MRes in Biomedical Sciences and Translational Medicine ...

MRes in Biomedical Sciences and
Translational Medicine
STUDENT HANDBOOK
2011 - 2012
Master of Research in Biomedical Sciences Strands:
Biology of Cancer
Cellular & Molecular Physiology
Drug Safety
Integrative Mammalian Biology (IMB)
Molecular and Clinical Gastroenterology
Molecular and Clinical Pharmacology
Stem Cells, Tissues and Disease
1

Section 1 Introduction
Student Handbook
2011/12
Contents
Section 2 Programme Organisation and Student Support
Section 3 Programme Overview & Timetable
Section 4 Assessment
Section 5 Research Projects
Section 6 Techniques and Frontiers in Biomedical Sciences
Section 7 Transferable Skills
Section 8 Attendance Monitoring & Absence Reporting
Section 9 Student Feedback and Representation
Section 10 Appendix
Page 3
Page 8
Page 16
Page 26
Page 31
Page 57
Page 80
Page 103
Page 105
Page 106
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Section 1
Introduction
1.1 A welcome to new students
I am pleased to welcome you as a new student into the Institute of Translational Medicine and hope
that you will find your time studying on the MRes in Biomedical Sciences and Translational Medicine
programme an enriching experience. The course combines hands-on laboratory research work with
lectures and tutorials to give you direct knowledge and experience of cutting-edge biomedical and
clinical research. You will also receive training in transferable skills, which will broaden your existing
skill set and help prepare you for your subsequent careers. Feedback from previous MRes students
indicates that you will need to work hard, but that the course is both enjoyable and rewarding.
This handbook contains essential information about all aspects of the MRes programme, so it is
important that you read and understand it. Additional information and announcements about the
programme will also be issued during the course, either electronically by email or through VITAL (the
University‟s online teaching resource), or via posters on the MRes notice boards. It is therefore very
important that you check your e-mail, relevant VITAL pages and the notice board every day, as there
may be important messages relating to the course or changes in schedule, etc.
One of the first things you will want to know is who to contact for help, information and advice. The
MRes programme is run by a team consisting of the Programme Director, the Programme Administrator
and the Strand Convenors. They are happy to help you if you are having any difficulties, whether
academic, administrative or personal in nature, including disability-related issues. Any problems should
initially be discussed with your Strand Convenor, who will either deal with the issue directly or will refer the
matter to the Programme Director or Administrator as appropriate. Prof Andrea Varro is the Director of
Postgraduate Studies of the Institute of Translational Medicine and she will be happy to discuss any
unresolved problems with you provided that the appropriate line of communication within the MRes
team has been followed and exhausted. Contact details for each member of the team can be found in
Section 2.1 of this handbook, along with a brief description of their area of responsibility, to guide you
to the most suitable person to deal with your question.
I hope that you find the MRes in Biomedical Sciences and Translational Medicine both useful and
enjoyable. Good luck with your studies.
Programme Director: Professor Alan Morgan
Email: amorgan@liv.ac.uk
Telephone: 0151 794 5333
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1.2 Induction Timetable for MRes Students
The first two weeks of the programme will provide you with essential introductory information and
practical training that will be of benefit to you throughout the programme. You should make every
effort to attend these activities on time and check you know how to find the activities that will take place
outside of the Sherrington Buildings.
MORNING
AFTERNOON
MONDAY
19 th Sept
10:00 – 10:30
Student arrival &
register
LOCATION: Common
Room, Physiology
Dept
10:30 – 11:00
Welcome by the
Programme Director,
Professor Alan
Morgan
11:00 – 12:00
Paperwork
completion and
finalising registration
using Spider Student
Web
12:00 – 13:00
Campus Tour
13:00 – 14:00
Lunch break
14:00 – 15:00
International students
to attend ONLY (bring
your passport and visa
for photocopying).
