Course-PM

BBT065 Industrial biotechnology lp4 VT23 (7.5 hp)

The course is offered by the department of Life Sciences

The schedule is available here

 

Contact details, teachers:

Carl Johan (Calle) Franzén, franzen@chalmers.se, 772 3808. (Course-responsible examiner)

Amparo Jimenez Quero,  amparo@chalmers.se, 772 2394 (Examiner, RPP)

Lisbeth Olsson, lisbeth.olsson@chalmers.se, 772 3805. (Lecturer)

Cecilia Geijer, cecilia.geijer@chalmers.se, 7723852 (Lecturer)

Adolf Krige, krige@chalmers.se (dry lab tutor)

Guest lecturers

 

Course purpose

The aims of the course are that the students should

• gain a quantitative understanding of different types of bioreactors and cultivation technologies
• obtain knowledge concerning the different demands on cultivation conditions and process control dictated by the metabolic and physiological characteristics of various cell systems such as bacteria, yeast, filamentous fungi as well as higher eukaryotes.
• obtain knowledge of industrial applications of such cell factories
• develop engineering competences like working with models, working with complex, open-ended problems, and communicating scientific problems in written and oral form within given time frames.

 

Schedule

TimeEdit

Detailed schedule 

 

Course literature

The course literature consists of handouts, scientific articles and book chapters referred to during the course. To avoid illegal copying, students must download the required articles via the E-journals and E-books available at the Chalmers library homepage: http://www.lib.chalmers.se/.

Compulsory literature:

Chapters 3 and 4 in: Stephanopoulos, Aristidou and Nielsen (1998), Metabolic engineering. Principles and methodologies. Academic Press. (Available as E-book via the Chalmers library)

Goldrick, S. et al. (2014) The development of an industrial-scale fed-batch fermentation simulation. Journal of Biotechnology. Vol 193, pp 70-82, 2015. DOI: 10.1016/j.jbiotec.2014.10.029

Mears L et al. (2017) Mechanistic Fermentation Models for Process Design, Monitoring, and Control.  Trends in Biotechnology, Vol. 35, Issue 10, p914–924

Mears, L., S. M. Stocks, G. Sin and K. V. Gernaey (2017). A review of control strategies for manipulating the feed rate in fed-batch fermentation processes. Journal of Biotechnology 245: 34-46.

Santos, L.O. et al. (2012) Nonlinear model predictive control of fed-batch cultures of micro-organisms exhibiting overflow metabolism: Assessment and robustness. Comput. Chem. Eng. 39, 143–151

 

Additional reading

Volumes 1-3 of: Moo-Young, M (editor) (2011): Comprehensive Biotechnology (Second Edition or other editions), Elsevier (available as E-book). (E.g.,chapters 1.19; 1.20; 1.48; 1.51; 2.02-2.07; 2.11; (2.14-2.22); 2.37-2.39; etc.)

The course literature used in KMB041 and KKR091 may also be used as reference books:

Madigan MT, Martinko JM, Stahl DA, Clark DP (2012) Brock biology of microorganisms (13^th edition). Pearson Education (or other editions)

Matthews, Appling, Anthony-Cahill, van Holde (2013) Biochemistry (4^th edition). Pearson education (or other editions)

Nielsen J, Villadsen J, Lidén G (2003) Bioreaction Engineering Principles (3^rd edition), Springer (available as E-book) (or other editions)

Larsson G (2017). Cultivation technology (8th edition). KTH Biotechnology.

 

Course design

Lectures

Lectures are an important part of the course, and will be the major basis for the final exam. Approximately half of the lectures will deal with the core of the course, namely physiologically based control of bioreactors. The other half is dedicated to theme lectures on different organisms, established processes, and the necessary considerations in choosing the right cultivation technology for various purposes.

The lectures will be given in class (mostly in KC). We will also stream and record via Zoom, but encourage everyone to participate in class.

 

Research Project Proposal (RPP)

This assignment will be described separately in more detail. It will be done in groups of three students. Students can choose project partners themselves. The RPP includes writing of a MSc project proposal on an industrial biotechnology research question. The project title (topic) should be selected and proposed to the course leaders no later than Thursday, March 28, at 18.00. To pass the course, students must hand in an acceptable literature assignment (research project grant application), and present it at an oral presentation.

If the RPP is submitted before Friday, May 3, 18.00, the assignment will also contribute to the final grade with a maximum of 30 points, with the following continuous grading scale:

Grade:	Acceptable		Good		Excellent
Points awarded for report:	10	15		20		25
Points awarded for oral presentation:	1		3		5

The oral presentations (compulsory attendance) will take place on Tuesday, May 14, and Thursday, May 16, according to a separate schedule.

The students will receive no points if the assignment is submitted too late. However, the assignment must still be submitted for passing the course. Detailed criteria for the assessment of the proposals will be given in class. The report must be written by the students themselves, and will be tested for plagiarism. You are allowed to use language bots (like ChatGPT or Bing) for studying and learning, but not for examination. Hence, you are not allowed to use text that has been generated by ChatGPT, or similar apps, in the final report. 

