Cursos Internacionais

Cursos Internacionais PPGBB

Os Cursos Internacionais PPGBB têm como objetivo intensificar o desenvolvimento da internacionalização e a excelência da educação no Programa de
Pós-graduação em Biociências e Biotecnologia, e contribuir para o processo de internacionalização da pós-graduação stricto sensu e da ciência, tecnologia e inovação.

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Cursos anteriores

International Course on Bioinformatics Analysis of Human Whole Exome Sequencing Data

Coordinator: Fabio Passetti

Collaborating Professors: Dr. Lucía Spangenberg and Dr. Hugo Naya from the Institut Pasteur de Montevideo

Course Load: 24 hours

Period: November 22 to 24, 2022

Schedule: Tuesdays and Fridays, from 1:00 PM to 3:00 PM

Syllabus:

Day 1: Introduction to Next-Generation Sequencing (NGS); mapping and quality analysis using Linux and R; and mapping with calibration of Whole Exome Sequencing (WES) data.
Day 2: Identification of genetic polymorphisms; types of genetic variants and quality analysis; and practical session with GATK software for identifying genetic polymorphisms in WES data.
Day 3: Epidemiology applied to genetics; population genomics; and exercises with case discussions.
Em Combining induced pluropotent …

Combining induced pluripotent stem cells and structural approaches to study neurodegenerative diseases

Coordinator: Tatiana de Arruda Campos Brasil de Souza

Collaborating Professor: Dr. Helen Cristina Miranda (Case Western University)

Course Load: 30 hours

Period: October 24 – 28, 2022

Schedule: 9:00 AM – 5:00 PM

Syllabus:

Module I
Available from October 17, 2022: Theoretical and practical classes on the use of visualization and manipulation programs for three-dimensional structures such as PyMOL, Chimera, etc. Analysis of protein-protein interactions. Online program for three-dimensional structure modeling.

Module II
October 24 – Theoretical classes on basic concepts of stem cells, isolation, culture, characterization, and differentiation of adult and pluripotent stem cells.

October 26, 2022 – How to model neurological diseases using 2D and 3D human stem cell cultures.

Genomic Biomarkers and their Interpretation in Hematologic Malignancies

Invited professors

Adam C. Smith – University of Toronto
José-Mario Capo-Chichi – University of Toronto
Hubert Tsui – University of Toronto

Invited professors

Adam C. Smith – University of Toronto
José-Mario Capo-Chichi – University of Toronto
Hubert Tsui – University of Toronto

Provide students with an overview of the classification of hematological malignancies and the techniques capable of detecting the genetic alterations associated with these diseases.

Understand the updated classification of hematologic malignancies launched in 2022 by the World Health Organization and the International Consensus Classification.
Discuss the differences and problems related to the diagnosis of these diseases.

Review the use of cytogenetics and cytogenomic techniques to detect structural variants. Understand and apply the International Standard for Cytogenetic Nomenclature (ISCN) in practical cases and scenarios. Review cytogenetic techniques related to diagnosis.

Review the techniques used in Molecular Genetics laboratories.
Compare the advantages and disadvantages of various techniques.

Use the acquired knowledge in specific objectives 1-3 for application in practical cases and scenarios.
Discussion of testing approaches in “resource-rich” and “resource-poor” environments. Investigate new applications for genetic testing in Onco-Hematology, including proposing hereditary leukemias and other special topics.

Part 1

Basic concepts of Biology of Cancer and Hematological Neoplasms: 8 hours
Genomic Basis of Hematological Neoplasms: 4 hours
WHO and ICC classification of Hematological Neoplasms: 4 hours

Part 2

Cytogenetic and Molecular Methods Molecular Nomenclature (HGNC): 2 hours
Cytogenetic Nomenclature (ISCN) : HGNC and ISCN Nomenclature Workshop : 4 hours

Part 3

New Generation of Biomarker Testing and characterization of Acquired Hematologic Neoplasms Using NGS: 4 hours
Optical genome mapping (OGM) applied to Hematological Neoplasms: 4 hours
Workshop – Case examples with report using mock NGS and GMO results: 4 hours
Additional Topics of Interest: What is CHIP and CCUS (Clonal Hematopoesis of Interdeterminant Potential and Clonal Cytopenia of Undetermined Significance): 2 hours
Hereditary Predisposition to Hematologic Neoplasms: Case Discussion: 4 hours

Integration of Structural Biology Approaches for Studying Macromolecules

The aim of this workshop is to give some tips and tools to researchers interested in studying the structure-function relationships in macromolecules and macromolecular complexes. To get a deep understanding of a biological process, an integration between biophysics, biochemistry, bioinformatics and structural biology is important. It is also important to stress the fact that one cannot be expert in each and every field, but each expertise is important to build the puzzle. Nevertheless, having an idea of which are the possibilities, and the possible pitfalls of several techniques will be fundamental to choose the right collaboration and to better follow their approaches and results. Therefore, I shall present some of the techniques with specific examples, also in relationships with the possibilities offered by Synchrotrons.

Responsible teacher

Adriana Erica Miele – teacher of Biochemistry and Biophysics at the University Claude Bernard Lyon 1. Lyon,

Researchgate: https://www.researchgate.net/profile/Adriana-Miele

The theoretical classes will be offered in a hybrid format only for participants outside of Curitiba.
The practical class will be limited to 18 participants. Those interested in the practical class should indicate their intention by sending a text justifying their interest.