LOCATION: Common
Room, Physiology
15:00 – 16:00
Overview of the MRes
in Biomedical Sciences
talk by Professor
Morgan
16:00 – 17:00
Strand Inductions
17:00 – onwards
Welcome reception
LOCATION: Common
Room, Physiology
TUESDAY
20 th Sept
INTERNATIONAL
STUDENT
INDUCTION
EVENT ALL DAY
No scheduled
activities for
Home/EU
students
INTERNATIONAL
STUDENT
INDUCTION
EVENT ALL DAY
No scheduled
activities for
Home/EU
students
WEDNESDAY
21 st Sept
09:00 – 10:00
Introduction to
Research Ethics by
Professor Andrea
Varro
LOCATION:
Physiology Seminar
Room
10:30 – 11:30
School Safety Talk
by Mr Adrian Walsh
LOCATION:
Physiology Seminar
Room
11:30 – 12:30
Q&A session with
Professor Morgan
(a chance to seek
guidance with any
issues that may
have arisen)
LOCATION:
Physiology Seminar
Room
14:00 – 17:30
Institute
Postgraduate Event
Postgrad Society
LOCATION: Cedar
House Rm 521,
opposite
Sherrington
Building main
entrance
17.30
Drinks reception
(Physiology
Common Room)
THURSDAY
22 nd Sept
09:00 – 12:30
Preparation for
research project
14:00 – 15:00
Understanding
Plagiarism Talk by
Mr Stuart
McGugan
LOCATION:
Physiology
Seminar Room,
Physiology Dept
15:30 – 16:30
Introduction to
the Harold Cohen
Library
LOCATION: Mr
Ken Linkman will
meet the group in
the foyer of the
Harold Cohen
Library
FRIDAY
23 rd Sept
09:00 – 12:30
Preparation for
research project
14:00 – 17:30
Preparation for
research project
4

MORNING
AFTERNOON
MONDAY
26 th Sept
09:00 – 12:30
Preparation for
research project
14:00 – 17:30
Preparation for
research project
TUESDAY
27 th Sept
09:00 – 17:00
Prospective
Licensee Training
Course
(All Strands to
attend day 1 & 2)
LOCATION: 126
Mount Pleasant
An exam follows
on Wednesday 5 th
October
WEDNESDAY
28 th Sept
09:00 – 17:00
Prospective
Licensee Training
Course
(All Strands to
attend day 1 & 2)
LOCATION: 126
Mount Pleasant
An exam follows
on Wednesday 5 th
October
THURSDAY
29 th Sept
09:00 – 17:00
Prospective
Licensee Training
Course
(Only IMB & Drug
Safety strands to
attend day 3)
LOCATION: 126
Mount Pleasant
An exam follows
on Wednesday 5 th
October
FRIDAY
30 th Sept
09:00 – 10:00
Feedback and
Q&A session with
Professor Alan
Morgan (a chance
to give your views
on the induction
period and to
seek guidance
with any
remaining issues)
LOCATION:
Physiology
Seminar Room,
Physiology Dept
14:00 – 15:00
Preparation for
Research
Project
5

LATER EVENTS:
Some induction activities are scheduled to take place after the first 2 weeks. Details of these are given below:
Event: University Safety Seminar
Date: 4 th October
Time: 2pm – 4pm
Location: Lecture Theatre 1 Sherrington Building
Event: Prospective Licensee Training Course Examination
Date: 5 th October
Time: 11.00am
Location: 126 Mount Pleasant
Event: University Radiation Protection (BASIC)
Date: 12 th October (Not Yet Confirmed)
Time: 14:00 – 16:00
Location:
Event: English Language Classes for International Students
Date: Classes will run throughout the academic year on a Friday starting 14 th October
Time: 09:00 – 10:00
Location: Physiology Seminar Room
Event: Demonstrator Training Workshop
Date: 21 st October
Time: 9.30am – 12.30pm
Location: 126 Mount Pleasant
Event: University Radiation Protection (LASER)
Date: 26 th October (Not Yet Confirmed)
Time: 14:00 – 16:30
Location:
Event: Biostatistics Workshop
Date: 3 rd November (Not Yet Confirmed)
Time: To Be Confirmed
Location: Physiology Seminar Room
6

1.3 Using the Handbook
This handbook is to be used in conjunction with other information you may be given about different
aspects of the MRes Programme, and compulsory courses organized by the University of Liverpool. It
provides essential information required for the Degree Program; you should read it carefully and keep it
in a safe place. It also presents information on how the student charter is implemented in this course.