Amparo will be available for consultation at certain times, indicated in the course schedule. Detailed contact information will be given in class.

 

Simulation assignment

The simulation assignment deals with dynamic mass balances, oxygen transfer, physiologi­cally based control of bioreactors, biochemically structured models for microbial growth and product formation, and with industrial bioprocessing. Students must submit a final report on these simulation exercises. The assignment exercises and report will be done in groups of three persons. The examiner will randomize and assign groups with mixed backgrounds as far as possible.

You are allowed to discuss the exercises and solution procedures with other students and groups but each group must write its own solutions, programs and report. References to external sources that are influential for your solution (including personal communication) must be clearly presented. Each person in the group must be able to explain the content of the report and simulations, and students may be asked individually to explain the report to the examiner. You are allowed to use chatbots (like ChatGPT or Bing) for studying and learning, but not for examination. Hence, you are not allowed to use text nor code that has been generated by ChatGPT, or similar apps, in the final report. 

To support the development of the required programs, there are exercises that are intended to train the basic theoretical concepts of the first lectures and help the students generate the code necessary for solving the more demanding assignment. Further information will be given during the exercises.

To pass the course, students must submit an acceptable simulation report and be able to explain the contents in a follow-up discussion with the teacher. To help meeting the final deadline, the matlab code for solving Exercise B4 must be submitted no later than Friday, April 19, at 18.00. To improve the final report, students have the opportunity to submit a voluntary draft report until Monday, May 6, 18.00. Carl Johan Franzén will give feedback on submitted drafts to support improvement. If the final report is submitted before Friday, May 17, 18.00, the reports will also contribute to the final grade with a maximum of 30 points, with the following continuous grading scale:

Grade:	Acceptable		Good		Excellent
Points awarded:	10	15	20	25	30

On Wednesday, May 22 through Friday, May 24 there will be 45-minute time slots for each group to book for final discussion of your reports and conclusions with Carl Johan Franzén.

No points will be awarded if the assignment is handed in after the deadline. If you will not meet the deadline, please contact the examiner. The assignment must still be submitted for passing the course. Detailed criteria for the assessment of the reports will be given in class. The report will be tested for plagiarism.

The interaction with the customer’s representative (i.e. Calle) will primarily be done in the computer studio.

You are allowed to use chatbots (like ChatGPT or Bing) for studying and learning, but not for examination. Hence, you are not allowed to use text nor code that has been generated by ChatGPT in the final report.

 

Written exam

The final exam is scheduled Friday, May 31, 2024 at 14:00. The location will be decided by the examination administration. The exam should be answered using Inspera, i.e. you can use the Safe Exam Browser (SEB) on your own computer. You will also have access to MS Excel within the SEB . No other aids are permitted during the exam.

The exam may include questions on all parts of the course, including guest lectures, exercises, assignments and literature. There may be both essay type questions as well as calculation problems. The maximum number of points in the written exam will be 60. To pass the course, the student must get at least 20 points at the final exam, regardless of the total sum of points which must be at least 50 for a pass grade.

 

Overall examination

Grading is based on the sum of the points given for the Simulation report, RPP (both written report and oral presentation), and the final exam. The maximum number of points is therefore 120. If the Simulation report and / or the RPP report are handed in too late, they will receive 0 points, but they must still be submitted in acceptable form for passing the course.

The final grade will be based on the total points gathered in the course as follows:

Grade 3: 50 points

Grade 4: 70 points

Grade 5: 90 points.

Note, that to pass the course, the student must also score a minimum of 20 points on the final written exam.

 

Changes made since the last occasion

• Slight updates in lecture order due to teacher availability.
  
• Amparo Jimenez Quero is new examiner for the RPP
• The goal of the RPP has changed from writing a three-year research project to a master thesis project proposal.
• The field trip mentioned in the study plan is canceled.
• The final written exam will be done using Safe Exam Browser and Inspera
• Adolf will give additional support during computer exercises.

 

Learning objectives and syllabus

Intended learning outcomes:

After completion of this course, the student should be able to:

• Describe how renewable raw materials can be used for production of fine and bulk chemicals using industrial biotechnology.
• Design common microbial cultivation techniques such as batch-, fed-batch, chemostat, and perfusion cultures, including cell recirculation.
• Make quantitative descriptions of growth and metabolic behaviour in industrial-like cultivation systems using biochemically structured mathematical models and simulation in Matlab
• Design strategies for development of microbial cell factories suitable for industrial applications, also considering the extra demands put on cell factories when using renewable lignocellulosic raw materials.
• Choose suitable cultivation techniques and cell systems for various manufacturing and research purposes and discuss the advantages and disadvantages of alternative  cultivation techniques and cell systems
• Design metabolically based control strategies for cultivation of different cell systems such as bacteria, yeast, filamentous fungi and higher eukaryotic cells.
• Formulate and communicate a proposal for a biotechnological research or development project, including choice of model organism, cultivation techniques, and analytical techniques.
• Describe some important industrial applications of microbiology.

 

Syllabus

See Study plan