Advanced Topics in Biochemistry and Molecular Biology IV

The course “Advanced Topics”
Is mandatory for graduate students of the Program in Biological Sciences-Biochemistry. Lecturers, who are Brazilian and foreign researchers, will present their recent research results and projects in the field of Biochemistry and Molecular Biology. This course is presented every semester. Along this course, graduate students in be in contact with recent advances and projects in a free discussion situation, so they should develop an analytical viewpoint of the lectures and topics discussed. This course aims to present a broad view of research projects, recent advances and methodologies in the field of Biochemistry and Molecular Biology. Institute of Chemistry (IQ) São Paulo main campus Students enrolled in this course should be familiar with the content of textbooks as Biochemistry (Voet & Voet), Principles of Biochemistry (Lehninger) and Genes (B. Lewin). Topics will be focused in the field of Biochemistry and Molecular Biology and they will be determined by the lecturers. Topics will include recent advances and research projects, approaches and methodologies, experimental results and published manuscripts. F_bio Lu_s Forti, Roberto Kopke Salinas, Alexandre Bruni Cardoso 60 QBQ5766 2 Students should present at least one written question to the speaker.

Introduction to risk analysis

The course is intended for students who have basic knowledge of probability such as random variables, distribution functions, generating functions and their basic properties. The basic concepts of risk analysis and their stochastic nature will be presented. The methodology presented in the course will broaden students’ knowledge area and show new applications of the probabilistic techniques in risk phenomena. Institute of Mathematics ans Statistics (IME) São Paulo main campus 1. Probability aspects of risk. 2. Distributions of total insurance paid in one year. 3. Principles of calculation of the premiums. 4. Exchanges of risk and re-insurance. Nikolai Valtchev Kolev 60 MAE5890 8

Quantitative Genetics and Genomics

Genome sequencing of domestic animals and advances in quantitative genetics have enable new approaches in animal breeding. This course will talk about recent advances in the area of quantitative genetics and genomics and the aplications in beef cattle breeding. The course will have the contribution of especialists in different areas. Provide the principles of quantitative genetics aplied to genome selection and genomics, so the students can understand a contribute to the development of this new area. Luiz de Queiroz College of Agriculture (ESALQ) Piracicaba campus The U.S. Beef Industry: Structure and Current Genetic Selection Programs; Priors in the Bayesian Alphabet; Developing Genomic Predictions: Training and Evaluation; Additive genomic relationship matrix and GBLUP; Haplotype-based models: BayesIM; Interpreting “genomic correlations” and pleiotropy; Tour of Genomics Center; Population structure in admixed populations; Reproducing kernel Hilbert spaces regression; GO enrichment analysis; MeSH enrichment analysis; GO / MeSH enrichment analysis in Bioconductor Luiz Lehmann Coutinho, Gerson Barreto Mour_o 75 LZT5869 4 University of Sao Paulo,Universidade de Campinas and Universidade Estadual Paulista Student participation and Exam.

Introduction to Programming and Computational Tools for the Social Sciences

The course offers an introduction to programming logic and computational tools for the social sciences graduate students. The course focus on procedures to (1) gather (2) organize and (3) present social data. The course aims to develop programming skills for handling data with academic purposes. Notice that this is not a methods, data analysis or computational social science course. The course is divided in two parts. In the first part we focus on preparing the computational enviroment, getting used with the tools and developing programming literacy in R, Git, SQL, Markdown, and other languages required in class. In the second part we apply the skills acquired in the first part to handle big datasets, webscrapping and third party APIs, digital files management for textual analysis, graphs, maps and other topics of interest. This course aims to fill a gap _common among social science students- providing the training in data management and computational skills Faculty of Philosophy, Languages and Human Sciences (FFLCH) São Paulo main campus 1 – Basics of R Programming 2 – Data structures and data management in R 3 – Tables and graphs in R 4 _ R + SQL basics 5 – Git basics 6 – Markdown basics 7 – LaTex basics 8 – Webscraping 9 – Text, corpus and natural language processing 10 – Maps and GIS 11 – Networks and graphs Glauco Peres da Silva, Leonardo Sangali Barone 40 FLS6397 8 Weekly activities (50%) and a final project (50%).

The Origins of Molecular Biology

The aim of this discipline is to present the students seminal papers of molecular biology. These papers will be analysed from a historical, methodological and scientific perspective. This discipline complements the basic knowledge acquired in regular disciplines of molecular biology. By discussing original articles, the students will analyze in depth the historical context and the methodologies used by the scientists that pave the way of molecular biology. This will ultimately give the students the tools to understand the basis of molecular biology and the development of scientific thought. Biomedical Sciences Institute (ICB) São Paulo main campus Every lecture will be followed by the discussion of an original article. The student will receive a questionnaire that will guide him/her through the reading of the paper, with the help of the instructors. Items to be discussed include the following topics: (1) Structure and function of DNA ; ( 2 ) RNA and the genetic code ; ( 3 ) Advent of genetic engineering and genomics. Carlos Eduardo Winter, Beny Spira 25 ICB5751 8 Written tests will be used to evaluate student progress during the course.