It includes details of:
� the broader aims and objectives of the MRes,
� the modules available
� the means by which the course will be assessed overall
� the assessment criteria that will be used.
� the aims and objectives of each individual module or similar unit of study and what you should be
able to achieve by the end of it.
� the teaching and learning methods that will be used and the means by which more general skills
(such as working in teams and making oral presentations) will be developed and assessed.
� the facilities and support services provided by the University that may be useful to you.
� the staff responsible for organising the programme and its strands or who undertake other duties
of relevance and their contact details
� the means by which your views on individual modules or units on courses of study overall and on
other aspects of your experience will be sought – both individually and collectively– and how
information on the responses to those views will be fed back to you.
� how you will be provided with systematic information on your individual progress, on your areas
of strength and weakness, and on the means by which you can improve your performance.
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Section 2
Programme Organisation and Student Support
The MRes in Biomedical Sciences and Translational Medicine programme is run by a team consisting of
Strand Convenors, Programme Director and Programme Administrator.. They are happy to help you if you
are having any difficulties, whether academic, administrative or personal in nature, including disabilityrelated
issues. In addition, the University provides many useful services to help you adjust to life on
campus and to help with various difficulties you may face. Any problems should initially be discussed with
your Strand Convenor, who will either deal with the issue directly or will refer the matter to the Programme
Director or Administrator, as appropriate. Prof Andrea Varro is the Director of Postgraduate Studies of
the Institute of Translational Medicine and she will be happy to discuss any unresolved problems with
you provided that the appropriate line of communication within the MRes team has been followed and
exhausted. Contact details for each member of the team can be found below, along with a brief
description of their area of responsibility, to guide you to the most suitable person to deal with your
question.
2.1 The MRes Team
Strand Convenors
Responsible for the organisation of the various MRes strands, convenors will help with any academic and
administrative problems relating to their specific MRes strand. Strand convenors will be able to help with
most issues and should normally be the first person you contact when problems arise. If they are unable
to help, they will refer you to the Programme Director/Administrator or other staff as appropriate. Contact
details for the various strand convenors are given below:
Biology of Cancer:
Dr. Eithne Costello-Goldring Tel: 0151 706 4178 email: Ecostell@liverpool.ac.uk
Dr. Carlos Rubbi Tel: 0151 706 4099 email: C.Rubbi@liverpool.ac.uk
Cellular & Molecular Physiology:
Dr. Jeff Barclay Tel: 0151 794 5307 email: Barclayj@liverpool.ac.uk
Prof. Alan Morgan Tel: 0151 794 5333 email: Amorgan@liverpool.ac.uk
Drug safety:
Dr. Dominic Williams Tel: 0151 794 5791 email: Dom@liverpool.ac.uk
Molecular and Clinical Gastroenterology:
Dr. John Jenkins Tel: 0151 794 6828 email: jrj1@liverpool.ac.uk
Integrative Mammalian Biology (IMB):
Dr. Laiche Djouhri Tel: 0151 795 4011 email: L.Djouhri@liverpool.ac.uk
Molecular and Clinical Pharmacology:
Dr. Andrew Owen Tel: 0151 794 8211 email: Aowen@liverpool.ac.uk
Stem Cells, Tissues and Disease:
Dr. Patricia Murray Tel: 0151-794 5450 email: embryo@liverpool.ac.uk
Dr. Jeff Barclay Tel: 0151 794 5307 email: Barclayj@liverpool.ac.uk
8

Programme Director – Prof Alan Morgan
Responsible for the overall organisation of the MRes programme, he will help with general academic and
administrative problems relating to the MRes course. He will also help with any specific issues that are not
able to be resolved by strand convenors. Alan‟s office, room G.37, is situated in Red Block on the ground
floor of the main Physiology Building on Crown Street (Building 313 on the campus map included at the
back of this handbook). He can be contacted by email, amorgan@liv.ac.uk, or by telephone on (0151) 794
5333.
