Bioremediation
A.Y. 2024/2025
Learning objectives
Bioremediation is the application of microorganisms to improve the environmental quality. These improvements include the treatment of contaminated waters and wastewaters, clean-up of industrial waste streams, and remediation of soils contaminated with hazardous and toxic chemicals.
The course will be composed by two teaching units: Environmental Microbiology and Biotechnological Remediation and Laboratory of Cell Biology.
The course will enable the students to learn and practice the basic and advanced techniques of manipulation of prokaryotic and eukaryotic cells in culture.
The course will introduce the students to the knowledge of environmental microbiology and of the basic microbiological treatment technologies to clean up contaminated environments. During the course, the students will also learn the basic genetic engineering techniques used to manipulate microorganisms not only for remediation purpose but also to build microbial biosensors to detect the presence of contaminants in the environment (teaching Unit: Environmental Microbiology and Biotechnological Remediation).
Moreover, the objective of the course is to provide to the students a deeping in a range of cellular techniques for the isolation, maintaining and manipulation of "in vitro" cell cultures as models for risk assess of environmental, pharmacological and natural toxic agents on specific cellular functions, including proliferation, viability (apoptosis, necrosis, autophagy, etc..), survival, migration, invasiveness, differentiation, adhesion, angiogenesis (teaching Unit: Laboratory of cell biology).
The course will consist of lecture-based teaching to provide background information on key concepts on bioremediation and in a laboratory-based section.
The course will be composed by two teaching units: Environmental Microbiology and Biotechnological Remediation and Laboratory of Cell Biology.
The course will enable the students to learn and practice the basic and advanced techniques of manipulation of prokaryotic and eukaryotic cells in culture.
The course will introduce the students to the knowledge of environmental microbiology and of the basic microbiological treatment technologies to clean up contaminated environments. During the course, the students will also learn the basic genetic engineering techniques used to manipulate microorganisms not only for remediation purpose but also to build microbial biosensors to detect the presence of contaminants in the environment (teaching Unit: Environmental Microbiology and Biotechnological Remediation).
Moreover, the objective of the course is to provide to the students a deeping in a range of cellular techniques for the isolation, maintaining and manipulation of "in vitro" cell cultures as models for risk assess of environmental, pharmacological and natural toxic agents on specific cellular functions, including proliferation, viability (apoptosis, necrosis, autophagy, etc..), survival, migration, invasiveness, differentiation, adhesion, angiogenesis (teaching Unit: Laboratory of cell biology).
The course will consist of lecture-based teaching to provide background information on key concepts on bioremediation and in a laboratory-based section.
Expected learning outcomes
Expected learning outcomes
At the end of the course, the student should have acquired knowledge on the microorganisms applied in bioremediation as well as on several techniques used in the laboratory of cell biology.
The student should be able to manipulate prokaryotic and eukaryotic cells in culture, and to apply specific cellular and molecular techniques.
Moreover, the student should be able to present and discuss scientific articles describing the techniques analysed in the course.
teaching Unit: Environmental Microbiology and Biotechnological Remediation
Upon completing this course, the students should be able to demonstrate an understanding of the basic aspects of environmental microbiology and of the influence of microorganisms on environmental pollution. Moreover, students should demonstrate to have acquired the ability to evaluate when each bioremediation strategy would be most applicable, based on the polluted site characteristics.
Finally, the students will gain capability to exploit the basic molecular techniques to build a bacterial biosensor to reveal environmental pollution.
teaching Unit: Laboratory of Cell biology
At the end of the course, the student should have a large knowledge about fundamentals of cell culture, principles of gene and protein expression, engineering strategies to study the gene function, methods to assess protein localisation, cell viability, survival and proliferation, and methods to assess cell adhesion, migration and invasion.
Moreover, the student should have acquired practical ability for manipulation of cell culture, transfection, cell migration, cell viability, and analysis of protein localization.
At the end of the course, the student should have acquired knowledge on the microorganisms applied in bioremediation as well as on several techniques used in the laboratory of cell biology.
