PLANT SC 2520WT - Microbiology and Biotechnology II

Waite Campus - Semester 1 - 2017

An introduction to the biology of microorganisms of importance in agriculture, food, wine and natural ecosystems and the application of biotechnology to increase the nutritional composition, yield and safety of food and beverages, for developed and developing nations. Microbiology topics to be considered include: microbial growth, energy sources and nutritional categories; form and function of major groups of microorganisms; classification and identification; features of saprophytic, pathogenic, symbiotic and commensal lifestyles; interactions of microorganisms with their environment, including plants and animals; case studies of natural and managed microbial ecosystems. Biotechnology examples include DNA marker-assisted selection in plant breeding, genetic modification (GM) approaches and enzyme engineering for efficient food processing and production, non-alcoholic and alcoholic fermentations, food additives. The role of the community, media and government in delivering safe, ethical and sustainable biotechnology solutions is investigated through current examples.

  • General Course Information
    Course Details
    Course Code PLANT SC 2520WT
    Course Microbiology and Biotechnology II
    Coordinating Unit School of Agriculture, Food and Wine
    Term Semester 1
    Level Undergraduate
    Location/s Waite Campus
    Units 3
    Contact Up to 7 hours per week
    Available for Study Abroad and Exchange Y
    Incompatible PLANT SC 2500WT and OENOLOGY 2501WT and PLANT SC 3500WT
    Assumed Knowledge BIOLOGY 1101 and BIOLOGY 1201 or equivalent
    Course Description An introduction to the biology of microorganisms of importance in agriculture, food, wine and natural ecosystems and the application of biotechnology to increase the nutritional composition, yield and safety of food and beverages, for developed and developing nations. Microbiology topics to be considered include: microbial growth, energy sources and nutritional categories; form and function of major groups of microorganisms; classification and identification; features of saprophytic, pathogenic, symbiotic and commensal lifestyles; interactions of microorganisms with their environment, including plants and animals; case studies of natural and managed microbial ecosystems. Biotechnology examples include DNA marker-assisted selection in plant breeding, genetic modification (GM) approaches and enzyme engineering for efficient food processing and production, non-alcoholic and alcoholic fermentations, food additives. The role of the community, media and government in delivering safe, ethical and sustainable biotechnology solutions is investigated through current examples.
    Course Staff

    Course Coordinator: Dr Karina Riggs

    Dr Karina Riggs
    Course Timetable

    The full timetable of all activities for this course can be accessed from Course Planner.

  • Learning Outcomes
    Course Learning Outcomes
    1 Explain the role and importance of microorganisms
    2 Describe the form and function of bacteria, fungi, viruses and protozoa
    3 Understand the principles of growth and reproduction of bacteria, fungi and viruses and of identifying and classifying organisms
    4 Discuss beneficial and deleterious activities of microorganisms in agriculture, food and wine
    5 Demonstrate an understanding of the processes involved in the recognition and manipulation of key groups of microorganisms
    6 Use terminology, appropriate to the field of biotechnology, correctly and contextually
    7 Apply a range of biotechnological solutions to improve the nutrition of food and/or the sustainability of food production for future generations
    8 Conduct, analyse and interpret results of experiments, and effectively communicate these in written reports
    9 Demonstrate efective information handling and communication skills
    10 Demonstrate the ability to work in a team
    University Graduate Attributes

    This course will provide students with an opportunity to develop the Graduate Attribute(s) specified below:

