1. business and industrial
2. business operations
3. management
4. project management

4th YEAR
MICROBIOLOGY
MANUAL
2013-14
“Our deepest fear is not that we are
inadequate. Our deepest fear is that we are
powerful beyond measure. It is our light, not
our darkness that frightens us. We ask
ourselves, who am I to be brilliant, gorgeous,
talented and fabulous? Actually, who are you
not to be? You are a child of God. Your
playing small doesn’t serve the world. There’s
nothing enlightened about shrinking, so that
other people won’t feel insecure around you.
We were born to manifest the glory of God
within us. It’s not just in some of us, it’s in
everyone. And as we let our own light shine,
we consciously give other people permission to
do the same. As we are liberated from our own
fear our presence automatically liberates
others.”
Marianne Williamson,
Return to Love: Reflections on the Principles of "A Course in Miracles", Harper
Collins, 1992.
1
Welcome to 4th year Microbiology!
This Manual describes the course offered in final year Microbiology. It aims to list
all the academic happenings during the year and you should keep it to consult throughout
the year. Any modifications to the course, as outlined in this manual, will be
communicated to you as soon as possible, normally via Blackboard. If you have any
questions about course requirements, contact the course coordinator Gerard Wall by email ([email protected]), ask one of your class representatives to do so on your
behalf, or drop into his office (Room 103, ground floor, Microbiology).
You are expected to attend all the sessions outlined in this manual. If, for any
reason, you are unable to attend, you should inform the course coordinator as soon as
possible and, where appropriate, give in a medical cert to the departmental secretary. As a
matter of courtesy you should also inform the staff member running the unit you have
been absent from as to the reasons for your absence.
Finally, take the opportunity to get to know the staff and postgrads throughout the
year, attend all the Departmental and MicroSoc nights out, enjoy the 4th Micro experience
… and welcome again to Micro!
Overview of this manual:
Section
A
B
C
D
E
F
G
Description
Introduction
Project
Self-study essays
Problem-Solving Papers
Demonstrating – 2nd Micro labs
Lecture Modules (6 Modules)
Appendices
1
Time
Week 1
Semester 1
Semester 1
Semester 2
Semester 1 or 2
Semester 2
Page
9
15
25
31
37
41
45
Staff
Dr Gerard Wall ([email protected]) is the overall course coordinator and
will be the main contact between you and the “Department”, either individually or
through your class representatives.
Dr Florence Abram will be responsible for timetabling and organising your
lecture Modules in Semester 2. She will present the Modules in week 1 of Semester 1,
and organise timetabling of lectures in Semester 2.
Dr Conor O’Byrne will be responsible for the self-study essays unit that you will
take in Semester 1. He will be assisted by Dr Florence Abram and Dr Cindy Smith.
Dr Paul McCay will run a series of data evaluation and handling tutorials during
weeks 1 and 2 of Semester 1. These form part of your laboratory project work and will be
of value when it comes to preparing your project thesis and for the Problem-Solving
exam papers in Semester 2.
Dr Carol Gately will co-ordinate and run 2nd year Microbiology lab practicals.
Caroline O’Connell ([email protected]) is the departmental
secretary and all documents must be submitted to her and signed off in her presence.
Please note the deadline (including time!) for submissions well in advance. Please also
note that most/all assignments must be submitted as both hard and soft copies.
Students
The class will elect two class reps who will act as a channel of communication
between the class and the course coordinator. The class reps typically also liaise with
MicroSoc (http://nuigmicrosoc.com/; join up also at www.facebook.com/microsoc.nuig
for updates on what’s going on) with respect to class availability for Departmental events
and are involved in organising other class social activities.
Communication and Feedback
There is a final year Class Notice Board (between Dunican theatre and
Microbiology ground floor corridor) for official communications, job adverts, seminar
2
announcements, etc. Notifications about meetings, tutorials, exams, etc will also be
posted on Blackboard. It is your responsibility to ensure you have access to Blackboard
and that you can receive email notifications from it throughout the year.
Throughout the year, there will be occasional informal class meetings on Mondays
in the Dunican lecture theatre at 10:00. Dates of these meetings will be announced in
advance by email and on Blackboard.
In addition to formal contacts, you will have regular informal contacts with staff
members throughout Microbiology. Use these contacts to discuss issues with the course,
your interests in microbiology, etc. Remember you are now members of Microbiology.
All illness and/or unavoidable absences from any element of the course must be
communicated to the course coordinator as soon as possible. All relevant medical
certificates must be given to the Departmental secretary.
Deadlines
Throughout the year you will be given deadlines for the submission of various
pieces of work. This manual gives some of the deadlines for different elements of the
course. However, these may change as the year develops. Any changes to these
deadlines will be communicated via email and on Blackboard. The attitude of
Microbiology to deadlines can be summarised easily: All deadlines must be met. There
will be a mark penalty for failing to meet a deadline.
For a variety of reasons but most frequently because of illness, individuals may
wish to negotiate a modified deadline for a particular piece of work. In such cases they
must, before that deadline has arrived, discuss their situation with the coordinator.
If the class as a whole wishes to alter a deadline, the class representatives should
inform the course coordinator of the desire to change a deadline. A decision on this
change will be made by the coordinator, in consultation with other members of
Microbiology, as appropriate.
With respect to all deadlines the Department’s decision (communicated through the
course coordinator) is final.
3
4
4th Year Microbiology Summary 2013-14
Week by Week Timetable - Semester 1
Week Date
Main activity
MUST DO events
Introduction session (9th)
Projects presentation (9th)
2nd year demonstrating session (10th)
Data handling – session 1 (10th)
Submission of projects (11th)
Tour of Microbiology (12th)
Introduction to self study essay unit (12th)
Project allocation (13th)
“Safety” seminar (13th)
Contact project supervisor (13th)
Start project & self-study essay (16th)
Data handling – session 2 (16th)
Data handling – session 3 (17th)
Data handling – session 4 (18th)
Data handling – session 5 (19th)
Library training (23rd / 24th / 25th)
Self-study essay marking (25th)
“Scientific Writing” seminar (2nd)
“Oral presentation” seminar (9th)
Submit self study essay (14th)
“Plagiarism” seminar (16th)
1
Sept 9th
Introduction
Self-study essay training
Project allocation
Safety training
Plagiarism seminar
Department tour
2
Sept 16th
Self-study essay training
Data handling training
Project and essay writing
3
Sept 23rd
Project and essay writing
4
5
6
Sept 30th
Oct 7th
Oct 14th
Project and essay writing
Project and essay writing
Project and essay writing
7
8
9
10
11
12
13
14
15
Oct 21st
Oct 28th
Nov 4th
Nov 11th
Nov 18th
Nov 25th
Dec 2nd
Dec 9th
Dec 16th
Project and essay marking
Project and essay marking
Project
Project
Finish project work
Write thesis
Write thesis
Prepare project presentation
Make project presentation
5
Finish marking self-study essays (30th)
Project presentations (7th, 8th)
Stop project work (22nd)
Submit Project Thesis (6th)
Give project oral (16th-18th)
4th Year Microbiology Summary 2013-14
Week by Week Timetable - Semester 2
Week Begins
th
1
2
3
Jan 6
Jan 13th
Jan 20th
4
Jan 27th
5
6
7
8
9
10
11
12
13
14
15
Feb 3rd
Feb 10th
Feb 17th
Feb 24th
Mar 3rd
Mar 10th
Mar 17th
Mar 24th
Mar 31st
Apr 7th
Apr 14th
16
April 21st
17-19
20
21
April 28th, May
5th, May 12th
May 19th
May 26th
Main activity
Session 1 Modules
Session 1 Modules
Session 1 Modules
Paper 5
Session 1 Modules
Paper 5
Session 1 Modules
Session 1 Modules
Session 1 Modules
Session 2 Modules
Session 2 Modules
Session 2 Modules
Session 2 Modules
Session 2 Modules
Session 2 Modules
Study break
Study break & Exams
Easter holidays &
Exams
Exams
External examiner
6
MUST DO events
Paper 5 (Part I) (31st)
Paper 5 (Part II) (7th)
Exams April 15th-16th
Easter Hols begin April 17th
Exams re-start April 24th
Exams end May 14th
External examiner (provisional)
… Results Party
Summary of evaluations timetable, 2013-14
Section of
manual
Evaluation
element
Type of product
required
Deadline /
date
Credits
available
( / 60)
Project seminar
Oral presentation
Thu Nov 7th,
Fri Nov 8th
Project thesis
Individual document
(1 copy)
Print and electronic
Fri Dec 6th;
15:00
Day book and
supervisor’s
assessment
Hand-written document Fri Dec 13th;
15:00
Project oral
20 (+ 10) min oral
presentation
Dec 16th-18th
C
Self-study essay
Essay
Mark
Mon Oct 14th;
15:00
Thu Oct
31 st
D
Problem solving
paper
Two written
examinations
Fri Jan 31st
AND
Fri Feb 7th
5
April 15th –
May 14th
5 per module
(x6)
B
F
Lecture unit exams Essays, project or 2 h
examination per unit
7
20
5
8
Section A: Introduction
9
10
Introduction
Weeks 1 & 2
Day
Time
Subject
Place
Mon 9th
10:00
Welcome/Introduction to the year (FA)
Introduction to the year; step-by-step account of the
key events and dates; collection of e-mail addresses,
mobile numbers; photo session.
Dunican
12:00
Project list distribution (FA)
Distribution of project descriptions
Dunican
all day
Staff available to discuss projects
Staff offices, labs
10:00
2nd year demonstrating session (CG)
Attendance compulsory.
Dunican
15:0017:00
Introduction to data handling sessions (PMC)
Attendance at this session is essential.
Dunican
am
Staff available to discuss projects
Staff offices, labs
by 15:00
Submission of project choices
Deptl. Office
10:0011:30
Departmental tour (Technical Staff)
Tour of facilities, including communal equipment and
rooms. Attendance essential.
Meet in Dunican
14:0015:00
Introduction to self study essay marking (COB)
Attendance at this session is essential.
Dunican
10:00
Project allocation (FA)
Attendance at this session is essential.
Dunican
12:00
Safety Lecture (GF)
Safety, lab etiquette, equipment use and maintenance,
keeping day books. Students cannot start laboratory
work until they have completed the safety course.
Dunican
*
Meet with project supervisor
Staff offices
Tue 10th
Wed 11th
Thu 12th
Fri 13th
* By arrangement with supervisor.
11
Day
Time
Subject
Place
All week: carry out project work by arrangement with project supervisor.
In addition, the following sessions must be attended.
Mon 16th
10:0013:00
Data handling – session 2 (PMC)
Dunican
Tue 17th
10:0013:00
Data handling – session 3 (PMC)
Dunican
Wed 18th
10:0013:00
Data handling – session 4 (PMC)
Dunican
14:0017:00
Introduction to self study essay unit (COB)
Attendance at this session is essential.
