Mission eDNA

What is environmental DNA?

We know that DNA is found in every cell of every living thing, so let’s imagine that a living thing loses a cell. What happens? A plant loses a leaf, a human being scratches himself and loses the superficial cells of his skin, an animal loses its hair, and so on. Living organisms constantly deposit genetic material in their environment.

DNA can be released into the environment via faeces, urine, gametes, mucus, saliva and skin, and it can also come from the decomposition of dead organisms. In aquatic environments, dead, decomposing organisms release a phenomenal amount of genetic material.

So, environmental DNA (eDNA) is the lost cells (intact or not) that we recover from the environment. Scientifically speaking, eDNA is genetic material derived from an environmental sample (freshwater, saltwater, sediment, humus, faeces, etc.).

Why is it useful? 

In a context of climate change, it is more than imperative to have a good understanding of the ecosystems that surround us, so that we can better protect them. To implement appropriate strategies and actions to protect our ecosystems, we need to know which species inhabit them. Using sequencing, eDNA identification enables researchers to gain an overview of the community of living beings that inhabit a particular ecosystem, and to deduce trophic links and key species.

Thanks to the eDNA we can extract from these water samples, we’ll have a better idea of the current state of biodiversity in the waterways around us, so we can better understand and protect them.

Mission eDNA : the project

Québec students, a major study of Québec’s waterways is underway, and genomics researchers need your help! Your job is to bring back water samples containing the DNA of various species that live in these ecosystems!

You’ll be working with a professional scientific team to use a powerful and very recent research tool: environmental DNA! It will enable you to recover the traces of DNA that living creatures (fish, invertebrates and microorganisms) leave behind in the water.

With the help of the environmental DNA you’ve collected, we’ll be able to better understand the state of biodiversity in the rivers selected for the project.

This project aims to:

The half-day activity will take place on the banks of a river. The results of the analyses will be revealed in the spring, during a live conversation between the students and the scientific team overseeing the project.

This initiative was developed in collaboration with the ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs and Université Laval’s Institute of integrative biology and systems. With financial support from the ministère de l’Économie et de l’Innovation.

Related documents

Here are all the documents you need to prepare and run the activity (French only):

How-to videos

Here are the three stages of the project (French only):
PHASE 1: Collecting data – Students

This project couldn’t happen without your help! Your students will be the budding researchers who get this project off the ground. You’ll follow a precise research protocol established by a professional scientific team. This will enable you to collect and filter high-quality water samples, from which the eDNA can then be extracted.

You must ensure that your students follow the scientific protocol.

PHASE 2: Analysis – The scientific team

Certifying the health of watercourses

Once the species have been identified, researchers and students will get together to talk about the health of Quebec’s waterways.

Experience overview

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Methodology

A. Sampling: A water sample is taken from a stream. It contains traces of DNA from fish, invertebrates and microorganisms. This is eDNA.

B. Filtration: The water sample is passed through a fine filter by the students to recover the DNA fragments.

C. Hypothesis: Students are asked to formulate a hypothesis.

Phase 2 : Scientific team

D. Extraction: The DNA is cleaned and preserved, while everything else is discarded (debris, dust, sediment, etc.).

E. Amplification: Our sample contains much more microbial DNA than fish and invertebrate DNA. As in the vast majority of ecosystems, the community of microorganisms in our river, though microscopic, is much larger than that of macroscopic species. The quantities of DNA collected will reflect this difference, and we can therefore expect our sample to contain 90% microbial DNA, compared with 10% DNA from other sources (fish, invertebrates, amphibians, humans, plants, etc.). In order to compensate for the possible biases this may entail during analysis, we amplify (copy in multiple copies) the DNA from fish and invertebrates, since these are the species we also want to study. Amplification takes place using a polymerase chain reaction (PCR). This technique, which takes place over several three-step cycles at different temperatures, produces millions of copies of a DNA molecule using the Taq DNA polymerase enzyme.

