2021 MICR2000 lab manual v2 PDF

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School of Chemistry & Molecular Biosciences, Faculty of Science

LABORATORY NOTES

MICR2000 Microbiology & Immunology Semester 2, 2021

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School of Chemistry and Molecular Biosciences Academic Prizes The School of Chemistry and Molecular Biosciences recognises students with outstanding academic performance across all our disciplines and study levels each year. This recognition is in the form of a number of prizes awarded at the annual SCMB award ceremony. A list of the prizes are below.

Bing and Ross Barnard Biotechnology Prize Awarded to a student in the Bachelor of Biotechnology, for the highest overall mark in their honours year.

Biochemistry Alumni Prize 1 Awarded to the biochemistry student with the highest mark in second level biochemistry.

Biochemistry Alumni Prize 2 Awarded to the biochemistry student with the highest mark in four level three biochemistry courses.

Biochemistry Alumni Prize 3 Awarded to the biochemistry student with the highest overall mark in their honours year.

Chemistry Honours Research Prize Awarded to student who has achieved a high level in the research component of the honours program and demonstrated a high potential for independent research.

Edward Taylor Memorial Prize Awarded to the student with the greatest proficiency in three second level chemistry courses.

John and Jan de Jersey Biochemistry and Molecular Biology Prize Awarded to the student with the highest marks in 8 units of level 3 courses and is enrolled in an honours program in biochemistry.

Lesley Merle Williams Memorial Prize Awarded to the student who achieved the highest marks in the practical component of Advanced Immunology and Biomedical Parasitology.

SCMB Postgraduate Coursework Prize Awarded to the student with the highest Grade Point Average (GPA) for their program.

Microbiology Prize Awarded to the student who achieved the highest overall marks for 8 units in third level microbiology.

Thermo Fisher Biotechnology Communication Prize Awarded to student who achieved the highest marks in seminars as part of the Biotechnology Honours program.

School of Chemistry and Molecular Biosciences Academic Excellence Award in Biochemistry Awarded to the student with the best marks in 4 units of second level biochemistry and 8 units of third level biochemistry.

School of Chemistry and Molecular Biosciences Academic Excellence Award in Microbiology and Parasitology Awarded to the student with the best marks in 4 units of second level and 8 units of third level microbiology and/or parasitology.

School of Chemistry and Molecular Biosciences | Academic Prizes

T.G.H. Jones Award for Academic Excellence in Chemistry Awarded to the student who achieved the best overall marks in 4 units of level 2 and 8 units of level 3 chemistry.

UQ Rowe Scientific Chemistry Award – 2nd Year Laboratory Prize Awarded to the student who achieved the greatest proficiency in the second level course, Experimental Chemistry.

UQ Rowe Scientific Chemistry Award – 3rd Year Laboratory Prize Awarded to the student who achieved the greatest proficiency in the third level course, Advanced Experimental Chemistry.

Wilmar Sugar Prize in Chemistry Awarded to the student who achieved the highest standard in the field of chemistry in their honours year.

Prize information correct at time of publishing. Please refer to scmb.uq.edu.au/student-support/scholarships-prizes for a full list of available prizes and further details regarding SCMB Academic Prizes.

