge.

 

Students need to have already covered “what is DNA” (deoxyribonucleic acid), briefly introducing the cell (including nucleus and chromosomes), and if possibly having touched on transcription and translation (there are useful OER resources on this like this). For background you can also show students BrainPop on DNA.

 

For an introduction to what is the genetic code, see the BBC’s resources on this.

For an overview of Human Chromosomes and Genes, see also CK12 for additional material.

Task 1: What is a Genome?

What is a Genome?

First coined by Hans Winkler in 1920 (translated from German) as:

“I propose the expression Genom for the haploid chromosome set, which, together with the pertinent protoplasm, specifies the material foundations of the species.”

I.e. all the genetic code in an organism. In the human that would be all the DNA from the 23 pairs of chromosomes.

How big is the human genome?
The human genome, all the instructions to code a living person is 3 billion basepairs (bp) in length. Referred to as 3Gbp (“Giga basepairs”), or 6Gbp if you count we are diploid (have two sets of chromosomes from each parent).

Stretching out all of the DNA in a human cell, end-to-end would stretch out 2 meters long,

Stretching out all of the DNA in all your 50 trillions cells would stretch to the moon and back 100,000 times.

Source.

Opening

What is a genome?

Do you know what a genome is?

All the genetic code in an organism. In the human that would be all the DNA from the 23 pairs of chromosomes.

How large is the human genome?

The human genome, all the instructions to code a living person is 3 billion basepairs (bp) in length. Writing these letters out in a book would produce roughly 1,000 volumes of the size of the Bible. All this is wrapped up into an organisms cell.

Stretching out all of the DNA in a human cell, end-to-end would stretch out 2 meters long,

Stretching out all of the DNA in all your 50 trillions cells would stretch to the moon and back 100,000 times.

http://i1.wp.com/bauhiniagenome.hk/wp-content/uploads/2016/04/chromosome_lg_adv.jpg

If you've not already covered the genetic code, see the BBC’s resources on this. For an overview of Human Chromosomes and Genes, see also CK12 for additional material.

Task 2: Main lesson plan on genomes, bauhinia flowers and more

How do you read the genome, and what is the human genome project?

What is DNA sequencing?
Fred Sanger received his second Nobel prize for figuring out how to read the genetic code with his DNA sequencing method, developed in 1977. This was slow, used radioactive chemicals and gels, but people subsequently sped up and automated this technique using light, sensors and computers to read and interpret data. This newer technique provides a faster and more reliable means of sequencing (see study.com and pbslearning for more).

What is the human genome?
Some good videos on this including these two embedded examples.

After realizing we could read the stretches of the DNA code, in 1985 the US Department of Energy proposed to sequence all 3 billion letters of the genetic code of the human. Starting in 1990, and eventually completed in 2003, the human genome project was the biggest ever project carried out in biology, and cost an estimated $3 billion US dollars to sequence one reference genome.

See timeline: source.

Thanks to incredible improvements in technology, the sequencing of one human genome can now be competed in a matter of days or weeks, and for a tiny fraction of the cost (roughly $1000 dollars by 2015).

See: NHGRI sequencing cost graph.

Step 1: Work Time

How do you read a genome, and what is the human genome project?

What is DNA sequencing?
The British scientist Fred Sanger received his second Nobel prize for figuring out how to read the genetic code with his DNA sequencing method, developed in 1977. This was slow, used radioactive chemicals and gels, but people subsequently sped up and automated this technique using light, sensors and computers to read and interpret data. This newer technique provides a faster and more reliable means of sequencing (see study.com and pbslearning for more on this this if you are interested).

What is the human genome?

What is the human genome?
Demystifying the human genome

After realizing we could read the stretches of the DNA code, in 1985 the US government proposed to sequence all 3 billion letters of the genetic code of the human. Starting in 1990, and eventually completed in 2003, the human genome project was the biggest ever project carried out in biology, and cost an estimated $3 billion US dollars to sequence one reference genome.

With the first genome costing billions of dollars and taking over a decade, things have changed rapidly. Thanks to incredible improvements in technology, the sequencing of one human genome can now be competed in a matter of days or weeks, and for a tiny fraction of the cost (roughly $1000 dollars by 2015).

costpergenome2015_4

Why sequence genomes?
On top of the importance for understanding human health and disease, there are amazing things that can be done studying biodiversity (environmental DNA studies and DNA barcoding, see this profile), the human microbiome (“our other genome”, with up to 10x more microbial cells in an on us than human cells), single cell sequencing to understand cancer evolution, DNA forensics, and ancient DNA sequencing.

