DNA analysis: the last frontier for biologists Lesson 1 of MEFF Spring 2007 Taught by Dr. Matteo...
-
date post
19-Dec-2015 -
Category
Documents
-
view
216 -
download
0
Transcript of DNA analysis: the last frontier for biologists Lesson 1 of MEFF Spring 2007 Taught by Dr. Matteo...
DNA analysis: the last frontier for biologists
• Lesson 1 of MEFF Spring 2007
• Taught by Dr. Matteo Garbelotto
Terrestrial ecosystems containing Terrestrial ecosystems containing maximum biodiversitymaximum biodiversity
Huge role in geological protection Huge role in geological protection from erosion, floods, etc.from erosion, floods, etc.
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
Aerial view of a single fungal Aerial view of a single fungal individual growing in the soil individual growing in the soil
and killing plantsand killing plants
Tens of acres occupied by a single individual, older than Tens of acres occupied by a single individual, older than
5000 years!!!! (Northern Michigan)5000 years!!!! (Northern Michigan)
Thanks to their web-like indefinite Thanks to their web-like indefinite growth in soil and plant substrates growth in soil and plant substrates and their way of digesting nutrients and their way of digesting nutrients fungi play a critical role in recycling fungi play a critical role in recycling
nutrients which can then be nutrients which can then be reutilized by plants reutilized by plants
•Fungi like this one will actually decay the woody matter and physically free space for new generations of trees, besides recycling the nutrients
The weblike structure of fungi, usually The weblike structure of fungi, usually immersed in the soil or in plant matter is immersed in the soil or in plant matter is involved in an essential symbiosis that involved in an essential symbiosis that
greatly enhances the ability of plants to growgreatly enhances the ability of plants to grow
•pianta
•fungo
The visible part of root tips of The visible part of root tips of most trees is actually a mantle most trees is actually a mantle of fungal hyphae fused with the of fungal hyphae fused with the
plant tissueplant tissue
What is the deal of this mutualism?
• Fungus absorbs nutrients for plants• Plant gives fungus carbohydrates it produces via
photosynthesis
There are thousands of mycorrhzial fungal There are thousands of mycorrhzial fungal species, and only at times do they produce the species, and only at times do they produce the
classical fruit body (e.g.mushrooms) above classical fruit body (e.g.mushrooms) above groundground
•In absence of fruit body: how can we identify them?
DNA can be extracted from any part of an DNA can be extracted from any part of an organism, like the web-like hyphae emanating organism, like the web-like hyphae emanating
from this root tipfrom this root tip
•DNA sequence identified these threads as Tricholoma matsutake
Tricholoma matsutakeTricholoma matsutake grows in Eurasia and is grows in Eurasia and is prized enormously by the Japanese who pay prized enormously by the Japanese who pay
over 1000 dollars a poundover 1000 dollars a pound
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Using DNA data we were able to prove Using DNA data we were able to prove Tricholoma matsutakeTricholoma matsutake also grows in the also grows in the
eastern US and in Mexicoeastern US and in Mexico
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
The mexican fungus is sold in Japan and the The mexican fungus is sold in Japan and the revenues make up to 30% of the economy of revenues make up to 30% of the economy of
some mountain communitiessome mountain communities
What about planting pines What about planting pines where these fungi, essential for where these fungi, essential for
the growth of pines, do not the growth of pines, do not exist?exist?
In the soil under pines we found In the soil under pines we found DNA sequences of an imported DNA sequences of an imported
fungusfungus
Fungi and fungus-like Fungi and fungus-like organisms are responsible for organisms are responsible for
90% of plant diseases90% of plant diseases
•Affecting a portion of a plant
•Affecting low• numbers of trees
•Epidemics (exotic diseases)
•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
Like the conquistadores brought Like the conquistadores brought diseases that were lethal to diseases that were lethal to those who had never been those who had never been
exposed to them, so do exotic exposed to them, so do exotic diseases cause true devastation diseases cause true devastation in plant communities because of in plant communities because of
lack of coevolution between lack of coevolution between hosts and microbeshosts and microbesQuickTime™ and a
TIFF (LZW) decompressorare needed to see this picture.
Fungal pathogens are true Fungal pathogens are true invadersinvaders
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
•Invasions are more frequent before frequency and intensity of movement of goods and people are greatly on the rise
How can people transport How can people transport pathogenspathogens
• By transporting plants and plant partsBy transporting plants and plant parts– Crops, and seedsCrops, and seeds– Raw foodRaw food– Ornamental plantsOrnamental plants
Untreated lumberUntreated lumber
SoilSoil
Insects vectoring fungiInsects vectoring fungi
HOW to identify species and HOW to identify species and possibly provenance of possibly provenance of
pathogenspathogens
• Microscopic organisms with few Microscopic organisms with few differentiating featuresdifferentiating features
• Often cannot be culturedOften cannot be cultured
: USING DNA SEQUENCES: USING DNA SEQUENCES
•Species I Species II(more virulent)
•Europa
•Nord America
A
B
C
D
ABCD are four sequences ABCD are four sequences uniquely found in the four types uniquely found in the four types
of pathogof pathogensens
• 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 containsEcah 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 Let’s read the DNA sequence of a variable portion of a a variable portion of a
chromosomechromosome
•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 Let’s build an evolutionary or family tree using these sequencesusing these sequences
•AGT GAA CCA G
Uncle Scroodge
• AGA GAA CCA G
Donald Duck
•AGA GAG CCA G
Hewey
•EVE
Lewy
Dewey
Who is Who is AGA GAG CCA G
•AGT GAA CCA G
Uncle Scroodge
• AGA GAA CCA G
Donald Duck
•AGA GAG CCA G
Hewey
•EVE
Lewey
Dewey
And if the culprit were And if the culprit were AGA GAT CCA G ?
•AGT GAA CCA G
UNCLE SC
• AGA GAA CCA G
DD
•AGA GAG CCA G
H
•EVE
L
D
If the culprit were If the culprit were AGA GAT CCA G ?
•AGT GAA CCA G
US
• AGA GAA CCA G
DD
•AGA GAG CCA G
H
•EVA
L
D
•Maybe•But which one?
And if the culprit were And if the culprit were GGC AAA TCT G ?
•AGT GAA CCA G
US
• AGA GAA CCA G
DD
•AGA GAG CCA G
H
•EVE
•AGA GAT CCA G
D
•AGA GAC CCA G
L
If the culprit were 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 ScienceThe last frontiers in Science11
• To sequence an entire genome to understand how it functions
We sequenced to genomes of We sequenced to genomes of related fungus-like organisms related fungus-like organisms
(Science)(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 ScienceThe new frontiers of Science22
• To sequence one gene, one locus, for hundreds of species to increase our databases regarding communities and entire ecosystems