Model organisms in biological research

obligatory courses

Knowledge about prokaryotic and eucaryotic cell structure, genetics and biochemistry.

Classroom

Despite the great variety of life, many biological processes progress in a similar or identical fashion in most or even all species. However, some organisms are easier to study than others. Therefore, research on a limited number of species has played a very important role in broadening our knowledge of many biological processes. The lecture presents and characterizes the most important model organisms used in experimental biology, with the emphasis on features that determined their selection as models. It also summarizes main findings of studies on discussed organisms and presents their perspectives.

1. Escherichia coli

Species characteristic. E. coli – a model to study fundamental biological processes: replication, transcription, recombination, proteins synthesis, control and regulation of gene expression. E. coli long-term evolution experiment (LTEE) (dr hab. Renata Godlewska)

2. Bacillus subtilis

B. subtilis as a model organism. Studies on the regulation of gene expression and sporulation, which is a simplified example of cellular differentiation. The use of Mycoplasma as one of the models in genetic engineering and synthetic biology. (dr hab. Renata Godlewska)

3. Viruses

Characteristics of model viruses. Mild bateriophages: phage λ (lambda phage, lytic and lysogenic cycle, gene expression control), lytic bacteriophages eg T4. Contribution to bacteriophage research in the development of molecular biology and biotechnology. Eucaryotic viruses: tobacco mosaic virus, oncogenic viruses eg Retroviridae, Papillomaviridae. (dr hab. Monika Adamczyk-Popławska)

4. Yeasts

Evolutionary divergence of yeasts. Most important model yeast species: Saccharomyces cerevisiae, S. pombe, Candida sp.). Classical and molecular yeast genetics. Yeasts as a model for molecular biology, genomics and systems biology (high throughput technique for phenotypic screening).

Yeast models of human diseases – selected examples. (prof. dr hab. Paweł Golik)

5. Filamentous fungi

Filamentous fungi in biotechnology (production of antibiotics, enzymes and heterologous protein expression). Filamentous fungi as important human, animal and plant pathogens. Aspergillus nidulans, Neurospor. crassa and Fusarium fujikuroi as model organisms. Filamentous fungi as eukaryotic model for regulation of gene expression at transcriptional and post-transcriptional level and for cell biology. (dr hab. Agnieszka Dzikowska)

6. Drosophila melanogaster

Characteristics of the species - biology, development and ecology of the group. The overview of the use of D. melanogaster as a model species. The uniqueness of the system, related to insect biology and molecular research methodologies. Advantages and disadvantages of D. melanogaster as a model organism in molecular biology. To which studies we mostly use D. melanogaster - examples in the field of developmental biology, physiology, ecology. Explain why D. melanogaster is an excellent object for basic research. The fruit fly as a tool in the analysis of molecular processes - production of mutants and transgenic insects. The fruit fly as an object in epigenetic research. (dr Piotr Borsuk)

8. Daphnia

Daphnia is a genus of cosmopolitan, planktonic crustaceans living in freshwaters of America, Europe and Australia. Daphnia pulex was the first crustacean to have its genome sequenced - due to an extensive gene duplication it contains ~28,000 genes (8000 more than the human genome). Daphnia displays great phenotypic plasticity (morphological as well as behavioral), which is easily inducible under laboratory conditions. Mode of reproduction is parthenogenetic for most of the year (daughter are true copies of mothers), enabling studies on strictly environmentally-induced phenotypic plasticity. Moreover, Daphnia is easy to culture and has a short lifespan, making for a good model in research of behaviour and research of environmental adaptation as well as stress tolerance and response. (dr hab. Mirosław Ślusarczyk)

9. Caenorhabditis elegans

C. elegans due to its simple anatomy and compact genome, and also because it has the rudiments of nearly all types of tissue is an excellent model to study molecular mechanisms of cell differentiation and organogenesis. (prof. dr hab. Marek Maleszewski)

10. Danio rerio

The aim of the lecture is to teach the students about biology of a model vertebrate. Students will learn that zebrafish (Danio rerio) is commonly used in the studies of development, organogenesis, genetics, physiology, and on other issues known under the name of Evo-Devo (evolutionary development). On a smaller scale fish from the genus Danio serves as a model for studies in ecology, toxicology and environmental protection. Zebrafish, like other typical model species, is cultured very easily under the laboratory conditions, has a short life cycle, and at the beginning of the development the body is transparent, which makes the observation easy. (dr Piotr Bernatowicz)

11.Domestic chicken (Gallus gallus domesticus L.)

