. "Vertebrate evolution (tetrapods)"@en . . "7.5" . "In the first year, students with 'Biogeosciences and Evolution' specialization should choose four courses out of these five specialization courses offered.\n\nThis course goal is To understand the development of terrestrial vertebrates during the history of the earth. A major focus is on feeding adaptations, in context of evolution, palaeogeography and palaeoclimatology.\n\nContent\nTaxonomy, comparative anatomy and phylogeny of major tetrapod groups will be discussed, from Paleozoic to Recent times. An important topic will be the physiological and morphological adaptations from an insectivorous or carnivorous lifestyle to a herbivorous lifestyle. The acquisition of herbivory in vertebrates is an important innovation, and is considered to be an important factor in the diversification of life on earth.\n\nEvolution of feeding adaptations in tetrapods will be discussed , in connection with evolution of plants and insects, palaeogeography and palaeoclimatology. In several hands-on exercises comparative morphology of skeletons (extant species) and functional morphology of skulls (extant and extinct species) will be studied. Also included is a visit to Naturalis Biodiversity Center.\n\nBy the end of the course, the student will have acquired:\nKnowledge and insight:\nAn advanced understanding of the evolutionary development of terrestrial vertebrates during the history of the earth, in context with evolution, palaeogeography and palaeoclimatology. An advanced understanding of the adaptation to diet as expressed in the morphology of skull and skeleton, and of convergent evolution due to dietary adaptations. \n>Acquired by reading of the literature, hands-on exercises, the discussions during the oral presentations, and the exam.\n \nApplication of knowledge and insight:\nthe student is capable of exploring the relevant scientific literature and information, and of critically examining, analyzing, and evaluating the information;\n- is able to use and analyze relevant information from other earth-sciences related disciplines (such as chemistry and biology);\n- has obtained the ability to analyse and interpret the data from the hands-on exercises at a high level, including data and information gathered from research-articles.\n>Acquired by the exam, the hands-on exercises, the discussions during the oral presentations, and by writing the report and essay.\n \nJudgement:\nthe student has obtained expertise of the underlying processes in the field of vertebrate evolution and evolution of the earth through time.\n>Acquired by the exam, the hands-on exercises, the discussions during the oral presentations, and by writing the report and essay.\n \nWritten communication skills\nthe student has developed writing and presentation skills and is able to produce written papers on vertebrate evolution in English.\n>Acquired by the writing of the report and essay.\n \nVerbal communication skills\nthe student has developed general listening and presentation skills, also for non-specialist audiences; is able to give an oral presentation, in English, using appropriate presentation techniques, and tuned to a specific public.\n>Acquired by the oral presentation and discussions during the oral presentations." . . "Presential"@en . "TRUE" . . "Basic of molecular biology"@en . . "6" . "Obligatory base module 2 \nLearning outcomes\nGraduate has a basic knowldge on the mechanisms of biological information flow.\nBrief description of content\nOverview of structure and stability of biologically important macromolecules and of structure-function relationship of macromolecules participating in three basic genetic processes: DNA replication, RNA transcription, and protein translation. Other genetic processes (DNA repair and recombination, RNA processing, modification of RNA and proteins, protein folding, transport, and degradation) are discussed using specific examples.\nCourse and its lectures are based on 'Molecular Biology of the Gene' by Watson, et al, 6th or 7th edition." . . "Presential"@en . "TRUE" . . "Cell biology"@en . . "6" . "Obligatory base module 2 \nLearning outcomes\nThe student who passed the course:\n1. Knows the basic postulates of cell theory;\n2. Is able to characterize the cell structure, chemical composition, gene structure and expression specificity in pro- and eucaryotes;\n3. Is able to describe the structure of membranes and how membranes connect different cell compartments to each other and with environment;\n4. Is able to describe structure and main reactions in different organelles;\n5. Will understand the cellular components underlying mitotic cell division and cell cycle regulation;\n6. Will apply their knowledge of cell biology to selected examples of changes or losses in cell function.\n7. Is able to characterize basic methods of cell biology (different microscopy and chromatography types, marked antibodies, flow cytometry)\nBrief description of content\nAn overview of cells as elementary units of life and their main principles of functioning.