BIOLOGY TEACHING ORGANISATION

PERSONAL ACHIEVEMENT RECORD
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LABORATORY RESOURCES
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Most laboratory skills are learned as integral components of the courses in year 1 to 3 and culminate in the extensive Honours Project.

Some of the specific skills that you may need to develop (depending on your subject specialisation) are shown below, with links to resources.

• Calculation of molarities, concentrations, dilution factors (needed by all bench scientists)

• Understanding the basic metabolic pathways (click on web sites below):

Metabolic problem set
Metabolic pathways of biochemistry
DIY Glycolysis

• Understanding chemical formulae and reactions (click for exam questions and answers from the Cell Metabolism & Regulation 2h course)

Additional laboratory resources::

• Safety and conduct in a biological laboratory (This links to the part of the University's Health & Safety Policy that covers biological laboratories. In addition, you should expect to be guided on health and safety matters in your Course Book and verbally in the laboratory classes.)
• Safety in the laboratory (Short guidance notes from the Origin & Diversity of Life 1h course)
• Experimental design - sampling, replication, etc.
• Accurate experimental manipulations
• Accurate recording and record keeping
• Construction and testing of hypotheses
• Report writing, summary and conclusions

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SAFETY IN THE LABORATORY

(Short guidance notes provided for the course Origin & Diversity of Life 1h, but with issues relevant to other courses)

The University Safety Policy

The Safety Policy and its procedures are contained in the University of Edinburgh Safety Handbook, a copy of which is available in the laboratory together with the Institute's own Safety Instructions. You should be aware of the policy and its procedures before undertaking any practical work in the laboratory. Much thought has been given to the safety aspects of the practical work and the laboratory. Nevertheless your own safety and that of your colleagues depends on your actions. So, work carefully and if you encounter any situation where you consider you are at risk inform a Demonstrator or the Floor Leader immediately.

Make sure you know what to do if things go wrong

In the event of any incident, or if you observe any practice that is potentially unsafe, inform the person in charge of the laboratory immediately.

Report any cut, minor accident, or spillage of any materials to a Demonstrator or the Floor Leader.

Remember the locations of the first aid box on the wall just outside the rear doors of the laboratory; the fire extinguishers on the pillars in the centre of the laboratory; the fire exit at the rear right-hand corner of the laboratory; the assembly point on the grass at the front of, and away from, the building.

First aid will be administered by a person trained in first aid techniques.

General protection

You are required to wear a laboratory coat at all times in the laboratory. It is sensible to buy one of good quality and to launder it regularly and repair it when necessary. Never wear your laboratory coat anywhere outwith the laboratory area.

Safe conduct

Avoid cluttering your bench space and the corridors between benches with coats and bags. Undertake your work without haste and do not take risks to complete a task quickly.

Take care:-

a) When handling hot ovens.

b) Using a scalpel, particularly when fitting a new blade.

c) When fitting a rubber bulb to a glass pipette or the pipette to a filler.

d) Using electrical apparatus: particularly when inserting or removing a plug and when using wet conditions on the bench. Remember that water is a good electrical conductor.

Never pipette liquids by mouth, always use a pipette filler. Never use any piece of laboratory apparatus such as a beaker for drinking: remember that eating (even sweets), drinking and smoking within a laboratory are strictly forbidden. Never distract the attention of anyone working with chemicals or delicate glass apparatus or with a bunsen burner. Extinguish any bunsen burner when it is not in use; or if required for aseptic conditions, set the flame so that it can be easily seen.

Use:-

Gloves that are provided for protection. But avoid touching your face or rubbing your eyes while wearing contaminated gloves; contact with certain substances can sometimes cause dermatitis and an allergic response. If you develop any such skin disorder report the fact to the Student Health Service at once.

Safety Glasses when they are required. If any chemical or biological material gets into your eye wash it out immediately under a running tap with your head positioned so that the water falls away from your face, not over it.

Adopt the sensible habit of washing your hands carefully after each practical session. Enjoy your practical work safely, but please do not skylark in the laboratory. If you should feel ill during a practical always inform the Floor Leader.

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NOTES ON SCIENTIFIC REPORT WRITING

[Notes produced by Maria Chamberlain to guide students in writing their Group Project Reports for the course Environmental & Community Biology 1h. They might be of more general value, but for all your course assignments you will be given specific instructions on the length and type of report that is required]

• The report should have a title and can be structured under the usual headings: Introduction, Materials and Methods/ Procedure, Results, Discussion, References, Acknowledgements. You can subdivide some of the sections, but if you do so, then use a different kind of font for the sub-headings, e.g. italics.
  
