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CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

Course Instructor : Professor John BARFORD Room 4552 ext 7237 (2358-7237) barford@ust.hk Teaching Assistant: Ms XU Jing Jing Lab 7104 Ext 7149 (2358-7149) kejing@ust.hk Mr Kelvin WONG will assist with some tutorials / computations during class times Lab 6114 kelvwong@ust.hk

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CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

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  1. Course Instructor : Professor John BARFORD Room 4552 ext 7237 (2358-7237) barford@ust.hk Teaching Assistant: Ms XU Jing Jing Lab 7104 Ext 7149 (2358-7149) kejing@ust.hk Mr Kelvin WONG will assist with some tutorials / computations during class times Lab 6114 kelvwong@ust.hk ext 8828 (2358-8828) CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  2. Class Times: Monday and Friday : 4505 (Lift 25/26) 4.30 pm - 5.50 pm Also booked: Monday and Friday: Computer Barn C (Room 4578 – Lift 27/28) 4.30 pm - 5.50 pm (Students will be advised when sessions in the Computer Barn will be held) There are no formal tutorials assigned to this course – some tutorials may replace some lecture time and these will be advised. Thursday 6-7pm is available for additional tutorials, if necessary. Room 3006 (Lift 4) has been reserved for this purpose. CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  3. Conduct in the Classroom Classrooms are for learning. Teachers and students must work together so that the classroom is a good place to learn. You can help by following a few simple rules. These rules are mostly just common sense and common courtesy. By following them, you show respect to your fellow students as well as your teachers. Please try to get to class on time. When you come in late, you disrupt your class. As a general rule, if you are more than 10 minutes late, you should not enter the classroom. If you arrive late, but need to see the instructor or pick up lecture notes, please return at the end of the class period.

  4. Conduct in the Classroom You should not do things during class that disrupt the class or distract your classmates – such as talking while the instructor is lecturing. If you have a pager or cellular phone, turn if off when you are in class. Once in class, you should stay until the class is over. If you know you have to leave early, ask the instructor’s permission before the class starts. And please pay attention to the signs that tell you not to eat or drink in the classrooms.

  5. Conduct in the Classroom Assignments, tests and examinations are an integral part of the learning experience. Students who cheat disrupt this process. The instructor has a responsibility to make cheating difficult, but cheating is wrong even when you can get away with it. Don’t give in to the temptation to cheat, and be critical of those who do. Your instructor has the authority to make other rules that he or she feels are necessary to help you learn. For example, some instructors may require that you attend a minimum number or percentage of their classes. If you do not follow these rules, it may affect your grade.

  6. Conduct in the Classroom You are investing several years of your life in your university education. Learning to accept responsibility is an important part of that education. The classroom is a good place to begin showing that you are ready for the responsibilities of being an adult.

  7. Conduct in the Classroom Class attendance is highly recommend and participation in the classroom discussions are an important aspect of the “learning process”. Lectures are also where the important concepts are presented and the notes on the web “put into perspective” ATTENDANCE RECORDS WILL NOT BE TAKEN It also allows the instructor to monitor whether the major concepts are being understood It is essential that studentsgive feedback to the instructor. An anonymous website will be set up for this purpose - http://www.cbme.ust.hk/course/ceng365/ceng365.htm In addition to identifying problems it is also very helpful to offer practical solutions / alternatives so that these can be considered. Please try to make this process a positive one.

  8. Previous “Student Concerns” and Proposed “Solutions” “Concerns”: Extensive Class Notes (Reading or Printing?) Instructors accent and speaking too fast Use of the white board during lectures – writing too small or hard to read “Solutions”: The major concepts will be clearly identified and stated in the lectures. Any material which may be considered “supplementary” will be identified as such. Material that is examinable will be clearly identified A summary of the main concepts of each lecture will be given. These concepts are the only examinable component of the course Students encouraged to interact in class and to raise concerns during the lecture (e.g. can’t read the material written on the board)

  9. Examinations Examinations will test the understanding of concepts and will not require students to memorise major formulas or large amounts of qualitative information. When marking exams, I will be looking for the student to demonstrate that they understand the concepts both qualitatively and quantitatively. For example, when a short qualitative questions is asked, a direct answer to the question illustrates such an understanding. Writing large quantities of qualitative information, only a small fraction of which actually addresses the question asked, does NOT illustrate such understanding.