F. Sequencing: DNA fragments are read by a sequencer. The affinity of the base pairs is used to decode the order in which they are arranged. To do this, a single-stranded DNA fragment is deposited in a solution containing modified free nitrogenous bases. Luminescent molecules have previously been linked to the various nitrogenous bases. (e.g. Adenine – red, Cytosine – yellow, Thymine – green and Guanine – blue). The modified nitrogenous bases are left to form the DNA strand complementary to our fragment. The nitrogenous bases always associate with the same specificity: adenine with thymine (A-T or T-A) and cytosine with guanine (C-G or G-C). With the sequencer, we can read the “colored” sequence attached to our initial DNA fragment. For a given sequence: red-blue-green-yellow-green-blue-red-red, we can deduce that the sequence of luminescent nitrogenous bases is: A-G-T-C-T-G-A-A and that the initial DNA sequence was: T-C-A-G-A-C-T-T. Record these readings in a computer file.

G. Bioinformatics analysis: Public databases contain the complete genome sequence of the different species studied, so we can compare the sequence we have read with those recorded. So we search the databases of fish, invertebrates and microorganisms for the species to which the DNA we’ve collected and sequenced belongs.

Phase 3: Together

H. Results and interpretation: The researchers analyze the results and try to understand what they mean.

  • Why do we find more microorganisms in one river than another?
  • Why isn’t such and such a species of fish found in this stream?
  • What do these data say about the health of the streams we sampled?
Activities
Virtual lab

Virtual lab

 Educational games

Educational games

 Mission eDNA

Mission eDNA

 Strawberry DNA extraction

Strawberry DNA extraction

 In search of DNA

In search of DNA
Bookings

If you have any questions, comments, or feedback, we would love to hear from you.

Please contact us at the following email adress : education@genomequebec.com

Careers in Genomics

Working in genomics

àGenomics offers a range of career opportunities that require different levels of education. 

Biomedical Laboratory Technician*

Required level of education: College

Biomedical laboratory technicians conduct control tests on product samples based on specifications, protocols and standard operating procedures. They provide technical support to various departments: analytical, control or bio-analytical. Technicians use a variety of laboratory techniques to carry out chemical, biochemical or genetic tests.

Examples of typical duties:

  • Conducting physical, chemical, biological, biochemical or microbiological testing on samples of raw materials or finished products.
  • Performing analytical problem solving.
  • Producing documents on the results of sample testing.

Biochemist

Required level of education: University

Biochemists study and analyze chemical reactions and biological processes that occur at the molecular level of living organisms in order to enhance scientific knowledge. They also seek out real-world applications for research in areas such as medicine, pharmaceuticals, genetics, agriculture, industry and even biotechnology. 

Examples of typical duties:

  • Studying the chemical processes involved in the various functions of organisms, such as digestion, energy conversion in living matter, growth and aging.
  • Isolating and characterizing enzymes, hormones or genes and identifying their impact on the human body.
  • Using genetic engineering techniques.
  • Developing tests and new drugs.
  • Producing reports and recommendations on research results.

Biologist 

Required level of education: University

Biologists study living beings. They strive to understand how cells work. They focus on areas such as DNA replication and animal or plant cells in order to discover new therapeutic substances. They also study the chemical reactions in biological entities. They are fascinated by the interactions between active substances and living organisms. They are also interested in microorganisms, such as viruses, fungi and bacteria.

Examples of typical duties:

  • Studying manifestations of life in living organisms.
  • Conducting experiments on the growth, heredity and reproduction of plants and animals.
  • Studying the repercussions of human activities on the environment.
  • Studying the relationships among individuals (plants and animals) and their environment.

Microbiologist

Required level of education: University

Microbiologists study the structure, functions, ecology, biotechnology and genetics of microorganisms (viruses, bacteria, yeasts, fungi, algae) by conducting experiments and research to enhance scientific knowledge and develop practical applications for society and industry.

Examples of typical duties:

  • Taking samples from living tissue.
  • Isolating, identifying and harvesting specimens in the lab.
  • Studying the action of microorganisms on living tissue (infectious diseases) and examining how they propagate as infectious agents.
  • Studying microorganisms that decompose organic matter and fertilize soil.
  • Controlling the safety of food and water.
  • Controlling the quality of pharmaceuticals, drugs, cosmetics, pesticides, etc.

