Ecology, diversity, taxonomy, and phylogeny of nitrogen fixation and nodulation in legumes

CAPES-PRINT Short Course

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Professors

Dr. Euan Kevin James | The James Hutton Institute | Scotland UK
Prof. Dr. Leonardo M. Cruz | Depto. de Bioquímica e Biologia Molecular - UFPR | 1o andar, sala 283

Course general information

Course load: 15h

Course enrolment: Secretaria do Programa de Pós-Graduação em Ciências - Bioquímica

Venue

Class: Anfiteatro 314 do Programa de Pós-Graduação em Ciências - Bioquímica | Terceiro andar do Departamento de Bioquímica e Biologia Molecular
Lab activities: Laboratórios do Núcleo de Fixação de Nitrogênio

Schedule

Every day from 09:00h AM to 12:00h AM
Start on 06 Feb (Monday) | End on 10 Feb (Friday)

Topics to be covered (short)

1. Theoretical

  1. Ecology, biochemistry and molecular biology of nitrogen fixation
  2. Nodulation process
  3. Taxonomy of rhizobia
  4. Rhizobia and ligume symbiosis
  5. Taxonomic identification and phylogeny of rizobia base on marker genes and genomic sequences

2. Practical

  1. Isolation and characterization of beta-rhizobia
  2. Sequence analysis
  3. Microscopy

Supporting Material

DAY 1 (06-02-2923)

Presentation
Beta-rhizobia-legume interaction presentation

DAY 2 (07-02-2023)

Presentation
Use of Transmission Electron Microscopy (TEM) in studies of Plant-Microbe Interactions presentation

DAY 3 (08-02-2023)

Class | Phylogeny

Presentation
Phylogeny - Introduction presentation
More About Phylogenetic Analysis presentation
Activity
Building a phylogenetic tree using MEGA11
Building a phylogenetic tree using the online tool NGPhylogeny.fr (coming soon)
YouTube Video
Creating a Phylogenetic Tree (vídeo no YouTube 8:50min)
Recommended reading
=== Web sites ===
1. Phylogenetics - an Introduction. Online Tutorial - EMBL-EBI Training
2. How to read a phylogenetic tree. Andrew Rambaut
3. Understanding Evolution. UC Museum of Paleontology – University of California, Berkeley
4. Misconceptions about evolution. UC Museum of Paleontology – University of California, Berkeley
=== Text ===
1. Baum DA, Smith SD, Donovan SS. Evolution. The tree-thinking challenge. Science (New York, N.Y.). 2005 Nov;310(5750):979-980. DOI: 10.1126/science.1117727. PMID: 16284166.
2. Baldauf SL. Phylogeny for the faint of heart: a tutorial. Trends in Genetics : TIG. 2003 Jun;19(6):345-351. DOI: 10.1016/s0168-9525(03)00112-4. PMID: 12801728.
3. Kolekar, P; Kale, M; Kulkarni-Kale, U. Chapter 1. Molecular Evolution and phylogeny: what, when, why and how? In: Lopes, HS; Cruz, LM (ed.) Computational biology and applied bioinformatics. InTech, 2011
4. Cruz LM et al. Chapter 5. Protein Function Prediction. In: Kaufmann, M.; Klinger, C.; Savelsbergh, A. (eds.) Functional Genomics - Methods and Protocols. Third Edition - Methods in Molecular Biology 1654 - Springer protocols. Humana Press.
5. Barry G. Hall. Building Phylogenetic Trees from Molecular Data with MEGA. Molecular Biology and Evolution, 30(5):1229-1235, 2013

DAY 4 (09-02-2023)

Lab | Fluorescence microscopy; Bacteria identification by mass spectrometry; Bacteria isolation from legume nodules

DAY 5 (10-02-2023)

Class | Evolution of legume-rhizobia symbiosis

Presentation
The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes presentation