2nd Micro lab
10:0012:00
Data handling – session 5 (PMC)
Dunican
Thu 19th
12
Semester 1 meeting / seminars / training
Date
Time
Meeting / seminar
Venue
Mondays (dates tba)
10:00
Class meetings (GW)
Dunican
Fri 13th Sept
12:00
Safety lecture (GF)
Dunican
Mon 23rd Sept
OR
Tue 24th Sept
OR
Wed 25th Sept
10-11:00
Safety, lab etiquette, equipment use and
maintenance, keeping day books.
Library training and database searching
Library
Wed 2nd Oct
10:00
Training sessions on how to search for, and
access, scientific information, in electronic
journals, etc. Essential for students to gain
competence in database searching for the
self-study essay and project. 3 sessions;
you will be allocated to 1.
On scientific writing (VOF)
Dunican
10:00
How to deal with the fear and terror that
having to write normally produces.
On oral presentation (CC)
Dunican
10:00
How to prepare and deliver an oral
presentation.
On avoiding plagiarism (GC)
Dunican
What plagiarism is and how to avoid it.
EndNote training
Library
Wed 9th Oct
Wed 16th Oct
Dates tbc
14-15:00
10-11:00
(groups)
Training sessions on how to use EndNote
(or EndNote Web) to build literature
databases and cite papers in your thesis, etc
13
14
Section B: Project Work
15
16
MI405: Project
Course Instance
Module CoOrdinator
Module
Title &
Description
Microbiology 4th year Dr Gerard Wall Project The Project is an 8‐10 week training period in molecular, cellular and process techniques relevant to environmental, biomedical and/or marine microbiology. Students work in groups, typically pairs, to investigate a research problem in the laboratory. Background literature and initial protocols are provided at the beginning of the work. Students develop and progress the initial project plan through formulation of original ideas and reading of relevant literature. Results interpretation and experimental troubleshooting are important for successful completion of the described project. Examination is through preparation of a ~25‐page thesis describing the project and presentation and defence of the project work in a 30‐min oral presentation upon completion of the lab work. “Dry” projects may also be offered. In this case, students will carry out a library‐ and web‐based project, typically involving identification and critical appraisal of key papers relevant to a specific question. Critical analysis of the literature will identify gaps in the scientific knowledge and a research proposal will be produced to address these. Appropriate objectives and hypotheses will be proposed, usually in the form of development of a research proposal. Examination is by thesis and oral presentation, as for lab‐based projects. Module
Code
ECTS
MI405 20 Assessment Sitting
st
1 Sitting
2
nd
Sitting
Semester/
Trimester
(Taught)
Module Type
Core 1 Is Module taught via
Blackboard: No
Assessment Type
Exam Session
Duration
Evaluation of labwork; Thesis; Oral presentation
Semester 1
Continuous; n/a; 30 mins
17
Others involved
in delivery of the
module
Drs Florence Abram, Thomas Barry, Aoife Boyd, Cyril Carroll, Gavin Collins, Gerard Fleming, Conor O’Byrne, Cindy Smith; Prof Vincent O’Flaherty, Prof. Jim O’Gara Over the Duration of the Module
Other forms of
Ongoing laboratory‐ or computer‐based work for 8‐10 weeks. educational
activity
Learning
Outcomes or
Competences
For laboratory projects, the student should be able to: 1. 2. 3. 4. 5. 6. demonstrate an understanding of and discuss the scientific literature related to the project. demonstrate good ability in lab techniques relevant to the research topic. design experiments and troubleshoot technical problems that arise. work in a team with project partners to plan and maximise the amount of work carried out. identify novel approaches to progress the project. discuss and critique published research papers in the field of the project. In the case of “dry” projects, the student should have: 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. Suggested
Reading (list)
studied in depth a topic in contemporary biology. used resources in the library, information databases and original literature. collected, organised, synthesised and critically reviewed a large body of information. written an extensive, structured report. presented aspects of the work in an oral presentation. identified a related area of research which needs further investigation. explained why this topic is worth investigating. outlined the experimental approaches appropriate to the investigation. showed an understanding of appropriate controls and statistical analyses. communicated and justified the concepts of the research project to a diverse range of target audiences. Staff members responsible for individual projects will provide relevant review and /or research papers at the beginning of the project. Protocols for practical techniques will also be provided where appropriate. Students will source other reading material from literature databases and the web throughout the project. 18
19
MI405: Project
The primary aim of the project is to provide students with some experience of
practical laboratory science. In the process, we hope that students will develop the very
important (and transferable) skills of teamwork, written and oral communication. The
emphasis will be on good experimental design rather than on exciting results. Nobel
prizes are rarely awarded on the basis of fourth year project work.
Projects are not evaluated on the basis of the results obtained but rather on the quality
of the work and the quality of its presentation. Thus “success” in getting the “right” result
is of no importance. A well-designed project with adequate controls that fails to meet its
goals is infinitely superior to a poorly controlled study that appears to be “successful”.
Project success is a matter of luck. Experimental design is a matter of skill.
The major elements of project work are:
B 1 Selection of project
A list of all projects on offer will be made available in Week 1. You must submit
your choice of projects (choose 1,2,3 in order of choice) to the Departmental office by the
deadline provided. Like all submissions throughout the year, you must hand your choices
to Caroline and sign the required page in her presence. Projects allocation will be based on
(i) submission of selection on time and (ii) performance in end of year 3rd year exams.
Students whose selected projects have already been filled will be offered a choice of the
remaining projects. Confirmation of allocated projects will occur at the end of Week 1. It is
essential that you attend this session. Projects will normally be carried out by students
working in pairs. Due to the allocation of projects according to performance in 3rd year,
you cannot choose your partner for the project.
B2
Project work
This section will involve the performance of an experimental or computer-based
project. This section will occupy you from September 16th through to November 22nd. As
there is considerable pressure on laboratory space, final year students carrying out
computer-based projects will not be allocated laboratory space. In addition, lab-based
students should not use laboratories for writing up work or for storing their personal
effects and must take care to work in a tidy and considerate manner.
Remember, postgraduates will be a valuable resource for you. Remember too they have
20
their own projects and it is very unwise to antagonise them by your behaviour in their lab.
B3
Day Books
Throughout your project you will be expected to keep a professional day-book of
you daily activities. Read Appendix 4 for a detailed description of what a day-book is and
how to keep one. A lecture to be given on Fri Sept 13th will also cover this topic.
Although you are working in teams, each student must keep an individual day-book
record of what they do themselves. Your day-book must be available for your project oral
and after that should be handed to your project supervisor.
B4
Project seminar
During the first half of your project you will be required to give a seminar on the
background to your work. This seminar is primarily a teaching element and it is included to
give you experience in oral presentation. While the seminar is not marked per se, students
who do not attend and present will lose 1% from their overall project mark. Further details
will be provided during the Semester.
B5
Project Thesis (see Appendix 1)
The project thesis must be accompanied by a declaration, signed by your project
supervisor, stating that you have left your laboratory space tidy and in a satisfactory state
of cleanliness. It must be submitted to the Departmental Secretary in printed form, and by
e-mail, by the deadline above (p.7). Note TIME of submission deadline also. A single
copy of printed theses should be submitted and these should include a title page. Each
student will be required to produce an individual project thesis.
Project supervisors are allowed to provide editorial guidance with the preparation
of the Materials and Methods and Results sections of your thesis. They will not provide
any input into any other sections of the thesis.
B6
Project orals
Each individual student will be required to present a 20 min (+ 5-10 min questions)
talk on his or her project to three staff members (not including project supervisor). These
talks should cover:
21
•
A brief background to the topic studied
•
The methods employed and the results obtained
•
The relationship of the results obtained to those obtained by other workers
•
A critical discussion of the overall project.
It is recommended that students take time and care to prepare the visual aids they
wish to use during their oral presentation. The quality of these will be assessed. A
seminar on oral presentations and the use of visual aids will be given in October.
Evaluation of Project
The project section will carry 20 ECTS credits of the total 60 credits awarded for
the overall 4th year programme. These marks will be compiled from a variety of sources
including supervisor’s assessment, Project Thesis and Project Orals. One third of the
marks awarded for the project will come from each of these areas. You should ensure that
you understand the requirements of project work, and the criteria used for evaluation of
laboratory performance, written and oral presentations. Read the instructions, attend the
tutorials provided for you and ask your supervisor if you are in any doubt.
Assistance Sessions
Tutorial sessions will be held to help you with the preparation of written reports and
oral presentations.
Data handling sessions: this series of 5 tutorials (see below) will focus on
developing data processing and data presentation skills (PMC).
Oral presentations: this session will cover how to give an oral presentation. Tips
and guidelines will be given (CC).
Writing: these sessions will cover how to write in science and the use of graphics,
tables and statistics in project reports (VOF). They will also explain what plagiarism is
and Microbiology’s policy on dealing with it (GC).
See p. 13 for further details of this seminar series.
22
Data Handling/Problem Solving Sessions
The aim of this series of tutorials is to give students experience in problem solving
and data handling, skills that are essential for any qualified microbiologist. There are two
sections within the series. The first of these sections will involve “data handling”.
Modern microbiology uses a variety of techniques that can produce vast arrays of raw
data. These data sets require processing, and importantly, simplifying, for publication,
and to make any sense of the experiments.
Within this module, all students will be presented with a scientific paper.
Accompanying this paper will be a spreadsheet of the raw data used to put the paper
together originally. Some of the data points in the paper will be blacked out. All students
will be, by the end of the sessions, expected to process the raw data in the same method
as that described in the paper (using Excel), and thus be able to fill in the missing data
points of the paper. There are a number of other problems to be solved along the way,
each of which are designed to aid students’ use of Excel, and some basic statistics.
These skills will aid all students in their final year project (either in Excel use, or
their ability to dissect a scientific publication) and in their preparation for the problemsolving exams papers to be carried out in Semester 2.
The paper that will be used in these sessions (“Possible application of noninhibitory concentrations as in vitro proxy indicators for the lower limit of the mutant
selection window”) is presented in Appendix 3. All students must read this document
carefully before the start of the first session in week 1. Likewise, students are expected
to read up on Area Under the Curve measurements. Further to this, there is an online
Excel
sheet
that
details
(https://www.dropbox.com/s/dmsf3reyr4dxo5l/AreaUnderCurve.xls).
AUC
Each
of
the
components will be explained thoroughly within the module. The sessions will strive to
be as inclusive as possible and therefore, will require feedback from the students, and a
discussion of the problems at hand. Students are urged to participate fully in class, and to
gain as much information from the sessions as possible.
A second section of the module deals with experimental design. Again, all students
will be presented with a data series produced as a part of an experiment. Students will be
expected to deduce, from the design of the experiment, what the initial aim of the
23
experiment was. Likewise, they will be expected to pick out potential flaws of the
experimental design, and to suggest alternative experimental designs. This will probably
be a new phenomenon to most students, and so you will be urged to participate as much
as possible in class.
