Research in molecular biology and biochemistry (LÍF114F)

This course is important for all graduate students in molecular biology and related fields. It is divided into two main parts: 1) presentation of a research article (journal club) and presentation of the research project (work in progress). For the research article students select a recent research article of interest and give a presentation on the aims and results. The goal is to train reading research articles in a critical way and present to others. The students have also as an assignment to bring up questions when other students present articles. The aim is to enhance critical approaches concerning scientific aims and methods used to reach the aims. In the project presentations students are expected to concentrate on the aims give a backgrounds and details of the methods used, results and the planned continuation. The students are expected to train in getting the message of the project in a clear way. The project presentation can lead to suggestion from other students that are useful for the approach.

This course is in English and has been on both spring and autumn term. The student can take this course four times giving max 8 ECTS.

Attendance is obligatory.

Introduction to Research Studies and the Scientific Community (LÍF128F)

Introduction to Research Studies and the Scientific Community for M.sc. and Ph.D. students. The scientific community. Ethical, professional and practical information for research students. The research student's rights and responsibilities. Career opportunities. Lab safety and professionalism. Scientific method, conflict of interest and proper scientific conduct. What you can expect and not expect from supervisors. Duties and responsibilities of graduate students. Experimental design and how to write and publish results. Bibliographic software, tables and figure presentation. Techniques for poster and oral presentations. Writing scientific papers. Writing science proposals.

Grant writing and opportunities, cover letters, publishing environment and options. Thesis completion and responsibilities around graduation.

Format. Lectures, practicals, student projects and reviewing. Indvidual and group projects.

The course is run over 11 weeks in the fall.

Final Project (LOS401L)

• The topic of the master's thesis must be chosen under the guidance of a supervisor. The thesis is usually 90 and sometimes 60  credits. The thesis work is expected to amount to 3 semesters of work (2 semesters in the case of a 60 credit project).
• Master's student has a supervisor from the academic staff of the department of biochemistry and molecular biology.  The MS committee shall have at least one extra member. The MS committee guides the student, regarding choice of course, project design and completion. In case of a main supervisor that is not a member of the department of biochemistry and molecular biology, a faculty coordinator has to be appointed (a permanent academic staff member of the department).
• The choice of topic is the responsibility of the student in collaboration with the project supervisors (and faculty coordinator when applicable). The topic of the project should fall within the field of biochemistry and molecular biology.
• Final project exam is divided into two parts: An oral examination and an open lecture.
• Present at the oral exam are the student, supervisor, external examiner and members of the Master's committee. The student provides a brief introduction to the project. It is important that the objectives and research question(s) are clearly stated, the main findings and conclusions drawn from the project.
• According to the rules of the Master's program, all students who intend to graduate from the School of Engineering and Natural Sciences must give a public lecture about their final project. There are three Master's Days at the School per year (one for each graduation) where students can present their projects.
• All students graduating from the University of Iceland shall submit an electronic copy of the final version of their masters thesis to www.skemman.is. Skemman is a digital repository for all Icelandic universities and is maintained by the National and University Library. 
• According to regulations of University of Iceland all MS thesis should be open access after submission to Skemman.

Human Genetics (LÍF513M)

Lectures: Mendelian genetics, organization of the human genome, structure of chromosomes, chromosomal changes and syndromes, gene mapping via association and whole genome sequencing methods, genetic analysis, genetic screening, genetics of simple and complex traits, genes and environment, cancer genetics, gene therapy, human and primate evolution, ethical issues concerning human genetics, informed consent and private information. Students are expected to have prior knowledge of the principles genetics.

Practical: Analyses of genetic data, study of chromosomal labelling, analyses of genetic associations and transcriptomes.

Microbiology II (LÍF533M)

The aim of this course is to introduce different applications of microorganisms and to help students develop independent research skills. In the first part of the course, students will visit a geothermal area and subsequently work on a research project where they isolate, identify and study bacterial strains.

The second part will introduce different fields of microbial biotechnology and how they have been shaped by recent progress in microbiology, molecular biology and biochemistry. State of the art will be covered regarding subjects such as microbial diversity as a resource of enzymes and biocompounds; bioprospecting, thermophiles, marine microbes and microalgae, biorefineries (emphasis on seaweed and lignocellulose), enzymes (emphasis on carbohydrate active enzymes), metabolic engineering (genetic engineering, omics), energy-biotechnology, cultivation and fermentation technology. The course will exemplify Icelandic biotechnology where applicable. Cultivation/production technology and yeast will be presented specifically in practical sessions in the brewing of beer.

The third part will cover environmental sampling, microbial communities and biofilms, microbes in aquatic and terrestrial environments, indoor air quality and the impact of molds. Also, water- and food-borne pathogens, risk assessment and surveillance, water treatment, microbial remediation, methane production and global warming. Students will visit waste management and water treatment plants and review and present selected research articles.

Additional teaching one Saturday in end of September or beginning of October.