  10. Bioremediation: Application of Biological Process Principles To The of Groundwater, Soil and Sludge Contaminated With Hazardous Wastes Bioremediation is defined by the American Academy of Microbiology as "the use of living organisms to reduce or eliminate environmental hazards resulting from accumulations of toxic chemicals and other hazardous wastes" (Gibson and Sayler, 1992). Biotechnology: Biotechnology = The Application of Scientific and Engineering Principles to the Processing of Materials by Biological Agents to Provide Goods and Services Environmental Biotechnology: Application of Biological Process Principles and Engineering Principles For The Treatment of Liquid, Solid and Gaseous Wastes CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  11. Red biotechnology is biotechnology applied to medical processes. Some examples are the designing of organisms to produce antibiotics, and the engineering of genetic cures to cure diseases through genomic manipulation. White biotechnology, also known as Grey biotechnology, is biotechnology applied to industrial processes. An example is the designing of an organism to produce a useful chemical. White biotechnology tends to consume less in resources than traditional processes when used to produce industrial goods. Green biotechnology is biotechnology applied to agricultural processes. An example is the designing of transgenic plants to grow under specific environmental conditions or in the presence (or absence) of certain agricultural chemicals. One hope is that green biotechnology might produce more environmentally friendly solutions than traditional industrial agriculture. An example of this is the engineering of a plant to express a pesticide, thereby eliminating the need for external application of pesticides. An example of this would be Bt com. Whether or not green biotechnology products such as this are ultimately more environmentally friendly is a topic of considerable debate. Blue biotechnology has been used to describe the marine and aquatic applications of biotechnology, but its use is relatively rare. . Biotechnology and the Environment

  12. O.E.C.D. (Organisation For Economic Cooperation and Development) 1994 ‘Biotechnology For a Clean Environment” Estimated the worldwide potential market for environmental biotechnology at: 1990 $40 billion 2000 $75 billion In 2000, USA – there are about 130 biotreatment companies U.S Market for Environmental Biotech Products for Waste Treatment Worth $261.3 million by 2013 http://www.przoom.com/news/34779/ Environmental biotechnology accounts for about 30-40% of all environmental technologies CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  13. Example of Potential: Petroleum contaminated soil and groundwater resulting from leaking underground storage tanks USA About 750,000 exisiting sites Over 50% contain petroleum hydrocarbons Over 1/3 of these are leaking Cost per site for clean-up : $100,000-$250,000 If 10% undergo biological treatment : $ billions CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  14. HOW BIG IS THE INDUSTRY ?? The water industry mat be compared in size and capital to the pharmaceutical industry and the oil industry In 2005 ,waste water treatment plants in China numbered 2000 with a value of 40 billion Yuan CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  15. China Wastewater Treatment Market http://www.ide.go.jp/English/Publish/Ideas/pdf/machine_02_1.pdf CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  16. WHY BIOTECHNOLOGY? CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  17. Biotechnology approaches are replacing / augmenting chemical production due to: Higher specificity Lower temperature , pressure Less energy Less waste products Less harmful end products CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  18. 2001 OECD (Organisation of Economic Cooperation and Development) asked the following question: What if Industrial Biotechnology were used more widely?? In posing this question, they attempted to undertake an initial, but limited, analysis of potential environmental and resource conservation benefits that might acrue to certain targeted industrial sectors CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  19. CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  20. CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

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  24. Basic Understanding of Microbiology Basic Understanding of Biochemistry Quantitative Understanding of Microbial Growth and Metabolism Quantitative Understanding of Biological Reactions and Reactors Ability to make relevant design calculations (e.g. reactor size etc) Ability to synthesise 1-4 above to quantitatively understand existing and new biological metabolisms and processes What “Basic Skills” are Required?

