CMB2000 : Essential Biomedical Research Skills
- Offered for Year: 2017/18
- Module Leader(s): Dr Nick Morris
- Lecturer: Dr Joe Willet, Dr Jennifer Wilkinson, Professor David Lydall, Professor Elaine McColl, Dr Matthew Bashton, Mr David McGeeney, Professor Brian Morgan, Dr Rachel Dickinson, Dr Geoff Bosson, Dr George Schlossmacher, Dr Damian Parry, Dr Lindsey Ferrie, Mr Jan Deckers
- Practical Supervisor: Dr Beth Lawry
- Owning School: Biomedical Sciences
- Teaching Location: Newcastle City Campus
|Semester 1 Credit Value:||20|
This module provides an integrated approach to modern molecular biology and aims to give the student an understanding of technique principles via lectures and then through laboratory work a basic level of competence in performing some of the key techniques and interpretation of the results. This includes an ability to utilise a range of informatics, bioinformatics and statistical software. The module will also provide an awareness and understanding of health and safety and ethics impacting on scientific research.
Outline Of Syllabus
The syllabus for this module can be considered under four interrelated strands;
• Practical - Molecular biology techniques covered in practical laboratory classes are; DNA (plasmid)
isolation/purification, heat shock transformation of E coli, PCR, agarose gel electrophoresis,
restriction enzyme digest, SDS-PAGE, Western Blotting / immunoprobing and ELISA.
• Informatics - The complexity of molecular biology and vast amount of data generated means that
students need a clear understanding of how computers can be used to search for, and interrogate
information effectively. The informatics tools and databases covered in this module include
PubMed, OMIM, DOI, BLASTp and BLASTn alignments, Prosite, SMART and Pfam. Appropriate
use of Wikis.
• Statistics - The analysis of data requires the application of statistics, including basic data
analysis, probability (including Hardy-Weinberg equation), normal distribution, inference, t-Test,
correlation and regression.
• Ethics - Much of the scientific research introduces a number of ethical dilemmas and questions that
students (as scientists) must be aware of and consider throughout their career. A series of
lectures will examine the concepts of ethical reasoning and extend this to animal and human
research and clinical trials.
|Scheduled Learning And Teaching Activities||Lecture||32||1:00||32:00||This includes 28 lectures plus 4 post practical feedback sessions.|
|Scheduled Learning And Teaching Activities||Practical||5||1:00||5:00||Statistics IT practical sessions|
|Scheduled Learning And Teaching Activities||Practical||1||6:00||6:00||Practical 4: Measurement of novel protein concentration by Enzyme Linked Immunosorbent Assay (ELISA)|
|Scheduled Learning And Teaching Activities||Practical||1||4:00||4:00||Practical 3: Evaluation of expression of recombinant proteins in Escherichia coli|
|Scheduled Learning And Teaching Activities||Practical||1||6:00||6:00||Practical 2: SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting.|
|Scheduled Learning And Teaching Activities||Practical||4||3:00||12:00||Practical 1: Analysis of recombinant plasmid|
|Scheduled Learning And Teaching Activities||Small group teaching||1||1:00||1:00||Ethical debate and group discussion|
|Scheduled Learning And Teaching Activities||Small group teaching||1||2:00||2:00||Informatics Seminar. 5 slots over 5 days (morning preferred).|
|Guided Independent Study||Independent study||1||132:00||132:00||N/A|
Teaching Rationale And Relationship
The didactic lecture is still the most efficient means of providing knowledge of method principles (K1, K2) and concepts in ethics (K3).
Basic experience and practical competence in the core molecular techniques is important to all students irrespective of the degree programme (S1). Emphasis will be made on the link between techniques by investigating a putative gene that has sequence similarity to other proteins involved in transmembrane transport (K1). The techniques progress from isolation of genetic material, engineering genes into plasmids and transformation of organisms to produce the protein product. Characterisation of the protein, expression, identification and quantification follow (S2).
Although frequently referred to as bioinformatics, the module does look at wider informatics (S3). BLAST searching and interpretation of results on several commonly used bioinformatics websites provides students with sufficient knowledge to use the tools without becoming bioinformaticians. The need to revisit the avoidance of plagiarism is timely at this point as students start to write more essays and gain a better understanding of scientific writing (S4). As much as we might want to ignore them, Wikis are widely used and therefore including their use here is relevant. ‘Cloud-based’ documents and databases are increasingly popular and will be used to handle some of the data and link the laboratory practical and informatics strands. Students will have the ability to access a formative interactive on-line practical that they can perform as many times as they wish individually or as a study group prior to the on-line assessment. Drop-in workshops will be available for students who are struggling with any aspect of this practical.