Literature study for the Master´s Degree in Biochemistry and Molecular Biology (LOS301F)

The aim is to broaden the student‘s knowledge and understanding of a selected topic within the field, tangential to their main research project.  The student meets with a supervisor on a regular basis to discuss literature such as book chapters, journal papers or methodology.  The course ends with an oral presentation, report or short thesis as appropriate.

The student can register for the literature study course in biochemistry and molecular biology for up to 12 credits.

Supervisor approval is a prerequisite for registration.

Thesis skills: project management, writing skills and presentation (VON001F)

Introduction to the scientific method. Ethics of science and within the university community.
The role of the student, advisors and external examiner. Effective and honest communications.
Conducting a literature review, using bibliographic databases and reference handling. Thesis structure, formulating research questions, writing and argumentation. How scientific writing differs from general purpose writing. Writing a MS study plan and proposal. Practical skills for presenting tables and figures, layout, fonts and colors. Presentation skills. Project management for a thesis, how to divide a large project into smaller tasks, setting a work plan and following a timeline. Life after graduate school and being employable.

Applied Biochemistry (LEF509M)

Aimed at introducing students to aspects of applied biochemistry and biotechnology with emphasis on protein biotechnology. Lectures: Use of proteins in industry and medicine. Industrial use of enzymes. Enzyme reactors. Applications of immobilized enzymes. Biosensors. Use of recombinant DNA technology to genetically engineer organisms for production of biochemicals. Analytical biochemistry. Automaton in bioanalysis. Purification of bioproducts; scaling up of production lines and downstream processing. Tutorials: Recent research papers presented and discussed.

Teaching methods:
Lectures (about 40). Student lectures based on selected scientific papers.

The course is taught together with ILT102F - Introduction to Applied Biotechnology. Students can only take one of the courses, not both. 

Methods in Molecular Biology (LÍF118F)

Lectures: Theoretical basis of common molecular-biology techniques and their application in research. Course material provided by teachers. Laboratory practice in molecular biology techniques: Model organisms: E.coli, S. cerevisiae, C. reinhardtii, A. thaliana, C. elegans, D. melanogaster, M. musculus. Laboratory notebooks and standard operating procedures (SOP's), using online tools. Culture and storage of bacteria, yeasts and other eukaryotic organisms and cells. DNA and RNA isolation and quantification (Southern and Northern blotting, PCR, RT-PCR, qRT-PCR), restriction enzymes, DNA sequencing techniques and data analysis. Gene cloning and manipulation in bacteria yeasts and other eukaryotes. Protein expression and analysis. How to raise antibodies and use them. Western blotting, immunostaining, radioactive techniques. Microscopy in molecular biology. Methods used in recent research papers will be discussed. Essay and oral presentation discussing a selected technique. Problem based learning group assignment for graduate students: Experimental design and grant writing exercise with oral presentation of a research project.

Final Project (LOS401L)

• The topic of the master's thesis must be chosen under the guidance of a supervisor. The thesis is usually 90 and sometimes 60  credits. The thesis work is expected to amount to 3 semesters of work (2 semesters in the case of a 60 credit project).
• Master's student has a supervisor from the academic staff of the department of biochemistry and molecular biology.  The MS committee shall have at least one extra member. The MS committee guides the student, regarding choice of course, project design and completion. In case of a main supervisor that is not a member of the department of biochemistry and molecular biology, a faculty coordinator has to be appointed (a permanent academic staff member of the department).
• The choice of topic is the responsibility of the student in collaboration with the project supervisors (and faculty coordinator when applicable). The topic of the project should fall within the field of biochemistry and molecular biology.
• Final project exam is divided into two parts: An oral examination and an open lecture.
• Present at the oral exam are the student, supervisor, external examiner and members of the Master's committee. The student provides a brief introduction to the project. It is important that the objectives and research question(s) are clearly stated, the main findings and conclusions drawn from the project.
• According to the rules of the Master's program, all students who intend to graduate from the School of Engineering and Natural Sciences must give a public lecture about their final project. There are three Master's Days at the School per year (one for each graduation) where students can present their projects.
• All students graduating from the University of Iceland shall submit an electronic copy of the final version of their masters thesis to www.skemman.is. Skemman is a digital repository for all Icelandic universities and is maintained by the National and University Library. 
• According to regulations of University of Iceland all MS thesis should be open access after submission to Skemman.

Guest lectures and conferences (LOS401F)

During the program, students attend at least 15 lectures related to their field at the University of Iceland (outside of classes), or elswhere. There is a limit to the umber of credited lectures attended at conferenes. Students keep logbooks where they record organizer´s confirmations of their attendance, as well as their reflections and critiques.

The supervisor reviews the logbook and verifies the completion of the course.  The credits may be registered as late as at the end of the final semester. 

Research in molecular biology and biochemistry (LÍF223F)

This seminar course is an important contribution to the education of all continuing students in the field of molecular biology. It is divided into two parts: journal club and work in progress. For the journal club students will present a recent article about an interesting area of research. The aim is to learn to read articles and to be able to present them to others. This should encourage students to be critical and ask questions about the methods used and the general approach of the research described. The work in progress part includes a detailed description of the project the student is working on, including aims, introduction, materials and methods and discussion with future work. The aim of this is to teach the student to present their work in a concise and organized manner. This also often helps to solve problems in the study due to the input of the other students and group leaders present.