School of Chemistry and Molecular Biosciences | Academic Prizes

School of Chemistry and Molecular Biosciences

Laboratory Safety Information The following laboratory safety rules apply specifically to practicals and other activities in the Molecular Biosciences Building and Chemistry Building undergraduate teaching laboratories. You are required to pass the U/G Student Lab Safety Induction Assessment (see Blackboard under Training Courses: UQ Workplace Inductions and OHS Training) before commencing practical work For all practical work to be undertaken in this course: • Health, safety and environmental aspects of the practical have been considered and risk assessments have been carried out on the chemicals and procedures involved. • Safety equipment has been provided where necessary. • Appropriate information and supervision necessary for the safe execution of each practical is provided. Specific information about particular hazards and how to avoid, eliminate or minimize your exposure to them is given in the relevant sections in the laboratory manual. • Additional information on chemical hazards is available from the Chemwatch Database. Students are required to: • Avoid, eliminate or minimize hazards of which they are aware. • Comply with all occupational health and safety instructions. • Make proper use of all safety devices and personal protective equipment. • Not wilfully place at risk the health and safety of themselves or any other person. • Seek information or advice where necessary or when in doubt before carrying out new or unfamiliar work. • Wear protective clothing and footwear. • Be familiar with emergency and evacuation procedures of each laboratory space they use • Report all accidents and near miss incidents. Emergency Evacuation and Safety Equipment • In an emergency and during practice evacuations, move quickly and carefully from the laboratory to the stairwell or nearest emergency exit. Proceed to the designated assembly area (demonstrator will advise) and wait there until permission is given to re-enter the building. • Never run in the laboratory or along corridors. • Make sure you are aware your nearest emergency and other exits. • Ensure you are aware of safety facilities in the laboratory, including safety showers and eyewash stations. Laboratory dress code • Enclosed footwear must be worn at all times in the laboratory including tutorials, exams, PBL and poster sessions etc. and when using designated general use computers. • ‘Enclosed’ requires that the heel and upper foot be covered (refer to posters on teaching laboratory doors). You will be denied entry to the laboratory unless wearing suitable footwear. If you are changing shoes before or after the practical, this must be done outside the laboratory. • Safety glasses are mandatory and must be worn at all times during laboratory work, unless you are explicitly instructed that eye protection is not required. • Prescription glasses alone are not sufficient – safety over-glasses must be worn in addition to these. • You are required to provide your own safety glasses or over-glasses which must have Standards markings on them to indicate they are approved (AS/NZS 1337, AS/NZS 2243.1 or AS/NZS 1336). • If you wear contact lenses during practicals involving potential exposure to chemical fumes, vapours or splashes, you should remove them at the first sign of any eye redness or irritation. Contact lens wearers are strongly recommended to wear safety goggles rather than safety glasses to reduce exposure. • A clean laboratory coat must be worn when conducting practical work and must be fastened (all buttons done up). • Sleeves must be rolled down. • You must remove your lab coat when leaving the laboratory for any reason.

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Store your laboratory coat in a plastic bag between practicals to reduce the risk of transferring contaminants to your books and other articles. Laboratory coats on which chemicals or biological materials have been spilled must not be taken out of the laboratory and must be left with the Preparation Laboratory staff for decontamination. In the case of tutorials, exams (except practical exams), PBL or poster sessions, it is not necessary to wear a laboratory coat if explicit instructions are given. Where gloves are required, they must be worn. They must be removed if you leave the laboratory for any reason and disposed of in the appropriate bin. Long hair must be tied back. If a headscarf or hijab is worn, the ends must be tucked into the front of the lab coat. Peaked caps are not permitted in practical classes where gas burners are being used (unless worn backwards) as they constitute a fire risk. Cuts and other skin wounds must be covered for protection. Special conditions apply to the designated general use computers in the Chemistry Building Level 5 teaching laboratories. • Gloves and laboratory coats must be removed when working at these. It is also permitted for safety glasses to be removed at these computers. Covered footwear is still compulsory. • Instruments and their associated computers are part of the main laboratory and all safety equipment must still be worn while they are being used.