Issues that cannot be resolved by the Programme Director will be referred to the Institute Director of
Postgraduate Studies (Prof Andrea Varro).
Programme Administrator – Helen Barclay
Responsible for the general administration of the MRes programme, she will help with non-academic
problems related to the course, including attendance issues, deadlines, schedule alterations, etc. Helen‟s
office is situated in Red Block on the ground floor of the main Physiology Building on Crown Street
(Building 313 on the campus map included at the back of this handbook). Helen can be contacted by email
on helen@liv.ac.uk or by telephone on (0151) 794 5313.
Institute Senior Postgraduate Administrator – Lisa Crimmins
Responsible for recruitment and registration onto the MRes programme, including supervisor registration,
she will help with problems related to these areas. She will also assist with wider University level
postgraduate issues, such as financial arrangements, visa problems, etc. Lisa‟s office, room 1.09, is
situated on the 2 nd floor of the Nuffield Wing on Ashton Street (Building 312 on the campus map). Her
email address is crimmins@liverpool.ac.uk, her phone number is (0151) 794 5455.
9

2.2 Academic Staff involved in the MRes programme
In addition to those listed above involved in organizing the MRes, a large number of staff contribute to
the delivery of the course and supervision of research projects. Most staff are based in the Institute of
Translational Medicine, although staff from other Institutes and Research & Business Services also
contribute to the programme. Students will be registered in the Faculty of Health and Life Sciences.
The contact details for all academic staff contributing to the MRes are listed below:
Staff Name Telephone E-mail
Dr. Ana Alfirevic 0151 794 5551 Ana.Alfirevic@liverpool.ac.uk
Prof. David Back 0151 794 5547 D.J.Back@liverpool.ac.uk
Dr. Jeff Barclay (Joint Strand
Convenor, Stem Cells, Tissues &
Disease and Cellular and Molecular
Physiology)
0151 794 5307 Barclayj@liverpool.ac.uk
Dr. Richard Barrett-Jolley 0151 794 4225 Rbj@liverpool.ac.uk
Dr. Chen Bing 0151 706 4075 bing@liverpool.ac.uk
Dr. Mark Boyd 0151 706 4185 Mboyd@liverpool.ac.uk
Dr. Vivian Bubb 0151 794 5509 Jillbubb@liverpool.ac.uk
Dr. Ted Burdyga 0151 794 4971 Burdyga@liverpool.ac.uk
Prof. Bob Burgoyne 0151 794 5305 Burgoyne@liverpool.ac.uk
Dr. Barry Campbell 0151 794 6829 B.J.Campbell@liverpool.ac.uk
Prof. Mike Clague
Dr. Eithne Costello- Goldring (Joint
0151 794 5310 Clague@liverpool.ac.uk
Strand Convenor, Biology of Cancer) 0151 706 4178 Ecostell@liverpool.ac.uk
Dr. Sarah Coupland 0151 706 5885 S.E.Coupland@liverpool.ac.uk
Dr. David Criddle 0151 794 5355 Criddle@liverpool.ac.uk
Dr. Michael Cross 0151 794 5556 M.J.Cross@liverpool.ac.uk
Dr. Judy Coulson 0151 794 5850 J.Coulson@liverpool.ac.uk
Prof. Rod Dimaline
Dr. Laiche Djouhri (Strand Convenor,
0151 794 5334 R.Dimaline@liverpool.ac.uk
IMB) 0151 795 4011 L.Djouhri@liverpool.ac.uk
Prof. Graham Dockray 0151 794 5324 G.J.Dockray@liverpool.ac.uk
Prof. David Edgar 0151 794 5508 Dhedgar@liverpool.ac.uk
Dr. Geoff Edwards 0151 794 5552 Ge1000@liverpool.ac.uk
Prof. John Field 0151 794 8901 J.K.Field@liverpool.ac.uk
Prof. Chris Foster 0151 706 4480 Christopher.Foster@liverpool.ac.uk
Dr. Chris Goldring 0151 794 5979 C.E.P.Goldring@liverpool.ac.uk
