Tuesday, 9 May 2017

Lab report guidelines

Bioprospecting for antimicrobials MBB265

Key format guidelines

  • Include your: name, U Card number and the date (also identify    your colleagues in your group) 
  • Summary/Abstract (50% A4) 
  • Conclusion and future suggestions (50% A4) 
  • Detailed diagram of protocol and results (A4 page) 
  • Submission date Monday 15th May (before 16.00)

The Abstract should capture the whole experiment, background, experimental, results and conclusion, in general terms. You may refer to your figure (although this isn’t usual in abstracts, it is fine here) [25% marks]

The Conclusion should summarise your key finding(s) and suggest further work or ways in which you might overcome any failures in the experiment [25% marks]

The Diagram can be hand drawn, may contain photographs, but should capture the essential stages of the work from start to finish. Importantly, it must be accompanied by a detailed legend and labels as appropriate [50% marks]

The sample figure below has a detailed legend, but it also needs a title?


Microcin C induces persistence in growing Escherichia coli cultures.
A. Growth curves of MG1655 (wt) strain after McC treatment. An overnight culture was diluted 100
fold in LB and growth was allowed to continue at 37°C. When OD600 reached 0.5 the indicated concentrations of McC were added to culture aliquots and further growth was monitored by following OD600 at indicated time points.
B. As in А, but showing the number of colony forming units (CFUs) on LB agar plates at various time points after the McC addition.
C. An example of killing curves obtained after ciprofloxacin (Cfx) treatment of MG1655 (wt) culture with or without McC (1.5 μM). Cultures were grown as in A. After 30 min incubation with McC, 1 mg/l Cfx was added. The incubation was continued and culture aliquots were removed at various time points followed by CFUs determination. Mean values and standard deviation obtained from three independent experiments are shown.
D. For each killing curve obtained with or without McC, percentage of surviving cells (for details see Experimental Procedures) after 4
h incubation in the presence of Cfx (see panel C) was calculated. Error bars show standard deviations of mean values of at least 3 independent experiments.

A couple of ideas for figures are given below 

Monday, 8 May 2017


Image result for green coconutsThe current level 2 class in MBB (MBB265) has become known locally as the coconut lab, mainly because we use coconuts as one of the sources of antimicrobial, natural products. As we approach the end of the experiment, I thought I would make a few observations about the highlights, the unexpected events. However, my main reason is to provide some additional support for the students who are about to collect their results and write their lab reports. The objectives of the coconut lab are several-fold. At one level, it is intended to bring together a number of skills that have formed part of the undergraduate experimental labs at Sheffield in Molecular Biology and Biotechnology, such as Microbiology and Biochemistry with some generic analysis methods thrown in. However the most important reason for the lab classes is to give students their first exposure to running an experimental research project. The instructions provided to students during the the first session are simply:
  • Brainstorm ideas
  • Organise and prioritise your ideas
  • Develop an experimental plan
  • Assemble reagents and equipment
  • Begin
The Learning Objectives The first session, as you might imagine, was a little animated, students were coming to terms with the general responses to questions they would ask of the demonstrators: I don't know, what do you think? But everyone got used to it eventually and the questions were soon framed more thoughtfully. I was planning on using 6 discs on my plates, is this too many? Or, would you use distillation to separate aqueous and solvent phases, or centrifugation? It was clear that the ability to trouble shoot and make decisions had come on leaps and bounds and, while some students would clearly prefer a more structured lab class experience, with standardised protocols, this is unlikely to be closer to the kind of experimental work they will encounter in a PhD or commercial laboratory setting. 

The second aspect of the lab class that is different to regular classes, is that any failure to plan appropriately (i.e. make up solutions in advance or inoculate cell cultures in a timely way etc.) is met with a shrug of the shoulders and a suggestion to re-plan in a less ambitious way, or try and find a suitable replacement sample from a colleague. Again, placing the responsibility on the students' shoulders. And I say students, since this is a small group project and so poor planning and organisation should be minimised, providing the team share the responsibilities evenly.

Image result for bioprospectingThe Science In addition to the general lab skills and research experience, the project has a relevance to understanding simple drug discovery strategies, in particular the search for new antimicrobial compounds. And in particular, an appreciation of the world of Natural Product Chemistry and Bioprospecting. The students are expected to develop an experimental strategy to establish whether extracts from a range of fruits, vegetables, roots etc., are capable of inhibiting the growth of one or more classic strains of bacteria: Proteus, Staphylococcus, E.coli and Pseudomonas.

Materials and Methods The students are asked to draw on their knowledge and lab skills to devise natural product extraction and testing protocols. They must choose the source material based on availability in the lab and then devise a way of making extracts and preparing them alongside a set of their own controls, in order to collect any evidence of growth inhibition. Students across the class may choose to prepare extracts from any or all parts of the plants. They may choose to look at aqueous or solvent based protocols and are free to use separation methods of their choosing, combined with ion exchange enrichment should they wish.

Data collection and analysis The impact of the extracts on growth may be monitored on plates, with or without top-agar or in broth culture. Both methods are satisfactory, the choice method(s) for plotting the data, to obtain a quantitative measure of growth inhibition (compared with common antibiotics), is at the students' discretion and I am looking for creativity in presentation of data as well, of course as critical evaluation. (I will add a supplement after I have looked through the lab reports). Communication of the results and design of follow up experiments is a critical part of the report. It is absolutely fine to discuss mistakes made, controls omitted: as long as lessons are learnt!

A final note on writing The communication of Scientific work, or indeed any form of evidential document (legal, historical etc) requires a high standard of English and precision: clarity of explanation and a careful avoidance of ambiguity, combined with a slightly formal style, is the "Gold Standard" here. A creative and attractive style of Science writing is also something you should strive for, but it is the icing on the cake and is often reserved for "reviews" or popular articles.

Finally, the story so far....The pattern of response to this kind of class is pretty standard. Students are generally a little anxious at first, but most embrace the freedom and the opportunity to follow their own ideas. The usual problems of inadequate labelling, mis-calculating concentrations crop up, but this is usually "contained" by the team approach. Estimating volumes of media for plating, and anticipating problems such as the premature setting of top agar etc and a general, or the need for a starter culture first thing in the morning are all apparent. However, I have been pleased with the planning and timetabling awareness: a key part of time management. 

Let's see what the results look like....