• The Introduction should be brief (usually not more than one or two paragraphs) and state the problem clearly, referring to the most relevant literature. If you are carrying out a qualitative study or a review of a problem, then you should state its relevance and what interests you about it. Avoid the personal pronoun in all your writing. Write "the study was done…" rather than "we decided to study…". If your project involves primary research and you have some quantitative data, then state the null hypothesis clearly. A null hypothesis might be that there are equal numbers of men and women in the class, because there are more or less equal numbers of men and women in society as a whole. Then you can use a statistical test to see if your findings depart from this.
  
• The Materials and Methods section can also be called Procedure. Again, avoid the personal pronoun. You should give as much detail as is necessary for somebody to be able to repeat the work you have done or to decide how strong your findings are. If you are carrying out a survey or questionnaire it is essential that you state the numbers sampled. You should include the questionnaire in the Appendix.
  
• The Results section should describe your findings in words, tables, graphs, diagrams or photographs. If you include diagrams or photographs, then you must scan them electronically into your file. All graphs, tables, etc. should be numbered and should have a legend that states clearly what they show (with the sample size). Any material copied or adapted from published literature (including web sites) should clearly acknowledge the source at the end of the legend. The graphs, diagrams and photographs should be called Figure 1, Figure 2 etc.; the tables should be called Table 1, Table 2 etc. You should always refer to them in the text, not leave them "hanging". You should never show the same results as a table and a graph – choose one or the other. Your results may lend themselves to a statistical analysis. Consult your tutor about this. In any case, be careful to state your findings realistically. It is misleading to state that 75% of respondents to a questionnaire said "yes" if there were only 4 responses. Also avoid spurious accuracy. If 51 out of the 157 people you questioned said "yes" then state that about 32% said yes (not 32.48%). Always explain what the findings mean in their biological context.
  
• The Discussion should analyse the findings critically. You should discuss the results with what you might have expected to find and with what other workers in the field have found in previously published literature. Suggest how you might explain any unexpected results and point out the deficiencies of the procedure e.g. small sample size. If your project does not lend itself to primary data, then you can discuss the advantages and disadvantages, costs etc., comparisons of views, legal aspects. You might wish to suggest any further studies which you might want to undertake, if you had the time and resources.
  
• You should summarise the whole report in a concise Conclusion.
  
• References should be cited in the text and listed alphabetically at the end. You should only cite references that you have read; refer to any others as "cited by ----". Use the following format for references in the text: " The findings agree with those of May and Will (1989), who worked on… but Day (1997) showed that…". If you are citing something from a personal contact, then write: "According to Dobson, 1998 (pers. comm.)….". Your reference list should give the full details so that anybody could find the reference in a library:

Day, D. (1997) Sexual Behaviour of Plants. (3^rd ed), Cambridge University Press, Cambridge.

May, J. and Will, B. (1989) Inbreeding and outbreeding in Snortia. Journal of Plant Psychiatry 18, 6-9.

Internet sources should be cited as: Jones, J. (if the author is known), title of the web page, date (if known) then the full URL, such as http://www.ed.ac.uk/bto.htm

• In the Acknowledgements you should thank your contact, and anybody else who helped you in the project, giving their first name, surname and address.

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RECORDING PRACTICAL WORK

(Guidance based on the Origin & Diversity of Life 1h course book)

General

Practical work should always be recorded directly into a bound lab book, never on loose-leaf sheets. Every entry in the lab book should be dated, and your own observations (including comments such as the difficulties you found in doing certain procedures, or ideas that occurred to you) should be written down as a permanent record.

Do not keep a rough, "working" lab book and then copy from this into another book later. Instead, recognise that your lab book is the true record of what you did and observed at the time. You can (if you wish) use the back pages of your lab book for making calculations, notes, etc.

Drawing and observation

Scientific observation involves not only looking but also making a careful record of what you see: which often means drawing the object. Shape, proportion and position can each be accurately recorded by anyone who has observed properly. Speed, though not essential, and clarity are improved by omitting unnecessary detail and not using 'artistic' shading. Rather, contrast of light (H) and dark (HB or B) pencil lines drawn with the same pressure with a sharp pencil can be used to emphasise important details. Every line should be essential to the drawing and precise: lines should not end 'in space' but rather always link up with another. Throughout the schedules you will find suggestions about what to draw. Do not make your drawings too small, rather size them as illustrations in a book.

A complete account of your practical work will include descriptive notes to supplement the drawings. Among the features that cannot be easily shown in drawings yet should be recorded in appended note form are: size, colour, movement, intricate details which would obscure the main features of the drawing, variation and comparisons between individual organisms. Drawings without the necessary title and descriptive labels, an indication of size and explanatory notes (for example, age, stage, culture conditions where relevant) are of very little subsequent scientific use.

