Posted: May 13th, 2023

Microbial Diagnostics Research paper

Microbial Diagnostics Research paper

 

The major piece of assessment in this module will be the production of a scientific paper on the design and validation of a diagnostic PCR assay for detection of UPEC. You will write the paper as indicated in the instructions to authors for the Journal of Clinical Microbiology (http://jcm.asm.org/site/misc/journal-ita_org.xhtml#02)

 

The paper should introduce the concept of wishing to detect UPEC in urine samples, and the problems associated with this. You should then provide methods as appropriate for a journal article in this journal. You should then provide concise and relevant results from your bioinformatics analysis through to your primer design and the results of your PCR tests to validate the assay.

 

You are strongly encouraged to look at similar types of J Clin Microbiol articles to gauge how much detail and how many figures tables you should be adding to your paper. The article is worth 60% of the module mark and will be assessed as follows:

 

• The word count should be around 3,000 words excluding title, abstract, figures, tables, and references.

 

 

Abstract – as per authors instructions, concise and informative 5%

 

Introduction – fully introduces background and rationale of the research 15%

 

Firstly, write about Escherichia coli in general and about the virulence factors

You must say why we used these three genoms

CFT073( UPEC)

MG1655( K12)

EDL933( EHEC)

and write about them. So, write all the information the Reader want to understand and to avoid any confusion.

You also should include why UPEC is important and has been a big problem, inn addition, why PCR is very good.

 

 

Aim:

In this paper, three strains of E. coli will be compared in order to evaluate as well as determine which among the three strains of E. coli has the capability of becoming UPEC. Then the study will design a novel PCR to test one gene that has potential factors, to cause UPEC among these strains.

 

Methods – concise, relevant and in appropriate style 10%

 

MATERIALS AND METHODS:

(1): Bioinforatics Steps

(2): primer Design Steps

(3): PCR Steps

You should write for each program and website why we use and how these programs work.

 

Results – Concise relevant and well presented, with appropriate supporting commentary, avoiding addition of numerous irrelevant tables and figures 45%

 

Discussion – discuss your results in light of recent literature   20%

 

Recommendation for the future in the discussion is important

 

 

References – relevant, recent references in correct style format   5%

I. Assessment Requirements

 

The major piece of work for this module (60% of the mark) is research article based on all of you practical work during the module

• Guidelines for how to format the review article should be taken from the Instructions for Authors from Journal of Clinical Microbiology.
• The word count should be around 3,000 words excluding title, abstract, figures, tables, and references.

• It should be written in MS Word and submitted as a single file.
• It will be examined using Turnitin anti-plagiarism software before it is marked by your tutor.

 

II. Assessment Scenario

 

Writing a review article

Research articles provide a concise presentation of new knowledge in a particular area for fellow scientists. The articles provide a forum in which the writers can share their most interesting and relevant data. They also provide an opportunity to critically analyse the literature. The best research articles are concise and to the point and provide a clear advance to the field.

 

Your task is to write the best-possible article using your bioinformatics and lab data. We are not looking for just a compilation of data, but also evidence of original and analytical thought. This must be evidence-based, using primary sources (i.e. original research articles).

The assessment criteria below show clearly what we are expecting

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Class/ Grade   Assessment Criteria	Exceptional Distinction (includes all features of Disctinction with the additional characteristics listed below)	Distinction Low | Mid | High	Commendation Low | Mid | High	Pass Low | Mid | High	Marginal Fail	Fail Low | Mid	Zero
Abstract/Summary (0.10 weighting)	Abstract is written to engage the reader. Synthesis of ideas is a major feature	A concise abstract that selects the most significant findings and states them concisely. Some evidence of synthesis	Abstract covers all the important points of the review in a balanced manner and shows good understanding	Abstract is a fair summary of the contents of the article, possibly with minor omissions or imbalances	Abstract is significantly imbalanced with omissions. May contain some minor inaccuracies. May be poor in structure.	Abstract is over-brief with significant omissions and inaccuracies or does not reflect the content of the review.	No submission or penalty
Introduction, Aims (0.10 weighting)	Shows an excellent grasp of the context of the problem, including latest developments in related fields.	States the aims of the article clearly and concisely. Introduction is well-structured and explains the context of the article with clarity, using current literature.	Aims of the article are explicit and appropriate. The background information is well summarised and current, with few omissions.	The introduction contains a factual account of the background to the problem. Most relevant ideas are mentioned. Aims are clearly stated	Introduction may be too short or too long. It is imbalanced and may have omissions or slight inaccuracies. Aims may be mentioned and/or reflect confusion	Introduction may be too short. It may have major omissions or inaccuracies. It may contain much irrelevant material. Aims are absent
Quality of results (0.40 weighting)	The results provide a clear descriptiopn of the main findings using only relevant figures and a clear concise supporting commentary. It has no obvious omissions.	The results provide a good description of the main findings using well chosen figures and a supporting commentary	A clear question is is answered using a reasonable choice of figures and tables. Most citations are from primary literature, and many are recent. Methodology of the review is mentioned .	Supporting figures and tables have not been carefully shosen, rather a list of raw data with little supporting commentary	No clear problem is investigated and answered. No sturcutre to data presented. No supporting commentary	No clear investigation is presented
Discussion and Interpretation (0.30 weighting)	The article presents strongly-evidence-based arguments that in places include original synthesis of ideas by the student. Recommendations show insight into the potential of current and developing technologies.	A critical evaluation of primary sources is evident Contentions are supported by citations Conclusions are sound and cover the material discussed adequately. Recommendations for future research in the field show a thorough understanding of the problem.	There is evidence of an analytical and critical approach, with many arguments supported by citations. The student makes a clear and valid summary of their findings, with some indication of gaps in current knowledge	Arguments are mostly clear and logical. The balance is towards the descriptive rather than the analytical. A few minor misunderstandings may be present. Ideas and information are adequately summarised.	There is much description but no evidence of analysis. There may be a tendency to make unsubstantiated assertions.	Significant concepts may be misunderstood Arguments are poorly structured in places and discussion may be difficult to follow. Conclusions may not be present or they may not be valid.
Quality of written presentation (0.10 weighting)	Uses quality of scientific English expected for publication of findings. The Instructions to authors are followed exactly.	Uses high-quality scientific English giving overall clarity to the work. The specified instructions for authors are followed with few errors. All references are pertinent to the discussion and most are recent. They are cited correctly Statistics are used correctly where appropriate	Writes in appropriate scientific style. The English is generally easy to follow with few   errors. The structure of the work is recognisably that of the specified journal, with adherence to the majority of the conventions. There is some use of numerical methods where appropriate. Citations in the text are matched by references at the end. References are listed in journal format with only a few errors	The work is mainly in good scientific English, but with some errors of spelling and/or grammar. Language may be too informal in places. The work is clearly structured, with a resemblance to the specified journal style. Statements in the text are supported by citations. There may be a slight mis-match between citations and the reference list. The reference list is well-formatted but may deviate from journal style.	Language may be too informal and/or there may be major errors of grammar. Structure of the writing is lacking in places. Citations may be limited in the text, but a list of references is present. Formatting of references may be poor.	The work lacks structure and there is little evidence of the student following a journal style. Writing may be disorganised and contain major grammatical errors. References may be absent or limited in number. There may be a mis-match between these and any citation in the text

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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