Students will be expected to work on the problems given to them at each session
and to submit their work before the next session. The work submitted by the student will
inform the next session’s content and discussion. As such, students will be required to
submit their work on time. A record will be kept of all submissions and level of student
engagement throughout the series of tutorials. This information will be available to staff
for consideration at the Microbiology Exam Board meeting in May 2014.
24
25
Section C: Self-Study Essay
26
27
MI406: Self-Study Essay
Course Instance
Module CoOrdinator
Module
Title &
Description
Module
Code
ECTS
Microbiology 4th year Dr Conor O’Byrne Self‐Study Essay A critical skill for any professional scientist is the ability to write coherent, well structured, properly referenced scientific documents. Progress in science is driven by the dissemination of such written material and is also shaped by the critical peer evaluation that such documents receive (i.e, the process of peer review). The self‐study essay module aims at combining essay writing with peer evaluation to develop these key research skills. Students will research and write a 2500 word essay on a topic chosen from a selection of 20 essay titles provided. The essay topics span a whole range of different areas of microbiology. Students will be expected to consult the primary scientific literature and to cite this literature appropriately in their essays. The essays will be marked by peer evaluation. Each essay will be independently evaluated by 5 peers. Then this group of 5 will convene to agree a final overall mark for the essay. The essays will be evaluated on 5 categories: Clarity and readability; Structure and presentation; Depth and level of detail; Creativity and use of novel arguments; Bibliography and citations. In order to train students in the peer evaluation process the essay writing will be preceded by a sample marking exercise, where students get to access essays from a previous year. This process will mirror exactly the process that will be used for the real peer evaluation. MI406 5 Semester/
Trimester
(Taught)
28
Module Type
Core 1 Is Module taught via
Blackboard: Yes
Assessment Sitting
Assessment Type
Exam Session
Duration
1st Sitting
Departmental Assessment
Semester 2
n/a
Total no. of hours
of educational
activity
6 2
nd
Sitting
Others involved
in delivery of the
module
Dr Florence Abram, Dr Cindy Smith Over the Duration of the Module
No. of Lectures
1 No. of Tutorials
Other forms of
educational
activity
1 h Tutorial
Duration
2* 6 h * "Tutorials" consist of 2 3‐hour group marking sessions. The essay writing takes approximately 3 weeks and 2 weeks for essay marking. Lecture Duration
Learning
Outcomes or
Competences
(list)
The student should be able to: Suggested
Reading (list)
No set reading ‐ the self study essay requires the students to access literature relevant to the topic they choose to write about. (i) Access information from the primary scientific literature; (ii) Write a coherent scientific essay; (iii) Evaluate scientific essays; (iv) Cite the scientific literature correctly; (v) Understand the key elements of well written essay; (vi) Understand the concept of peer evaluation in science. 29
This part of the 4th year programme will be organised and run by Dr Conor
O’Byrne (Room 105B, ground floor Micro; email [email protected]) with the
assistance of a number of Microbiology staff.
Dates to note:
Thu 12th Sept, 14:00-15:00: Introduction to self-study essay unit; Dunican
Wed 25th Sept, 14:00-17:00: Introduction to self-study essay marking; 2nd Micro lab
Mon 14th Oct, deadline 15:00: Submit self-study essay; Microbiology office
Wed 30th Oct, 14:00-17:00: Mark and submit self-study essay mark; 2nd Micro lab
All further information on the self-study essay, format, marking, revision of
submission dates if necessary, etc will be provided by Conor at the sessions detailed
above.
30
31
Section D: Experimental Design and Analysis /
Problem Solving Paper (“Paper 5”)
32
33
MI413: Problem Solving Papers I & II
Microbiology 4th year Dr Gerard Wall Course Instance
Module CoOrdinator
Module
Title &
Description
Module
Code
ECTS
Problem Solving Papers I & II The ability to read, understand, distil and process data and information from scientific papers and other sources is an essential skill for any professional scientist. In this module, students will receive training in mathematical calculations; reading and summarising scientific papers; and interpreting and critiquing scientific data and results. The module is broadly divided into 3 parts: (i)
Mathematical calculations (ii)
Reading and summarising papers (iii) Evaluation and interpretation of experimental data. The module will be largely run on a self‐directed learning basis. Students will have access to past exam papers and will be encouraged to attempt questions from these. Tutorials, both formal class‐based and informal, small‐group meetings, will be held to solve sample problems from past papers as guidance in how to answer questions. MI413 5 Semester/
Trimester
(Taught)
Module Type
Core 1 Is Module taught via
Blackboard: No
Assessment Sitting
Assessment Type
Exam Session
Duration
1st Sitting
Written examinations
Semester 2
2x 3‐h exams (in‐house)
Others involved
in delivery of the
module
Total no. of hours
Various Microbiology staff of educational
activity
Over the Duration of the Module
34
6 No. of Lectures
No. of Tutorials
0 4‐6 Lecture Duration
Tutorial Duration
1 h Learning
Outcomes or
Competences
(list)
Upon completion of the module, the student should be able to: Suggested
Reading (list)
No set reading – the self‐directed learning process begins with past exams papers from the module. (i) Complete basic mathematical calculations based on laboratory problems; (ii) Understand, summarise and write an appropriate title of anonymised research papers; (iii) Evaluate and understand experimental data from (micro)biologically relevant studies; (iv) Critically assess experimental data and results and express opinions on those results. 35
Experimental Design and Analysis /
Problem Solving Paper (“Paper 5”)
Towards the beginning of second semester (Fri Jan 31st and Fri Feb 7th) students
will sit the Problem Solving Paper of their final examination. This paper carries 5 ECTS
credits of the final year 60 ECTS total. The paper is in two parts, with six questions in
total. All questions are compulsory but the lowest mark obtained is discarded before the
final mark is assessed.
Part A consists of two questions. One question involves the writing of a summary
of a published scientific paper. This paper will be on a topic that has not necessarily been
covered in any lecture course. The second question involves mathematical calculations
relevant to practical microbiology. This second question is essentially an expanded
version of the mathematical question in the 3rd science practical examination.
The aim of Part 2 is to test the student’s ability to handle experimental data. Each of
the 4 questions will present experimental data and the student will be asked to make
observations concerning the experiments involved and the meaning of the data.
The topics investigated in these experiments may not have been covered in any
lecture course. However, the questions are set with the intention that theoretical
knowledge of the subject matter of the experiments is not essential.
Tutorial sessions on how to approach and solve Paper 5 questions will be given at
the beginning of Semester 2. Dates will be posted on Blackboard and communicated by
email.
It is advisable to attempt to answer questions from previous years’ exam papers –
mathematical and data manipulation – before attending tutorials in order to benefit as
much as possible from the tutorial and to be able to avail of the opportunity to ask
questions. Past exam papers will be available on Blackboard.
36
37
Section E:
Demonstration of 2nd year Microbiology labs
38
39
Demonstration of 2nd year Microbiology labs
The ability to communicate laboratory skills and techniques is an essential part of
being a scientist. It is also a skill employers will expect you to have. During your project
you will benefit (hopefully) from the ability of the postgrads in your lab to communicate
lab skills to you. Attendance at all allocated practical sessions is compulsory.
Microbiology will take into account your attendance record for these practicals in
their end-of-year grading meeting.
To help you develop an understanding of what is involved in communicating
laboratory skills you will be appointed to demonstrate to Second year practical classes.
Each student will be appointed to a group of second years (6 groups: Mon, Tue, Wed in
Semester 1 or 2) and will be responsible, under Dr Carol Gately’s direction, for
demonstrating to them for an academic semester. Demonstrating will give you an
experience of taking part in a group activity and exploring how well you can fulfil a
commitment to those junior to you. These are important professional skills.
At the end of each semester the Second years will be asked to provide a formal
feedback on the quality of the help they received from you. The results of this feedback
will be communicated to the class and to the academic staff. The results of this feedback
will not be used in constructing your final mark for the year. The feedback is not,
therefore, an evaluation. Staff members are free, however, to use the results of the
feedback to inform any references they might write for you.
To prepare you for this Section a session on “Demonstrating to Second Years” will
be provided on Tue Sept 10th at 10:00 (Dunican). The lists of students assigned to
particular days and times will not be given out at this session but will be mailed after
project allocation has been completed. Attendance at this session is compulsory.
2nd Micro practical times and dates:
Semester 1: Monday 30th September – Wednesday 20th November
Semester 2: Monday 13th January – Wednesday 5th March
Lab times:
Mondays 14:00-17:00; Tuesdays 10:00-13:00; Wednesdays 13:00-16:00
40
41
Section F: Lecture Modules
42
43
Introduction
Appendix 6 of this manual consists of a Module Booklet. This booklet contains a
short description of all Modules on offer in 2013-14. Unlike in previous years, there is no
need to choose lecture Modules in 2013-14 – you will attend all 6 Modules on offer under
the new “Simplified” system.
Modules are divided into two Sections (see timetable below) of 3 Modules each.
Please note that formal registration for Modules with the Examinations Office, as
with all M401 components, is the responsibility of each student. Register carefully
with the University in order to avoid difficulties with Examinations Office at exam time.
The timetable of lecture Units for 2013-14 is as follows:
Teaching Session 1 (Jan 6th – Feb 21st)
Code
Module Name
Dynamics of microbial gene regulation
The Meaning of Life: Bioinformatics
Marine Microbial Ecology and Nutrient Cycling
Teaching Session 2 (Feb 24th – April 4th)
Bacterial Pathogenesis
Bioprocessors and recombinant protein production
Anaerobic Biotech & Systems Biology
44
45
Section G: Appendices
46
47
Appendix 1
Written Documents
48
49
Written Documents
Layout and style
All documents must be produced in the style specified in Microbiology’s
Instructions to Authors presented in Appendix 2.
All documents should be submitted both as printed and electronic documents.
Printed documents should be in Times 12pt font with 1.5 line spacing with a page
number at the bottom of each page.
All electronic versions should be Word documents (save as .doc) and sent by e-mail
to [email protected].
All written material should have a cover page, printed on normal (white) paper that
must include:
The project or essay title,
The student name(s),
The student’s examination number,
Where relevant the supervisor’s name should also be on the title page,
The University logo on the cover page.
Plagiarism and authenticity declarations
Your project thesis must include a declaration that the student has read, accepted
and has complied with the plagiarism policy of the Department (Appendix 5). A
suggested wording is;
“I have read, understood and have accepted the plagiarism policy of the Department. To
the best of my ability, I have complied with its requirements. Signed; A. Student”
All essays must also include a declaration that the work submitted for examination
is the unaided work of the student who submits it.
Project Theses must also contain a declaration, signed by the supervisor stating that
the laboratory has been left in a suitable condition and a specific authenticity declaration
(see below).