Many other professions require the use of genomics  

College level:

  • Analytical chemistry technician
  • Chemical process technician
  • Inspector
  • Crime scene technician

University level:

  • Biophysicist
  • Chemist
  • Coroner
  • Biotechnology engineer

To learn more about the various careers related to genomics, talk to your school guidance counsellor or consult the programs of study offered by the schools in your area. 

*Source : www.reperes.qc.ca (French only)

DNA
DNA and RNA

DNA day
DNA modification

Mutations: Driving biodiversity

Mutations are permanent changes to one or more nitrogenous bases in a DNA sequence. These genetic changes may be harmful or beneficial or may have no consequences for the organism. 

Mutations in the DNA sequence always occur randomly. However, beneficial mutations that give the organism a better chance of survival are more likely to be passed on to the next generation. This is how species evolve and adapt to changes in their environment. 

Mutations affecting a single nitrogenous base are very common. They’re called point mutations and they come in three categories:

Point mutationThis common type of change involves a single pair of nitrogenous bases
SubstitutionOne nitrogenous base is replaced with another
InsertionAn additional nitrogen base is inserted into the DNA sequence
DeletionA base is deleted from the DNA sequence
  • Substitutions can lead to a change in amino acid in the encoded protein.
  • Insertions and deletions create frameshifts by changing how codons are read, which disrupts the amino acid sequence and often produces a non-functional protein.

Mutations are also described according to the effect they produce.

Silent mutationsThese mutations cause no change in the final protein, as the amino acid in question can be encoded by different codons.  
Nonsense mutationThese mutations create a premature stop codon. The resulting proteins are incomplete and generally non-functional.
Missense mutationsThese mutations create a different amino acid in the final protein.

Other mutation typesThese mutation types involve more than one pair of nitrogenous bases
Tandem repeat mutations These mutations increase or decrease the number of repeats of a specific sequence of nitrogenous bases.
Chromosomal rearrangementsThese changes in the structure of chromosomes can disrupt normal gene function by putting genes under the control of incorrect regulators or changing their expression.
  • Breakdown in natural DNA repair mechanisms.
  • Exposure to mutagens such as toxic chemicals (e.g., in cigarettes), viruses and UV radiation from the sun.
  • Errors introduced during the DNA replication or genetic recombination that occurs during sex cell formation.

Cancer

Cancer is a disease characterized by the uncontrolled growth of abnormal cells in the body. The genetic mutations behind cancer change the mechanisms that control the cell cycle and apoptosis (programmed cell death) and allow cells to grow out of control and never die. These cells constantly divide and form tumours, which can then invade and harm the body’s tissues.

Understanding mutation mechanisms is therefore a vital part of cancer research. Identifying the specific types of mutations in cancer cells and understanding their causes lets researchers develop targeted methods to treat different types of cancer.

The study of genetic mutations has important implications for many other fields, such as evolution, developmental biology and research into hereditary diseases.

Mutation and evolution

Mutations are important from an evolutionary standpoint because they give rise to genetic diversity. Every mutation creates a new, unique version of a gene. If a mutation occurs in a sex cell, it can be passed on to the organism’s offspring.

When beneficial mutations give an organism an advantage in its specific environment, the organism is more likely to survive and reproduce. The frequency of a beneficial mutation that increases in a population over multiple generations is known as natural selection, a key concept in Charles Darwin’s theory of evolution.

Natural selection also tends to weed out mutations that hinder the survival of an organism, as individuals carrying these mutations will be less likely to reproduce and pass them on to their children.

Generation length is an also important factor in an organism’s ability to adapt to a changing environment. Organisms with shorter life cycles can potentially evolve faster, as they have more opportunities to generate offspring that carry beneficial mutations.