Dr. Melita Gordon 0151 794 6863 magordon@liverpool.ac.uk
Dr. Tim Green 0151 794 5564 Tpgreen@liverpool.ac.uk
Dr. William Greenhalf
Dr Dharani Hapangama (Joint Strand
0151 706 4184 Greenhaf@liverpool.ac.uk
Convenor, Womens, Children and
Perinatal Health) 0151 702 4114 Dharani@liverpool.ac.uk
Dr. Lee Haynes 0151 794 6861 Leeh@liverpool.ac.uk
Dr. Tim Helliwell
Dr. John Jenkins (Strand Convenor,
0151 706 4492 Trh@liverpool.ac.uk
Gastroenterology) 0151 794 6828 John.Jenkins@liverpool.ac.uk
10

Dr. Nagesh Kalakonda
0151 706 4593 Nagesh.Kalakonda@liverpool.ac.uk
Dr. Graham Kemp 0151 706 4124 G.J.Kemp@liverpool.ac.uk
Prof. Youqiang Ke 0151 706 4515 Yqk@liverpool.ac.uk
Dr. Neil Kitteringham 0151 794 5548 Neilk@liverpool.ac.uk
Dr. Saye Khoo 0151 794 5560 S.H.Khoo@liverpool.ac.uk
Dr. Stuart Marshall-Clark 0151 794 5457 stumc@liverpool.ac.uk
Dr. Silvia Mora 0151 794 5405 S.Mora@liverpool.ac.uk
Prof. Alan Morgan (Programme
Director; Joint Strand Convenor,
Cellular & Molecular Physiology) 0151 794 5333 Amorgan@liverpool.ac.uk
Dr. Diana Moss 0151 794 5521 D.Moss@liverpool.ac.uk
Dr Patricia Murray (Joint Strand
Convenor, Stem Cells, Tissues and
Disease) 0151 794 5450 embryo@liverpool.ac.uk
Dr. Dean Naisbitt 0151 794 5346 D.J.Naisbitt@liverpool.ac.uk
Dr. John Nash
Dr. Andrew Owen (Strand Convenor,
0151 706 4487 J.R.G.Nash@liverpool.ac.uk
Pharmacology)
0151 794 8211 Aowen@liverpool.ac.uk
Dr Luminita Paraoan
0151 706 4101 Luminita.Paraoan@liverpool.ac.uk
Prof. Kevin Park (Head of Institute) 0151 794 5559 B.K.Park@liverpool.ac.uk
Dr. Lucy Pickavance 0151 794 4234 Lucyp@liverpool.ac.uk
Prof. Munir Pirmohamed 0151 794 5549 Munirp@liverpool.ac.uk
Dr. Tony Plagge 0151 795 4991 A.Plagge@liverpool.ac.uk
Dr. Ian Prior 0151 794 5332 Iprior@liverpool.ac.uk
Dr. Mark Pritchard 0151 794 5772 Mark.Pritchard@liverpool.ac.uk
Dr. John Quayle 0151 794 5446 Jquayle@liverpool.ac.uk
Prof. John Quinn 0151 794 4770 Jquinn@liverpool.ac.uk
Prof. Jonathan Rhodes 0151 706 4073 J.M.Rhodes@liverpool.ac.uk
Dr. Carlos Rubbi (Joint Strand
Convenor, Biology of Cancer) 0151 706 4099 C.Rubbi@liverpool.ac.uk
Dr. Steve Royle 0151 795 4984 S.J.Royle@liverpool.ac.uk
Prof. Chris Sanderson 0151 794 4180 C.Sanderson@liverpool.ac.uk
Dr. Jean Sathish 0151 794 5477 Jean.Sathish@liverpool.ac.uk
Prof. Soraya Shirazi-Beechey 0151 794 4276 Spsb@liverpool.ac.uk
Prof. Ross Sibson 0151 343 4307 D.R.Sibson@liverpool.ac.uk
Dr. Graeme Sills 0151 529 5469 drwindy@liverpool.ac.uk
Dr. Alec Simpson 0151 794 5510 Awms@liverpool.ac.uk
Dr. Joe Slupsky 0151 706 4318 J.R.Slupsky@liverpool.ac.uk
Dr Kevin Southern (Joint Strand
Convenor, Womens, Children and
Perinatal Health) 0151 228 4811 kwsouth@liverpool.ac.uk
Prof. Robert Sutton 0151 706 4187 R.Sutton@liverpool.ac.uk
Prof. Alexei Tepikin 0151 794 5351 A.Tepikin@liverpool.ac.uk
Dr. Swamy Thippeswamy 0151 794 4242 T.Thippeswamy@liverpool.ac.uk
Dr. Cheng-Hock Toh 0151 706 4324 C.H.Toh@liverpool.ac.uk
Dr. Sylvie Urbe 0151 794 5432 Urbe@liverpool.ac.uk
11

Dr Marta van der Hoek (Strand
Convenor, Biostatistics) 0151 794 4750 martaf@liverpool.ac.uk
Prof. Andrea Varro (Institute Director of
Postgraduate Studies) 0151 794 5331 A.Varro@liverpool.ac.uk
Dr. Nikolina Vlatkovic 0151 706 4172 Vlatko@liverpool.ac.uk
Dr. Helen Wallace 0151 795 4008 Hwallace@liverpool.ac.uk
Dr. Dominic Williams (Strand Convenor,