Ancient DNA: Is Jurassic park possible?
We have sequenced DNA from ancient humans, and extinct species such as woolly mammoths. The oldest species sequenced to date is 700,000 years old, and we have now determined the half life of DNA is 521 years, meaning that even in cold environments all detectable levels of DNA would have been degraded in a million years.

Writing DNA. Synthetic Biology and Genome Editing.
“Synthetic biology is a) the design and construction of new biological parts, devices and systems and b) the re-design of existing natural biological systems for useful purposes.”

Definition source: Synthetic Biology.org.

As we have machines that can synthesize DNA sequences to order, we now how the equivalent of DNA printers that can synthesise sequences designed on computer, treat parts like interacting lego bricks, and even design and create entire organisms.

Adventures in Synthetic biology webcomic.

The first entirely synthetic organism was produced in 2010, Mycoplasma laboratorium, designed on a computer and assembled by a team lead by DNA researcher Craig Venter. The synthesized genome was transplanted into the existing empty cell of another bacterium that had had its DNA removed. This viable “synthetic” bacterium, nicknamed Synthia, is now be followed up by moves to synthesize larger synthetic organisms such as yeast and eventually nematode worms.

See this cartoon for further on the story of Synthia.

Would you and your students like to participate?
The International Genetically Engineered Machine (iGEM) Competition is the premier student competition in Synthetic Biology. Since 2004, participants of the competition have experienced education, teamwork, sharing, and more in a unique competition setting that involves students and the public in the development of this new field of synthetic biology.  In 2015 more than 260 teams participated from across the world (including four teams from Hong Kong), representing universities, high schools and community labs. Check out their homepage to see who is competing this year:

http://igem.org/Main_Page

Synbio101 Definition of Synthetic Biology.

FAQ on Synthetic Biology.

Step 2: Work Time

Why study genomes? Why are they important? What is Synthetic Biology?

Why sequence genomes?
On top of the importance for understanding human health and disease, there are amazing things that can be done studying biodiversity (environmental DNA studies and DNA barcoding, see this profile), the human microbiome (“our other genome”, with up to 10x more microbial cells in an on us than human cells), single cell sequencing to understand cancer evolution, DNA forensics, and ancient DNA sequencing.

Ancient DNA: Is Jurassic park possible?
We have sequenced DNA from ancient humans, and extinct species such as woolly mammoths. The oldest species sequenced to date is 700,000 years old, and we have now determined the half life of DNA is 521 years, meaning that even in cold environments all detectable levels of DNA would have been degraded in a million years.

Horse DNA

Writing DNA. Synthetic Biology and Genome Editing.
“Synthetic biology is a) the design and construction of new biological parts, devices and systems and b) the re-design of existing natural biological systems for useful purposes.”

3257cab1d1bcc20f4c8e5d7cc6e73004
As we have machines that can synthesize DNA sequences to order, we now how the equivalent of DNA printers that can synthesise sequences designed on computer, treat parts like interacting lego bricks, and even design and create entire organisms.

See the adventures in Synthetic biology webcomic here.

The first entirely synthetic organism was produced in 2010, Mycoplasma laboratorium, designed on a computer and assembled by a team lead by DNA researcher Craig Venter. The synthesized genome was transplanted into the existing empty cell of another bacterium that had had its DNA removed. This viable “synthetic” bacterium, nicknamed Synthia, is now be followed up by moves to synthesize larger synthetic organisms such as yeast and eventually nematode worms.

See this cartoon for further on the story of Synthia.
Would you like to participate?
The International Genetically Engineered Machine (iGEM) Competition is the premier student competition in Synthetic Biology. Since 2004, participants of the competition have experienced education, teamwork, sharing, and more in a unique competition setting that involves students and the public in the development of this new field of synthetic biology.  In 2015 more than 260 teams participated from across the world (including four teams from Hong Kong), representing universities, high schools and community labs. Check out their homepage to see who is competing this year: http://igem.org/Main_Page

Further Reading.
Synbio101 Definition of Synthetic Biology.
FAQ on Synthetic Biology.