The student should be able to manipulate prokaryotic and eukaryotic cells in culture, and to apply specific cellular and molecular techniques.
Moreover, the student should be able to present and discuss scientific articles describing the techniques analysed in the course.
teaching Unit: Environmental Microbiology and Biotechnological Remediation
Upon completing this course, the students should be able to demonstrate an understanding of the basic aspects of environmental microbiology and of the influence of microorganisms on environmental pollution. Moreover, students should demonstrate to have acquired the ability to evaluate when each bioremediation strategy would be most applicable, based on the polluted site characteristics.
Finally, the students will gain capability to exploit the basic molecular techniques to build a bacterial biosensor to reveal environmental pollution.
teaching Unit: Laboratory of Cell biology
At the end of the course, the student should have a large knowledge about fundamentals of cell culture, principles of gene and protein expression, engineering strategies to study the gene function, methods to assess protein localisation, cell viability, survival and proliferation, and methods to assess cell adhesion, migration and invasion.
Moreover, the student should have acquired practical ability for manipulation of cell culture, transfection, cell migration, cell viability, and analysis of protein localization.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Course syllabus
Environmental Microbiology and Biotechnological Remediation:
Environmental biotechnology utilizes microorganisms to improve the environmental quality. These improvements include the treatment of contaminated waters and wastewaters, clean up of industrial waste streams, and remediation of soils contaminated with hazardous and toxic chemicals.
This course will introduce the students to the scientific principles of microbiological treatment technologies to clean up contaminated environments and to the basic DNA engineering techniques to manipulate microorganisms for these purposes. Moreover, the students will acquire experience on molecular methods /techniques used to monitor the presence of contaminants by the construction of a microbial biosensor. The course will consist of lecture-based teaching to provide background information on key concepts on bioremediation and in a laboratory-based section where the students will construct and use a microbial biosensor.
The lecture-based section will include the following topics: (1) fundamentals of environmental microbiology, (2) principles of bioremediation of organic contaminants and toxic molecules, (3) engineering strategies for bioremediation and biosensors construction.
Laboratory section
Day 1: Extraction of genomic DNA from suitable bacterial strain and quantification.
Day 2: Amplification of regulative gene and promoter by PCR, check on agarose gel and excision from agarose gel. Enzymatic digestion of fragment DNA.
Day 3: Plasmid DNA extraction (Midiprep) and purification. Enzymatic digestion.
Day 4: DNA fragment/plasmid excision from agarose gel, set up of the ligation mixture and overnight incubation.
Day 5: Competent Escherichia coli cells preparation and transformation. Overnight incubation.
Day 6 (second week): Plasmid preparation (Miniprep) from transformants and screening by restriction analysis.
Day 7: Growth of the reporter E. coli and control strains in the presence of different xenobiotic compounds and samples collection.
Day 8: β-galactosidase assay. Conclusions.
Laboratory of Cell Biology Cell culture techniques are commonly used in cell biology, pharmacology and toxicology. Starting from basic approaches and considerations, this course aims to provide the theoretical and practical skills needed for designing cell culture-based experiments. It will also provide an overview of the technologies available for manipulating the gene expression of cultured cells and integrating this approach into a research project. The lecture-based section will include the following topics: (1) fundamentals of cell culture; (2) novel cell culture technologies; (3) fluorescence-based techniques; (4) methods to assess cell proliferation, viability and survival; (5) methods to assess cell adhesion and migration; (6) transient and stable gene overexpression; (7) other technologies of genetic manipulation. The practical section will include demonstrations on cell culture and manipulation.
Environmental biotechnology utilizes microorganisms to improve the environmental quality. These improvements include the treatment of contaminated waters and wastewaters, clean up of industrial waste streams, and remediation of soils contaminated with hazardous and toxic chemicals.
This course will introduce the students to the scientific principles of microbiological treatment technologies to clean up contaminated environments and to the basic DNA engineering techniques to manipulate microorganisms for these purposes. Moreover, the students will acquire experience on molecular methods /techniques used to monitor the presence of contaminants by the construction of a microbial biosensor. The course will consist of lecture-based teaching to provide background information on key concepts on bioremediation and in a laboratory-based section where the students will construct and use a microbial biosensor.
