Bioremediation

A.Y. 2020/2021
7
Max ECTS
88
Overall hours
SSD
BIO/13 BIO/19
Language
English
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.
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.
Course syllabus and organization

Single session

Responsible
Lesson period
Second semester
Regarding Environmental Microbiology and Biotechnological Remediation:
During the emergency phase teaching, the program will be maintained with the following changes, necessary for a good online use of the course, originally designed for face-to-face teaching:
-Teaching methods:
Lecture-based lessons will be held in class. When this will not be possible, lectures will be held as synchronous videoconferences using Microsoft Teams.
All synchronous videoconference lectures will be recorded and made available on the Ariel teaching website.
Laboratory-based lessons will be held in a blended format: with 22 hours of synchronous videoconferences and video-tutorials and 10 hours of laboratory in presence.
Any communication will be posted on the Ariel website in due course.

-Program and reference material:
The program and reference material will not change for the lecture-based lessons. For the laboratory-based lessons, during the 10-hour practical course, students will apply the following techniques: PCR, agarose gel electrophoresis, plasmid-DNA purification, analysis of a bacterial culture and β-galactosidase assay.

-Learning assessment procedures and assessment criteria:
If the situation allows it, the exam will be done in presence through a presentation by the students of a scientific article on bioremediation, according to the procedures described in the section "Exam procedures". Alternatively, the exam will be done using the Microsoft Teams platform, according to the same format as described above.

Regarding Laboratory of cell biology:
During the emergency teaching phase, the course program, the materials and the training objectives will not change.
Teaching methods: The course foresees lessons in presence (if possible) and at the same time by videoconference using the Teams platform. When this will not be possible, lectures will be held as synchronous or synchronous videoconferences using Microsoft Teams. All lessons will be recorded and made available on the Ariel or Teams platforms.
The criteria for participating to lectures in presence, as well as any notice related to Covid-19 will be published in due time on the Ariel page of the course.
The mandatory laboratory lecturers will be delivered using the Teams platform, while the laboratory practices will be performed by the students in the University laboratories.


Learning verifications: The exam is oral and will take place in videoconference by using Microsoft Teams. During the examination, students should demonstrate to have acquired a solid knowledge, and they should demonstrate to have acquired an accurate and specific language allowing them to communicate the most relevant topics in the field of Bioremediation.
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
The effects of toxic agents can be studied on cellular models. Thus the principles of cell biology and cell culture manipulation will be given in this course. Specifically, the students will learn the basic principles of cell cultures including the use of primary and immortalised mammalian cells. Further an overview of the techniques used to study gene and protein expression, as well as gene knockdown and knockout will be given. Further the students will learn how to transfect cells, how to measure proliferation survival, viability, adhesion. migration and invasion. Examples of these methods will be given by presenting articles related to these subjects.
The lecture-based section will include the following topics: (1) fundamentals of cell culture, (2) principles of gene and protein expression, (3) engineering strategies to study the gene function (4) methods to assess protein localisation, cell viability, survival and proliferation; (5) methods to assess cell adhesion, migration and invasion. The practical section will include demonstrations on cell culture, transfection, cell migration and protein localisation.
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.
Teaching methods
The course is composed by lessons with the support of slides as well as laboratory exercises.
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:

-Environmental Microbiology/ Ian L. Pepper, Charles P. Gerba, Terry J. Gentry. Third Edition. Amsterdam (etc.) Academic Press
-Brock Biology of Microorganisms/ Michael Madigan, John Martinko, Kelly Bender, Daniel Buckley, David Stahl. 14 Edition. Pearson Press
Edwards SJ, Kjellerup BV. Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals. Appl Microbiol Biotechnol. 2013. 97(23):9909-21. doi: 10.1007/s00253-013-5216-z.

Regarding Laboratory of cell biology:
Material consisting of slides and articles will be provided by Professor.
Assessment methods and Criteria
Regarding Environmental Microbiology and Biotechnological Remediation:
the examination consists of an oral exam covering all topics discussed during classes (lectures and laboratory).
Regarding Laboratory of cell biology: the examination consists in a group presentation (2-4 people) of one article regarding techniques and methods discussed during the course

Students will be asked to demonstrate to have acquired a solid knowledge, and they should demonstrate to have acquired an accurate and specific language allowing them to communicate the most relevant topics in the field of Bioremediation.
Environmental Microbiology and Biotechnological Remediation
BIO/13 - EXPERIMENTAL BIOLOGY - University credits: 0
BIO/19 - MICROBIOLOGY - University credits: 0
Individual laboratory activities: 32 hours
Lectures: 8 hours
Professor: Sperandeo Paola
Laboratory of Cell Biology
BIO/13 - EXPERIMENTAL BIOLOGY - University credits: 0
BIO/19 - MICROBIOLOGY - University credits: 0
Individual laboratory activities: 32 hours
Lectures: 16 hours
Professor: Rusmini Paola
Professor(s)
Reception:
Monday, 11.00-12.00
Via Balzaretti, 9
Reception:
By email appointment
Via Balzaretti, 9. 4th floor