The practice and training in making an accurate and complete record will be essential to any future scientific work: it is a skill you require to learn. Your record will be valuable also for revision, examinations and perhaps for later courses. In some practicals you will need to decide for yourself what your priorities for drawing and note-taking should be, and the most economical way of making your record: for example, partial drawings, tables, an outline sketch with separate details.

Students differ in the rate and the way in which they work. If you find you have covered the work in less than the time allotted, make sure that your approach has not been too superficial before finishing: it almost certainly has! If you find yourself short of time, make sure that you are working efficiently and that you are not doing more with each example than can be reasonably expected in the time. If you are still short of time, first ensure that you have completed the section to which special attention is drawn at the start of each practical and then that you have investigated at least some of the material associated with each of the remaining sections. Be guided by the posed questions: these are designed to focus your attention. Most of the questions can be answered by observation of the specimens provided, a few may require recourse to the study notes and/or a textbook.

Experimental work

There is little point in performing an experiment unless the procedure and results are recorded. Your record should state why and how the experiment was done, what happened and offer an interpretation of the results. It should be clear and concise, and should be readily understandable by another person on a subsequent occasion because much of scientific investigation involves precise repetition for conformation. A complete record of an experiment is best set out under specific headings: Title, Introduction and Aims, Materials and Methods, Results, Discussion and Conclusions. Many of the simple exercises in the Course practicals do not require anything so elaborate, but bear these headings in mind when recording your experiments.

Title, Introduction and Aims: When working from a class schedule, give a brief statement of your aims, possibly combined with the title, and refer the reader to the schedule.

Materials and Methods: Give an account in sufficient detail for another worker to repeat the experiment in exactly the same way. For a class experiment you might write 'see schedule' and attach the schedule. But you should note carefully any modifications you introduce.

Results: Record your results as they are obtained, concisely and in a logical order. Often the best way is to make a table in which the different groups or treatments or conditions may be clearly shown with the results. If you enter a value (datum) in error cross it through with a line and insert the correct value along side: do not erase the original value for with hindsight you might not have been wrong. Table columns must be labelled and units of measurement given. Make any necessary calculations: for example, from your repeated test results derive a mean and standard deviation for the data set. Do not quote dimensions as, for example, 10.55 µm when the method used could not safely distinguish between 10 and 11. Record all data to the same number of significant figures. Always write 0.1 rather than .1 since it is very easy to miss the '.' subsequently.

Supplement your data with drawings or diagrams, graphs or histograms as appropriate: in each case provide a caption and other labels so that they make sense without reference to the text.

Graphs are a good way of presenting data, but they are useful and intelligible only if you remember and use the basic rules about how to set them out:-

1 All graphs, as any diagram, must have a clear title.

2 The axes must be labelled and the units stated. Mark the way your axes are divided into numbers clearly. It is usual for the independent variable that you are altering (time or the concentration of a solution) to be plotted on the horizontal x-axis (the abscissa), and the dependent variable that you are measuring (rate of growth or amplitude of a response) on the vertical y-axis (the ordinate).

3 Choose a scale so that the graph uses all the paper: but to facilitate labelling, the axes should be drawn three or four squares in from the edge of the paper. It should be quite clear how many units correspond to a division on the paper.

4 Make the data points bold and clear so that anyone can see them.

5 The origin is always at the bottom left-hand corner. If zero is not included on one or other scale show this clearly.

6 If the points are clearly not linear do not draw a straight line through them. Rather, join them by a best-fitting, smooth curve: you can usually do this quite easily by eye. Consider the nature of the data you are displaying and decide whether a smooth curve or a series of straight lines is the more appropriate way of linking the points.

7 When for comparison you plot more than one curve on the same graph use a different symbol for each curve and where necessary to avoid confusion a different style of line to join the points. Remember to include a legend to identify the individual curves.

8 Most graphs are plotted on arithmetical paper where the axes are both linear, however, it is sometimes useful if one or both of the axes are in logarithms. Remember that zero can never appear on a log scale since log 0 has no meaning, and if you want to plot numbers ranging from 0.1 to 100, for example, you will have to use paper designed with three-cycles of logs. Log paper is used when you require to include a wide range of values in a single graph.

Discussion and Conclusions: Do not simply repeat the results. Interpret and relate them to each other, and to any other relevant information. Distinguish carefully between inferences made from your experimental data and those based on other information, the sources of this additional information must be cited (in a Reference List). The reasoning on which your inferences are based should be made explicit.

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Calculating molarities, concentrations, dilution factors etc.