50
Submission
All written documents (except Day Books) must be submitted to the departmental
secretary in printed and in electronic form.
Printed versions must be handed to the Departmental secretary in her office.
Students are responsible for ‘signing-in’ each piece of work when they submit it.
The electronic versions should be sent by e-mail as Word documents (.doc) to
[email protected].
Binding
With respect to Project Theses (2 copies), hard copies must be submitted to the
Departmental secretary unbound.
Essays can be bound but should, as a minimum, be held together in some sort of
folder.
Help with written documents
There are three written sources that have been designed by the Department to help
you write your documents in away that will appeal to examiners.
1. The Microbiology Instructions to Authors in Appendix 2 of this manual.
The instructions in this appendix are MANDATORY. You must follow them;
failure to do so will impact severely on your essay or project thesis mark. Spelling, syntax
and the use of standard scientific language and style will also be evaluated in the
assessment of all written documents. There are a variety of books in the library on how to
write in English. These are valuable resources and consulting them is a good habit to get
into.
2. The Departmental Policy on Plagiarism in Appendix 4 of this manual.
This is a VITALLY IMPORTANT document. You must read it and you must
understand what it is saying. Plagiarism is taken very seriously by the University. If you
fail to follow the instructions laid out in this Appendix it is entirely possible that you will
receive NO MARKS at all.
51
If you are in any doubt about plagiarism you should consult the departmental
plagiarism adviser, Dr Gavin Collins.
3. Writing in Science; a guide to the perplexed.
This is also available on the Microbiology Web site and aims to help you with the
psychological problems you will encounter in writing.
You are strongly advised to consult this booklet before you start writing
anything.
There will also be two seminars that will help you prepare written documents
“On Avoiding Plagiarism”
“On Scientific Writing”
and training in the use of EndNote for building and managing bibliographies (see dates
and details of these seminars and training sessions on p.13).
52
1. PROJECT THESIS
THE PROJECT THESIS IS AN INDIVIDUAL ACTIVITY.
Each student will prepare a final thesis containing the following sections and
formatted appropriately.
Cover page
Authenticity declaration
Plagiarism declaration
Abstract
Introduction
Materials and Methods
Results
Discussion
Bibliography.
Authenticity declaration
The thesis should be an authentic document. It should, therefore, include a signed
statement by its authors confirming that they are the sole authors of the work and that the
report is an accurate representation of the work they performed. This statement should be
signed by each student in the project group. A suggested wording for this declaration is as
follows:
“This project thesis is an accurate and faithful representation of the work performed by
us between (date) and (date). The authorship of any data included in this report, which
was not generated by our own work, is clearly indicated”.
Printed name, Signature, date.
Lab clearance declaration
No thesis will be accepted unless it contains a declaration that the student has left
the laboratory in a clean, tidy and satisfactory state. This declaration must be signed by
the project supervisor.
53
Critical review is an essential part of the scientific process. In its scientific sense
‘critical’ is not limited to faultfinding. Critical is used to describe “a skilful judgment as
to truth, merit etc.” (Random House Dictionary). Thus a critical review involves an
assessment of the validity of experimental methods employed, a discussion of the
suitability of experimental designs and an evaluation of the extent to which conclusions
may be drawn from the available data. Critical review may suggest faults in these
processes and indicate the limited validity of conclusions but it may equally well find
merit and confer praise.
Project Thesis
(i)
Laboratory-based projects
The Project Thesis for laboratory-based projects should include: Introduction;
Materials and Methods; Results; Discussion (which together must make up no more than
25 A4 pages), a ½-page Abstract, and a Bibliography.
The Abstract should provide a short (½ page) description of the work performed
and the major results obtained. It should not be divided into sections and should not
contain abbreviations. Read abstracts from scientific journals in your research field to
become familiar with their typical setup, content and wording.
The Introduction should address the background to the work performed by critical
reference to the published literature. These published sources may include in-lab reports
and previous theses and/or project reports produced in the lab provided they exist in
written form. Anecdotal information from research personnel in the laboratories (or other
sources) may also be included as personal communications. A statement of the project
aims should be included at the end of the introduction section.
The aim of the Materials and Methods section is to provide sufficient details of
the materials and methods used that another scientist could exactly replicate the work.
The scientist should be able to do this by reference to the materials and methods section
and to the cited references it contains. Suppliers of chemicals or reagents used, for
54
example, should be identified. Manufacturers and the model nos. of any equipment used
should also be provided. Any protocols used to check the performance of reagents or
equipment should be mentioned in this section. If standard methods, or methods that have
been adequately described in the published literature, are used, they can be referenced
and need not be described in detail.
The Results section should provide a clear written description of the results
obtained. This should make the details of the work performed comprehensible to another
scientist who has no previous experience of the specific field (i.e. avoid lab jargon and
non-standard abbreviations). This section should primarily be a written text, but tabular
and graphical presentations of data can be used when relevant. Although this section is
primarily aimed at presenting results it is acceptable to include some discussion of these
results if it serves to explain why subsequent experiments were performed.
Note:
In the results section graphical or tabular presentation of data with minimal
accompanying text or no text at all is NOT acceptable.
Note 2:
There is no requirement for you to present the results of all the experiments you
performed. Some of your experiments may have been disasters or may have been invalid
for some technical reason.
If, however, you do decide to present the results generated in a particular
experiment it is totally unacceptable to omit, falsify or invent any data obtained in that
experiment. This will be treated as CHEATING and will be severely punished.
If, in an experiment you have chosen to present, you obtained an odd or really
weird data point, you must include it in your thesis even if it is obviously absurd or the
result of a mistake. The only exceptions to this rule are;
i) When you apply a specified statistical test to eliminate ‘outliers’. In this case you
must specify both the statistical test you used and where you used it.
ii) Where you possess evidence, obtained prior to your reading the results, that you
55
had suspected that there was something wrong with your performance of an experimental
protocol. Such evidence is only legitimate if it was recorded in your Day Book at the time
the error was made. It is not legitimate if the entry was made only after the results have
been obtained.
Note 3:
As a general rule the thesis should not include any data that were generated by
people other than those signing the document. If it is considered essential that such data
be included, then the authors of the report must make it totally clear who was
responsible for performing the experiments or calculations involved.
The Discussion should cover three main areas:
It should critically discuss the results presented in the thesis.
It should compare the data generated during the project with other data available.
It should propose future actions and experiments that are indicated by the data
generated during the project. These may include improvements in experimental design or
the use of alternative approaches to the topic being studied.
Project Thesis
(i)
Computer-based projects
The overall Aim of evidence-based literature review and research proposal-based
final year projects is similar to that of lab bench-based projects: to help students become
effective independent learners, using a research-led and enquiry-based approach. Also, it
aims to enhance students’ written and verbal communication skills.
This form of “dry” final year project will focus on a topic in contemporary biology
or microbiology, under the supervision of a member of staff. It will provide experience in
the use of information databases to access literature in the library and on-line. The
student’s task will focus on the identification and critical appraisal of key papers relevant
to the identified question. Critical analysis of the key papers will identify gaps in the
scientific knowledge and a research proposal will be produced to address these.
56
Appropriate objectives and hypotheses will be proposed, and an achievable programme
of work, using appropriate experimental methods developed.
Format of thesis:
Technical Abstract: (not to exceed 250 words)
This could include the aims and context, including the objectives of the work and the
main methods to be adopted. It should be written in a way that enables the reader to
understand the scope and main conclusions of the work without having read the rest of
the script. It should be clear how the proposed work will move the field forward.
Keywords:
Up to 6 keywords to cover the scope of the project.
Lay Abstract: (not to exceed 250 words)
A description of the work that could be understood by a scientifically-competent nonspecialist – somebody with Leaving Cert Biology.
Introduction: (not to exceed 2,000 words)
This section should include:
•
An introduction to the research question
•
Why is this problem significant?
•
Review of the relevant literature (include controversies, unresolved questions,
recent developments and different viewpoints)
•
Description and critical evaluation of five key papers you have identified (e.g.
why you think they are important, approach used, their key findings, significance
of their results, shortcomings you may have noted).
Aims and Hypothesis:
•
What is the overarching aim of the study?
•
What hypothesis(es) do you want to test?
•
Objectives of the study (e.g. at the end of this study we will have…).
57
Methodologies:
List the appropriate methods, techniques and scientific instruments you will use to
address the hypothesis(es). Outline in detail the next logical experiment(s) to advance the
specified scientific field, both short- (up to 3 months) and medium-term (up to 3 years).
Provide details of experimental controls and appropriate statistical analyses you would
use to interpret your (expected) results. Be clear how the information and data you expect
to generate will help you to answer your initial experimental objectives. Where
appropriate, justify your approach by including relevant references to similar pieces of
work that have employed your methodologies. Include a Gantt chart to indicate major
milestones and key deliverables of the proposed work over a three year period.
Strategic Relevance and Impact (not to exceed 250 words)
It is increasingly important to justify spending on research to the public and to funding
bodies. This section should outline the expected impact of your study on end users (e.g.
in agriculture, medicine, conservation bodies, governments, industry, etc), on scientific
excellence, on the development of Irish industry and economy, or on prosperity and/or
quality of life of Ireland’s citizens.
Note on citing published literature:
In scientific writing the source of all factual statements must be provided. In a
Project Thesis factual statements may derive either from your own work or from
literature you have read. If the source is your own work then reference should be made to
the specific Table or Figure in your Thesis. If the source is the published literature then
reference to that source should be made in the manner outlined in instruction to authors in
Appendix 2.
Note on critical analysis:
Particularly at the level of a final year project, finding fault with one’s approach or
58
one’s experimental design is not a sign of weakness. In contrast, an over grandiose
interpretation of one’s own work, an inflation of its importance, is a sign of serious lack
of judgment. A balanced evaluation, based on rational arguments, is the approach that
will gain the highest marks. Read "Writing in Science; a guide for the perplexed" for
further information on what the examiner will be looking for in your review.
One hard copy (unbound) and an electronic version of the final thesis should be
submitted to the Departmental Secretary.
The absolute deadline for submission is provided above (p.7).
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60
Appendix 2
Microbiology Instructions to Authors
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62
Microbiology Instructions to Authors
This document provides information on the editorial style required by the
Department. You must follow these instructions and will be evaluated on your ability to
do so. For examples of these guidelines being applied in papers and reviews, consult a
recent issue of the Society for General Microbiology journal “Microbiology”.
1. GENERAL
All written documents must, unless specifically stated, be submitted in both printed
and in electronic form. Spelling, syntax and the use of appropriate scientific language and
style will be evaluated in the assessment of all written documents. All documents should
be printed in Times 12pt font with 1.5 line spacing. All pages should be numbered. Page
numbers should appear on the bottom of each page.
2. SECTIONS
Sections and sub-sections within documents should be clearly numbered and titled,
e.g. 1. INTRODUCTION
1.1 Anaerobic microbiology
1.2 Methanogens
1.2.1 Methane from acetate
etc.