The lecture-based section will include the following topics: (1) fundamentals of environmental microbiology, (2) principles of bioremediation of organic contaminants and toxic molecules, (3) engineering strategies for bioremediation and biosensors construction.
Laboratory section
Day 1: Extraction of genomic DNA from suitable bacterial strain and quantification.
Day 2: Amplification of regulative gene and promoter by PCR, check on agarose gel and excision from agarose gel. Enzymatic digestion of fragment DNA.
Day 3: Plasmid DNA extraction (Midiprep) and purification. Enzymatic digestion.
Day 4: DNA fragment/plasmid excision from agarose gel, set up of the ligation mixture and overnight incubation.
Day 5: Competent Escherichia coli cells preparation and transformation. Overnight incubation.
Day 6 (second week): Plasmid preparation (Miniprep) from transformants and screening by restriction analysis.
Day 7: Growth of the reporter E. coli and control strains in the presence of different xenobiotic compounds and samples collection.
Day 8: β-galactosidase assay. Conclusions.
Laboratory of Cell Biology Cell culture techniques are commonly used in cell biology, pharmacology and toxicology. Starting from basic approaches and considerations, this course aims to provide the theoretical and practical skills needed for designing cell culture-based experiments. It will also provide an overview of the technologies available for manipulating the gene expression of cultured cells and integrating this approach into a research project. The lecture-based section will include the following topics: (1) fundamentals of cell culture; (2) novel cell culture technologies; (3) fluorescence-based techniques; (4) methods to assess cell proliferation, viability and survival; (5) methods to assess cell adhesion and migration; (6) transient and stable gene overexpression; (7) other technologies of genetic manipulation. The practical section will include demonstrations on cell culture and manipulation.
Prerequisites for admission
Regarding Environmental Microbiology and Biotechnological Remediation:
the course requires a basic knowledge in Microbiology.
Regarding Laboratory of cell biology:
the course requires a basic knowledge in Biology.
the course requires a basic knowledge in Microbiology.
Regarding Laboratory of cell biology:
the course requires a basic knowledge in Biology.
Teaching methods
The course is composed of in-person lectures with the support of slides as well as practical laboratories.
The slides are available to students in the webpage dedicated to the "Teaching materials" on the website of the Professor in the Ariel platform.
The slides are available to students in the webpage dedicated to the "Teaching materials" on the website of the Professor in the Ariel platform.
Teaching Resources
Regarding Environmental Microbiology and Biotechnological Remediation:
-Brock Biology of Microorganisms/ Michael Madigan, John Martinko, Kelly Bender, Daniel Buckley, David Stahl. 14 Edition. Pearson Press. Chapters: 19, 20, 22.
-Slides from the lectures.
Regarding Laboratory of cell biology:
Lecture slides will be provided by the Professor.
-Brock Biology of Microorganisms/ Michael Madigan, John Martinko, Kelly Bender, Daniel Buckley, David Stahl. 14 Edition. Pearson Press. Chapters: 19, 20, 22.
-Slides from the lectures.
Regarding Laboratory of cell biology:
Lecture slides will be provided by the Professor.
Assessment methods and Criteria
The examination consists of a written test lasting 60 minutes and consists of 30 multiple choice questions with 3/4 answers for each question with only one true answer. The questions concern the whole program (lectures and laboratories). The evaluation is in thirtieths.
Environmental Microbiology and Biotechnological Remediation
BIO/19 - MICROBIOLOGY - University credits: 3
Individual laboratory activities: 32 hours
Lectures: 8 hours
Lectures: 8 hours
Professor:
Sperandeo Paola
Shifts:
Turno
Professor:
Sperandeo Paola
Laboratory of Cell Biology
BIO/13 - EXPERIMENTAL BIOLOGY - University credits: 4
Individual laboratory activities: 32 hours
Lectures: 16 hours
Lectures: 16 hours
Professor:
Fontana Fabrizio
Shifts:
Turno
Professor:
Fontana FabrizioProfessor(s)