    University Graduate Attribute Course Learning Outcome(s)
    Deep discipline knowledge
    • informed and infused by cutting edge research, scaffolded throughout their program of studies
    • acquired from personal interaction with research active educators, from year 1
    • accredited or validated against national or international standards (for relevant programs)
    1-7
    Critical thinking and problem solving
    • steeped in research methods and rigor
    • based on empirical evidence and the scientific approach to knowledge development
    • demonstrated through appropriate and relevant assessment
    8, 9
    Teamwork and communication skills
    • developed from, with, and via the SGDE
    • honed through assessment and practice throughout the program of studies
    • encouraged and valued in all aspects of learning
    10
    Career and leadership readiness
    • technology savvy
    • professional and, where relevant, fully accredited
    • forward thinking and well informed
    • tested and validated by work based experiences
    1-7
    Intercultural and ethical competency
    • adept at operating in other cultures
    • comfortable with different nationalities and social contexts
    • Able to determine and contribute to desirable social outcomes
    • demonstrated by study abroad or with an understanding of indigenous knowledges
    8-10
    Self-awareness and emotional intelligence
    • a capacity for self-reflection and a willingness to engage in self-appraisal
    • open to objective and constructive feedback from supervisors and peers
    • able to negotiate difficult social situations, defuse conflict and engage positively in purposeful debate
    9-10
  • Learning Resources
    Required Resources
    A lab coat and closed foot wear must be worn in every practical session in the laboratory.
    Recommended Resources
    Recommended Reading

    Communication

    Cargill M and Bellotti M (2004) Written Communication in the Agricultural and Natural Resource Sciences. Theu University of Adelaide.
    http://www.agwine.adelaide.edu.au/students/external/carwripg1.pdf


    General microbiology and bacteria

    Madigan MT. Martinko JM et al. (20-12) Brock Biology of Microorganisms (13th edn.). Pearson (earlier editions, 200 onwards are also suitable).

    Wiley JM, Sherwood LM and Woolverton CJ (2014) Prescott's Microbiology (9th edn.). McGraw-Hill (earlier editiions, 2005 onwards are also suitable).


    Fungi

    Deacon JW (2006) Fungal Biology (4th edn.). Blackwell Publishing.

    Gow NAR and Gadd GM (1995). The Growing Fungus. Chapman and Hall.

    Ingold CT and Hudson HJ (1993). The Biology of Fungi (6th edn.). Chapman and Hall.


    Applied Microbiology

    Agrios GN (1997, 2005 or electronnic resource) Plant Pathology (4th, 5th edn.). Academic Press

    Fleet GH (1992) Wine Microbiology and and Biotechnology. Harwood Academic Publishers

    Fugelsang KC (1996) Wine Microbiology. Chapman and Hall

    Fugelsang KC and Edwards CG (electronic resource) Wine Microbiology. Springer.

    Pitt and Hocking AD (1997) Fungi and Food Spoilage (2nd edn). Blackie Academic Publishers.

    Pitt J and Hocking AD (electronic resource) Fungi and Food Spoilage (3rd edn.) Springer.


    Virology


    Hull R( 2009 or electronic resource) Comparative Plant Virology (2nd end.). Academic Press.

    Mahy BWJ, Van Regenmortel MVH et al. (2010) EDesk Encyclopedia of Plant and Fungal Virology. Academic Press.

    Wagner EK and Hewlett MJ (2004) Basic Virology (2nd edn.). Blackwell Publishing.


    Biotechnology


    Belitz HD and Grosch W (1987) Food Chemistry (2nd edn.) Springer Verlaf. Berlin.

    Burton RA et al. (2006) Cellulose synthase-like CsIF genes mediate the synthesis of cell callus (1,3;1,4)-B-D-glucans. Science 311: 1940-1942.

    Collin P et al. (2004) The safe threshold for gluten contamination in gluten free products. Can trace amounts be accepted in the treatment of coeliac disease? Ailment Pharmacol Ther. 19: 1277-1283.

    Hansen HB et al. (2004) Grain characteristics, chemical composition and functional properties of rye as influenced by genotype and harvest year. J Agric Food Chem. 52: 2282-2291.

    Hischenhuber C et al. (2006) Review article: Safe amounts of gluten for patients with wheat allergy or coeliac disease. Ailment Phamrmacol Ther. 23: 559-575.

    Holtekjolen ADK et al. (2006) Contents of starch and non- starch polysaccharides in barley varieites of different food origin. Food Chem. 94: 348-358.

