Microbial Cell Factories, 6 credits

Mikrobiella cellfabriker, 6 hp

TFKE70

Main field of study

Engineering Biology

Course level

Second cycle

Course type

Programme course

Examiner

Martin Karlsson

Director of studies or equivalent

Magdalena Svensson

Education components

Preliminary scheduled hours: 52 h
Recommended self-study hours: 108 h

Available for exchange students

Yes
ECV = Elective / Compulsory / Voluntary
Course offered for Semester Period Timetable module Language Campus ECV
6CKEB Chemical Biology, Master of Science in Engineering (Industrial Bioprocesses) 7 (Autumn 2023) 2 1 Swedish/English Linköping C
6CTBI Engineering Biology, Master of Science in Engineering (Industrial Bioprocesses) 7 (Autumn 2023) 2 1 Swedish/English Linköping C

Main field of study

Engineering Biology

Course level

Second cycle

Advancement level

A1X

Course offered for

  • Master of Science in Engineering Biology
  • Master of Science in Chemical Biology

Prerequisites

Cell Biology, Microbiology, Gene Technology.

Intended learning outcomes

Based on knowledge obtained in earlier courses the course gives knowledge about, and an understanding of, how microorganisms can be used in e.g. food industry and environmental biotechnology. In addition, it covers how microorganisms can be used and modified for fermentation-based production of a wide spectrum of products such as energy carriers, biochemicals, drugs etc.

The basis for the above is knowledge about the living conditions, growth, metabolism and gene regulation of microorganisms, and further, a large number of methods in microbiology, molecular biology and biotechnology of microorganisms. 

After the course the student should be able to:

  1. describe and differentiate between the main differences between prokaryotic and eukaryotic microorganisms with respect to cell morphology, cellular systems and biochemicals synthesis routes.  
  2. describe and account for the properties, the requirements for growth/production, and areas of use, of the most commonly used microorganisms in industrial biotechnology. 
  3. describe microbial production of proteins/enzymes, and describe the properties of microbial cell factories for efficient production, purification and use of protein/enzyme products.
  4. describe central metabolic pathways and their regulation for the production of industrially relevant primary and secondary metabolites for sustainable development and production of e g biofuels and biopolymers from renewable raw materials.
  5. describe various methods to analyze the flows in metabolic pathways and account for how obtained information, together with novel methods in synthetic biology and gene editing, can be used for metabolic engineering, aiming at increased yield or new products.
  6. independently evaluate experimental data and information from scientific articles in the field and draw conclusions based on several methods/sources, to be reported orally and in writing with the correct terminology. 

Course content

Naturally occurring microbial processes used for production of e.g. food, biofuels and other biological processes such as waste water treatment. 

The cell structure of prokaryotic and eukaryotic microorganisms and the sub-cellular localization of various metabolic processes. 

Properties, needs and areas of use of the most commonly used cell factories including E. coli, B. subtilis, P. pastoris, Y. lipolytica, Streptomyces sp, S. cerevisae and micro algae.

The use of microorganisms for the recombinant production of peptides, proteins and enzymes, and for that, the associated issues of codon usage, post-translational modifications, protein folding/-processing and the influence on down-stream purification/activation. 

Specific metabolic processes to produce biotechnologically relevant products from primary or secondary metabolism, such as organic acids, biofuels and biopolymers.

Fundamental methods in analysis of metabolic flows and their control systems via various omics approaches (genomics, transcriptomics, proteomics, metabolomics).

CRISPR/Cas based methods for gene editing of microorganisms and how methods in synthetic biology, gene editing and protein engineering can be used for metabolic engineering of microbial cell factories for new products and/or enhanced product yield.

Teaching and working methods

The theory is covered in lectures. The laboratory work illustrates various theoretical aspects. For passing the laboratory course the students need to be actively participating and to provide an approved written report. A literature project is to be performed in group, to cover a relevant use or modification of a microbial cell factory. The literature project is to be presented in a written report and orally presented at a seminar.

Examination

PRA1Project assignment, oral and written presentation1.5 creditsU, G
TEN1Written examination3 creditsU, 3, 4, 5
LAB1Laboratory work with written report1.5 creditsU, G

For a passed laboratory work an approved written report is necessary. For a passed project a written and oral report is necessary. The written exam provides a measure of how well the student fulfills the requirements.

Grades for examination modules are decided in accordance with the assessment criteria presented at the start of the course.