The red junglefowl (Gallus gallus L.) is thought to be the source of all domestic chickens breeds. Analysis of mitochondrial DNA suggests that domestication took place probably more than 8000 years ago. Since that time this species is an agricultural animal and has served as a model organism in many areas of biology. The lecture introduces a historical overview of domestic chicken in experimental biology including its role in the development of genetic, embryology, immunology and physiology. The contribution of avian genomics researches in the recognition of terms such as alleles, genetic linkage and epistasis is discussed. The chicken limb bud development as a model of molecular patterning in vertebrates is presented. Moreover, chickens as an important model in immunology including oncology as well as chronobiology having in its self the biological clock mechanism recognition is emphasized. (dr hab. Paweł Majewski)

12. Mouse

Mouse is the most important mammalian model organism. Mouse embryonic stem cells can easily and efficiently be isolated and cultured in vitro. In consequence mice bearing programmed modifications of their genome (knock in, knock out, conditional mutations) can be produced. Genetically modified mice are currently one of most important tools in biomedical research – they allow to analyze how genes control the development and functions of the organism. Models of genetic diseases are created by obtaining genetically engineered mice. (prof. Marek Maleszewski)

13. Arabidopsis thaliana (L.) Heynh

Biology of Arabidopis thaliana, its advantages and disadvantages as a model organism in laboratory research (short growth period, high seed productivity, fully sequenced genome, broad availability of physiological, biochemical and molecular methods, multiple databases and mutant stocks). Extensive utilization of Arabidopsis thaliana in basic research related to plant physiology, hormone and stress signal transduction, resistance to pathogenic organisms, general metabolic pathways including RNA metabolism and RNA interference in particular. Perspectives in plant research using Arabidopsis thaliana.(prof. dr hab. Joanna Kufel)

14. Zea mays

Anatomy, physiology, and systematics of maize. Maize genome. Maize domestication as the effect of changes in regulatory regions of several genes. Adaptative success of maize in different climates as the result of intraspecific diversification of maize genome. Maize as a crop – economical importance, an introduction to maize breeding. Maize mutants, maize transformation. Maize as a model C4 grass. (prof. dr hab. Paweł Sowiński)

A Guinea Pig's History of Biology by Jim Endersby; Harvard University Press

Mouse as a Model Organism. From Animals to Cells. Cord Brakebusch and Taina Pihlajaniemi, Springer

and reference list provided by each of the teachers

Knowledge

- Has broad knowledge in the fields of biotechnology, molecular biology and genetic engineering of microorganisms. Understands the importance of research with model organisms. Understands which features make an organism a good model.

- Has up-to-date knowledge in the main areas of biotechnology including the scientific terminology , the most recent researches, discoveries and applications of model organisms in, physiology, genetics, developmental biology.

- Has knowledge concerning most important model organism, Understands basic terminology categories of: biotechnology, genetics, physiology.

Abilities

Has knowledge of a modern language (Polish or English) sufficient for using electronic resources and scientific literature devoted to broadly defined molecular biology and biotechnology.

Is able to draw proper conclusions and interpret research results and discuss them in relation to the literature available.

Is able to study on his/her own on the study area.

Social competences

- Is careful and critical about mass-media information concerning science and biotechnological achievements

- Is willing to engage in continued education and acquire up-to-date scientific knowledge

- Understands the need for informing the public about latest advances in biology achived through the stadies of model organisms.

The course will be evaluated based on a written test examination.

Multiple choice questions. Student should receive a minimum of 51% of the highest score in the tests.

No