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DNA analysis: the last frontier for biologists. Lesson 1 of MEFF Spring 2007 Taught by Dr. Matteo Garbelotto. Forest pathology and mycology: the P.I. THE LAB . IMPORTANCE OF FORESTS. Aesthetic value. Production of timber and fuel. Terrestrial ecosystems containing maximum biodiversity.

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dna analysis the last frontier for biologists
DNA analysis: the last frontier for biologists
  • Lesson 1 of MEFF Spring 2007
  • Taught by Dr. Matteo Garbelotto
what are fungi
WHAT ARE FUNGI ?
  • Individuals belonging to the kingdom fungi
  • They are actually more closely related to animals than plants (cell wall contains chitin, do not photosynthesize)
  • The feed by extrogenous digestion (food base digested outside their cells and then simple elements absorbed )
  • Indefinite growth: size can range from unicellular organisms) to the largest beings in the world
slide17

Thanks to their web-like indefinite growth in soil and plant substrates and their way of digesting nutrients fungi play a critical role in recycling nutrients which can then be reutilized by plants

slide19

Fungi like this one will actually decay the woody matter and physically free space for new generations of trees, besides recycling the nutrients

slide20

The weblike structure of fungi, usually immersed in the soil or in plant matter is involved in an essential symbiosis that greatly enhances the ability of plants to grow

pianta

fungo

slide21
The visible part of root tips of most trees is actually a mantle of fungal hyphae fused with the plant tissue
what is the deal of this mutualism
What is the deal of this mutualism?
  • Fungus absorbs nutrients for plants
  • Plant gives fungus carbohydrates it produces via photosynthesis
slide23
There are thousands of mycorrhzial fungal species, and only at times do they produce the classical fruit body (e.g.mushrooms) above ground

In absence of fruit body: how can we identify them?

slide24
DNA can be extracted from any part of an organism, like the web-like hyphae emanating from this root tip

DNA sequence identified these threads as Tricholoma matsutake

slide25
Tricholoma matsutake grows in Eurasia and is prized enormously by the Japanese who pay over 1000 dollars a pound
slide26
Using DNA data we were able to prove Tricholoma matsutake also grows in the eastern US and in Mexico
slide27
The mexican fungus is sold in Japan and the revenues make up to 30% of the economy of some mountain communities
fungi and fungus like organisms are responsible for 90 of plant diseases
Fungi and fungus-like organisms are responsible for 90% of plant diseases

Affecting a portion of a plant

Epidemics (exotic diseases)

Affecting low

numbers of trees

slide31

Native diseases play a fundamental role of eliminating overcrowding and eliminating the weakest individuals, but exotic diseases can negatively change ecosystems by wiping out entire populations

slide33

Like the conquistadores brought diseases that were lethal to those who had never been exposed to them, so do exotic diseases cause true devastation in plant communities because of lack of coevolution between hosts and microbes

slide35

Invasions are more frequent before frequency and intensity of movement of goods and people are greatly on the rise

how can people transport pathogens
How can people transport pathogens
  • By transporting plants and plant parts
    • Crops, and seeds
    • Raw food
    • Ornamental plants

Untreated lumber

Soil

Insects vectoring fungi

how to identify species and possibly provenance of pathogens
HOW to identify species and possibly provenance of pathogens
  • Microscopic organisms with few differentiating features
  • Often cannot be cultured
using dna sequences
: USING DNA SEQUENCES

Species I Species II(more virulent)

Europa

Nord America

C

A

D

B

abcd are four sequences uniquely found in the four types of pathog ens
ABCD are four sequences uniquely found in the four types of pathogens
  • If association of sequence and pathogen is unequivocal, sequence can be used for diagnostics
  • If you were and official in the US which sequence (I.e. pathogen) should you be most concerned abou….t
what is dna
What is DNA?
  • The code of life, four different bases are arranfed in triplets of different combinations, each triplet codes for an amminoacid. Aminoacids are assembled to form proteins

DNA is a tight double helix and is arranged in physical sticks called chromosomes

ecah chromosome contains
Ecah chromosome contains

Portions that are garbage they do not code for a protein, these evolve more rapidly, and are more likley to differentiate organisms

Portions that code for proteins, the more essential is the protein, the less the DNA will be allowed to mutate, less useful to differentiate organisms

let s read the dna sequence of a variable portion of a chromosome
Let’s read the DNA sequence of a variable portion of a chromosome

AGT GAA CCA G

Mutation-evolution

AGA GAA CCA G

Further mutation-evolution

AGA GAG CCA G

let s build an evolutionary or family tree using these sequences
Let’s build an evolutionary or family tree using these sequences
  • AGT GAA CCA G

Uncle Scroodge

EVE

  • AGA GAA CCA G

Donald Duck

  • AGA GAG CCA G

Hewey

Lewy

Dewey

who is ag a ga g cca g
Who is AGA GAG CCA G
  • AGT GAA CCA G

Uncle Scroodge

EVE

  • AGA GAA CCA G

Donald Duck

  • AGA GAG CCA G

Hewey

Lewey

Dewey

and if the culprit were ag a ga t cca g
And if the culprit were AGA GAT CCA G ?
  • AGT GAA CCA G

UNCLE SC

EVE

  • AGA GAA CCA G

DD

  • AGA GAG CCA G

H

L

D

if the culprit were ag a ga t cca g
If the culprit were AGA GAT CCA G ?
  • AGT GAA CCA G

US

EVA

  • AGA GAA CCA G

DD

  • AGA GAG CCA G

H

Maybe

But which one?

L

D

slide49

AGT GAA CCA G

US

EVE

  • AGA GAA CCA G

DD

  • AGA GAG CCA G

H

  • AGA GAT CCA G

D

  • AGA GAC CCA G

L

and if the culprit were ggc aaa tct g
And if the culprit were GGC AAA TCT G ?
  • AGT GAA CCA G

US

EVE

  • AGA GAA CCA G

DD

  • AGA GAG CCA G

H

  • AGA GAT CCA G

D

  • AGA GAC CCA G

L

if the culprit were ggc aaa tct g
If the culprit were GGC AAA TCT G ?
  • With the available database it would be impossible to identify the culprit
  • By enlarging the database we may fiund the match in somebody else not present in the current database. E.g. Mickey mouse
the last frontiers in science 1
The last frontiers in Science1
  • To sequence an entire genome to understand how it functions
we sequenced to genomes of related fungus like organisms science
We sequenced to genomes of related fungus-like organisms (Science)
  • Discovered that they produce hundreds of molecules to relate with plants
  • The kingdom called Straminopila has seen the fusion of photosynthetic and non-photosynthetic organisms
the new frontiers of science 2
The new frontiers of Science2
  • To sequence one gene, one locus, for hundreds of species to increase our databases regarding communities and entire ecosystems
sequencing of groups of organisms
Sequencing of groups of organisms
  • Sequencing all of the organisms on the island of Moorea
  • Sequencing all the species in an herbarium
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