3. ABBREVIATIONS
With the exception of standard systeme internationale (SI) units, all names that you
wish to abbreviate must be written in full (followed by the abbreviation in brackets) the
first time you use them. All subsequent mentions can be the abbreviation. Abbreviation
symbols should not be followed by a full stop unless they occur at the end of a sentence.
There are similar rules for abbreviation bacterial names, which are always written
in italics. The first mention should be in full (e.g. Escherichia coli). In all subsequent
cases the generic name can be abbreviated to a single letter (E. coli).
3.1 Compound units
These should be written as g 1-1 not g/l and 10 g ampicillin 1-1 not 10 g 1-1
ampicillin.
In any compound unit at least one of the unit should be the base SI unit, e.g. mg 1-1
63
not µg ml-l.(the litre is the base SI unit of volume)
Always introduce a space between number and unit, e.g. 10,000 g not 10,000g. The
exception to this rule is the symbol % for percentage that may be placed immediately
after the number.
3.2 Concentration
Given in g l-1, etc., or molarity, M, not normality, N. The term ‘%’ should be
defined as ‘w/v’, ‘w/w’ or ‘v/v’ if this is necessary to avoid ambiguity.
3.4 Figures
Refer to in text as Fig. 1(a) not FIG 1A, Figure 1(A), etc.; or as (Fig. 1a) not
(Figure 1A). Multipart figures should be labeled (a), (b), etc., not A, (A), or B, (B).
3.5 Genes, genotypes and phenotypes
Always use italics for gene names: gyrA not gyrA or gyr A; also use hyphens: arg1 not arg1 or arg I, etc.
Abbreviations of phenotypes are not italicised but the first letter is capitalized, e.g.
Gal not gal or gal
3.6 Molecular mass
Given in Da, e.g. 31500 Da or 31.5 kDa. In table headings and figure axes, for
values >1000 use kDa or 10-3 x Mr.
3.7 Pressure
Given in Pa or kPa (I p.s.i. = 6.9 kPa).
3.8 Radioactivity
Given in Ci (I Ci = 3.7 x 1010 Bq).
3.9 Restriction enzymes
Eco RI not EcoRI, etc.; Hin dIII not HindIII, HindIII, HindIII, etc.
3.10 Spectrophotometry
Absorbance, A, absorption of monochromatic light; for clear solutions or for
absorbing molecules in turbid suspensions.
Optical density, OD, for non-monochromatic light or for turbid suspensions.
64
In either case (A or OD) wavelength and instrument must be stated.
3.11 Suppliers
Give the name of the company without Ltd., Co., Corp., etc.; no address.
4. REFERENCES (according to the style of the journal Microbiology)
The most common fault in final year written documents is that referencing
guidelines are not followed correctly. Read this section and apply the guidelines in your
documents – don’t lose silly marks!!
4.1 In-text citation.
For citing a reference in the text, the surname(s) of the authors (no initial or first
names) and the year of publication should be inserted in the text. There are two ways of
doing this.
“The instructions on how to write an essay (Smith, 2008) were easy to
understand.”
“The instructions on how to write an essay that were provided by Smith (2008),
were easy to understand.”
When a cited paper had two authors use; ‘&’ not ‘and’. For example use Smith &
Wall (2006) not Smith and Wall (2006).
When the cited paper had three or more authors use italic ‘et al.’. For example, use
Smith et al. (2005) or (Smith et al., 2005).
If you are citing two papers by the same author(s) that were published in the same
year, these should be differentiated by placing either ‘a’ or ‘b’ after the year. For example
“Both Wall (2008a) and Wall (2008b) argued that this gene was essential for virulence.”
4.1.2 Example of in text citation
According to Smith & Wall (2007), issuing appropriate instructions should make it
impossible for a final year student to produce an imperfectly referenced essay or thesis.
However, previous studies (Moran & O’Flaherty, 2001; O’Byrne et al., 2003; Carroll,
2004) have demonstrated a remarkable reluctance on the part of students to read such
65
instructions. Barry et al. (2005) have reported a statistically significant correlation
between the failure of students to read the instructions and incidences of elevated blood
pressure in examiners. Smith (2008) is about to embark, once again, on an ambitious
quest to correct this sad state of affairs by appealing to students to follow the
instructions. The only reason for hoping that this attempt will have a higher success rate
is that, this year, examiners have been instructed to penalise those who persist in
ignoring the advice given to them (V. O’Flaherty, pers. comm.).
4.2 Bibliography
The bibliography must contain a full reference to all of the papers cited in the text.
In the bibliography these references should be presented in the alphabetical order of the
first author. If you are providing references to more than one paper with same first author,
those where he/she is the sole author come first and are arranged in chronological order.
The rest of the papers are then organised alphabetically by considering the name of the
second author.
In preparing the bibliography, the position of all spaces, commas, italics and
bold print in the following examples must be followed. Failure to prepare
bibliographies consistently and according to provides guidelines can result in
manuscripts being rejected or returned without review from scientific journals. Failure to
do so in your thesis will lead to a marks penalty.
4.2.1 How to reference a journal paper:
Cerde-Cuellar, M., Rossello-Mora, R. A., Lalucat, J., Jofre, J. & Blanch, A. (1997).
Vibrio scophthalmi sp. nov., a new species from turbot (Scophthalmus maximus). Int J
Syst Bacteriol 47, 58-61.
Pasta, F. & Sicard, M. A. (1996). Exclusion of long heterologous insertions and
deletions from the pairing synapsis in pneumococcal transformation. Microbiology 142,
695-705.
4.2.2 How to reference a whole book:
Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory
66
Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
4.2.3 How to reference a book chapter or section:
Romano, A. H. & Saier, M. H. (1992). Evolution of the bacterial phosphoenolpyruvate
sugar phosphotransferase system. In The Evolution of Metabolic Function, pp. 171-204.
Edited by R.P. Mortlock. Boca Raton, FL: CRC Press.
4.2.4 How to reference a Ph.D. Thesis:
Jones, J. L. (1997). Anaerobic Digestion of Sulphate-Containing Wastewaters. Ph.D.
Thesis. National University of Ireland, Galway.
4.2.5 How to reference a Web site:
Microbiologist, J. K. (1999) (10 October 1999). DNA Sequences [On-line]
http://www.nuigalway/micro/eusus. [20 November 1999].
The first date refers to the date the site was last amended; the second to the last date you
accessed it.
5. FIGURES
These must be selected to illustrate specific points and be clearly referenced in the
text. Figures should be numbered and should be given a short title printed in bold type.
Any additional information that is required should be presented in a footnote or in the
legend. Clearly define symbols used in the figure legend. Use symbols coherently in a
related set of figures, e.g. for two graphs of glucose utilisation versus time, the same
symbol should be used for glucose. If there is a possibility that the graphs will be visually
compared, similar axes should be used. If it is not possible to use similar axes, this should
be pointed out in the figure legend. Graphs may be printed only in black and white or
greyscale.
6. TABLES
These must also be clearly referenced in the text. Tables should be numbered and
should be given a short, self-explanatory title printed in bold type. Any additional
information that is required should be presented in a footnote. They should be broadly
comprehensible without reference to the text, but should not include detailed descriptions
of methods.
The use of abbreviated column headings, (for example etc.) should be avoided
where possible, but if used these must be clearly defined in footnotes.
67
The symbols * ‡ : Ψ: § should be used for footnotes rather than superscript letters
and numbers.
7. STATISTICS
The symbol p for probability is always italicised. It should always be associated
with the name of the statistical test employed. The words 'significant', 'significantly' and
'insignificant' must only be used in their statistical sense in scientific writing.
68
Appendix 3
Data handling tutorial series
69
70
Data handling tutorial series
Paper for discussion:
Possible application of non-inhibitory concentrations as in vitro proxy indicators for
the lower limit of the mutant selection window.
Mc Cay, P.*, Fleming, GTA., Smith, P.
Department of Microbiology, National University of Ireland Galway, Ireland
* Corresponding author: [email protected]
71
Abstract
Any concentration of an antibacterial agent capable of retarding the growth of
fully sensitive bacteria will exert a selective pressure for the enrichment of variants with
an increased resistance to that agent. This work reports determinations of the highest
concentration of cefotaxime, ciprofloxacin, gentamicin , levofloxacin, polymyxin B,
rifampicin and tetracycline that did not exert any negative impact on the growth of
Escherichia coli ATCC 25922 in in vitro batch culture. These values, the non-inhibitory
concentrations, were compared to the minimum inhibitory concentrations required to
prevent growth under the same conditions. For polymyxin B the values of these two
parameters were similar. However, for ciprofloxacin, tetracycline and gentamicin, the
non-inhibitory concentrations were approximately xx fold lower than the corresponding
minimum inhibitory concentrations and for cefotaxime they were xx fold lower. These
data suggest that, for some agents, concentrations well below the minimum inhibitory
concentration could exert a selective pressure for the emergence of resistant variants. It is
argued that these observations have implications for our attempts to model the conditions
that result in the selection of resistant variants both inside and outside the host.
72
Sir,
Traditionally, two parameters have been used to characterise the in vitro activity
of antibacterial agents; the minimum bactericidal concentration (MBC), the concentration
needed to kill, and the minimum inhibitory concentration (MIC), the concentration
needed to prevent growth. A third, potentially useful parameter, the non-inhibitory
concentration (NIC), has been defined as the highest concentration that does not exert any
negative effect on the growth of the bacterium1. Theoretical considerations and limited
experimental data2 suggest that any concentration that retards the growth of wild-type
(WT) strains3 would exert a selection pressure favouring the emergence of non-wild-type
(NWT) variants. For this reason, we investigated the relationship between MIC and NIC
for seven antimicrobial agents against Escherichia coli ATCC 25922, a control strain
recommended in the Clinical and Laboratory Standards Institute standard M7-A84.
The media, inoculum preparation and incubation conditions used were those
specified in the micro-dilution protocol of M7-A84 with the modification that five
overlapping two-fold dilution series of the antimicrobial agents were employed1. Optical
densities (OD595) were measured at 15 min intervals in a Genios 96 well plate reader
(Tecan Trading AG, Switzerland) and plotted against time. Prism 5 software (GrahPad,
Inc) was used to calculate the area under the curve (AUC) of these plots and to perform
modified Gompertz model fitting. The seven antimicrobial agents (cefotaxime,
ciprofloxacin, gentamicin , levofloxacin, polymyxin B, rifampicin and tetracycline) were
all obtained from Sigma (Steinheim, Germany). MIC and NIC values were calculated in
three independent assays.