  25. What are the “Engineering Issues”?? Alternatively – what are chemical engineers interested in ?? Rates – v- Yields (That is HOW FAST a process works and HOW EFFICIENTLY it works) A quantitative understanding of a process or operation , so that relevant design calculations can be made to ensure optimal performance (for example, reactor size, oxygen requirements, heating / cooling requirements, nutrient supplementation requirements The use of computer design packages are now commonplace in environmental biotechnology. The activated sludge models (ASM), mathematical descriptions of flocs and films, computational fluid dynamics etc are some examples of these. CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  26. Rate: What if the maximum rate possible? What factors influence it? Yield: What is the “relevant” yield? What is the maximum “growth associated” and non-growth associated yield? Is there a relationship between rate and yield ? That is, is the a “trade-off”? Is it desirable to achieve the highest yield?? What problems does high yield create? Rates and Yields – Relevant Engineering Questions

  27. Common Organisms for Bioremediation Type of Contaminant (Genus) Petroleum Pseudomonas, Proteus, Bacillus, Penicillum,Cunninghamella Aromatic Rings Pseudomonas, Achromobacter, Bacillus, Arthrobacter, Penicillum, Aspergillus, Fusarium, Phanerocheate Cadmium Staphlococcus, Bacillus, Pseudomonas, Citrobacter, Klebsiella, Rhodococcus Sulfur Thiobacillus Chromium Alcaligenes, Pseudomonas Copper Escherichia, PseudomonasFungi are italicized Microbiology – Why?

  28. Microbiology – Why? Public Health Microbiology (Bacterial Pathogens, Opportunistic Bacterial Pathogens, Viral Pathogens, Protozoan Parasites, Blue Green Algae, Exotoxins and Endotoxins)

  29. Biodegradation of Problem Environmental Contaminants Synthetic Detergents Pesticides Hydrocarbons BTEX, MTBE Poly Aromatic Hydrocarbons (PAH’s) Chlorinated Solvents Halogenated Aliphatic Hydrocarbons Polychlorinated Biphenyls Explosives

  30. ENZYMES and PATHWAYS The CARBON Cycle The NITROGEN cycle The PHOSPHOROUS Cycle The SULFUR Cycle Biochemistry – Why??

  31. hydrolysis Acidogenisis Organic C (aq) VFA CH4 + CO2 Organic C (s) Biological Carbon Cycle in Wastewater Treatment Aerobic Anaerobic Anoxic

  32. Biological N - Mechanism

  33. Biological P - Mechanism

  34. Sulfur Metabolism

  35. Anaerobic Digestion Process – An Example of Multi -organism and Multi-pathway

  36. Microbial Growth Kinetics Energy Formation Electron Acceptance Degradation Pathways Co-Metabolism Integration of Pathways Integration of Microbiology, Biochemistry

  37. Biological process are very significantly affected by environmental factors such as pH, temperature, presence of sufficient carbon, nitrogen, phosphorous , growth factors, vitamins, salt etc. In addition, actions taken during biotreatment may also have an influence on the biological processes. For example, pH modification using NaOH or NH4Cl may have very different consequences (Na+ inhibition or increased oxygen demand by NH4+). Environmental Factors