Grades

Four-grade scale, LiU, U, 3, 4, 5

Other information

About teaching and examination language

The teaching language is presented in the Overview tab for each course. The examination language relates to the teaching language as follows: 

  • If teaching language is “Swedish”, the course as a whole could be given in Swedish, or partly in English. Examination language is Swedish, but parts of the examination can be in English.
  • If teaching language is “English”, the course as a whole is taught in English. Examination language is English.
  • If teaching language is “Swedish/English”, the course as a whole will be taught in English if students without prior knowledge of the Swedish language participate. Examination language is Swedish or English depending on teaching language.

Other

The course is conducted in a manner where both men's and women's experience and knowledge are made visible and developed. 

The planning and implementation of a course should correspond to the course syllabus. The course evaluation should therefore be conducted with the course syllabus as a starting point. 

The course is campus-based at the location specified for the course, unless otherwise stated under “Teaching and working methods”. Please note, in a campus-based course occasional remote sessions could be included.  

If special circumstances prevail, the vice-chancellor may in a special decision specify the preconditions for temporary deviations from this course syllabus, and delegate the right to take such decisions.

Department

Institutionen för fysik, kemi och biologi

Course literature

Books

  • Singh, Vijai, (2021) Microbial cell factories engineering for production of biomolecules. London : Academic Press, 2021.
    ISBN: 9780128214787, 0128214783, 9780128214770, 0128214775

Other

  • Material provided from the institution in the form of lecture notes and laboration instructions.

Code Name Scope Grading scale
PRA1 Project assignment, oral and written presentation 1.5 credits U, G
TEN1 Written examination 3 credits U, 3, 4, 5
LAB1 Laboratory work with written report 1.5 credits U, G

For a passed laboratory work an approved written report is necessary. For a passed project a written and oral report is necessary. The written exam provides a measure of how well the student fulfills the requirements.

Grades for examination modules are decided in accordance with the assessment criteria presented at the start of the course.

Course syllabus

A syllabus must be established for each course. The syllabus specifies the aim and contents of the course, and the prior knowledge that a student must have in order to be able to benefit from the course.

Timetabling

Courses are timetabled after a decision has been made for this course concerning its assignment to a timetable module. 

Interruption in and deregistration from a course

The LiU decision, Guidelines concerning confirmation of participation in education (Dnr LiU-2020-02256), states that interruptions in study are to be recorded in Ladok. Thus, all students who do not participate in a course for which they have registered must record the interruption, such that the registration on the course can be removed. Deregistration from or interrupting a course is carried out using a web-based form: https://www.lith.liu.se/for-studenter/kurskomplettering?l=en

Cancelled courses and changes to the course syllabus

Courses with few participants (fewer than 10) may be cancelled or organised in a manner that differs from that stated in the course syllabus. The Dean is to deliberate and decide whether a course is to be cancelled or changed from the course syllabus. 

Guidelines relating to examinations and examiners 

For details, see Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, Dnr LiU-2020-04501  (http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592).

An examiner must be employed as a teacher at LiU according to the LiU Regulations for Appointments, Dnr LiU-2021-01204 (https://styrdokument.liu.se/Regelsamling/VisaBeslut/622784). For courses in second-cycle, the following teachers can be appointed as examiner: Professor (including Adjunct and Visiting Professor), Associate Professor (including Adjunct), Senior Lecturer (including Adjunct and Visiting Senior Lecturer), Research Fellow, or Postdoc. For courses in first-cycle, Assistant Lecturer (including Adjunct and Visiting Assistant Lecturer) can also be appointed as examiner in addition to those listed for second-cycle courses. In exceptional cases, a Part-time Lecturer can also be appointed as an examiner at both first- and second cycle, see Delegation of authority for the Board of Faculty of Science and Engineering.

Forms of examination

Principles for examination

Written and oral examinations and digital and computer-based examinations are held at least three times a year: once immediately after the end of the course, once in August, and once (usually) in one of the re-examination periods. Examinations held at other times are to follow a decision of the faculty programme board.

Principles for examination scheduling for courses that follow the study periods:

  • courses given in VT1 are examined for the first time in March, with re-examination in June and August
  • courses given in VT2 are examined for the first time in May, with re-examination in August and January
  • courses given in HT1 are examined for the first time in October, with re-examination in January and August
  • courses given in HT2 are examined for the first time in January, with re-examination in March and in August.

The examination schedule is based on the structure of timetable modules, but there may be deviations from this, mainly in the case of courses that are studied and examined for several programmes and in lower grades (i.e. 1 and 2). 

Examinations for courses that the faculty programme board has decided are to be held in alternate years are held three times during the school year in which the course is given according to the principles stated above.

Examinations for courses that are cancelled or rescheduled such that they are not given in one or several years are held three times during the year that immediately follows the course, with examination scheduling that corresponds to the scheduling that was in force before the course was cancelled or rescheduled.