In batch culture, antibacterial agents may increase the lag phase, slow growth
during the logarithmic phase and/or reduce the terminal OD of the culture. Lambert &
Pearson1 suggested that the AUC of a plot of OD against time represented a measure that
could integrate all of these effects. They measured the AUC for various concentrations of
the agent (AUCc) and calculated the values of AUCc/AUC0, where AUC0 was the AUC
obtained in the absence of the agent and used modified Gompertz model fitting to
determine MIC and NIC values. We compared the MIC and NIC values obtained using
this approach with those estimated from a visual examination of the plots of AUCc/AUC0
against log concentration. For some agents, particularly those where the MIC and NIC
73
values were close, Gompertz analysis and visual examination generated similar estimates
of these parameters. For other agents, however, the plot of AUCc/AUC0 against log
concentration, over the range of concentrations from NIC to MIC, was complex. In these
cases, Gompertz analysis resulted in higher MIC and NIC values than were suggested by
visual examination. Therefore, in this work, NIC values for all agents were estimated by
determining the highest concentration of the agent that resulted in an AUCc within two
standard deviations of the mean of AUC0 (n = 5). The MIC values were calculated
according to M7-A84. Table 1 presents the mean and range (n = 3) of MIC/NIC ratios
calculated for the seven agents investigated. These showed a wide variation ranging from
xx for polymyxin B to xx for cefotaxime.
The mutant selection window (MSW) model5 represents an attempt to quantify
the conditions under which a selective pressure for the emergence of NWT variants
would occur in vivo. Drlica suggested that a variant of the standard MIC would represent
an acceptable in vitro proxy measurement of the lower boundary of the window5.
However, it is reasonable to presume that agent concentrations > NIC and < MIC,
determined for wild type (WT) strains3, would exert a selection pressure for the
emergence of NWT variants. If this assumption were to be experimentally validated, it
would suggest that the NIC rather than the MIC would provide the most appropriate
proxy indicator for the lower boundary of the MSW. The limited observations presented
here, if expanded and confirmed, would suggest that the use of NIC values rather than
MIC values would result in increases, in some cases large increases, in the size of the
window.
Practical applications of the MSW model are based on the assumption that
selection for the emergence of NWT variants can be minimised by designing dosage
regimen that result in in vivo concentrations that are greater than its upper limit5. Thus, it
could be argued that reducing the lower boundary of the MSW might have little impact
on the design of therapeutic dosage regimen. The major value of using NIC values to
estimate the lower limit of the MSW might, therefore, relate to an improvement of our
understanding of selection for resistance that occurs outside the treated host where it is
reasonable to expect that concentrations < MIC will occur more frequently6.
74
Funding
The work reported here was funded entirely from the internal resources of the
Department of Microbiology, NUI Galway.
Transparency
None of the authors have received any financial support from any company or
institution that might have an interest in the work presented and none of them have any
financial interests in any such companies or institutions.
References
1. Lambert RJW, Pearson J. Susceptibility testing: accurate and reproducible minimum
inhibitory concentration (MIC) and non-inhibitory concentration (NIC) values. J Appl
Microbiol 2001;188: 784-790.
2. O'Reilly A, Smith P. Development of methods for predicting the minimum
concentrations of oxytetracycline capable of exerting a selection for resistance to this
agent. Aquaculture 1999; 180: 1-11.
3. European Committee on Antimicrobial Susceptibility Testing (EUCAST). Clinical
Breakpoints and Epidemiological Cut-off Values: Definitions of Clinical Breakpoints
and Epidemiological Cut-off Values.
http://www.srga.org/eucastwt/eucastdefinitions.htm (5 February 2009, date last
accessed).
4. Clinical and Laboratory Standards Institute. Methods for dilution antimicrobial
susceptibility tests for bacteria that grow aerobically-Eighth Edition: Approved
standard M7-A8. CLSI, Wayne, PA. USA, 2009.
5. Drlica K. The mutant selection window and antimicrobial resistance. J Antimicrob
Chemother 2003; 52: 11-17.
6. Kümmerer K. Resistance in the environment. J Antimicrob Chemother 2004; 54: 311320
75
Table 1. Ratio of minimum inhibitory concentrations (MIC) to non-inhibitory
concentrations (NIC) for seven agents against Escherichia coli ATCC 25922.
Agent
MIC*/NIC ratios (n = 3)
Range
Mean
polymyxin B
Xx - xx
Xx - xx
levofloxacin
Xx - xx
Xx - xx
rifampicin
Xx - xx
Xx - xx
ciprofloxacin
Xx - xx
Xx - xx
tetracycline
Xx - xx
Xx - xx
gentamicin
Xx - xx
Xx - xx
cefotaxime
Xx - xx
Xx - xx
* All MIC values for all agents were within the acceptable range specified in M7-A84.
76
Appendix 4
What Is A Day-Book
77
78
What Is A Day-Book
Get the daybook habit.
It is part of becoming a professional scientist.
Your memory is not 100% reliable.
If the details of an experiment are not recorded in your day-book,
the experiment does not exist.
In industrial research accurate record keeping of all scientific activities in a
laboratory is an essential component of the requirement of such regulatory agencies such
as the FDA or ISO-9000. It is also absolutely required for compliance to GLP (good
laboratory practice) and GMP (good manufacturing practice). Similar standards are
required in medical and forensic science.
In research laboratories there are no stringent regulations, laid down by external
agencies, as to how scientific activity should be recorded. A record is, however,
necessary. An accurate record is extremely helpful to the scientists themselves and is
essential in situations of conflict such as allegations of fraud, dishonesty or
incompetence.
The keeping of a DAY-BOOK is the suggested method for record keeping in
academic research laboratories and the requirements for such a day book are outlined
below.
Keeping a day-book is time consuming and boring but it is essential. It is certain
that there will come a time when you will be grateful that you have an accurate record of
your work.
79
DAY-BOOK RULES
1.
A day book is a personal document. It is the essential, primary and complete record
of all your scientific activity for every day that you are in the laboratory.
2.
Physically a day-book should be a substantial hard bound copy and pages should
never be removed or inserted. Corrections should be carried out so that any deleted
material is still legible. Tipex or similar products must never be used to delete material.
3.
A day-book must be written up every day, dated and signed. A day book is not a
work of literature. It is not necessary that the rules of syntax, grammar and spelling be
adhered to. The only essential feature is that it is adequate for the aims outlined in rule 4.
4.
The aim of a day-book is to provide sufficient information for another scientist to
be able to replicate, exactly, your day’s laboratory work by reference to your day book
and other references you cite in it.
5.
Any data recorded in your day-book must be primary data. Mathematically
processed data may also be recorded in addition.
Example; The actual number of colonies counted on a plate must be recorded in
your day-book. The calculated number of colony forming units in the original suspension
may also be recorded.
6.
An important element of a day book is that it must contain all errors, omissions and
accidents that occur in a days work.
Example; "In the determination of the standard curve the 2mg/ml sample of
oxytetracycline was spilled and was not analysed. Standard curve was derived from the
remaining samples"
Actually in the real world of day-books what is written will more likely be, "lost 2 mg/ml
got st curve from others"
7.
Any standard or routine methods used during a day may be entered in your daybook by reference to a previous entry in the day book or any other reference source. Any
deviation from the method must be noted.
Example; "The TSB culture used was 31 h not 24 h."
8.
The calibration status of any piece of equipment used must also be recorded in your
day-book. The date of the last calibration of apiece of equipment, for example a pH
meter, pipette or incubator, together with the name of the person who performed the
calibration must be entered in your day book. You do not need to enter the calibration
80
status of equipment every day you use it. The most recent entry in your day-book about
the status of apiece of equipment will be considered as the evidence of its calibration
status. The use of uncalibrated equipment can invalidate any experiment in which it is
used. If, for example, you recorded in your day-book that you had made a buffer and the
last record of a calibration of the pH meter in your day book was four months ago, your
buffers would have no validity and all experiments in which they were used will also be
invalid.
9.
If you use any solutions or reagents that were not made up by you personally, the
name of the person who made them and date they were made should be recorded in your
day-book. Actually it is a good rule NEVER to use solutions made up by anybody else.
10. Your day-book should include observations on your day’s results and plans for
future modification of methods.
Example; "The spreading of the colonies on plates in the total viable count
suggested that the plates were insufficiently dried. Plate drying will in future be
increased to 30 min" - Real world translation "f**k all cols spread – prob not dried
enough! try 30 min next time”
11. It is often helpful if your day-book contains a simple outline of the aims of a
particular experiment.
12. Plans for future experiments need not be recorded in your day-book (exception see
10 above). Many scientists find it useful to record these plans in the same physical book
as the day book, often in a separate section at the end of the book.
13.
A day book is a personal document. It would be very surprising if the day-books of
two students working on the same project contained the same information. It would also
be surprising if the two day-books did not refer to each other.
Submitting day-books
Day-books are not evaluated and need not be submitted. However, they must be
available to the examiners at your oral presentation.
The examiners may wish to consult your day-books if:
1.
There is an apparent discrepancy between the accounts of a piece of work
provided by two partners.
2.
More details of a particular experiment are required.
81
82
Appendix 5
Microbiology policy on Plagiarism
83
84
Microbiology policy on Plagiarism
What is plagiarism?
Copying somebody else’s words and passing them off as your own. Plagiarism is a
major crime in all writing but in an examination context, Plagiarism is CHEATING and
will be treated as such.
For
a
good
discussion
of
plagiarism
see
the
Wikipedia
entry
(http://en.wikipedia.org/wiki/Plagiarism#cite_note-4). Please note that not all Wikipedia
entries can be trusted, however, this one is pretty good.
How is plagiarism detected?
The increasing availability of written material on the Web has made plagiarism
easier. It is now child’s play to access material on a Web site and to copy and paste it into
your own work. However, the Web has also made such plagiarism much easier to detect.
Turnitin is a software programme that is capable of scanning any piece of writing and
identifying every single case where words have been copied from a document already
available on the Web.
All course material must be submitted electronically as well as in hard copy.
This is so that it can be checked with “Turnitin” to identify plagiarised material,
extensive copy/pasting from the Web, etc.
You Have Been Warned
Why is it so difficult not to copy other people’s work?
When you first start writing in science you will encounter what looks like a
paradox. You are supposed to follow two rules that appear to contradict each other.
Rule 1 You are expected to derive all the facts and most of the opinions you write about
from the published literature and you are also expected to give the source from which you
obtained those facts. (The only exception to this is in your thesis report were you are also
allowed to discuss the data you produced yourself.)
85
Rule 2 It is required that the words you use are your own. It is not legitimate to use the
words somebody else has used, even if they were the person who generated the data or
expressed the opinion in the first place.
Thus, what you are required to do is to describe the facts that somebody else has
produced but, when you are describing them, you are not allowed not to copy the words
they used.
YOU MUST USE THEIR FACTS BUT YOU MUST NOT USE THEIR WORDS
This may seem a little weird at first. If a senior researcher has already described
something well, why do you have to re-describe it in your own words. Why not use
theirs? Surely they are more experienced than you and the words they used are, in all
probability, better than the ones you will come up with?
However, it is an absolute rule of academic writing that it is not acceptable to
copy chunks out of other people's work.