Drug Safety) 0151 794 5791 Dom@liverpool.ac.uk
Dr. Bettina Wilm 0151 795 4988 B.Wilm@liverpool.ac.uk
Dr Michael Weindling (Joint Strand
Convenor, Womens, Children and
Perinatal Health) 0151 702 4119 a.m.weindling@liverpool.ac.uk
Prof. Sue Wray 0151 794 5306 S.Wray@liverpool.ac.uk
Dr. Lugang Yu 0151 794 6820 L.Yu@liverpool.ac.uk
2.3 Safety
Mr. Adrian Walsh is the Safety Officer for the Institute of Translational Medicine. He can be contacted
by telephone on 0151 794 5468 or by email at A.A.Walsh@liverpool.ac.uk. All students must attend a
safety talk given by Mr Walsh in the first week and will receive written guidelines from him on safety
within the Institute. You are also required to attend University training sessions dealing with general
safety and radiation protection, as detailed in the induction timetable in Section 1.2. Additional safety
information will be given by Departmental safety officers within the Departments in which you conduct
your Research Projects. Risk assessment forms must be completed for your Research Projects and
copies of these provided to the appropriate safety officers in your department.
Working with human subjects and/or human material
Supervisors have a responsibility to ensure that all work involving human subjects is covered by
appropriate Ethics Comittee Permission. They should also ensure that students conducting research
projects involving human subjects and/or material understand the permission given for their work, and
in writing their dissertation, they make a clear statement of the Ethics Comittee Approval for the work.
Working with animals
Supervisors have a responsibility to ensure that the appropriate Home Office Authority (both personal
and project licence) are in place before working with experimental animal is started. They should also
ensure that students conducting research projects involving experimental animals understand the
permission given for their work, and in writing their dissertation, they make a clear statement of the
Home Office Approval for the work.
You need to read carefully and obey all the instructions regarding safety that have been given to you
before commencing experimental work in the laboratory. Normal working hours are 9.00-5.30 Monday
– Friday. Work outside these hours, including weekends, is only permitted if either your
supervisor or a suitably qualified person approved by your supervisor is present.
2.4 Mail and Messages
Mail coming into the Institute addressed to students will be left in the MRes Students pigeon holes in
the Institute Office, on the first floor foyer of the Nuffield Building. Urgent messages received for
12

students, wherever possible, are relayed either by telephone or email. There are also MRes notice
boards in two locations: outside the Seminar Room in Physiology, near to the main entrance; and on
the second floor of the Nuffield Building, close to the Program Administrator‟s office. Information and
announcements about the programme will also be issued during the course, either electronically by
email or through VITAL (the University‟s online teaching resource), or via posters on the MRes notice
boards. It is therefore very important that you check your e-mail, relevant VITAL pages and the notice
board every day for important information and schedule changes etc.