    Keegstra K and Walton J (2006) Beta-glucans: brewer's bane, dieticians delight. Science .311: 1872-1873.

    Shewry PR and Halford NG (2002) Cereal seed storage proteins: structures, properties and role in grain utilisation. J Exp Bot. 53: 947-958.

    Spaenij-dekking L et al. (2005) Natural variation in toxivity of wheat. Potential selection of non toxic varieties for coeliac disease patients. Gastroenterology. 129: 797-806.

    Tamine AY et al. (1998) Laboratory made Kishk from wheat, oat and barley: 1. Production and comparison of chemical and nutritional composition of Burghol. Food Res Intl. 30: 311-317.

    Online Learning
    Teaching and course materials will be posted in MyUni (http://myuni.adelaide.edu.au/). Lectures will be recorded and posted on MyUni. Tutorial topics for microbiology will be posted for discussion. A series of videos demonstrating common microbiological techniques will be available on MyUni. Interative pre-laboratory activities using the software Articulate Storyline will be used in formative and summative assessment. Online quizzes will be available to help with review and revision (formative assessment).
  • Learning & Teaching Activities
    Learning & Teaching Modes

    Lectures are used to deliver content relevant to the specified course objectives. Lectures include the opportunity for open discussion, questions and problem solving activities. Selected biotechnology lectures are supported by formative pre-lecture online activities to support in class activities and discussions. The microbiology project work in weeks 4-6 allow students to synthesise and apply the skills learned in the course to address practical situations.

     

    Tutorials aim to develop and support the material covered in the lectures as well as provide a forum for acquiring skills and knowledge necessary to complete the assessment tasks. The tutorials take the form of class discussions, demonstrations and problem-solving activities.

     

    Practicals aim to apply the knowledge and skills covered in the lectures and tutorials linking theory to practice.

    Workload

    The information below is provided as a guide to assist students in engaging appropriately with the course requirements.

    A student enrolled in a 3 unit course, such as this, should expect to spend, on average 12 hours per week on the studies required. This includes both the formal contact time required to the course (e.g., lectures and practicals), as well as non-contact time (e.g., reading and revision).

    The information below is provided as a guide to assist students engaging appropriately with course requirements:
    Lectures: 2 hours per week
    Practicals: 4 hours per week
    Reading: (lecture material and practical manual) and preparation for practicals and tutorials (including pre-laboratory online exercises): 6 hours per week
    Preparation of project poster: 6-8 hours (total)
    Revision for exams: 20 hours
    Estimated average weekly workload: 12 hours
    Learning Activities Summary

    Week 1
    Lecture 1: Introduction & Role and importance of microbiology in agriculture and related areas
    Lecture 2: Microbial growth and its control
    Tutorial: Overview of course and assessment
    Practical: Microbila culture techniques, use of dissecting and compound microscope

    Week 2
    Lecture 3: Bacteria form and function
    Lecture 4: Fungi form and function
    Practical: Single- celled microorganisms: form and function, methods for counting cells

    Week 3
    Lecture 5: Viruses, identification and classification
    Lecture 6: Identification and classification of microorganisms
    Tutorial: (small groups) Bacteria and fungi- structure and function
    Practical: Complete work on singel-celled microorganisms, Multi-celled microorganisms- form and function

    Week 4
    Lecture 7: Microbial ecosystems- introduction
    Lecture 8: Food microbiology
    Tutorial: Introduction to project
    Practical: Project work on beneficial and deleterious activities of microorganisms

    Week 5
    Lecture 9: Plant microbe interactions- disease
    Lecture 10: Plant disease and control
    Practical: Project work (continued, 1hour) Microbes as pathogens: bacteria, fungi and virus diseases

    Week 6
    Lecture 11: Plant microbe interactions- rhizobium
    Lecture 12: Bioremediation, compost, silage
    Tutorial: (optional over lunch): Preparation for mid semester written exam
    Tutorial: (small groups): Review progress in project and discuss assessment
    Practical: Project work continued

    NOTE: Time and location of lectures and tutorials will change for weeks 7-12. Tutorials will begin 10-11am. Lectures will begin 11.10am - 1pm. Location will be advised.