The rules governing the copying of other people's words and presenting them in
your own work are simple.
1.
Copying a whole essay from any source is never legitimate. This will be treated as
CHEATING and it will be reported to the University authorities and will incur very
severe penalties.
2.
Copying a paragraph from any source is rarely, if ever, legitimate. You would
have to have a very good defence to obtain any marks from work where this extent of
copying was identified.
3.
Copying a phrase, sentence or maximally, two sentences, may be legitimate but
only when you do it properly.
4.
If you include more than a single phrase of another author's work, you must
acknowledge the source by including an appropriate citation to it and you must put the
words you have borrowed in inverted commas.
86
If you have read this Appendix and you have attended the seminar on plagiarism,
you are still in doubt about plagiarism and you should consult Dr Gavin Collins, the
departmental plagiarism adviser.
Note
An essay or thesis that contains sentences copied from other texts will not, if the
relevant rules are followed, be considered as evidence of plagiarism. An essay that
contains many such sentence will, however, normally be considered as a bad piece of
scientific writing and will not get very many marks.
When is it legitimate to copy material from somebody else or from a site you have
accessed on the Web?
Copying material can, on occasions, be legitimate and, in some cases, it may be
necessary. The most frequent legitimate reason for copying a sentence (or more) is that is
contains a definition that has legal consequences or represents a definition arrived at by a
reputable international (or national) agency.
The Clinical and Laboratory Standards Institute (CLSI) are a major international
standards agency and has spent many hours arriving at a definition of the category
“resistant” in the context of antimicrobial susceptibility testing. Thus, in discussing the
meaning given by CLSI to the term resistant, it is better to copy their exact words. If you
make it very clear that you have copied their words, then this is not plagiarism. You
could, for example write the following.
The CLSI guideline M37-A3 (CLSI, 2008) state that “resistant isolates are not
inhibited by the usually achievable concentrations of the agent with normal dosage
regimens and/or fall in the range where specific microbial resistance mechanisms are
likely (eg, β-lactamases), and clinical efficacy has not been reliable in treatment studies.”
In this example, although words have been directly copied, it has been made clear
that this has been done and the original source has been identified. As there is no attempt
to pass these words off as your own you will not have committed plagiarism.
87
How to copy text and avoid plagiarism
Let’s consider the following two sentences that I might have included in this note
on plagiarism.
There are a number of defences that have been used against
charges of plagiarism. Some individuals caught plagiarizing in
academic or journalistic contexts claim that they plagiarized
unintentionally, by failing to include quotations or give the
appropriate citation.
Turnitin would have detected that the second sentence had been copied directly
from Wikipedia. Thus, its inclusion in my text would have been plagiarism.
However, I could have avoided plagiarism by writing the following sentence.
In discussing the possible defences that might be offered when a person is
charged
with
plagiarism,
Wikipedia
(http://en.wikipedia.org/wiki/Plagiarism#cite_note-4) have commented; “Some
individuals caught plagiarizing in academic or journalistic
88
contexts
claim
that
they
plagiarized
unintentionally,
by
failing to include quotations or give the appropriate citation.”
Turnitin would still have identified Wikipedia as the source of a portion of the
text. However, as I have clearly demonstrated that I have copied these words (inverted
commas) and provided the information as to where I copied them from (citation), this
would not have been plagiarism.
It would also have been legitimate (not plagiarism) for me to have written;
Failure to include quotation marks where they would have
been appropriate or the failure to include appropriate citations
have been offered as defences against the charge of plagiarism
((http://en.wikipedia.org/wiki/Plagiarism#cite_note4).
Here I have re-phrased the Wikipedia comment and have cited the source of the
opinion. Thus, I have avoided plagiarism.
89
How does Microbiology react to suspicions of plagiarism?
1.
If plagiarism is suspected, either by the reader or because of data yielded by
Turnitin analysis, the case will be brought to the attention of the Microbiology
plagiarism adviser (GC).
2.
The plagiarism adviser will consider all relevant material and, at his discretion, may
also hold a meeting with the student concerned. The adviser will arrive at a
recommendation as to the most appropriate course of action the Discipline should
take. In making his recommendations the adviser will take account of the
University regulations and current practice within the School.
3.
The plagiarism adviser’s recommendation will be made to the Microbiology
Plagiarism Committee which shall consist of the Head of Discipline (or his
nominee), the Microbiology plagiarism adviser and the academic staff member to
whom the work in question was submitted.
4.
The plagiarism adviser’s recommendation will also be made available to the student
concerned.
5.
The Plagiarism Committee will meet the student whose work has been brought into
question.
6.
The Plagiarism Committee will issue a decision as to the action to be taken.
Possible departmental actions in the case of plagiarism
In cases where the infringement is sufficiently minor they may recommend that no
action be taken and that the work be marked, as submitted, in the normal manner.
In cases where the infringement is considered minor they may recommend that the
work be marked as submitted and in the normal manner but that a certain percentage
should be deducted because of the failure to follow the rules on plagiarism.
In cases where the infringement is considered major they may recommend that no
marks be awarded.
In cases where the infringement is considered major and severe they may
recommend that no marks be awarded and that the case should be referred to the
University authorities.
90
91
Appendix 6
Modules Brochure
92
93
Modules Brochure
This is a list of the 6 lecture Modules that will be offered this year.
You will have to register for and present yourself for examination in ALL 6 of
these Modules.
Teaching Session 1 (Jan 6th – Feb 21st)
Code
Module Name
Dynamics of microbial gene regulation
The Meaning of Life: Bioinformatics
Marine Microbial Ecology and Nutrient Cycling
Teaching Session 2 (Feb 24th – April 4th)
Bacterial Pathogenesis
Bioprocessors and recombinant protein production
Anaerobic Biotech & Systems Biology
94
95
ACADEMIC YEAR 2013-14
Bioprocessors and Recombinant Protein Production
Description
This module will examine how recombinant proteins are engineered in the context of
productive microbial cell factories and how traditional and advanced bioprocess
technologies are employed for the industrial-scale production of such products.
The course will introduce expression systems – E. coli, yeast and mammalian cells,
and cell-free – commonly used in recombinant protein production. Factors affecting
the choice of expression host and approaches to identifying bottlenecks in expression
of biomedically and biotechnologically important products will be reviewed. The unit
will also review recombinant biotherapeutics currently available on the market and
consider how they are produced.
Bioprocess technology will investigate the production of biomass, primary and
secondary metabolite production on the industrial scale by means of technologies
associated with submerged cultures and solid-state fermentations.
Module Owner / Lecturer
Module Administrator Details
Dr Gerard Fleming
Dr Gerard Fleming
Email: [email protected]
Module Code
Module Type
Core for MI401
ECTS: 5
Semester Taught: Semester 2
Module Assessment
Assessment Type
Semester Examined: Semester 2
Exam Session
Duration
1st Sitting
Written Paper
Spring
2nd Sitting
n/a
PART B
Module Schedule
No. of Lectures Hours
24
No. of Tutorials Hours
0
No. of Labs Hours
Recommended No. of self study hours
75
Lecture Duration
Tutorial Duration
Lab Duration
Placement(s) hours
96
2 Hours
1h
0
Module Learning Outcomes
On successful completion of this module the learner should be able to:
1. Describe the common eukaryotic, prokaryotic and cell-free expression systems in
which recombinant proteins can be produced.
2. Identify limitations and advantages of each of these systems.
3. Explain how recombinant protein production experiments can be evaluated.
4. Make and explain rational choices of expression systems for the production and
purification of target recombinant proteins.
5. Show evidence of understanding of the underlying principles of the design and
operation of submerged and solid-state bioprocessor systems by being able to describe
and classify the key components and operational parameters of these reactors.
6. Be able to critically discuss and evaluate the relative merits of these systems for the
production of cell biomass, primary /secondary metabolites and recombinant proteins.
7. Be able to translate their understanding of bioprocess systems by evidential
composition and evaluation of practices as described in the published literature.
Module Learning, Coursework and Assessment
Assessment type
% weighting
Written paper
100
Indicative Content (Marketing Description and content)
Overview of recombinant protein production. Escherichia coli: strains, vectors,
modifications, limitations as an expression host. Protein expression in yeast, fungi
insect and animal cells. Cell-free expression systems based on cell extracts and
purified components. Monitoring and troubleshooting recombinant protein
production. History of classical and biotechnology-based fermentations. Role of
strain, medium and process in biotechnological fermentations. Classical and
recombinant strain selection and improvement. Inoculum preparation and medium
design. Design of laboratory scale, pilot and production- scale bioprocessors.
Biosafety and containment. Operational parameters and control. Detailed examples of
commercial production of primary and secondary metabolites of biotechnological
importance. Solid substrate fermentations. Production of Plant growth Hormones and
Quorn Biomass. Downstream-processing.
Module Resources
Suggested Reading Lists
Will be provided in class
97
ACADEMIC YEAR 2013-14
Marine Microbiology and Nutrient Cycling
Description
This module will introduce students to the fundamentals of molecular microbial
ecology and the advances such approaches have bought about in the field. Students
will be introduced to, and will critically assess, the techniques employed in molecular
microbial ecology. Students will then focus on microbial mediation of nitrogen (N)
and carbon (C) cycling in the marine environment. Finally, future perspectives in
molecular microbial ecology linking community structure and function will be
addressed.
Module Owner / Lecturer
Module Administrator Details
Dr Cindy Smith
Email: [email protected]
Dr Cindy Smith
Module Code
Module Type
Core for 4BS Microbiology,
4EV, 4MR
ECTS: 5
Semester Taught: Semester
Semester Examined: Semester
Requisite(s)
Modules
Pre-Req
MI3XX Marine
Microbiology
PART B
Module Schedule
No. of Lectures Hours
16
Lecture Duration
1h
No. of Tutorials Hours
2
Tutorial Duration
1h
No. of Labs Hours
6
Lab Duration
3hX2
Recommended No. of self study hours 75 Placement(s) hours
0
Other educational activities and hours
3 dedicated, prescribed hours of time when the
allocated
lecturer will be available on a dedicated Twitter
account to answer questions and drive
discussions
Module Learning Outcomes
98
On successful completion of this module the learner should be able to:
1. describe, compare, contrast and critique the principle state-of–the-art molecular
techniques used to study microorganisms in the environment;
2. IDENTIFY, DESCRIBE and EXPLAIN the importance of, and list the main
microbial species associated with, the different stages of the marine Carbon &
Nitrogen Cycles;
3. DISCUSS the challenges of linking microbial ecology with function in the marine
environment.
Module Learning, Coursework and Assessment
Outcomes
assessed
Assessment type
Written exam
Report on high-impact paper in Microbial Ecology
1-3
1-3
% weighting
80
20
Indicative Content (Marketing Description and content)
The content will include lectures on: the ‘Plate-Count Anomaly’; cultureindependent techniques in microbial ecology; the N & C cycles in the marine; and
microbial ecophysiology to link ecology (identity) and physiology (activity) of
microbial communities.