Here are some simple calculations that every biologist should be able to do while working at the bench. Read the short introductory notes (for guidance, if you need it) then try the questions and check your answers.

Introductory notes:

• A molar solution contains the relative molecular mass (mole) of a substance (in grams) in 1 litre of solution. For example, a molar solution of sodium chloride contains 58.5 g NaCl in 1 litre, because the molecular mass (one mole) of NaCl is 58.5 (Na atomic mass 23 + Cl atomic mass 35.5).
• 1 millilitre (ml) is one thousandth (10^-3) of a litre
• 1 microlitre (m l) is one millionth (10^-6) of a litre
• 1 milligram (mg) is one thousandth (10^-3) of a gram
• 1 microgram (mg) is one millionth (10^-6) of a gram
• The term "parts per million" (ppm) is no longer used; it is equivalent to mg/ml

Problem 1:

The molecular mass of NaCl is 58.5.

Question (i). How much NaCl (milligrams) is present in 1 ml of a molar (1M) solution?
[Answer]

Question (ii). How much NaCl would you add to 1 litre of water to make a millimolar (1mM) solution?
[Answer]

Question (iii) How much NaCl is present in 100 ml of a 0.5M solution?
[Answer]

Problem 2:

The molecular mass of KOH is 56.

Question (i) You are asked to prepare 200 ml of a 0.2M solution of potassium hydroxide (KOH). How much KOH would you use?
[Answer]

Question (ii) If you took half of this 0.2M solution and added it to 400 ml water, what would be the molarity of your new solution?
[Answer]

Question (iii) What weight (in grams) of KOH would be in this final solution?
[Answer]

Problem 3:

In preparing microbial growth media we often express the concentrations of major nutrients (sugars, etc.) as a percentage. In fact, you need to do this with complex mixtures of nutrients such as peptone (a meat digest containing several amino acids) because you do not know the molecular mass. A 1% solution contains 1 gram of the substance in a volume of 100 ml.

Question (i) If you were asked to make 1 litre of a 1% glucose solution, what weight (grams) of glucose would you use?
[Answer]

Question (ii) Given that the molecular mass of glucose (C₆H₁₂O₆) is 180, what is the molarity of your solution? Express this in terms of both molar (M) and millimolar (mM).
[Answer]

Problem 4.

Some plants (and many fungi) can use either nitrate (NO₃^-) or ammonium (NH₄⁺) ions as their only form of nitrogen for growth. We might want to compare the growth of a plant (or fungus) when supplied with only nitrate or only ammonium ions. To do this, we add these ions as salts (e.g. sodium nitrate NaNO₃ or ammonium chloride NH₄Cl). But we must use the same amount of NO₃^- (for one of our treatments) as we use NH₄⁺ (for the other treatment). In other words, these ionic concentrations must be the same. Otherwise, we could be supplying more nutrients in one treatment than in the other, which would bias our results. [Remember that plants and fungi take up ions and convert them into amino acids, etc. - they do not split the ion into its elements and then take up nitrogen (N); only some nitrogen-fixing bacteria can use N as such.]

The atomic weights are as follows: Na = 23, N = 14, O = 16, H = 1, Cl = 35.5

Question (i) Calculate the molecular mass of NaNO₃ and of NH₄Cl, and the contribution of each N-containing ion to each molecular mass.
[Answer]

Question (ii) If we choose to supply 0.1M NaNO₃ to one treatment, what molarity of NH₄Cl should we supply to the other treatment, to provide the same concentration of nitrogen-containing ion?
[Answer]

Answers:

Problem 1(i) 58.5 mg
Problem 1(ii) 58.5 mg
Problem 1(iii) 2.925g (because you would use 5.85g to make 100 ml of a molar solution, and half of this for a 0.5M solution)

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Problem 2(i) A 1M solution of KOH would contain 56 g in 1 litre. So a 0.2M solution would contain 11.2 g (56 ¸ 5) in 1 litre, or 2.24 g (11.2 ¸ 5) in 200 ml.
Problem 2(ii) 0.04M
Problem 2(iii) 1.12g, calculated as 0.04 x 56 x 0.5, because you have 500 ml of solution, not 1 litre)

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Problem 3(i) 10g
Problem 3 (ii) 0.055M, calculated as 10 ¸ 180; or 55 mM

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Problem 4 (i) NaNO₃ = 85, of which NO₃ = 62 (73%). NH₄Cl = 51.5, of which NH₄ = 18 (35%)
Problem 4 (ii) 0.208M NH₄Cl, calculated as 0.1(73 ¸ 35)M. You can verify this from your answer to Q 4(i) - there is about half as much of the nitrogen-containing ion in NH₄Cl than in NaNO₃

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