When a course, or a written examination (TEN, DIT, DAT), is given for the last time, the regular examination and two re-examinations will be offered. Thereafter, examinations are phased out by offering three examinations during the following academic year at the same times as the examinations in any substitute course. If there is no substitute course, three examinations will be offered during re-examination periods during the following academic year. Other examination times are decided by the faculty programme board. In all cases above, the examination is also offered one more time during the academic year after the following, unless the faculty programme board decides otherwise. In total, 6 re-examinations are offered, of which 2 are regular re-examinations. In the examination registration system, the examinations given for the penultimate time and the last time are denoted. 

If a course is given during several periods of the year (for programmes, or on different occasions for different programmes) the faculty programme board or boards determine together the scheduling and frequency of re-examination occasions.

Retakes of other forms of examination

Regulations concerning retakes of other forms of examination than written examinations and digital and computer-based examinations are given in the LiU guidelines for examinations and examiners, http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592.

Course closure

For Decision on Routines for Administration of the Discontinuation of Educational Programs, Freestanding Courses and Courses in Programs, see DNR LiU-2021-04782. After a decision on closure and after the end of the discontinuation period, the students are referred to a replacement course (or similar) according to information in the course syllabus or programme syllabus. If a student has passed some part/parts of a closed program course but not all, and there is an at least partially replacing course, an assessment of crediting can be made. Any crediting of course components is made by the examiner.

Registration for examination

In order to take an written, digital or computer-based examination, registration in advance is mandatory, see decision in the university’s rule book https://styrdokument.liu.se/Regelsamling/VisaBeslut/622682. An unregistered student can thus not be offered a place. The registration is done at the Student Portal or in the LiU-app during the registration period. The registration period opens 30 days before the date of the examination and closes 10 days before the date of the examination. Candidates are informed of the location of the examination by email, four days in advance. 

Code of conduct for students during examinations

Details are given in a decision in the university’s rule book: http://styrdokument.liu.se/Regelsamling/VisaBeslut/622682.

Retakes for higher grade

Students at the Institute of Technology at LiU have the right to retake written examinations and digital and computer-based examinations in an attempt to achieve a higher grade. This is valid for all examination components with code “TEN”, “DIT” and "DAT". The same right may not be exercised for other examination components, unless otherwise specified in the course syllabus.

A retake is not possible on courses that are included in an issued degree diploma. 

Grades

The grades that are preferably to be used are Fail (U), Pass (3), Pass not without distinction (4) and Pass with distinction (5). 

  • Grades U, 3, 4, 5 are to be awarded for courses that have written or digital examinations.
  • Grades Fail (U) and Pass (G) may be awarded for courses with a large degree of practical components such as laboratory work, project work and group work.
  • Grades Fail (U) and Pass (G) are to be used for degree projects and other independent work.

Examination components

The following examination components and associated module codes are used at the Faculty of Science and Engineering:

  • Grades U, 3, 4, 5 are to be awarded for written examinations (TEN) and digital examinations (DIT).
  • Examination components for which the grades Fail (U) and Pass (G) may be awarded are laboratory work (LAB), project work (PRA), preparatory written examination (KTR), digital preparatory written examination (DIK), oral examination (MUN), computer-based examination (DAT), home assignment (HEM), and assignment (UPG).
  • Students receive grades either Fail (U) or Pass (G) for other examination components in which the examination criteria are satisfied principally through active attendance such as tutorial group (BAS) or examination item (MOM).
  • Grades Fail (U) and Pass (G) are to be used for the examination components Opposition (OPPO) and Attendance at thesis presentation (AUSK) (i.e. part of the degree project).

In general, the following applies:

  • Mandatory course components must be scored and given a module code.
  • Examination components that are not scored, cannot be mandatory. Hence, it is voluntary to participate in these examinations, and the voluntariness must be clearly stated. Additionally, if there are any associated conditions to the examination component, these must be clearly stated as well.
  • For courses with more than one examination component with grades U,3,4,5, it shall be clearly stated how the final grade is weighted.

For mandatory components, the following applies (in accordance with the LiU Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592): 

  • If special circumstances prevail, and if it is possible with consideration of the nature of the compulsory component, the examiner may decide to replace the compulsory component with another equivalent component.

For possibilities to alternative forms of examinations, the following applies (in accordance with the LiU Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592): 

  • If the LiU coordinator for students with disabilities has granted a student the right to an adapted examination for a written examination in an examination hall, the student has the right to it.
  • If the coordinator has recommended for the student an adapted examination or alternative form of examination, the examiner may grant this if the examiner assesses that it is possible, based on consideration of the course objectives.
  • An examiner may also decide that an adapted examination or alternative form of examination if the examiner assessed that special circumstances prevail, and the examiner assesses that it is possible while maintaing the objectives of the course.

