BGS course student manual#

Welcome to Bacterial Genome Sequencing course. Each lab week will have a separate lab manual with all the details and instructions you need. This is a guide to the BGS course structure, and a way in which we can highlight the important stuff,guiding you (we hope) to do well.

601137 Bacterial Genome Sequencing is a 40-credit 2-semester course and part of the final-year-projects umbrella of modules. We will work together to characterise bacterial species from a clinical environment. We will prepare DNA, construct a DNA sequencing library, and run a modern minION DNA sequencer in the lab to generate DNA sequences and construct a genome assembly. In semester 2 we will annotate the bacterial genome to identify genes involved in antibiotic resistance. Finally you can test your personal assessment of the bacterial resistance to specific antibiotics (determined from the sequence) by applying antibiotics. You will have lots to write up.

There will be five full weeks in the lab spread over 2 semesters. This is not a practical class, this is real scientific research. You are doing things that have never been done before, analysing totally new data, and drawing unique conclusions. Scientists do not work in isolation, you will be working in groups, working with academic staff, helping out others, and learning as a team. We have designed this so that your fate is in your own hands though, your assessments are mostly individual and you will not be dependent on others for good marks.

Goals of the Course#

Try to think what you want to get out of this course. Perhaps you just want 40 credits, perhaps to learn very modern lab skills, perhaps to sequence a bacterial genome because it’s fun and fascinating. There are lots of other things you might want.

We want to teach a good course. We want to provide an alternative to the standard IRP project format to promote a diversity of learning methods. We want to interact with students and guide them through research because it’s fun and rewarding and something we don’t often get to do. We want to teach students cutting edge lab techniques to prepare them for research or industry. We want to sequence bacterial genomes because it’s fun and fascinating.

We can arrange this course so that both students and staff get what they want, but we need to collaborate. We are working hard in the background to prepare everything and to teach the material. You will also need to work hard behind the scenes reading papers, learning methods and skills, thinking and asking questions. You can get great marks on this course (and remember it’s 40 credits) but it will require very strong engagement, you will have to work for it.

Assessments#

  1. Portfolio 25%

  2. Group presentation 25%

  3. Manuscript 50%

The assessments are briefly outlined below but we will explain and guide you much more as the course progresses. Each assessment will have a help page on Canvas and also a help session before it is due to be submitted.

Portfolio#

You will individually prepare and submit a document (portfolio) outlining the different work you have done. This has two compulsory components

  1. Electronic Lab Notebook, a reproducible record of all your research activities

  2. Evidence of achievement of competencies, briefly document the completion of specific research activities that are assigned to you (eg run a gel, summarise a paper, trim DNA sequences)

Group presentation#

You will present your work as a small group (~4 students) in a 10 minute talk to the other students. You will present your preliminary analyses and results describing what they mean. You are not assessed on how slick you are at presenting, but more on how well you explain the system and results to the class. This assessment is a great way to get detailed feedback that will feed into your final assessment, the scientific manuscript. We have run these for years and it is both teaching and assessment, you will learn a lot during the discussions. Also, there may be biscuits.

Manuscript#

You will individually write a scientific manuscript (ie short journal article) of your bacterial genome sequencing work. You will have plenty of guidance, opportunities for verbal feedback, and be able to submit a draft version for detailed comment before your final submission. This format is used across all the project courses, and also by real scientists publishing their work.

Course Work#

Labs#

You will spend 5 full weeks in labs (we label these weeks A-E). You will be expected to attend every day during the set hours. If you do not attend fully you will be letting down the entire group, and will be asked to transfer to a different module.

We do of course recognise that there will be times when you can’t attend for genuine reasons, and as long as we are made aware then we can come to some suitable arrangement. Some students will have to step out to attend lectures on other courses, this will be fine, but please keep us informed well ahead of time.

Hardy Lab 301 is a specifically designed lab for this type of research. It will be yours for these 5 weeks. We may also break out to other rooms for seminars, computing, or whatever works best.

Study#

To really succeed in the course you will need to gain detailed knowledge as well as lab skills. We will be setting reading, holding informal journal clubs to discuss papers, and giving seminars to explain the science. You will need to contribute to these, learning interactively rather than passively.

Things for your CV#

There are many skills that will look great on your cv. We are happy to discuss with you how you can best represent your new knowledge and abilities in this way. Some things that you may be able to include at the end of the course include:

  • Microbiology techniques. Plating, culturing and gram staining bacteria from clinical isolates

  • Bacterial DNA extraction, construction of DNA sequencing library and running of minION nanopore DNA sequencer

  • Knowledge of the unix command line. Basic command line skills to navigate, inspect and manipulate large data sets

  • Genome assembly and annotation. Basic skills to assemble a bacterial genome from DNA sequence data, and annotate to discover antibiotic resistance genes

  • Reproducible research skills. Understanding of modern reproducible research skills including archiving data and metadata, electronic laboratory records, and open practices.