    Week 7
    Lecture 13: Biotechnology for wine makers and food technologists
    Lecture 14: Molecular markers for protection of crops, yeasts, sustainability and human health
    Tutorial: Databases for finding scientific resources
    Practical: Techniques for the identification and comparison of Genetically Modified Organisms- Part 1

    Week 8
    Lecture 15: Genetically modified (transgenic) plants
    Lecture 16: Genetic manipulation of cereals, other food crops and grape vines
    Practical: No practical this week due to optional exam
    Thursday (am)- Optional redeemable (non compulsory) mid-semster written exam: content from weeks 1-6 (Microbiology)

    Week 9
    Lecture 17: Limitations and risks of GM crops- OGTR/FSANZ
    Lecture 18: Biotechnology in food safety, quality control and nutrition
    Tutorial: Project poster presentation- mini conference
    Practical: (continued) Techniques for the identification and comparison of Genetically Modified Organisms- Part 2

    Week 10
    Lecture 19: Commercial use of enzymes in industry - Part 1
    Lecture 20: Commercial use of enzymes in industry - Part 2
    Practical: Use of a recombinant enzyme to reduce viscosity in the food and beverage industry- Part 1

    Week 11
    Lecture 21: Plant cell walls, carbohydrates and human health
    Lecture 22: Plant cell walls and renewable biofuel production
    Tutorial: Plotting graphs in Excel and enzyme purification calculations
    Practical: (continued) Use of a recombinant enzyme to reduce viscosity in the food and beverage industry- Part 2

    Week 12
    Lecture 23: Fermentation in wine and food - Part 1
    Lecture 24: Fermentation in wine and food - Part 2
    Tutorial: Exam preparation
    Practial: No practical this week

    Specific Course Requirements
    Attendance at practicals and tutorials is compulsory.
    Small Group Discovery Experience


    Groups of 4 students

    Project on microbial activities- identification of spoilage organisms on a food item, planning of experiments, performing experiments, analysing results, preparing poster as a group and individual journal, peer assessment.

    Interactions with mentors- meet the mentors in the practical session (1 x 2hrs)

    mentors attend practical sessions in specified week (2 occassions up to 4 hrs over 3 weeks)

    mentors attend poster presentation session (min conference)( 1 x 1 hr)


    Students undertake project work in weeks 4-6 inclusive in groups of 4. Each group selects a topic to explore the beneficial and deleterious activities of microorganisms, then plans and conducts experimental work in the laboratory. Students will work in conjunction with an academic mentor. Each group presents their work as a poster which is presented academic staff and peers at a mini-conference.

    Students are required to assess their contribution and that of their group members to the project as part of the assessment (peer assessment).

    Each student documents his or her individual contribution through a journal.

    Guidance is provided throughout by academic staff and demonstrators and exemplars of posters and journals are provided.

  • Assessment

    The University's policy on Assessment for Coursework Programs is based on the following four principles:

    1. Assessment must encourage and reinforce learning.
    2. Assessment must enable robust and fair judgements about student performance.
    3. Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
    4. Assessment must maintain academic standards.

    Assessment Summary
    Assessment Task Type of assessment Percentage of total assessment for grading purposes Hurdle (Yes or No) Learning Outcome
    Online quizzes for learning and revision Formative

    0%

    No 2,3,4,6
    Online practical and tutorial quizzes Formative and summative

    5%

    No 1-8
    Practical reports

    1. Single & multicelled
        organisms

    2. Plant disease

    3. Identifying GMOs

    4. Recombinant proteins

    Summative
    30% (Total)


    5%

    5%

    10%

    10%
    No
    2,3,4,6

    1,5,6,9,10

    7,9

    7,9
    Microbiology project work & presentation Summative 15% No 1-5,6,9,10
    Non-compulsory mid-semester theory exam Formative and Summative 0-25% No 1-6
    Final Written exam(s) Summative 25-50% Yes 1-8
    Assessment Related Requirements

    To pass the course, a student must obtain 40% for the written exam(s) (i.e. 24 out of 60). Students who miss assessed practicals because of illness, bereavement (or other compassionate grounds) or unavoidable commitments are given an assignment in lieu of the assessment piece (replacement assessment). No other additional assessment is available for Practical Components.