\nAn overview of the pro- and eucaryotic cell structure as well as of the structure, composition and processes in main organelles (nucleus, nucleolus, chloroplast, mitochondrion, endoplasmatic reticulum, Golgi complex, lysosome, peroxisome, proteasome). The role of and interactions between various cell organelles. The cytoskeleton: microfilaments and microtubules, its motor proteins. The structure and composition of biomembranes, membrane transport. The cell cycle and its regulation. The methods for the investigation of the cell structure and composition" . . "Presential"@en . "TRUE" . . "Systems biology"@en . . "4" . "Learning outcomes\nRecent advances in technology have revolutionized biology enabling the collection of large sets of genomics, metabolomics and proteomics data. The new discipline of systems biology aims to meet the most important challenge of the 'post-omics' era: to understand the mechanisms of the biomolecular networks. The course presents the design principles of biological systems, and highlights the recurring circuit elements that make up biolomolecular networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits.\nBrief description of content\nThe course is introductory, specialist terms are largely avoided, focusing instead on several well-studied biological systems that concisely demonstrate key principles.\nThe course will present an integrated approach in which the quantitative experimental data from biochemical and cell biology research is used to create predictive models of cellular systems. Examples will be discussed to demonstrate how cell-level functions arise and why mechanistic knowledge of the biochemical systems allows us to predict behaviors leading to different cell fate decisions, and also to disease states and drug responses." . . "Presential"@en . "TRUE" . . "Applied synthetic biology"@en . . "6" . "Learning outcomes\nThe students will know:\n1) the recent major general breakthroughs in the field of synthetic biology;\n2) major applications of synthetic biology in bio-economy;\n3) major applications of synthetic biology in medicine;\n4) major applications of synthetic biology in agriculture;\n5) major applications of synthetic biology in chemical and material industry;\n6) major applications of synthetic biology in the fields of biofuels, global warming, and in reaching the humanities goals of biosustainability.\nBrief description of content\nMicrobial cell factories unit (15 lectures and seminars)\nMicrobial cell factories yeast, bacteria. Cell factory construction in silico. Engineering of biosynthetic enzyme specificities and other applications of synthetic biology in cell factory technologies aimed for production of bio-based chemicals, proteins and bio-inspired materials. The topic of next generation biofuels and the role of synthetic biology tools to rewire the microbial metabolism for high-yield biofuel production will be discussed and exemplified with newest examples in industry (Loog, Lahtvee, Valgepea).\nMammalian cell factories unit (5 lectures and seminars): Synthetic biology application in virology and fighting mosquito-spread viral diseases will be covered by Prof. Andres Merits.\nSynthetic biology application in plant biology and agriculture (5 lectures and seminars; Prof. Hannes Kollist).\nMedical applications of synthetic biology (5 lectures and seminars) (Dr. Viljar Jaks)" . . "Presential"@en . "FALSE" . . "Molecular systems biology"@en . . "3" . "Learning outcomes\nThe course presents a more advanced approach as a subsequent step after the introductory course LTTI.00.008 Systems Biology (4 EAP).\nBrief description of content\nThe interface between systems biology and synthetic biology will be thoroughly discussed. The principle \"Build life to understand it\" will be analyzed and studied using specific examples. Conventionally, biologists have sought to understand life as it exists. Increasingly, however, from stem-cell reprogramming to microbial factories, researchers are describing what is and exploring what could be. A large part of the course will be dedicated to theoretical introduction into the mathematical modeling methods for systems biology. This part will serve as groundwork for the following practical modeling course using MATLAB (\"Systems Modeling\" 4EAP)." . . "Presential"@en . "TRUE" . . "The cell cycle: principles of control"@en . . "3" . "Learning outcomes\nThis course has two major objectives:\n1) To provide an overview of current topics in cell cycle control\n2) To provide experience in the critical reading and evaluation of research literature\nBrief description of content\nThe class will begin with a description of the phases and main events of the cell cycle and the main model organisms in cell-cycle analysis, including Xenopus, Drosophila, and yeasts. Later lectures will focus on the molecules and mechanisms of the cell-cycle control system, including the cyclin-dependent kinase family of protein kinases, the cyclins that activate them, and the signaling molecules that regulate them, and discuss cell-cycle control in development and the failure of controls in cancer.