The course is taught in english both in the autumn and spring semester. Students can take the course at least four times giving a total of 8 ECTS.

Genomics and bioinformatics (LÍF659M)

Genomics and bioinformatics are intertwinned in many ways. Technological advances enabled the sequencing of for instance genomes, transcriptomes and proteomes. Complete genome sequences of thousands of organisms enables study of this flood of information for gaining knowledge and deeper understanding of biological phenomena. Comparative studies, in one way or another, building on Darwininan thought provide the theoretical underpinnings for analyzing this information and it applications. Characters and features conserved among organisms are based in conserved parts of genomes and conversely, new and unique phenotypes are affected by variable parts of genomes. This applies equally to animals, plants and microbes, and cells, enzymatic and developmental systems.

The course centers on the theoretical and practical aspects of comparative analysis, about analyses of genomes, metagenomes and transcriptomes to study biological, medical and applied questions. The lectures cover structure and sequencing of genomes, transcriptomes and proteomes, molecular evolution, different types of bioinformatic data, shell scripts, intro to R and Python scripting and applications. The practicals include, retrieval of data from databases, blast and alignment, assembly and annotation, comparison of genomes, population data analyses. Students will work with databases, such as Flybase, Genebank and ENSEMBL. Data will be retrived with Biomart and Bioconductor, and data quality discussed. Algorithms for search tools and alignments, read counts and comparisons of groups and treatments. Also elements of python scripting, open linux software, installation of linux programs, analyses of data from RNA-seq, RADseq and genome sequencing.

Students are required to turn in a few small and one big group project and present the large project with a lecture. In discussion session primary literature will be presented.

Molecular Genetics (LÍF644M)

Lectures: The molecular basis of life (chemical bonds, biological molecules, structure of DNA, RNA and proteins). Genomes and the flow of biological information. Chromosome structure and function, chromatin and nucleosomes. The cell cycle, DNA replication. Chromosome segregaition, Transcription. Regulation of transcription. RNA processing. Translation. Regulation of translation. Regulatory RNAs. Protein modification and targeting. DNA damage, checkpoints and DNA repair mechanisms. Repair of DNA double-strand breaks and homologous recombination. Mobile DNA elements. Tools and techniques in molecular Biology icluding Model organisms.

Seminar: Students present and discuss selected research papers and hand in a short essay.

Laboratory work: Work on molecular genetics project relevant to current research. Basic methods such as gene cloning, gene transfer and expression, PCR, sequencing, DNA isolation and restriction analysis, electrophoresis of DNA and proteins will be used.

Exam: Laboratory 10%, seminar 15%, written final exam 75%.

Cell Biology II (LÍF614M)

The emphasis is on research articles. Resent research in various field with links to cell biology are included but can vary between years. For each lecture max three research articles are included.

Each student gives a seminar on one research article with details on methods and results. The students write a report (essay) on the article and discusses the results in a critical way.

Examples of topics included in the course: innate immunity, prions, the proteins pontin and reptin, polarized epithelium, development of trachea, data analyses and gene expression, autophagy, the origin of the nucleus.

Literature study for the Master´s Degree in Biochemistry and Molecular Biology (LOS402F)

The aim is to broaden the student‘s knowledge and understanding of a selected topic within the field, tangential to their main research project.  The student meets with a supervisor on a regular basis to discuss literature such as book chapters, journal papers or methodology.  The course ends with an oral presentation, report or short thesis as appropriate.

The student can register for the literature study course in biochemistry and molecular biology for up to 12 credits.

Supervisor approval is a prerequisite for registration.

Structure and Function of Proteins (LEF616M)

The characteristics of protein structures at the different structural levels. How structure determines the different properties of proteins. Structural classes of proteins and their characteristics. Relationship between molecular structure and biological function. Interactions that determine structural stability of proteins. Protein folding and unfolding. Effects of different parameters, e.g. temperature, pH, salts and denaturants on protein stability. Techniques used for determination structure and different properties proteins. Selected topics in protein structure function relationships.

Course plan: Lectures twice per week (2x40 min. each time). Computer lab once per week (2x40 min.). Lab sessions involve training using the WWW to study proteins. Tutorials and practice of using SwissPDBviewer program for solving specific assignments related to topics covered in lectures.

Biochemistry 4 (LEF617M)

This course focuses on methodology and recent innovations in biochemistry, emphasizing both analytical and computational techniques. It is divided into several modules, each taught by experts in their respective fields. While lectures form the core of the material, additional resources such as articles or book chapters may be assigned when appropriate. Practical demonstrations of research equipment may also be included. Students are expected to submit several written assignments throughout the semester.

The course will explore recent research in various specialized areas of biochemistry, and the content of the modules is regularly updated.

Topics covered may include single-molecule spectroscopy, protein mass spectrometry, structural biochemistry, binding affinity and thermodynamics, enzymology, and computational biochemistry.