    Assessment Detail
    Written examinations
    The written exam(s) account for 50% of the final mark (30% is for microbiology and 20% for biotechnology). The exam will assess the students’ knowledge, their ability to apply knowledge and their critical analysis skills. Questions will be set by each lecturer, with marks according to the number of lectures given. There is a non-compulsory mid-semester written examination in
    week 8 (worth potentially 30% of the final course grade).

    Mid-semester examination:
    There will be a non-compulsory mid-semester examination in week 8, covering material presented in weeks 1-6 (microbiology), potentially making up 30% in total of the final grade for the course. The mid-semester exam will be redeemable in the end of semester exam; there will be a separate section in the final exam (section A) that will correspond to the material covered in the
    mid-semester exam. Students may choose not to complete this section of the final exam, in which case the mid-semester exam marks will be used automatically to calculate the final grade and the final exam will have a weighting of 20%. If students attempt both the mid-semester exam and the corresponding section in the final exam, the best mark of their two attempts will be used to
    calculate the final grade. If students do not attempt the mid-semester exam, then they must attempt the corresponding section in the final exam, in which case the final exam weighting will be 50%.

    Students will be offered the opportunity to review their answers in the non-compulsory mid-semester examination with academic staff. Replacement/alternative assessment is not available for the mid-semester exam except on medical or compassionate grounds.

    Final examination:
    An end-of-semester written examination will be used to assess, summatively, understanding the course material. The examination will be divided into two parts:
    A. An optional section consisting of questions corresponding to those in the non-compulsory mid-semester exam (potentially 30% if used to redeem mid-semester exam mark).
    B. A compulsory section consisting of material covered in weeks 7-12 (biotechnology).

    Assessment of practical and work:
    Formative assessment; tutorial classes will include diagnostic and formative assessment to review information and understanding of the course material. Tutorial discussion topics and quizzes will be posted on MyUni.

    Summative assessment and submission of work for assessment; instructions for format, content and submission of practical reports, tutorial work and project work will be provided by the lecturer concerned.

    Practical reports, account for 30% of the final mark as follows:

    Practical 1: Single and multi-celled microorganisms; individual report,
    template distributed in class, data entered in practical sessions 2 &
    3  and tutorial 2, due at end of practical 3, (5% of final mark), addresses
    learning objectives 2, 3, 8, 9.

    Practical 2: Plant disease; prepared in pairs, template distributed in class,
    report due at end of practical 5, (5% of final mark), addresses learning
    objectives 1, 2, 3, 4, 8, 9.

    Microbiology project work and presentation account for 15% of the final mark as follows:

    Microbiology project report
    (Poster, journal and peer assessment); microbial activities- experiments and interpretation, presented as a team poster and individual journal, instructions in practical manual and tutorial 3, formative review of progress in tutorial 4,  due on specified date in week 9, (15% of final mark), addresses learning objectives 1, 4, 8, 9, 10.

    Practical 3: Identifying Genetically Modified Organisms (GMOs); individual report including Aims, Introduction, Results,  Discussion & Conclusion, due in week 10,  (10% of final mark), addresses learning objectives 6, 7, 8, 9.

    Practical 4: Purification and use of recombinant proteins; individual report focusing on data presentation and summarising key points from four different, but related experiments. A formative assessment component is included to provide students with feedback due in week 10 before submission of the final assessment task in week 12, (10% of final mark), addresses learning
    objectives 6, 7, 8, 9.