2.5 Common Rooms
Tea and coffee facilities and chilled water are available in the common room (room 3.02) on the 3 rd
floor of the Nuffield Building and in the Physiology Common Room, where you will also find a
microwave and vending machines. There are also two Meeting Rooms (3.04 or 3.09) available for
group interactions and group working in the 3 rd floor Nuffield Building, which can be booked via the
Course Administrator.
2.6 Computer, Library and Other Academic Services
There are three computers in the Physiology common room connected to University Network (Physiology
Cybercafé) for all students to use. In addition, room 3.06, HACB, 3 rd floor, Nuffield Wing has been
designed as a workspace for the MRes students. It is equipped with computer points and is also in
range of the wireless router. There is also a computer lab downstairs in the Sherrington Building (behind
the porters lodge) in the Medical School Teaching Centre (MSTC), which has 50 computers available for
general use (the room is occasionally booked; bookings are shown on a diary on the door). All students
registered for the MRes will also have access to all the University services. These are detailed in the
postgraduate handbook and on the University website. Students are expected to make full use of these
services.
2.7 Support for International Students
The International Support Team (IST) provides specialist advice to international students on a variety
of issues such as visas, accommodation and financial matters.
Services offered by the IST include:
� events for international students
� information about UK life
� support for international students with children
� workshops and presentations
� guidance notes and publications, including a monthly newsletter covering the latest issues
affecting international students.
Welcome event
The IST hosts a Welcome event in September, which all new international MRes students should
attend.
The event is designed to introduce you to the city and the University and to also give you the
opportunity to meet all the other new international students.
13

Contacts
For more information contact:
Tel: +44 (0)151 794 4716
Email: ist@liv.ac.uk
Web: www.liv.ac.uk/studentsupport/ist/
2.8 Students with disabilities
The University Disability Support Team co-ordinates and maintains the support required to help you
succeed on your course.
Practical support
The team can help you to:
� inform academic departments about your support requirements
� arrange appropriate support in using the libraries and other academic support services
� organise study assistants
� find financial support for services.
With consent, and when appropriate, the team can liaise on a continual basis with your academic
department and prepare documentation to confirm your support arrangements.
Advice
The Disability Support Team also provides advice on:
� support requirements
� how to apply for Disabled Students Allowance and other sources of funding
� who to contact for support and advice.
You can find further information and details of who to contact regarding disability issues from the
following website:
http://www.liv.ac.uk/studentsupport/disability/index.htm
2.9 Students with financial hardship
If you need help with managing your finances whilst at university, you can talk to the Financial Support
Team.The FST provides personalised, independent and confidential support on a wide range of
financial issues.
These include:
� government student loans and grants
� previous study and how it will affect your funding entitlement
� welfare benefits
� tax credits
14

� debt counselling and advice.
Contacts
Tel: 0151 794 6673
Email: fst@liv.ac.uk
Web: http://www.liv.ac.uk/admin/studentsupport/finance/
2.10 University Counselling Service
The counselling service can help you with any personal and emotional problems you might have while
at Liverpool. If you need to discuss anything in confidence you can talk to a counsellor, or use the daily
drop-in service. The contact details are below:
14 Oxford Street
Liverpool
L69 7WX
0151 794 3304
Email: counserv@liverpool.ac.uk
Web site: http://www.liv.ac.uk/counserv/
2.11 Student Charter
The University of Liverpool Student Charter is issued jointly by the Senate and Council of the
University and by the Liverpool Guild of Students. It makes explicit some of the reciprocal
responsibilities which members of the University, both staff and students, have to each other and which
policies and procedures in individual areas of the University should reflect. All new students will receive
a copy of the Charter as part of the publication 'Your University' upon arrival at the University. 'Your
University' is also available from the Student Administration and Support Division in the Foundation
Building.
Access to the Student Charter for all staff and continuing students is web based only.
The Student Charter can be downloaded from the following web pages:
Charter:
http://www.liv.ac.uk/tqsd/pol_strat_cop/uol_charter.pdf
Annexe:
http://www.liv.ac.uk/tqsd/pol_strat_cop/studchart_ann_2007-08.doc
15

Section 3
Programme Overview & Timetable
3.1 Aims & Objectives
Aims
The degree program aims to provide students with a first class training in research at Masters level, in
Biomedical Sciences and Translational Medicine.