  38. Course Aims: Understand the role of microorganisms in the treatment of solid, liquid and gaseous wastes Understand the range of bioremediation technologies available and the practical benefits and limitations of bioremediation Apply the knowledge of (1) and (2) above, to address a series of “real life” environmental problems by class problems, homeworks ad supervised project work Undertake quantitative calculations using Excel and PolyMath Modern computer design packages will be demonstrated since they are either not available or are beyond the scope of this course. In addition, specific programs developed in Excel, Excel VBA and PolyMath will be developed and/or demonstrated. Understand how molecular biology is impacting on environmental biotechnology processes CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  39. Topic 1 : Introduction (Engineering Design Using Biological Systems, What are the Engineering Issues?) Topic 2: Waste Characteristics / Standard Methods Topic 3: Microbiology (Types of microorganisms) Topic 4: Biochemistry (Structure of the Cell) Topic 5: Metabolism (Major Metabolic Pathways), Topic 6: Metabolism (Degradation of Aliphatic, Aromatic, Halogenated Compounds, Genetic Manipulation) CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  40. Topic 7: Reactor Systems (Liquid, Gas and Solid) including reactors specific to waste treatment (Trickling Filter, RDC, Biofilms etc) Topics 8-12: Bioremediation Technologies (Anaerobic Digestion, Aerobic Treatment Processes, Biological Nutrient Removal, Composting, Landfill, Large Scale Municipal Soild Waste Treatment Systems, Biofiltration, Artificial Wetlands) Topic 13: Introduction to Molecular Biology and its application to Environmental Biotechnology (selection of microbes for treatment of particular “target” chemicals; gene probes; fluorescent markers etc) Topic 14: Other Industrial Applications (Bioleaching / Sulfate Reducing Bacteria, Biominerals, Sediments, Biomonitoring, Biosensors, Biopesticides, Biodiesel etc) CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  41. Textbook: Extensive Lecture Notes will be provided. These will be posted on Teaching Web http://www.ust.hk/intranet/ then Teaching and Research then Teaching then Course List on Teaching Web then CENG365 These may be supplemented by the following reference books. Environmental Biotechnology Principles and Applications B.E.Rittman and P.L.McCarty McGraw-Hill,2001 Bioremediation Principles J.B.Eweis, S.J.Ergas, D.P.Y.Chang and E.D. Schroeder McGraw-Hill, 1998 Environmental Engineering G.Kiely McGraw-Hill, 1997 Wastewater Engineering – Treatment ,Disposal, Reuse Metcalf and Eddy 3rd Edition McGraw-Hill, 1991 CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  42. Major Reviews etc 1, New Biotech Tools For a Cleaner Environment 2. Microbial Degradation 3. OECD The Application of Biotechnology To Industrial Sustainability 4. Maximum Biodegradation Rate and Half saturation Constant 5. Bacterial metabolism in Waste Water Treatment Systems These reviews/notes will be posted on the web and are put there to further stimulate your interest in the topis – they will NOT be examinable CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  43. Web Resources: Biochemistry: bich122 (webpage to be advised) Microbiology: esce500 (available on LMES through HKUST webpage) https://access.ust.hk/cas/login?service=http%3A%2F%2Flmes2.ust.hk%3A80%2Flmes-login-tool%2Fcontainer CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  44. Other web resources: University Of Minnesota: Biocatalysis / Biodegradation Database: http://umbbd.ahc.umn.edu/ Useful Internet Resources For Microbial Biotechnolgy:http://umbbd.ahc.umn.edu/resources.html#pathways Molecular Biology: http://www.lib.berkeley.edu/BIOS/molebio.html Databanks: http://www.brenda-enzymes.info/ Pathways :http://www.genome.ad.jp/kegg/pathway.html EPA Reach It: http://www.epareachit.org/ Federal Remediation Technologies Roundtable: http://www.frtr.gov CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

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  46. Course Assessment Homework 15% Classwork 7% Project 20% (Report / Powerpoint Submission) (Biodegradation Pathways) (Bioremediation Technologies) Mid-Term Exam 25% Final Exam33% CENG 365 ENVIRONMENTAL BIOTECHNOLOGY

  47. Homework and Classwork will be due TWO WEEKS from the date of issue and should be handed to the Course Instructor in the Classroom or left in the Course Instructor’s mailbox in the CENG Administrative Office (Room Lift 27/28). They should NOT be left under the Course Instructors office door. All homeworks will be marked and count towards the course assessment. A selected number of classworks will be marked and contribute to the course assessment. Solutions will be posted on Teaching Web after the due date and no further submissions will be possible once the solutions have been posted. Assessment

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