    Practical reports will be promptly assessed to provide continual feedback to students and a sense of progressive accomplishment in the course. Students will receive written feedback on each of practical reports submitted for assessment.

    Formative online pre-laboratory quizzes: completion before the laboratory class, including safety information relevant to the practical and activities including practice calculations, plotting graphs in Microsoft Excel and writing informative figure legends. There is one pre-laboratory quiz for each practical (4 for microbiology and 4 for biotechnology), due before the practical class, addresses learning objectives 1, 2, 3, 4, 5, 6, 8, 9.



    Submission

    A completed assessment cover sheet must be attached to each practical/tutorial report. Practical/tutorial reports are submitted in class, online to Turnitin or to a designated drop box. Students will be notified in class where to submit reports for assessment.

    A student who misses an assessed exercise of whose work is impaired through illness or equivalent may be offered a replacement assessment task for the microbiology section of the course.

    Staff endeavor to return marked assessments and provide feedback to students within 2 weeks of submission.

    Late submission of assessments: If an extension is not applied for, or not granted then a penalty for late submission will apply.  A penalty of 10% of the value of the assignment for each calendar day that the assignment is late (i.e. weekends count as 2 days), up to a maximum of 50% of the available marks will be applied. This means that an assignment that is 5 days late or more without an approved extension can only receive a maximum of 50% of the marks available for that assignment.

    Course Grading

    Grades for your performance in this course will be awarded in accordance with the following scheme:

    M10 (Coursework Mark Scheme)
    Grade Mark Description
    FNS   Fail No Submission
    F 1-49 Fail
    P 50-64 Pass
    C 65-74 Credit
    D 75-84 Distinction
    HD 85-100 High Distinction
    CN   Continuing
    NFE   No Formal Examination
    RP   Result Pending

    Further details of the grades/results can be obtained from Examinations.

    Grade Descriptors are available which provide a general guide to the standard of work that is expected at each grade level. More information at Assessment for Coursework Programs.

    Final results for this course will be made available through Access Adelaide.

  • Student Feedback

    The University places a high priority on approaches to learning and teaching that enhance the student experience. Feedback is sought from students in a variety of ways including on-going engagement with staff, the use of online discussion boards and the use of Student Experience of Learning and Teaching (SELT) surveys as well as GOS surveys and Program reviews.

    SELTs are an important source of information to inform individual teaching practice, decisions about teaching duties, and course and program curriculum design. They enable the University to assess how effectively its learning environments and teaching practices facilitate student engagement and learning outcomes. Under the current SELT Policy (http://www.adelaide.edu.au/policies/101/) course SELTs are mandated and must be conducted at the conclusion of each term/semester/trimester for every course offering. Feedback on issues raised through course SELT surveys is made available to enrolled students through various resources (e.g. MyUni). In addition aggregated course SELT data is available.

    The University places a high priority on approaches tolearning and teaching that enhance the student experience. Feedback is sought from students in a variety of ways including on-going engagement with staff, the use of online discussion boards and the use of Student Experience of Learning and Teaching (SELT) surveys as well as GOS surveys and Program reviews.

    SELTs are an important source of information to inform individual teaching practice, decisions about teaching duties, and course and program curriculum design. They enable the University to assess how effectively its learning environments and teaching practices facilitate student engagement and learning outcomes. Under the current SELT Policy (http://www.adelaide.edu.au/policies/101/) course SELTs are mandated and must be conducted at the conclusion of each term/semester/trimester for every course offering. Feedback on issues raised through course SELT surveys is made available to enrolled students through various resources
    (e.g. MyUni). In addition aggregated course SELT data is available.

    In response to positive feedback in an informal survey in 2012 and course SELTs in 2013 and 2014 (for the co-taught course Microbiology and Invertebrate Biology II), the non-compulsory, redeemable mid-semester exam, which was run as a trial in 2012, is retained.

    In response to feedback from the program coordinator in 2016, timetabling has been changed so that the course remains on the same day for the entire semester to avoid clashes with courses on other campuses.








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