Registration for the practical class – https://forms.gle/ogxMegXnao4eC4cYA

Monday October 30th 2023

9:00-10:30 – Integrative structural biology

An introduction on the different methods that can be used to gain structural information on macromolecules, with emphasis on Microscopy (super resolution, atomic force and electron microscopies), NMR, crystallography and small angle X-ray scattering (SAXS)

11:00-12:30 – cryoElectron Microscopy (cryoEM)

A quick tour on the theory and practice of EM, including sample preparation and a few examples of applications.

Break

14:00-15:30 – Tutorial on SAXS

EMBL-Hamburg offers the package ATSAS for data analysis online as well as for download. The tutorial will show how to analyse protein SAXS data and which information can be obtained.

Tuesday October 31st 2023

9:00-10:30 – How to read a structure paper: a hitchhiker guide for non structuralists

Seeing is believing, but which are the possible pitfalls to avoid if you are not a specialists? A guided tour on a few examples.

11:00-12:00 – When structure meets function (or not)

Schistosoma mansoni is a complex multicellular parasite and an interesting biological puzzle, needing a multi-technical approach to be tackled.

In vitro and in vivo systems to study the immune response to pathogens and vaccines: Hepatitis B virus and Bacillus Calmette-Guérin models

The analysis of the immunological response to different pathogens represents an important tool for understanding the pathogenesis of infections, as well as for the development of vaccines and therapies.

One of the fundamental aspects of the immune response is the recognition of foreign invaders and the development of an immune response. At the cellular level, immune cells can sense pathogen associated molecular patterns (PAMPs) and start an immune response at the cellular level. Specifically for viral pathogens, cells sense the pathogens using different receptors and initiate the modulation of intrinsic cells factors and pathways (like type I IFN) which present antiviral activity. Understanding the role of these pathways may lead to the development of antiviral strategies, either specific or broadly to multiple viruses.

Additionally, from a systemic point of view one important characteristic of the immune response is the ability of immune cells to migrate to the site of infection, or even to circulate through different immune organs (lymph nodes, spleen and thymus). This property of immune cells is responsible for capturing non-self antigens in the periphery, initiating specific immune responses in immune tissues. Therefore, analyzing how this cell migration occurs in vivo is relevant to understand the dynamics of the immune response to antigens. Furthermore, this knowledge can be useful for the development of more efficient vaccines, or for the treatment of immunological disorders associated with cell migration to inflamed tissues.

For some pathogens these studies are quite limited, due to the handling biosafety level, or the difficulty of cultivating those microorganisms in vitro and/or in vivo. The hepatitis B virus (HBV) represents a classic example of a pathogen in which the in vitro and in vivo cultivation of the agent represents one of the main challenges. Although there is a safe and efficient vaccine for preventing acute and chronic infection with the virus, curing chronically infected patients still represents a key challenge. In vitro and in vivo culture systems for this pathogen, although useful, still have major limitations. Additionally, studies involving the infection/transfection of susceptible cells (HepG2 or Huh7.5 expressing the sodium taurocholate co-transporting peptide, NTCP receptor) have brought some advances, but there are still important limitations. Therefore, the course will focus on in vitro cultivation of HBV on HepG2-NTCP cells and the recently described HBV pregenomic RNA (pgRNA) system to study HBV biology and the antiviral immune response. Also, the Bacillus Calmette-Guérin (BCG), the vaccine against tuberculosis, will be used to study cell migration using protocols that allow cell tracking and enable the understanding of the migration dynamics of different cells in vivo.

Finally, students will have the opportunity to learn about new tools and protocols for studying the immune response against HBV and BCG, which can be adapted to other pathogens of interest.

Program

Day 1 (10/28/2024)

9:00-10:30h – Theoretical class I – General aspects of HBV biology

Lefteris Michailidis, PhD – Emory University, Atlanta, USA.

11:00-12:00h – Protocol Discussion I – Virus stock preparation, infection of HepG2-NTCP cells with HBV, and a cell culture system supporting the complete life cycle of HBV

Lefetris Michailidis, PhD – Emory University, Atlanta, USA

13:30-18:00h – Practical class I – Stock preparation, infection of HepG2-NTCP cells with HBV

Lefetris Michailidis, PhD – Emory University, Atlanta, USA

Day 2 (10/29/2024)

9:00-10:30h – Theoretical class II – Primary human hepatocytes as a model to study HBV biology and innate immune responses

Lefteris Michailidis, PhD – Emory University, Atlanta, USA

11:00-12:00h – Protocol Discussion II – Targeted arrayed overexpression and CRISPR KO screens for virus-host interaction studies in the context of HBV infection

Lefteris Michailidis, PhD – Emory University, Atlanta, USA

13:30-18:00h – Practical class II – Targeted arrayed overexpression and CRISPR KO screens for virus-host interaction studies in the context of HBV infection Lefteris Michailidis, PhD – Emory University, Atlanta, USA

Day 3 (10/30/2024)

9:00-10:30h – Theoretical class III – An RNA-based system to study HBV replication and evaluate antivirals