Genomics in Hong Kong. Why is this important here?
Hong Kong has since 2010 hosted the largest DNA sequencing facility in the world in Tai Po Industrial Estate (BGI HK profile), and also has researchers that have invented many of the key techniques that are making genomics a key technology used by medical doctors (see this interview with Dennis Lo, pioneer of circulating DNA diagnostics at the Chinese University of Hong Kong).

Genomics is also estimated in coming decades to overtake astrophysics, social media, and video streaming from youtube to become the biggest “big data” on the internet. Despite this very few people in Hong Kong know and understand what genomics is. It will be very important to provide genomics education and literacy to the public, and train a future generation of data scientists to work in this area. Hence this project.

What is the Hong Kong Bauhinia, and why is it relevant to genomics?
The emblem of Hong Kong is the beautiful Bauhinia flower. This is the flower of the orchid tree Bauhinia blakeana, which was first discovered in Hong Kong. What many people may not know is that it is a sterile hybrid, and how and why it ended up in Hong Kong is shrouded in mystery.  The tree was first discovered by a French missionary, Father Jean-Marie Delavay, in the 1880s, growing near Mount Davis on Hong Kong Island.  Being an expert in horticulture, Jean-Marie took cuttings and introduced to the Hong Kong Botanic Gardens and across the world. The species is a hybrid, likely a cross of two local species, Bauhinia variegata and Bauhinia purpurea, but this has yet to be confirmed definitively. One of the best ways to help uncover the secrets of any organism is by looking at its genetic code. Sequencing the genome of the Hong Kong Bauhinia can hopefully help determine exactly where the plant originally came from. The BauhiniaGenome.hk project has launched to fund and carry this work out in Hong Kong, inspiring students and others to join these efforts and learn the skills and what is involved in putting together a genome project.

Bauhinia is not actually an orchid. It is instead a legume, part of the same family of plants as peas and beans, and has nodules on its roots that enables special nitrogen fixing bacteria to produce their own fertilizer. This makes Bauhinia a special plant that is good for the soil by helping create its own fertilizer, and is also used as tasty food in India, Nepal, Thailand and Vietnam.

We have set up some resources for students spot the different Bauhinia species in Hong Kong, and they can use the hashtag #bauhiniawatch on social media or our checklist if they do. See also some videos on BauhiniaGenome, plus coverage in SCMP, on CNN, on the radio, and on the Bauhnia Genome Homepage:

http://bauhiniagenome.hk/

The sample collection, and RNA/DNA extraction was captured on film by CNN and featured on a “On China” special covering science in China in April 2016. You can see the clip here.

Step 3: Work Time

A blooming area of science. Hong Kong and Bauhinia Genomes.

 

 

Genomics in Hong Kong. Why is this important here?
Hong Kong has since 2010 hosted the largest DNA sequencing facility in the world in Tai Po Industrial Estate, and also has researchers that have invented many of the key techniques that are making genomics a key technology used by medical doctors.

Genomics is also estimated in coming decades to overtake astrophysics, social media, and video streaming from youtube to become the biggest “big data” on the internet. Despite this very few people in Hong Kong know and understand what genomics is. It will be very important to provide genomics education and literacy to the public, and train a future generation of data scientists to work in this area.

What is the Hong Kong Bauhinia, and why is it relevant to genomics?
The emblem of Hong Kong is the beautiful Bauhinia flower and appears on our flag and money. This is the flower of the orchid tree Bauhinia blakeana, which was first discovered in Hong Kong. What many people may not know is that it is a sterile hybrid, and how and why it ended up in Hong Kong is shrouded in mystery.  The tree was first discovered by a French missionary, Father Jean-Marie Delavay, in the 1880s, growing near Mount Davis on Hong Kong Island.  Being an expert in horticulture, Jean-Marie took cuttings and introduced to the Hong Kong Botanic Gardens and across the world. The species is a hybrid, likely a cross of two local species, Bauhinia variegata and Bauhinia purpurea, but this has yet to be confirmed definitively. One of the best ways to help uncover the secrets of any organism is by looking at its genetic code. Sequencing the genome of the Hong Kong Bauhinia can hopefully help determine exactly where the plant originally came from. The BauhiniaGenome.hk project has launched to fund and carry this work out in Hong Kong, inspiring students and others to join these efforts and learn the skills and what is involved in putting together a genome project.