\n1. Events of the eukaryotic cell cycle\n2. Model organisms in cell-cycle analysis\n3. The overview of cell-cycle control system\n4. Cell cycle switches and regulatory modules\n5. Chromosome duplication\n6. Early mitosis: Preparing the chromosomes for segregation\n7. Assembly of the mitotic spindle\n8. The completion of mitosis\n9. Cytokinesis\n10. Meiosis\n11. Control of cell proliferation and growth\n12. Cell-Cycle responses to DNA damage\n13. Systems level modeling of the cell cycle\n14. The cell cycle in cancer" . . "Presential"@en . "FALSE" . . "Synthetic biology 1"@en . . "5" . "no data" . . "Presential"@en . "TRUE" . . "Kinetics of cellular reactions"@en . . "5" . "no data" . . "Presential"@en . "FALSE" . . "Protein prediction"@en . . "8" . "no data" . . "Presential"@en . "FALSE" . . "Proseminar: intracellular motility"@en . . "5" . "no data" . . "Presential"@en . "FALSE" . . "Quantitative cell and tissue biology"@en . . "5" . "1) Introduction to Cell Biology\r\n\r\nThis part aims to introduce the students to the main basic principles of Cell Biology. The focus lies on the theoretical knowledge of these fundamental cell biology principles.\r\n\r\nFollowing aspects of cell biology will be discussed:\r\n\r\nUniversal features of eukaryotic cells\r\nThe plasma membrane\r\nThe cytoskeleton\r\nCompartmentalization of the cell: The nucleus, The endoplasmic reticulum, The Golgi apparatus, The mitochondrion\r\n \r\n\r\n2) Important cell biology techniques and their applications\r\n\r\nThis part aims to introduce the students to 3 main cell biology techniques, which are amply used in research (both in academia as in industry). The focus lies on both the theoretical knowledge of these fundamental cell biology techniques and an understanding of their applications.\r\n\r\nFollowing techniques will be discussed:\r\n\r\nManipulating DNA and proteins. This chapter includes: techniques for the fractionation of cell components, techniques for the isolation of proteins, techniques to isolate genes (PCR, reverse transcription, gene cloning, plasmid expression vectors, construction of transgenic mice)\r\nLight microscopy. This chapter includes: light as electromagnetic waves, light refraction, basis of a compound microscope, introduction to bright-field microscopy, introduction to dark-field microscopy, introduction to fluorescence microscopy (basics of fluorescence, filter sets, photodetectors), using fluorescence to visualize cells or cellular structures (functional dyes, immunofluorescence, fluorescent proteins, FRAP, FLIP, FRET), introduction to laser scanning confocal microscopy, introduction to two-photon microscopy.\r\nFlow cytometry and cell sorting. This chapter includes: the flow cytometric set-up, electrostatic cell sorting, compensation\r\n \r\n\r\n3) Mathematical modelling of complex cell biology systems (Enzyme kinetics and biochemical reaction networks)\r\n\r\nThis part aims to introduce the students to mathematical modelling of exemplary biological problems. The focus lies on applicability, rather than theoretical knowledge.\r\n\r\nFollowing aspects will be discussed:\r\n\r\nModelling chemical reaction networks (law of mass action, numerical simulations, separation of time scales and model reduction\r\nModelling biochemical reactions (enzyme kinetics)\r\nModelling gene regulatory networks (modelling gene expression)\r\n \r\n\r\n4) Tissue techniques. This part aims to introduce the students to the principle techniques for studying and manipulating tissue.\r\n\r\nThe following aspects will be discussed:\r\n\r\nCell and tissue culture techniques\r\nHistology and histological techniques\r\nElectron microscopy.\nLEARNING OUTCOMES\r\n1. Understand the working principles of techniques to culture cells and tissues\r\n\r\n2. Understanding of histology and histological techniques and being able to interpret histological coupes\r\n\r\n3. Understand various quantitative techniques for the quantitative analysis of cell morphology, cell properties, structure and function and be able to apply quantitative analysis\r\n\r\n4. Understand the relation between cell composition and cell function as inferred from the above-mentioned techniques" . . "Presential"@en . "FALSE" . . "Experimental microbiology"@en . . "3" . "no data" . . "Presential"@en . "FALSE" . . "In-depth microbiology"@en . . "3" . "This teaching unit will aim to deepen basic notions in Bacteriology and Mycology. You will learn to master the fundamental knowledge of microbiology, which will allow you to have a better understanding of biological phenomena. You will also acquire knowledge of the structure of microorganisms as well as their culture, their ecology, and their physiology. You will understand their interactions, whether pathogenic or not, with their environment and other living beings. You will learn about the concepts and methods specific to quality in microbiology in an industrial environment as well as the means of combating micro-organisms. The tutorials will illustrate the concepts acquired in lectures. Through research data, these concepts will be detailed and applied to case studies." . . "Presential"@en . "FALSE" . . "Applications in biology"@en . . "3.0" . "Information at: https://sigarra.up.pt/fcup/pt/ucurr_geral.ficha_uc_view?pv_ocorrencia_id=479357" . . "Presential"@en . "FALSE" . . "Introduction to cell biology"@en . . "20.0" . "https://portal.stir.ac.uk/calendar/calendar.jsp?modCode=BIOU1CE&_gl=1*zxnwpp*_ga*MTY1OTcwNzEyMS4xNjkyMDM2NjY3*_ga_ENJQ0W7S1M*MTY5MjAzNjY2Ny4xLjEuMTY5MjAzODY1MC4wLjAuMA.." . . "Presential"@en . "FALSE" . . "Introduction to cell biology"@en . . "20.0" . "https://portal.stir.ac.uk/calendar/calendar.jsp?modCode=BIOU1CE&_gl=1*7lcm2i*_ga*MTY1OTcwNzEyMS4xNjkyMDM2NjY3*_ga_ENJQ0W7S1M*MTY5MjAzNjY2Ny4xLjEuMTY5MjAzOTM5NC4wLjAuMA.." . . "Presential"@en . "FALSE" . . "Other Biology Kas"@en . . . . . . . . . . . . . . . . . . .