Reporting of examination results

The examination results for a student are reported at the relevant department.

Plagiarism

For examinations that involve the writing of reports, in cases in which it can be assumed that the student has had access to other sources (such as during project work, writing essays, etc.), the material submitted must be prepared in accordance with principles for acceptable practice when referring to sources (references or quotations for which the source is specified) when the text, images, ideas, data, etc. of other people are used. It is also to be made clear whether the author has reused his or her own text, images, ideas, data, etc. from previous examinations, such as degree projects, project reports, etc. (this is sometimes known as “self-plagiarism”).

A failure to specify such sources may be regarded as attempted deception during examination.

Attempts to cheat

In the event of a suspected attempt by a student to cheat during an examination, or when study performance is to be assessed as specified in Chapter 10 of the Higher Education Ordinance, the examiner is to report this to the disciplinary board of the university. Possible consequences for the student are suspension from study and a formal warning. More information is available at https://www.student.liu.se/studenttjanster/lagar-regler-rattigheter?l=en.

Regulations (apply to LiU in its entirety)

The university is a government agency whose operations are regulated by legislation and ordinances, which include the Higher Education Act and the Higher Education Ordinance. In addition to legislation and ordinances, operations are subject to several policy documents. The Linköping University rule book collects currently valid decisions of a regulatory nature taken by the university board, the vice-chancellor and faculty/department boards.

LiU’s rule book for education at first-cycle and second-cycle levels is available at http://styrdokument.liu.se/Regelsamling/Innehall/Utbildning_pa_grund-_och_avancerad_niva

Books

Singh, Vijai, (2021) Microbial cell factories engineering for production of biomolecules. London : Academic Press, 2021.

ISBN: 9780128214787, 0128214783, 9780128214770, 0128214775

Other

Material provided from the institution in the form of lecture notes and laboration instructions.

Note: The course matrix might contain more information in Swedish.

I = Introduce, U = Teach, A = Utilize
I U A Modules Comment
1. DISCIPLINARY KNOWLEDGE AND REASONING
1.1 Knowledge of underlying mathematics and science (G1X level)
X
Cell-/microbiology, biochemistry, gene technology
1.2 Fundamental engineering knowledge (G1X level)
X
Cell-/microbiology, biochemistry, gene technology
1.3 Further knowledge, methods, and tools in one or several subjects in engineering or natural science (G2X level)
X
X
PRA1
TEN1
Project
1.4 Advanced knowledge, methods, and tools in one or several subjects in engineering or natural sciences (A1X level)
X
TEN1

                            
1.5 Insight into current research and development work
X
X
PRA1
TEN1
Project
2. PERSONAL AND PROFESSIONAL SKILLS AND ATTRIBUTES
2.1 Analytical reasoning and problem solving
X
PRA1
LAB1
Laboratory work and project
2.2 Experimentation, investigation, and knowledge discovery
X
LAB1
Laboratory work with report
2.3 System thinking
X
X
PRA1
TEN1
LAB1

                            
2.4 Attitudes, thought, and learning
X
X
PRA1
TEN1
LAB1

                            
2.5 Ethics, equity, and other responsibilities
X
TEN1
Sustainable development, environmental biotech. 
3. INTERPERSONAL SKILLS: TEAMWORK AND COMMUNICATION
3.1 Teamwork
X
PRA1
LAB1
Laboratory work and project
3.2 Communications
X
PRA1
Written report and oral presentation 
3.3 Communication in foreign languages
X
PRA1
Written report in English
4. CONCEIVING, DESIGNING, IMPLEMENTING AND OPERATING SYSTEMS IN THE ENTERPRISE, SOCIETAL AND ENVIRONMENTAL CONTEXT
4.1 External, societal, and environmental context

                            
4.2 Enterprise and business context

                            
4.3 Conceiving, system engineering and management
X
X
TEN1
LAB1
Laboratory work and project
4.4 Designing
X
X
PRA1
TEN1
Metabolic engineering + project
4.5 Implementing

                            
4.6 Operating

                            
5. PLANNING, EXECUTION AND PRESENTATION OF RESEARCH DEVELOPMENT PROJECTS WITH RESPECT TO SCIENTIFIC AND SOCIETAL NEEDS AND REQUIREMENTS
5.1 Societal conditions, including economic, social, and ecological aspects of sustainable development for knowledge development
X
X
PRA1
TEN1
Project
5.2 Economic conditions for knowledge development

                            
5.3 Identification of needs, structuring and planning of research or development projects
X
X
PRA1
LAB1
Laboratory work and project
5.4 Execution of research or development projects
X
LAB1
Laboratory work
5.5 Presentation and evaluation of research or development projects
X
PRA1
Laboratory work with report

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