Food and Drink • Eating and drinking is prohibited in the laboratory. This includes sweets, gum and drinking from water bottles. Any food or drink must be left in your bag on the bag racks. • The staff and demonstrators have authority to dispose of any items of food or drink as necessary. • Special conditions apply to the Molecular Biosciences Building teaching laboratories. • You may not remove food or drink from your bag while inside the laboratory. This includes drinking from water bottles while standing at the bag racks. • If you need to access items of food and drink during the practical, take off your laboratory coat and gloves, wash your hands and exit the laboratory with your bag. Handling of Chemicals • All chemicals should be treated as potentially hazardous. Some are known to be toxic and others may be found to be so when more fully investigated. Chemicals should never be sniffed, tasted or allowed to come in contact with the skin. • Be aware of the conditions required for the safe handling of substances involved in the practical course. Information is provided in the laboratory notes, on the chemical container labels and/or on Chemwatch. If in any doubt, seek guidance from the laboratory demonstrator. • Most organic solvents are both volatile and flammable and thus pose a serious fire hazard. • Volatile chemicals also present a risk through inhalation and so their dispensing should be routinely performed in a fume hood. • No chemicals, including solvents, are to be put in ovens unless you are specifically told to do so by a demonstrator. • Chemicals should NEVER be removed from the laboratory – not even briefly (e.g. from one lab to another through a non-laboratory area), or taken into a computing area. • Special conditions apply to chemistry practical classes. • Open flames must not be used. • Electrical heating (steam baths, hotplates etc.) is provided, but even so, organic vapours can still ignite if critical concentrations come in contact with hot surfaces. • Consequently, any heating should be performed in a fume-hood and condensers must be used if boiling for any length of time. General Rules • Leave bags, jackets etc. on the bag racks. Do not block passageways or fire exits. Keep valuables with you. • Do not enter the Preparation Room without permission from laboratory staff or demonstrators. • Experiments may only be performed under the direct supervision of a demonstrator, during the scheduled hours of opening of the laboratory. Follow the instructions of the demonstrator at all times. • Unauthorised experimentation is strictly forbidden. Inappropriate conduct and disruptive behaviour may result in denial of further laboratory access. Laboratory Safety Information | S2 - 2021

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No reagent, specimen or equipment is to be removed from the laboratory without permission of the demonstrator or staff member in charge. Radiation sources (e.g. laser equipment, UV transilluminators and other UV sources, arc lamps etc.) must only be used under the direction of a demonstrator or member of staff. Sitting on laboratory benches is prohibited. Pipetting by mouth is prohibited. Automatic pipettes or other pipetting aids are provided. Take care not to contaminate these. Special care is required when attaching pipette fillers to a glass pipette. Consult a demonstrator if uncertain of the correct technique. Report any defective equipment or broken and cracked glassware to the demonstrator. Handle dissecting equipment with care. Store scalpel blades covered and secured inside the dissecting kit. Always remove blade from handle using a Qlicksmart device. Regard all microbiological cultures as potential pathogens (infectious). Work practices should aim to minimize the production of aerosols when working on the open bench. Keep hands, pens and other material that may become contaminated away from your face. Ensure that workbooks, lab manuals etc do not become contaminated. Mobile phones should be turned off and should not be used during the practical. They may not be used for photographing results in the lab or as timers. They should be kept in your bag or pocket and not placed on the bench where they could become contaminated. The use of ear-plug/headphone audio devices (iPods, MP3 players etc) is prohibited in the teaching laboratories. Spills must be reported to the demonstrator immediately. A staff member or demonstrator will clean up if the spill is hazardous. If microbiological cultures are spilled, remain seated and ask someone else to report to the demonstrator so that the contamination is not spread. Contaminated lab coats must be left with the Preparation Laboratory staff for decontamination. When working with microorganisms, swab the bench with 70% ethanol before commencing work and when you have finished. Special conditions apply to biochemistry and microbiology practical classes. Correct use of gas burners will be demonstrated. Be aware of the potential danger of unattended burners as the pilot light is often difficult to see. Before leaving the laboratory, turn the gas burner off at the tap.