Bauhinia is not actually an orchid. It is instead a legume, part of the same family of plants as peas and beans, and has nodules on its roots that enables special nitrogen fixing bacteria to produce their own fertilizer. This makes Bauhinia a special plant that is good for the soil by helping create its own fertilizer, and is also used as tasty food in India and Nepal.

We have set up some resources to spot the different Bauhinia species in Hong Kong, and you can use the hashtag #bauhiniawatch on social media or our checklist if you do.

http://i2.wp.com/bauhiniagenome.hk/wp-content/uploads/2015/11/KnowYourBauhinia.jpg

See more on the Bauhnia Genome Homepage:

http://bauhiniagenome.hk/
 

Bauhinia Genome

 

The sample collection, and RNA/DNA extraction was captured on film by CNN and featured on a “On China” special covering science in China in April 2016. You can see the clip here.

Bauhinia in CNN.

 

Task 3: How to extract DNA at home/in the classroom?

How to extract DNA at home/in the classroom?

Studying the DNA of a species is not just something very expensive high tech labs and universities can do. With the huge decrease in cost, genomics is getting increasingly democratized. Most genomics data is available for free on the internet to anyone who wants to use it, and there are growing numbers of DIYbio community labs around the world demonstrating what citizens can do at home. Extracting DNA is surprisingly easy, and there are some easy demos you can do in class if you have 15 minutes spare and all the suitable materials: fresh strawberries, salt, water, liquid detergent, coffee filters, ice cold rubbing alcohol, ziplock bag and a small beaker.

More detailed on instructions on how to extract DNA from strawberries is here.

From tougher species there are instructions here.

Strawberry DNA extraction

 

Performance Task

How to extract DNA from a species: a berry good example.

Your teacher will now attempt to demonstrate DNA extraction to you in about 15 minutes using strawberries and some common household ingredients. Or you can see the following example on this video. If you have the items to do this at home you can even have a go at this yourself.

Strawberry DNA example

 

Task 4: Final quiz on what you've learned about Bauhinia and Genomes

Included as a resource is a final short final quiz on what you have learned in the lesson today. This should take 5-10 minutes maximum, and can be carried out at the end of the lesson, during the digestion step of a DNA extraction demo, or as homework.

Answers if needed: 1). 3 billion (or 6 billion if you count being diploid). 2). 500 million. 3). 2m. 4). 100,000 times. 5). $3 billion USD. 6). Synthia (or Mycoplasma laboratorium). 7). Father Jean-Marie Delavay. 8). No, a legume (bean/pea family). 9). Produce their own fertizer (special bacteria in root nodules). 10). International Genetically Engineered Machine Competition.

Homework

Final quiz/homework/further reading.

Here we have a final short final quiz on what you have learned in the lesson today. This should take 5-10 minutes maximum. We hope you enjoyed learning about BauhiniaGenome, and if you'd like some further reading as homework see the following.

How to extract DNA at home

From strawberries: http://www.stevespanglerscience.com/lab/experiments/strawberry-dna/

From tougher species: http://learn.genetics.utah.edu/content/labs/extraction/howto/

More on Synthetic Biology

Adventures in Synthetic biology webcomic:
http://www.nature.com/nature/comics/syntheticbiologycomic/

iGEM competition:
http://igem.org/Main_Page

Bauhinia Genome

http:// bauhiniagenome.hk/

How to spot Bauhinia (use the hashtag #bauhiniawatch if you do):

http://bauhiniagenome.hk/get-involved/education/know-your-bauhinia/

How to cook Bauhinia: recipe for Bauhinia achaar (Nepali pickle):

http://bauhiniagenome.hk/get-involved/education/recipe-koirala-achaar/

Bauhinia Genome in SCMP:

http://www.scmp.com/magazines/post-magazine/article/1875917/unique-project-sequence-genome-hong-kong-bauhinia-tree

Follow us:

Twitter: @bauhiniagenome #bauhinawatch

Facebook: https://www.facebook.com/BauhiniaGenome
Website: http://bauhiniagenome.hk/
Youtube: https://www.youtube.com/channel/UC1zUwiLpoyeviqnDNAM40eg
Indiegogo: http://igg.me/at/bauhinia  

Bauhinia prize