DNA analysis: the last frontier for biologists

1. DNA analysis: the last frontier for biologists • Lesson 1 of MEFF Spring 2007 • Taught by Dr. Matteo Garbelotto

2. Forest pathology and mycology:the P.I.

3. THE LAB

4. IMPORTANCE OF FORESTS

5. Aesthetic value

6. Production of timber and fuel

7. Terrestrial ecosystems containing maximum biodiversity

8. Habitat for millions

9. Huge role in geological protection from erosion, floods, etc.

10. One of the most significant sinks for carbon

11. FORESTS ARE ESSENTIAL FOR LIFE ON THE PLANET

12. FUNGI ARE ESSENTIAL FOR FORESTS

13. 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

14. Largest living organisms in the world are fungi

15. Aerial view of a single fungal individual growing in the soil and killing plants

16. Tens of acres occupied by a single individual, older than 5000 years!!!! (Northern Michigan)

17. 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

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

20. 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

21. The visible part of root tips of most trees is actually a mantle of fungal hyphae fused with the plant tissue

22. What is the deal of this mutualism? • Fungus absorbs nutrients for plants • Plant gives fungus carbohydrates it produces via photosynthesis

23. 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?

24. 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

25. Tricholoma matsutake grows in Eurasia and is prized enormously by the Japanese who pay over 1000 dollars a pound

26. Using DNA data we were able to prove Tricholoma matsutake also grows in the eastern US and in Mexico

27. The mexican fungus is sold in Japan and the revenues make up to 30% of the economy of some mountain communities

28. What about planting pines where these fungi, essential for the growth of pines, do not exist?

29. In the soil under pines we found DNA sequences of an imported fungus

30. 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

31. 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

33. 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

34. Fungal pathogens are true invaders

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

36. Forest pathogens can never be eradicated

37. How can people transport pathogens • By transporting plants and plant parts • Crops, and seeds • Raw food • Ornamental plants Untreated lumber Soil Insects vectoring fungi

38. HOW to identify species and possibly provenance of pathogens • Microscopic organisms with few differentiating features • Often cannot be cultured

39. : USING DNA SEQUENCES Species I Species II(more virulent) Europa Nord America C A D B

40. 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

41. 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

42. 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

43. 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

44. 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

45. Who stole the cookies ? • AGA GAG CCA G

46. 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

47. 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

48. 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

49. 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

50. 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