Biological Sciences

This course provides an introduction to fundamental bioinformatics. Topics include biological databases, sequence alignment (pairwise and multiple), phylogeny, genomics, next generation sequencing, expression analysis, RNA-seq, RNA structure, and systems biology. 

Tropical forests are amongst the most species-rich biomes in the world. Yet, our understanding of their evolution, functioning, and development is far from complete. There are three main tropical rainforest areas, the Neotropics (Central and South America), Africa, and Asia, but this course mainly focuses on the Neotropics. The course examines what defines the tropical region, the differences, and similarities between the three large blocks of rainforest, and investigates the structure and biodiversity of tropical rainforests. The development of tropical forests, how biodiversity changes over time (ecologically and evolutionarily), and how trophic levels work within these forests are also reviewed. Furthermore, the role of tropical forests in relation to climate change and global carbon cycling is investigated, and a link between tropical savannas and dry tropical forests is made. Finally, the IUCN red list is investigated as well as the different dimensions (e.g., biological, cultural, and political) of nature conservation in tropical areas.

The course provides an introduction to statistical and computational methods of analyzing and interpreting genetics/genomics data. Emphasis is placed on statistical model application and interpretation. Students learn how to implement various statistical methods, analyze and visualize genetic data through programming in R and command line tools. The emphasis is on students doing analyses in class, and on the interpretation of the results. Programming forms a major part of this course. Students learn how to write their own scripts to perform advanced statistical analyses of genetic data. This is an advanced, fast-paced course with extensive programming assignments. We strongly advise students with no previous programming experience to undertake the R crash course. A short introduction to R at the start of the module will be given. If enrolling on the module with no previous programming knowledge, please be aware that programming skills can only be obtained through many hours of practice. Good performance in the course is dependent upon additional private study to further develop programming skills.

Major technological advances in affordable nucleic acid sequencing have allowed for an explosion of sequencing data and molecular tools available for researchers in biological sciences. This provides the opportunity for ecologists, evolutionary biologists, and molecular biologists to incorporate bioinformatic analyses into their existing research program to approach their research questions from an interdisciplinary angle. This course provides a general understanding of several major bioinformatics concepts and tools commonly used in biology and molecular biology.  Basic knowledge and practice in designing and executing bioinformatics procedures aimed at answering scientific questions in the fields mentioned above are gained. More specifically, the course gives an overview of the most commonly used methods within applied bioinformatics within the fields of biology and molecular biology. Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases, and subcellular localization prediction. Several downstream analyses are performed and their utility in applied ecology, evolutionary biology, and molecular biology research are discussed with guest speakers. An overview of the algorithms and statistics behind the bioinformatics methods is included, but the primary focus of course is on applicability, not on methodological details. 

The course provides an introduction to eukaryotic and prokaryotic cell biology, cell signaling, and virology. Topics include membrane structure and function, cellular organelles, cytoskeleton, cell signaling, cell division, cell physiology, bacterial cell biology, and basic principles of virology.

This course provides an overview of the main aspects of biochemistry by relating molecular interactions to their effects on the organism as a whole. Topics include metabolism, glycolysis and gluconeogenesis, the citric acid cycle, oxidative phosphorylation, the light reactions of photosynthesis, the Calvin cycle and the pentose phosphate pathway, glycogen metabolism, fatty acid metabolism, protein turnover and amino acid catabolism, biosynthesis of amino acids, nucleotide biosynthesis, the biosynthesis of membrane lipids and steroids, and integration of metabolism.

This course is part of the LM degree program and is intended for advanced level students. Enrollment is by consent of the instructor. This course discusses the morphology and function of specific organs and apparatuses of biotechnological interest in the context of clinical applications, correlates concepts of integrative physiology of the human organism with pathophysiology, and selects and interprets scientific data relevant to physiology and pathophysiology. Topics include cellular physiology; synaptic transmission; skeletal, smooth, and cardiac muscle; functional organization of the nervous system; cardiovascular function; respiratory function; and renal function.

This course examines invertebrates in nature. It covers how and why invertebrates are critical to the natural world and the role of invertebrates in life on earth.