Module Resources
Suggested Reading Lists
Will be provided in class.
99
ACADEMIC YEAR 2013-14
Bacterial Pathogenesis
Description
This module will explore the genetic basis of microbial pathogenicity, in
representative gram-positive and gram-negative pathogens. The module will address
virulence mechanisms, host pathogen interactions, immune evasion and microbial
colonisation (biofilm) mechanisms. Specific topics that will be covered include
pathogenicity islands and plasmids, virulence factors, type III secretion systems,
infection strategies, resistance mechanisms and regulation of virulence gene
expression.
Module Owner / Lecturer
Module Administrator Details
Prof. Jim O’Gara
Email: [email protected]
Prof. Jim O’Gara
Module Code
Module Type
Core for MI401
ECTS: 5
Semester Taught: Semester 2
Pre-Req
Semester Examined: Semester 2
3rd year Microbiology
Modules 
modules
Module Assessment
Assessment Type
Exam Session
Duration
1st Sitting
Written paper
Semester 2
2 hours
PART B
Module Schedule
No. of Lectures Hours
21
No. of Tutorials Hours
0
No. of Labs Hours
0
Recommended No. of self study hours
65
Other educational activities(Describe)
and hours allocated
Lecture Duration
Tutorial Duration
Lab Duration
Placement(s) hours
1h
0
Directed learning – 30 hours
Module Learning Outcomes
On successful completion of this module the learner should be able to:
1. Discuss the role of microbial biofilms in infectious disease.
100
2. Explain the regulatory mechanisms controlling the biofilm phenotype in
representative organisms
3. Discuss the genetic organisation of virulence genes and regulation of their
expression
4. Describe immune evasion strategies used by representative microbes to survive in
the host environment
5. Describe the molecular interactions that occur when bacteria invade into host cells.
6. Critically evaluate research papers in the field of bacterial pathogenesis.
7. Explain how bacteria manipulate host cell signalling pathways and host cell
behaviours
8. Discuss the benefits to the bacterium of manipulating host cell signalling pathways
and host cell behaviours
Module Learning, Coursework and Assessment
Outcomes
assessed
Assessment type
Written exam
1-8
101
% weighting
100
ACADEMIC YEAR 2013-14
The Meaning of Life: Bioinformatics
Description
The module will cover a range of topics in the theory of Bioinformatics, ranging
from fundamental concepts on the Central Dogma of Biology, through sequencing
technologies in genomics, transcriptomics, proteomics and metabolomics. It will
provide students with an insight into the potential impact of bioinformatics data can
have on our understanding of microbial phylogeny; microbial community
functioning; and microbial processes, including pathogenesis. It will also provide
training for students in the tools used to interpret DNA and amino acid sequence
information, including database interrogations; phylogenetic analyses; and
interpretation of protein structural motifs.
Module Owner / Lecturer
Module Administrator Details
Dr Gavin Collins
Email: [email protected]
Dr Gavin Collins
Module Code
Module Type
Core for 4BS Microbiology
Semester Taught: Semester 2
Pre-Req
PART B
Module Schedule
No. of Lectures Hours
ECTS: 5
Semester Examined: Semester 2
Modules
MCB module in 2nd
year
12
Lecture Duration
1h
No. of Tutorials Hours
2
Tutorial Duration
1h
No. of Labs Hours
12
Lab Duration
3hX4
Recommended No. of self study hours 75
Placement(s) hours 0
Module Learning Outcomes
On successful completion of this module the learner should be able to:
1. describe the Central Dogma of Biology and the importance of Bioinformatics in
modern Microbiology, medicine and environmental science;
2. discuss how next generation DNA sequencing technology can be used to advance
our understanding of microbial phylogeny, physiology, and pathogenicity;
3. describe the tools available for proteomics and protein informatics;
102
4. outline the strategies used for analyses of complex next-generation sequencing
datasets;
5. describe the steps in developing bacterial diagnostics assays based on molecular
targets;
6. perform intermediate-level analyses of DNA, RNA and protein sequences using
a range of tools, including sequence databases and alignment editors.
Module Learning, Coursework and Assessment
Assessment type
Outcomes assessed
% weighting
End of year exam
Bioinformatics Project
50
50
1-5
6
Indicative Content
Students will get an insight into the generation of the vast volumes of bioinformatics
data from genome sequencing, proteomics and metabolomics projects, and the impact
of these data on our understanding of phylogenetics and microbial processes, including
pathogenesis. Lectures will cover: overviews of the structure and function of nucleic
acids, genes and genomes, and their role in determining the activity of a cell;
sequencing technologies and strategies for data analyses, including for metagenomics
datasets; protein bioinformatics, including alignments, identifying functionally-related
proteins and conserved motifs; using tools to predict protein structure; peptide
fingerprinting of proteins; identification of proteins using mass fingerprints; using
genome sequencing to identify single nucleotide polymorphisms associated with the
regulation of antibiotic resistance, biofilm and virulence; global
transcriptomics/proteomics concepts and the associated adaptation responses of
bacteria mediated through dysregulation. Practical sessions – and associated lectures –
will focus on database interrogations and sequence analyses, with examples the
development and design of molecular-based infectious disease diagnostics assay.
Examples of Bioinformatics in research areas, wet-lab applications and in the
marketplace will be discussed.
Module Resources
Suggested Reading Lists
To be provided in class
103
ACADEMIC YEAR 2013-14
Anaerobic Microbial Biotechnology & Systems Biology
Description
This module will focus on the exploitation, and optimization, of complex microbial
communities in biotechnology. Important applications of anaerobic microbial
communities, including in wastewater treatment, biorefining and conversions into
energy, will be discussed. An EcoSystems [Micro]Biology approach to understanding
the structure and function of complex communities underpinning biotechnological
applications will be discussed in detail; this will include the application of genomics,
transcriptomics and proteomics to understand dynamic interactions between microbial
trophic groups in complex systems. Using this type of knowledge to optimise
technology – as well as optimizing the microbial community itself – will be considered.
Module Owner / Lecturer
Dr Florence Abram
Module Administrator Details
Dr Florence Abram
Email: [email protected]
Module Code
Module Type
Core for 4BS Microbiology,
4EV
Semester Taught: Semester 2
Pre-Req
ECTS: 5
Semester Examined: Semester 2
Modules
MI3XX Environmental
Microbiology
PART B
Module Schedule
No. of Lectures Hours
22
Lecture Duration
1h
No. of Tutorials Hours
2
Tutorial Duration
1h
No. of Labs Hours
0
Lab Duration
Recommended No. of self study hours 75
Placement(s) hours 0
Module Learning Outcomes
On successful completion of this module the learner should be able to:
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1. discuss the application of microbial communities for a range of biotechnologies,
including anaerobic digestion, microbial fuel cells and in biorefineries;
2. explain their understanding of techniques and approaches used in genomics,
transcriptomics and proteomics to study microbial communities;
3. discuss how Systems Biology approaches can be used to better understand potential
functions, and real activity, in complex microbial communities
4. Discuss future applications of this approach to optimise biotechnologies and the
activity of microbial communities.
Module Learning, Coursework and Assessment
Outcomes
assessed
Assessment type
End of year exam
1-4
% weighting
100
Indicative Content
This module will focus on the exploitation, and optimization, of complex microbial
communities in biotechnology. Important applications of anaerobic microbial
communities, including in wastewater treatment, biorefining and conversions into
energy, will be discussed. An EcoSystems [Micro]Biology approach to understanding
the structure and function of complex communities underpinning biotechnological
applications will be discussed in detail; this will include the application of genomics,
transcriptomics and proteomics to understand dynamic interactions between microbial
trophic groups in complex systems. Using this type of knowledge to optimise
technology – as well as optimizing the microbial community itself – will be
considered.
Module Resources
Suggested Reading Lists
Will be provided in class
105
ACADEMIC YEAR 2013-14
Dynamics of microbial gene regulation
Description
Bacteria inhabit almost every environment on the planet and they respond to the
different environmental conditions they encounter. Bacteria can sometimes adapt to a
single stressful condition and at other times they respond to multiple stresses.In this
module, we take an overview of multigene regulation, at both the DNA and RNA level,
in bacteria such as E. coli and Salmonella and explore examples of microbial responses
drawn primarily from different kinds of environmental stresses.
Module Owner / Lecturer
Dr Cyril Carroll
Module Administrator Details
Dr Cyril Carroll
Email: [email protected]
Module Code
Module Type
Core for 4BS Microbiology
Semester Taught: Semester 2
Pre-Req
ECTS: 5
Semester Examined: Semester 2
Modules
MI 301 (3rd year
Microbiology)
Module Assessment Assessment Type
1st Sitting
Written paper
Exam Session
Duration
Semester 2
2 hours
Continuous
n/a
assessment
n/a
Essay
PART B
Module Schedule
No. of Lectures Hours
24
Lecture Duration
1h
No. of Tutorials Hours
0
Tutorial Duration
1h
No. of Labs Hours
0
Lab Duration
Recommended No. of self study hours 100
Placement(s) hours 0
Module Learning Outcomes
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On successful completion of this module the learner should be able to:
1. Explain the dynamics of Microbial gene expression at both the RNA and DNA
level;
2. Demonstrate a broad comprehension of varied functions, roles and activities of
translated and nontranslated RNAs of the bacterial cell;
3. Describe the role of non-translated regulatory RNAs of the microbial cell;
4. Describe the underlying regulatory mechanism of bacterial response to
environmental stress at the DNA, RNA and protein transduction level;
5. Outline in detail the bacterial SOS response to DNA damage;
6. Explain the underlying regulatory mechanism of bacterial chemotaxis via protein
signal transduction pathway.
Module Learning, Coursework and Assessment
Outcomes
assessed
Assessment type
Written paper
1-6
% weighting
100%
Indicative Content
Bacteria inhabit almost every environment on the planet and they respond to the
different environmental conditions they encounter. Bacteria can sometimes adapt to a
single stressful condition and at other times they respond to multiple stresses. When
bacteria are exposed to a single stress, they typically express a fraction of their entire
proteome constitutively, while in situations where bacteria are exposed to multiple
stresses, they prove to be extremely versatile, turning on many different sets of genes
that permit them to survive a range of different stressors. All bacteria, including those
that grow in a relatively constant environment face changes that threaten their
survival. Our understanding of microbial stress responses is complicated by the fact
that bacteria experience multiple stresses simultaneously.
Typically, stress integration mechanisms fall into three categories: (1) constitutive
expression of responses to a constant or recurring stress, (2) global responses with a
hierarchal regulator for switching between different environments, and (3) distributed
independent responses to stress fluctuation without hierarchal control.
Module Resources
Suggested Reading Lists
Students will be provided with up to date literature
developments and reviews pertaining to the subject area.
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