Hygiene Practices when using Shared Equipment • Shared equipment can be a potential source of infection transmission. • Alcohol wipes impregnated with isopropyl alcohol are provided in the laboratory. Use these to clean shared equipment before and after use e.g. microscope eyepieces, UV viewers and any safety eyewear that you have borrowed. Waste Disposal • Waste must be disposed of strictly in accordance with the instructions in your laboratory notes or instructions given by a demonstrator or member of staff. Only dispose of waste via the sink if you are authorised to do so. • Hazardous chemical waste is to be disposed of in the correct labelled containers provided. • Disposable gloves should be placed into the yellow clinical waste bins. • Sharps (including Pasteur pipettes and plastic pipette tips) are to be disposed of into the yellow plastic sharps bins provided on the benches. Leaving the Laboratory • Wash your hands before leaving the laboratory, even if you have been wearing gloves. • At the end of the practical session and if you leave the laboratory for any reason during the practical, you must REMOVE your laboratory coat and gloves and wash your hands. Hand washing sinks and skin disinfectant are located in every laboratory. • If you are changing shoes at the end of the practical, this must be done OUTSIDE the laboratory. • The wearing of gloves and/or lab coat when using the water cooler in the corridor is prohibited. • Exercise care when opening and closing doors on entering and leaving the laboratory. First Aid • Report all accidents, injuries and illnesses to the demonstrator immediately. If required, trained personnel will administer first aid. All accidents, injuries and illnesses must be recorded via UQ’s OHS

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Incident Reporting Database. Non injury-causing incidents such as spills, electrical shorts etc must also be reported. Eye injuries (chemical/biological splash or mechanical injury) are serious. Treatment requires immediate and prolonged flushing with water (20 minutes minimum) at the eyewash station. Notify demonstrator immediately. If contact lenses are worn, remove these as soon as practical but do not delay irrigation while waiting for contact lens removal. Medical advice should always be obtained for an eye injury – if a chemical is involved the SDS (Safety Data Sheet) should accompany the student. Chemical or biological spills on skin - thoroughly wash affected area with copious quantities of water. Notify demonstrator immediately. Laboratory staff will consult SDS to determine appropriate first aid. SDS should accompany student if necessary to seek medical treatment. Burns including chemical burns – cool burnt area under running water (10 minutes for thermal burns, 20 minutes for chemical burns). Do not apply ice or any lotions or creams. Seek medical advice (take the SDS for chemical burns). Sharps injuries – notify demonstrator immediately. Wash the wound and encourage bleeding. Visit the University Health Service for a follow up consultation. If you are feeling unwell or dizzy when participating in a practical class, stop immediately, sit down and notify demonstrator.

Pregnancy and Allergies • Students who are pregnant or trying to fall pregnant may be at higher risk from exposure to certain chemicals and hazards. In addition, some students may develop allergies or may be sensitive to particular chemicals. • You must contact the course coordinator or academic running the practical class if this applies to you. • Suitable arrangements or modifications can then be made to minimise your exposure, if at risk, in consultation with the Occupational Hygiene Adviser from the OH&S Unit and/or a medical professional at the University Health Service. Immunisation • All students should be up to date for tetanus immunisation. If unsure, visit the University Health Service. Students who come in contact with human blood or blood products are strongly advised to have a course of Hepatitis B immunisation. Further advice on immunisation is available through the University Health Service. Students with disabilities • The University of Queensland has a number of policies that support its commitment to ensuring students with a disability have equitable access to study, and to fully participate in the life of the University. • Any student who has a physical impairment or a mental health condition that may impact upon their ability to safely conduct themselves in a laboratory must discuss their situation with the course coordinator. •

Students should be aware that the University provides support to students with disabilities through Student Services. This support may include: • Helping students to liaise with academic and administrative staff on the student’s behalf • Participation assistance • Counselling

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Consultations with UQ’s Disability Advisors are free. Appointments can be made through the UQ Student Support website.

Laboratory Safety Information | S2 - 2021

EYE PROTECTION MUST BE WORN AT ALL TIMES IN THE LABORATORY

Plagiarism Information Plagiarism occurs whenever you present someone else's work as your own without acknowledgement, and is defined by the University (PPL. 3.60.04, Student Integrity and Misconduct) as follows: "The act of misrepresenting as one's own original work the ideas, interpretations, words or creative works of another either intentionally or unintentionally. These include published and unpublished documents, data, results, images … and ideas gained through working in a group. These ideas, interpretations, words or works may be found in print and/or electronic media.” The following practices constitute acts of plagiarism and are a major infringement of the University’s academic values: •

Where paragraphs, sentences, a single sentence or significant parts of a sentence are copied directly, ...