How do transposable elements survive and proliferate, when their presence in the eukaryote genomes is rarely beneficial and often deleterious?

This assignment is based on a Research Proposal with a Literature Review component. You will be provided with an observation, question and reference which will be at the very bottom in quotation marks which will set the scene (Research Proposal Exercise Questions). From that information you will be expected to develop a research study and complete the attached proforma . While it does not have to be entirely original, you will hopefully be able to develop and provide some additional ideas as to how the research could be conducted.
A critical step in advancing scientific research is finding funds to pay for staff, laboratory facilities, equipment and consumables. It is not enough to have a good idea, you need to convince a funding body that you have expertise, a good research plan based on reliable past research findings, that your approach is sensible, feasible, safe and ethical. Most importantly, is it worth doing? Will the results be guaranteed and will anyone care? What will be the impact of your findings on advancing science, on medicine, food production, on society, on government policy? There is a long list, only certain ones may be relevant to the funding body, so a grant application must take that into account.
The attached proforma contains most of the typical components of a research proposal submitted to a major funding body, such as the Medical Research Council. The form has guidance notes on the right-hand side in blue. You should remove these notes prior to submission. All grant application forms have word or character limits and as they are often online, so they cannot be exceeded. Therefore, pay attention to the word limits, they are NOT flexible. You can write less, but you will lose credit if you don’t provide the necessary information and you will lose credit if you go over the limit.
The starting point for the exercise is the Literature workshop followed by the Literature practical in Semester A. Further support will be provided in tutorials with your BRM Tutor in Semester A and B. If you are completely lost and bereft of ideas, then consider choosing one or more experiments from a single research paper and base your proposal on that. Don’t copy it! You can make it more original by changing the species or changing parameters or slightly altering the objectives or aims.
Literature Review Component of the Proforma
As part of the Proposal you are required to produce a scientific literature review (Section C1) to help provide background and justification for the research proposal. This will form the main component of the assignment and completing this aspect FIRST will aid in the completion of the proforma since it will serve to provide you with understanding of the topic and the current state of the research.
The goal of a review is normally to present the current state of the art, which means a comprehensive search of the published peer reviewed research science that is currently available. It will identify the areas where research is incomplete or controversial, where questions remain unanswered and present new questions that have yet to be addressed and hypothetical answers. It is a valuable precursor to experimental research and is for example normally completed in the early stages of a PhD.
Your assignment review cannot be that ambitious as the literature alone will overwhelm you. If you are to be comprehensive, the topic is going to need to be very narrow. If the topic is broad you will have to be superficial. Therefore, choose your limits carefully so that your review appears well rounded with adequate depth. Avoid lengthy and detailed descriiptions of experiments or methods. Try and identify themes related to the question you are addressing to consider throughout your review.
Your introduction should contain background and explanations or definitions of terms that the reader needs to follow the rest of the review, but it should also contain information and what is to be covered.
The main body of the review should not repeat the introduction and should follow a logical sequence integrating and discussing information from different sources. The author should make valid and original points supported by evidence. Do not describe the evidence and expect the reader to work out the point.
The review needs a conclusion in which the main findings are drawn together and recommendations for further work are made.
Figures and tables can be included, but only if they are referred to and discussed in the text. Do not copy and paste from copyrighted sources, but you may include an original table or figure derived from published work and properly acknowledged. If you include images, they must be in the public domain. You don’t get extra marks for decorating your review or substituting copied figures for your original text.
You may wish to use popular science magazines and textbooks to aid your understanding, but not necessarily as a direct source, in which case you can list these in a “Bibliography” (not the reference list – the distinction is that all references cited in the text must be in the reference list, whereas references in the bibliography are not and can be regarded as further reading). Only relevant and useful sources of a broad range of information should be in the bibliography.
You must proof-read your report. As a guideline you should spend 12 hours in total on the assignment in addition to the normal study time for this module.
The review should be based on:
at least 10 references (there is no upper limit) from recent peer reviewed mainstream scientific journals.
at least two thirds of your references must be original research papers and not reviews.
in addition to the above you may include a few references (no more than a quarter of the total) from alternative, but reliable sources (eg. scientific databases like OMIM, not medical advice websites).
Observation- “ Transposable elements (TEs) are a major source of mutation, often deleterious, yet they are ubiquitous in eukaryotic genomes. They make up nearly 50% of the human genome, with one family, the L1 retroposons, responsible for more than a quarter”
Assigned question : “ How do transposable elements survive and proliferate, when their presence in the eukaryote genomes is rarely beneficial and often deleterious?”

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