Molecular Biology of Plasmodium falciparum: a Practical Course Biologia Molecular de Plasmodium Falciparum _ um Curso Pr_tico

This course aims to teach techniques dealing with recombinant DNA and enable the students to perform a number of basic methodologies frequently used in laboratories which research activities in gene expression, molecular cloning and manipulation of DNA and RNA in general. Another goal is to complement informations given in other regular lessons and transmit a global vision to the student. The course is supposed to give postgrad students the opprotunity to acquire knowledge about Plasmodium and apply moleculares techniques. Further, by applying practical techniques, they learn different aspects about Plasmodium biology and malaria disease. In addition, the students Will have the opportunity to present general topics related to malaria in a series of seminars held in English or Portuguese language. Biomedical Sciences Institute (ICB) São Paulo main campus 1) Cloning of different genes encoding antigens of Plasmodium falciparum; 2) Purification of recombinant proteins by affinity chromatography. 3) PCR; 4) SDS-PAGE; 5) Western blotting; 6) ELISA 7) Real time PCR 8) DNA edition soiftare (ApE). The complete methods are provided in a manual which is delivered in the beginning of the course. Gerhard Wunderlich, Carsten Wrenger 2 BMP5785 5 The course is mainly meant for undergrad students in the last semesters of Biology, Biomedicine or Pharmaceutical Sciences. In case that the offered seats are not occupied by undergrad students, the remaining slots can be distributed among interested postgrad students. Before the course, all selected students meet with the professor in order to organize working groups of two students and distribute seminar themes. The course is mainly meant for undergrad students in the last semesters of Biology, Biomedicine or Pharmaceutical Sciences. In case that the offered seats are not occupied by undergrad students, the remaining slots can be distributed among interested postgrad students. Written exam and seminar presentations.

Uses of Nuclear and Related Techniques in Studies of Animal Science

Within the strategic objectives of CENA, the “Productivity and Agribusiness Food” includes the programs for plant breeding and production and food preservation, whose scientific research deals in many cases with the use of nuclear techniques in biological systems. The course will provide the basics of different nuclear and related techniques used in developing research on agricultural productivity, aiming to secure and qualitative development of scientific works. Present nuclear and related techniques as tool for studying factors affecting animal productivity and its interaction with the environment, through nutritional evaluation of feeds, the study of nutrient metabolism, quantification and identification of bioactive molecules present in foods and by-products and studies for mitigating greenhouse gases by animals. Center of Nuclear Energy in Agriculture (CENA) Piracicaba campus The use of isotopic markers such as 13C, 51Cr, 32P, 45Ca and 15N and the radiation is discussed in understanding the way as the microorganisms in the rumen of animals digest forages and other foods; how the radiation may increase the digestibility of fibrous foods and how radioisotopes and radiation are important tools for studying the real absorption of minerals; besides being discussed the use of markers such as 125I and 3H for determination of hormones by immunohistochemical analysis to monitor reproductive functions of female domestic interest. It is also studied food and diet regarding the in vivo production of methane produced by ruminants by systems using single chambers and tracer gas SF6. Practical classes will analyze different products to follow techniques of chemical analysis; estimates of total digestible nutrients and gas production in the evaluation of food; Beyond the determination of minimum requirements of minerals in domestic animals; digestibility in vivo and in vitro determination of bioactive molecules in food and quantification of enteric methane. Adibe Luiz Abdalla, Helder Louvani 20 CEN5740 12 Assessment through seminars with the presentation of the results obtained in practical classes.

Seminar on Methods for Investigating the Aseptic Processing of Health Products and Healthcare Environment Decontamination

The growing production of knowledge in the context of aseptic processing of health products and healthcare environment decontamination, such as biofilms, endotoxins, and prion proteins, among organic residue, has required researchers develop suitable study designs. This course proposes to qualify students to develop research projects in the field of Nursing in Central Sterile Service Departments, taking into account the rigor required for producing knowledge in this specialty. • To discuss and analyze different research designs related to the aseptic processing of health products and healthcare environment decontamination, with the goal of broadening students’ information based on the topic so that their practice can be critical and transformative. To mobilize graduate students’ capacity of using and developing research methods suitable for producing new consistent knowledge. School of Nursing (EE) São Paulo, Pinheiros campus 1. Analysis of published studies on the aseptic processing of health products and healthcare environment decontamination. 2. Basic research designs for demonstrating security against the presence of endotoxins, biofilms and microorganisms in processed health products. 3. Analysis of developing research projects about the aseptic processing of health products and healthcare environment decontamination, identifying their theoretical and methodological basis. Kazuko Uchikawa Graziano 27 ENC5932 2 The course lasts one week and meets on 3 consecutive days with 8 hours of work per day. Presentation of and ability to discuss a developing graduate research project, incorporating pertinent suggestions from the course.