A close integration between didactic lectures and practical sessions in an IT cluster allow students to immediately apply theoretical knowledge. Each week students get a 1 hr lecture on one aspect of numerical data analysis (K2) followed by a 1 hr practical class in which commercially available statistical software will be used (S5). The sequence of topics develops an appreciation of statistics and an introductory competence in their use.
Ethics surrounding scientific research influences all areas of science and is therefore important to all degree programmes (K3). Lectures provide the most efficient means of providing information about ethics. This is supported by a seminar session to facilitate interactive debate and better prepare the student for the assessment.
The format of resits will be determined by the Board of Examiners
|Written Examination||120||1||A||50||Extended Matching Items and short answer questions.|
|Computer assessment||1||M||12||Informatics assessment; in-course online exercise, short answer questions|
|Prob solv exercises||1||M||12||Statistics in-course written worksheets and on-line assessment, short answer questions|
|Essay||1||M||20||Ethics essay, title will be provided 2 weeks before submission date and prior to ethics lectures. 1,000 word limit|
|Practical/lab report||1||M||6||Online EMI - Practical 1 Online EMI - Practical 2 Online EMI - Practicals 3 & 4|
Assessment Rationale And Relationship
As in prerequisite modules, the requirement for students to pass each strand with a minimum mark of 40% is required for students to pass the module. This system was introduced to ensure students who pass the module have achieved all learning outcomes. Failure in any of the four strands will result in a capped module mark of 35% only retrievable to a 40% pass on completion of any reassessment considered necessary to meet the learning outcomes.
The practical strand consists of Practicals 1, 2, 3 and 4 as outlined in the Teaching Activities table.
On-line and automatically marked worksheets comprising mainly EMI style questions will be used to provide immediate feedback and self-evaluation of student’s understanding of the laboratory practicals. These will have a nominal summative weighting (as described in the Assessment tables - Practical/lab report 1, Practical/lab report 2, and Practical/lab report 3 (Practical/lab report 1 consists of material from practicals 3 and 4)) to promote student engagement, but the majority of marks for the practical strand will be assessed under examination conditions with a single 2hr paper (again, please see Assessment tables - Written Examination 1).
The informatics strand consists of the Informatics lectures, along with the Informatics training session (please see Teaching Activities table), plus a three hour assessment (as described in the Assessment tables - Computer assessment 1). The 3-hour on-line assessment (Informatics Assessment in the Assessment table - Computer assessment 1) will test an individual student’s ability to find and interpret informatics data. The format will be almost identical to that undertaken as the formative informatics on-line practical. The material taught in this strand will also be examined as part of Written Examination 1 (see Assessment tables).
This consists of 5 lectures and 5 online sessions as outlined in the Teaching Activities table. The assessment (Prob solv exercises 1) will consist of a unique set of data for each student generated from their student ID number which is then used to test the student’s ability apply appropriate statistical methods and interpret the results. The assessment is able to provide feedback and marks quickly and efficiently. The analysis is weighted as described in the Assessment table (Prob solv exercises 1). The material taught in this strand will also be examined as part of Written Examination 1 (see Assessment tables).
This consists of the five ethics lectures, and the seminar.
This strand will be assessed by an essay. The title will be set before the ethics lectures and seminar allowing students to ask specific questions that relate to the ethical dilemma. Submission of the essay will be 2 weeks after title was set. The title will reflect the latest ethical dilemma in the news and will therefore change from year to year. The essay will be marked on sound arguments to resolve the dilemma and consideration of different aspects of ethics. This provides students with the opportunity to write discursive prose and weigh up the arguments for and against the resolution. The essay is weighted as described in the Assessment table. The material taught in this strand will also be examined as part of Written Examination 1 (see Assessment tables).
FMS Schools offering Semester One modules available as ‘Study Abroad’ will, where required, provide an alternative assessment time for examinations that take place after the Christmas vacation. Coursework with submissions dates after the Christmas vacation will either be submitted at an earlier date or at the same time remotely.
The form of assessment will not vary from the original.