Evolution is therefore driven by the tension between mutations, which create genetic diversity, and natural selection, which acts as a “filter” that promotes beneficial mutations and hinders non-beneficial ones. This ongoing process of mutation and natural selection is how populations adapt, how they evolve over the long term, and how new species emerge.

Biotechnology  

What is biotechnology?

Biotechnology is the study of living organisms to develop technologies that are useful to society. There are applications for biotechnology in many fields, such as medicine, agriculture, engineering and the environment.

Transgenic organisms are created through genetic engineering, a technique that allows scientists to insert the genes of one species into the genome of another to modify certain traits. A transgenic organism therefore carries a gene from another species in its genome. For example, agricultural crops that require fewer pesticides can be engineered using a gene for resistance to certain pathogens.

CRISPR-Cas9 is used as “molecular scissors” to add, remove or change target genes. Scientists adapted this gene-editing technique from an immune defence mechanism in bacteria and archaea as a way to cut DNA using Cas9 proteins. Guide RNA sequences accompany and direct the Cas9 proteins to specific genes. Once CRISPR-Cas9 binds to its target, it cuts the DNA, which triggers the cell’s natural repair mechanisms, which modify or replace the existing gene.

Some body tissues, such as those in the spinal cord, don’t repair themselves if damaged. In such cases, stem cells can be reprogrammed to trigger the repair and regeneration of the affected tissues.

Embryonic stem cells are cells from an early‑stage embryo that differentiate into all types of cells in the body (muscle cells, epithelial cells, etc.). Although their regenerative potential is immense, their use raises ethical questions since the cells are extracted from embryos.

Scientists can also use cell reprogramming techniques to transform cells that have already differentiated—such as skin cells—into stem cells that can change into other cell types. These cells are called induced pluripotent stem cells.

Cloning is a technique to create an organism that is genetically identical to another. A famous example is Dolly, a sheep that was cloned in 1996. Learn more about Dolly here: DOLLY – Britannica

Ethical issues

Biotechnology opens up a world of possibilities. However, it also raises ethical questions about human responsibility and respect for life.

Reproduction and heredity
DNA: The Code of Life!

What is DNA?

DNA, which stands for deoxyribonucleic acid, is a molecule found in the cells of all living organisms that contains the genetic information an organism needs to develop, grow and function.

The complete set of genetic material that makes up an organism’s DNA is called its genome. Genomes vary between species, as well as within species and between individuals.

A genome is like a big recipe book. Genes are the recipes in the book that are used to produce a specific component that the organism needs to function.

DNA structure

The double helix code

DNA is a very long molecule with two strands shaped like a twisted ladder. This shape is what gives it the name double helix.  

The DNA strands are made of alternating sugar (deoxyribose) and phosphate molecules. Each sugar molecule bonds to one of four nitrogenous bases called adenine (A), thymine (T), cytosine (C) and guanine (G). When these bases form pairs, A always goes with T and C always goes with G. These pairs link the two strands together to form the “rungs” of the ladder.

How is DNA decoded?

The term genetic code refers to the order that the nitrogenous bases follow each other on a strand of DNA, an example being A-C-C-A-T-T-C-G-C-T. Genetic sequencing lets us decipher this code. These letters can be thought of as an alphabet forming words in a recipe that help us understand how organisms are put together.

A genome is made up of both coding and non-coding DNA. Coding DNA contains information that creates a protein. This type accounts for about 2% of the genome. The non-coding parts include promoters, stop codons and enhancers that regulate the expression of certain genes. The role of some non-coding DNA is still not fully understood.

Where is DNA located?

All of an organism‘s cells, except its gametes, contain a complete copy of its genetic material.

Animal and plant cells are called eukaryotic, which means they have a nucleus that stores DNA. Organisms, such as many microorganisms, that do not have a nucleus in their cells are called prokaryotic. In these cells, the DNA floats in the cytoplasm and clusters into a mass called the nucleoid.

In eukaryotic cells, the DNA—which contains all of an organism’s genetic information—stays in the nucleus, where it is protected and compacted.