Principles of Research Data Management and Collection

The proposal of this course is to create an adequate infrastructure for data collection and management of the studies carried out in the scope of Post-Graduation Program. In order to achieve this goal, students will have access to the world’s most widely used system for electronic data collection and data management in scientific research, known as REDCap (Research Electronic Data Capture). This course will provide best practices and real case examples for data management in REDCap. This course aims to present critical concepts and practical methods to support planning, collection, storage, and dissemination of data in clinical research to enhance security, reliability and quality to the data collected for research purposes. School of Nursing (EE) São Paulo, Pinheiros campus Principles of data management in scientific research; Recommended practices for development of questionnaires; Modalities for data collection in scientific research; Privacy, confidentiality and data security requirements of human research data; REDCap _ key concepts and applications in scientific research; International data standards and best practices for data dictionaries definitions; Effective data management: reports, data export, graphical visualization and data quality monitoring; Considerations for conducting web-based surveys; Hands-on training: REDCap projects development (classical and longitudinal) and application of the main REDCap features. Katia Regina da Silva 20 ENC5966 2 Hands-on exercises.

Analysis of Nursing Conceptual Frameworks in Research

All research is grounded in a theoretical perspective. Nursing knowledge is only built through the development and testing of theories and conceptual frameworks. The purpose of this course is to enhance students understanding of how nursing conceptual frameworks are used to guide nursing research. Students will be able to aplly the knowledge learned in this course to guide their proposed research. 1. Describe the relationship between nursing science, philosophy, theory development and research; 2. Examine selected nursing theories and their application to research; 3. Apply the process of theoretical substruction in the analysis of nursing theory testing research. School of Nursing (EE) São Paulo, Pinheiros campus Structure of knowledge in the discipline of nursing; The value and purpose of nursing theory; Tipes of theories; Selected conceptual frameworks and nursing theories and their application to guide research; Theoretical substraction of nursing theories. Rita de Cassia Gengo e Silva 22 ENC5967 2 Each student will select a published nursing theory testing research article and complete a theoretical substraction on the conceptual framework of the study.

Observational Astrophysics

The observational activity is one of the pillars of Astrophysics, continuously feeding the theoretical elaboration. Observational training is essential both to researchers who produce the data as to theorists who should know evaluate them critically. Give to the graduate student fundamental notions of the instrumentation used in Astrophysics, as well as on observational techniques, data acquisition and reduction. In particular, give to the student conditions to plan the use of instrumentation to achieve specific scientific goals. Institute of Astronomy, Geophysics and Atmospheric Sciences (IAG) São Paulo main campus Effect of Earth’s atmosphere on observations in the optical and infrared; Telescopes and image quality; Effects of the interstellar medium; Detectors; Techniques of radio astronomy; Photometry; Spectroscopy; Elements of polarimetry ; Data acquisition handling; Space astronomy – X-rays Roberto Dell’Aglio Dias da Costa, Marcos Perez Diaz, Jorge Luis Melendez Moreno 30 AGA5802 11 Tests and practical exercises

Formation and Evolution of Galaxies

In this course we will discuss the main scenarios for the formation and evolution of galaxies in order to enable the students to know the main recent advances in the area and also to expose them to the questions and challenges still open. Some content discussed in other disciplines, especially Extragalactic Astronomy, will be briefly reviewed. The question of the origin and evolution of galaxies is one of the most important research topics in the present day in extragalactic astronomy and cosmology, both theoretically and observationally. The techniques used are quite varied and useful in various areas of research. The course should provide the elements for students to track progress in this area Institute of Astronomy, Geophysics and Atmospheric Sciences (IAG) São Paulo main campus Review of the properties of galaxies: structure, stellar populations, scale relations, dependence on the environment. Review of cosmology concepts relevant to the course. Gravity instability and structure formation. The first stars. The reionization. Semi-analytical models of galaxy formation. Star formation. Chemical evolution. Photometric-photometric evolution. Mergers of galaxies. Evolution of Morphology. Analysis of observational data. Laerte Sodre Junior, Gastao Cesar Bierrenbach Lima Neto, Paula Rodrigues Teixeira Coelho 25 AGA5906 11