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Novas Perspectivas em Estudos de Ecologia Microbiana

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Aula ministrada junto à disciplina “Microbiologia Ruminal: Abordagem Molecular” [Tópico: Novas Perspectivas em Estudos de Ecologia Microbiana], do curso de pós-graduação em Ciências (Energia Nuclear), do Centro de Energia Nuclear na Agricultura (CENA/USP).

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Novas Perspectivas em Estudos de Ecologia Microbiana

  1. 1. Novas Perspectivas em Estudos de Ecologia Microbiana Leandro Nascimento Lemos Doutorando em Biologia na Agricultura e no Ambiente Supervisor: Profa. Dra. Siu Mui Tsai Marc¸o/2017 Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  2. 2. Novas perspectivas em estudos de Ecologia Microbiana Descobrir novos microrganismos n˜ao-cultiv´aveis (biodiversidade desconhecida). Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  3. 3. Novas perspectivas em estudos de Ecologia Microbiana Descobrir novos microrganismos n˜ao-cultiv´aveis (biodiversidade desconhecida). Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  4. 4. Novas perspectivas em estudos de Ecologia Microbiana 1 Sequenciamento massivo de DNA. 2 Desenvolvimento de supercomputadores. 3 Desenvolvimento de novas ferramentas computacionais (de Bioinform´atica). Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  5. 5. Ciˆencia de Dados (Data Science) Acesso a informac¸˜ao e como transformar a informac¸˜ao em conhecimento; Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  6. 6. Ciˆencia de Dados (Data Science) Acesso a informac¸˜ao e como transformar a informac¸˜ao em conhecimento; https://www.youtube.com/watch?v=OE63BYWdqC4 Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  7. 7. Novas perspectivas em estudos de Ecologia Microbiana 1 Sequenciamento massivo de DNA. 2 Desenvolvimento de supercomputadores. 3 Desenvolvimento de novas ferramentas computacionais (de Bioinform´atica). Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  8. 8. 1. Sequenciamento massivo de DNA Illumina Hiseq: sequenciamento de at´e 2.000 genomas microbianos em uma ´unica corrida. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  9. 9. 1. Sequenciamento massivo de DNA Ebola em 2015. 28.599 casos 11.299 mortes na ´Africa Ocidental. Sequenciamento: Caracterizar o agente infeccioso e determinar as taxas de mutac¸˜oes. Ganhos: Identificac¸˜ao de trac¸os adaptativos e caracterizac¸˜ao de respostas do v´ırus a vacinas e tratamentos. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  10. 10. 1. Sequenciamento massivo de DNA MinIon: Sequenciador port´atil USB. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  11. 11. 1. Sequenciamento massivo de DNA MinIon: Strand sequencing - DNA passa intacto em um nanoporo prot´eico, sendo sequenciado em tempo real, assim que a mol´ecula ultrapassa o poro. https://www.youtube.com/watch?v=BNz880V52rQ Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  12. 12. 1. Sequenciamento massivo de DNA SmidgION - Mobile analyses Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  13. 13. 2. Desenvolvimento de supercomputadores Velocidade dos avanc¸os na capacidade de processamento e armazenamento de dados. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  14. 14. 2. Desenvolvimento de supercomputadores Lei de Moore: N´umero de transistores em um chip dobraria a cada 18 meses, mantendo ou diminuindo o custo de produc¸˜ao e o espac¸o ocupado pela pec¸a. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  15. 15. 2. Desenvolvimento de supercomputadores Alta capacidade de processamento, armanezamento e mem´oria; Illumina Hiseq (18.000.000/reads por amostra); 128 processadores e 2 TB de mem´oria ram. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  16. 16. 3. Bioinform´atica O que ´e: Aplicac¸˜ao da Ciˆencia de Dados na resoluc¸˜ao de problemas biol´ogicos; Desafio: processar uma avalanche de dados gerados por sequenciadores de nova gerac¸˜ao; Solu¸c˜ao: Produzir novas ferramentas computacionais. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  17. 17. 3. Bioinform´atica Ferramentas de Processamento: Ferramentas de Visualiza¸c˜ao: Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  18. 18. Bioinform´atica: Human Microbiome Project Explorar as relac¸˜oes entre doenc¸as humanas com alterac¸˜oes na microbiota; Desenvolvimento de novas ferramentas de Bioinform´atica Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  19. 19. Bioinform´atica: Human Microbiome Project Desenvolvimento de novas ferramentas de Bioinform´atica (IMG/M) Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  20. 20. Novas perspectivas em estudos de Ecologia Microbiana Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  21. 21. Estudos de comunidades microbianas (ou de microbiomas) T´ecnicas independentes de cultivo de microrganismos; Microrganismos n˜ao-cultiv´aveis s˜ao a maioria! Meta’omics: integrac¸˜ao de diferentes tipos de dados. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  22. 22. Reconstruc¸˜ao de genomas em amostras de metagenomas por Single-cell Separac¸˜ao de c´elulas de bact´erias n˜ao-cultiv´aveis; Extrac¸˜ao de DNA e amplificac¸˜ao do genoma total; Sequenciamento e Bioinform´atica. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  23. 23. Reconstruc¸˜ao de genomas em metagenomas por Single-cell Separac¸˜ao de 9.600 c´elulas e sequenciamento de 201 genomas de bact´erias e arqu´eias n˜ao-cultiv´aveis; Muitos grupos ainda desconhecidos (”microbial dark matter”); Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  24. 24. Reconstruc¸˜ao de genomas em metagenomas por Single-cell C´odon de parada UGA codifica uma glicina; S´ıntese de purina de arqu´eias presentes em bact´erias (transferˆencia horizontal de genes); Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  25. 25. Reconstruc¸˜ao de genomas em amostras do metagenoma total Metagenomas = m´ultiplos genomas presentes em uma amostra ambiental. Genomas microbianos s˜ao parecidos (evolu¸c˜ao) == dificulta o processo de separac¸˜ao (ou montagem); Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  26. 26. Reconstruc¸˜ao de genomas - Binning Soluc¸˜oes: Montagem e Binning Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  27. 27. Reconstruc¸˜ao de genomas - Binning Reconstruc¸˜ao do genoma de uma Firmicutes n˜ao-cultiv´aveis e com abundˆancia relativamente alta em compostagem. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  28. 28. Nova ´arvore da vida Pontos vermelhos indicam grupos que ainda n˜ao foram cultivados. Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  29. 29. Onde aprender? Coursera: https://www.coursera.org Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  30. 30. Onde aprender? Coursera: https://www.coursera.org Gut Check: Exploring Your Microbiome Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana
  31. 31. Obrigado pela aten¸c˜ao! Leandro Nascimento Lemos Novas Perspectivas em Estudos de Ecologia Microbiana

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