To get the genetic information out of the nucleus, the DNA is copied into RNA. Messenger RNA then leaves the nucleus to direct protein synthesis in the cytoplasm, while other types of RNA, such as ribosomal RNA and transfer RNA, actively help different parts of the cell to function.

In eukaryotic cells, DNA is also found in mitochondria and chloroplasts.

Mitochondria are organelles that produce energy (ATP). This type of DNA is different from nuclear DNA. It has a circular shape and is transmitted from one generation to the next through the mother’s egg cells. This means that an entire maternal line will have the same mitochondrial DNA! (Note: Although rare, mitochondrial DNA can be passed on from the father. Studies are ongoing to understand how this happens.)

Chloroplasts are organelles that conduct photosynthesis. For a long time, it was thought that chloroplast DNA was also circular, but studies show that it is more often linear. Chloroplast DNA is passed on through egg cells or pollen and allows the chloroplasts to synthesize some of their proteins.

Although viruses are not made of cells, they do contain genetic material in the form of DNA or RNA. To replicate and spread, they need to hijack the mechanisms and resources of the cell they invade, called the host cell.

A DNA virus will enter the nucleus and deliver its viral genome into the host cell’s DNA. The virus then takes control of the cell’s machinery to produce viral proteins.

RNA viruses take over the ribosomes of infected cells directly to produce viral proteins.

DNA compaction: Big information in a small package

DNA is extremely long, and each human cell contains about 2 metres of this molecule! To fit the entirety of its genetic information into the tiny nucleus of a cell, DNA is compacted and coiled into chromatin.

Compaction also regulates access to DNA and controls gene expression. This is because compacted regions cannot be reached by RNA polymerases and therefore can’t be transcribed into RNA.

Chromatin is formed through multiple stages of compaction:

1. Proteins called histones form a spherical structure called the nucleosome. The DNA winds around this structure like a spool.

2. These nucleosomes become compacted to form chromatin, or strands of coiled DNA that look like beads on a necklace.  

When cells divide, chromatin reorganizes itself into an even more compact form called chromosomes. 

Humans have 23 pairs of chromosomes, with each pair assigned a number from 1 to 23. The first 22 pairs of chromosomes are called autosomes. The 23rd pair are the sex chromosomes, and these come in two types in humans: X and Y. The 23rd chromosome pair may consist of:

  • two identical chromosomes (XX)
  • two different chromosomes (XY)

The sex chromosomes do not always come in pairs, as an individual may have:

  • a single X chromosome

Or

  • three chromosomes (XXX, XXY or XYY)

An image of the size, shape, number and structure of an individual’s chromosomes can be produced with karyotyping, which involves taking a snapshot of chromosomes during cell division when the chromosomes are most visible.

Karyotyping is frequently done by medical geneticists to diagnose genetic disorders.

Chromosomes are passed on by the parents during sexual reproduction. Reproductive cells, called gametes, have one pair of chromosomes each. During fertilization, the gametes merge to form a zygote, which then inherits a complete set of chromosomes.

Each parent therefore passes on half of their chromosomes to their offspring. 

From gene to protein
Educational games
DNA

DNA

 DNA and RNA

DNA and RNA

 DNA day

DNA day

 Matilda’s Revelation

Matilda’s Revelation

 True or False

True or False
Educational space

Welcome to the Educational space

This platform is aimed primarily at secondary school students and science and technology teachers. It presents the basic concepts of genetics, as well as introducing the more advanced notions of genomics. Génome Québec also offers free classroom activities to help students put their knowledge into practice.

A reliable and relevant resource

The platform was developed with teachers and educational consultants to meet their needs, as well as the requirements of the Québec Ministry of Education’s Science and Technology program. In addition, all content and activities were developed with the support of scientific teams.

Come meet us!

Virtual lab

Virtual lab

 DNA: The Code of Life!

DNA: The Code of Life!

 From gene to protein

From gene to protein

 The cell

The cell

 Reproduction and heredity

Reproduction and heredity

 DNA modification

DNA modification

 Lexicon

Lexicon

 Miscellaneous

Miscellaneous

 Activities

Activities
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