Overview

Teaching: min
Exercises: 480 min

Objectives

• Develop a hypothesis

• Get acquainted with the state of the art of phage research

• Choose one or more papers for inspiration

• Write down 1 or 2 research questions

• Make a plan on how to tackle the questions

To close off this course, we would like to give you the opportunity to design and work on your own research project. Viromics is a new field, the virosphere is huge, and there is a LOT of data, so there are more unanswered than answered questions. Looking back on the course, are there things you are wondering about or want more time to work on? For inspiration, you could refine the ideas below or look in the literature. It is important to have a clear hypothesis at the start of your project. Afterwards, make a bullet point plan of how you will be able to address it (methods), including any required statistics.

How to make a clear, data-driven hypothesis? Start with a specific question, which is neither too broad, now too narrow. For example: how does adding a target phage and host affect the virome community? This is a singular question that can be answered by comparing two datasets - one with the target phage/host and another without the target phage/host. It is crucial to manage your time in the set up and execution of your research project. After creating the hypothesis, you should also do some literature search, make a list of bullet points with methods and discuss your ideas with one of the teachers. You should finish all the aforementioned tasks this morning!

Our suggestions of projects were all inspired by the experiments done in the wet lab in the module “Viromics - Virome isolation and sequencing”:

• Calculate the abundance of the target phage of the wet lab experiments and compare different treatments
• Compare the predictions of bacterial hosts you already did with the 16S sequencing of the bacteria
• Compare the phylogenetic trees of two different proteins found in the same contigs during this module
• How does the addition of the target phage and host affect the abundances of other viruses in the community?
• What differences do we observe in the other phages in the virome when target phage/host are added?
• Can we track the target phage/host in the complex community along the samples? In which sample is it more abundant?

Documentation

Do not forget to document the development of the project in your lab book. Write down your hypothesis, any relevant papers, methods, databases, etc. Below are points that should be included in your documentation:

• A brief background on the topic
• A workflow for the steps you plan to take
• What will be the inputs and outputs?
• Which programs do you plan to use?

Presentation

The points below are what we expect to see in your final presentation:

• Background on the topic that lead to the research question (1-2 slides)
• Hypothesis and brief overview of the literature
• Workflow figure or bullet point list of methods
• A rationale for why you choose those methods
• What were the inputs?
• What did you get as output (table(s) and/or figure(s))
• Interpretation of the output
  • Consider interpreting your results on 3 levels: 1) what does the data say? 2) What does this mean for the biology of the organisms? 3) What does this mean for the ecology of the community?
  • Does it answer your initial question? It does not have to. In a negative case, can you say what you might do differently next time?
• Limitations and lessons learnt
• Things you found particularly interesting

Exercise

1. Create a clear, data-driven hypothesis, and discuss it with teachers and fellow students. Often your initial idea can be further refined based on discussions with others.
2. Make sure you check the literature Find at least one paper that is closely related to your project, and use it/them to refine your question.
3. Methods: Make a plan for tackling your question(s). Think about data sources, bioinformatic methods, possible outcomes, expectations, backup/follow-up plans, hypotheses, and interpretation.

Key Points