Objectives
� To conduct independent pieces of research and provide Masters level research training via three
10 week research projects in an interdisciplinary research environment.
� To demonstrate a critical awareness of a range of modern techniques and to enable students to
increase their knowledge of current research in Biomedical Sciences to Masters level.
� To provide the acquisition and training of transferable skills and knowledge, appropriate to
postgraduate research students.
Learning outcomes
The three objectives above directly map on to the three separately assessed components of the
programme: A) Research Projects; B) Techniques and Frontiers in Biomedical sciences; C)
Transferable Skills. The learning outcomes of each of these components are detailed below:
A) Research Projects
Students will be enabled to develop the skills required for:
� Data gathering and interpretation in an area of biomedical research.
� Planning and managing research and achieving goals.
� The presentation and discussion of scientific data, both verbally and in writing.
� The acquisition of a detailed knowledge of the experimental foundation of a specific area of
biomedical research.
� Working in a group to achieve a common objective.
� Communication in science.
� Accessing information, including the use of electronic systems, and PC technology.
B) Techniques in Biomedical Sciences
Students will be enabled to:
� Develop a critical understanding of the experimental methods that underpin modern ideas in
biomedical sciences.
16

� Appreciate current experimental limitations and likely technical developments
� Develop the ability to access, collate and discuss in writing the subject literature.
Frontiers in Biomedical Sciences
Students will be enabled to:
� Develop an understanding of the concepts fundamental to modern ideas in biomedical
sciences.
� Relate emerging and future developments to existing knowledge.
� Develop the ability to access, collate and discuss in writing the subject literature.
C) Transferable skills
Students will be enabled to:
� Develop the skills required to access information, including the use of electronic systems,
and PC technology.
� Develop the skills required for communication in science, to both specialists and nonspecialists
� Be appraised of the skills required, and mechanisms for, transferring basic science into a
business setting
� Develop the ability to access, collate and discuss in writing technical information e.g. for
reports, publications.
� Develop the skills of group working and leadership to achieve objectives
� Improve their management skills, in terms of personal time management and research
management.
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3.2 Programme Content
The programme has a modular framework and is based around 3 semesters (i.e. one year, full time). It
is delivered through lectures, tutorials, seminars, short courses and research projects with individual
tuition. Each of these activities contributes to one of the 3 components of the programme: A) Research
Projects; B) Techniques and Frontiers in Biomedical sciences; C) Transferable Skills. These 3 modules
are assessed separately, and contribute 60%, 20% and 20%, respectively, of the total marks available
for the MRes degree. An overview of each module is given below, but further detailed information can
be found later in this handbook.
A) Research Projects
Students will undertake three research projects, comprising 10 weeks of lab work followed by 2 weeks
in which to write a project report and prepare a presentation. In most strands the research project is
chosen by the student depending on the strand of interest after discussion with staff involved in the
program. In the Cellular & Molecular Physiology strand, the first two research projects are allocated to
students and are chosen to augment their existing technique and knowledge base. For example those
who have previously followed courses in molecular biology might do a project involving
electrophysiology and vice versa. The third project is chosen by Cellular & Molecular Physiology
strand students after discussion with staff involved in the program. During the course of the project, all
students will be encouraged to suggest experiments, design experimental protocols, as well as being
taught subject specific techniques and advanced knowledge in transferable skills. The research project
will include at least three different research techniques to enhance experimental training skills that
need to be clearly stated at the end of each 10 week project. Students will have regular (usually daily)
contact with the supervisors or other laboratory members for advice and guidance. Time will be
allowed to undertake the necessary literature searches during the 10-week experimental period, and a
further 2 weeks is to be spent out of the lab in order to write a project report and make an oral or a
poster presentation to the Institute at the end of each project. Students will be assessed on their
project report, their presentation and their general performance in the lab.
B) Techniques and Frontiers in Biomedical sciences
Techniques in Biomedical Sciences
This part of the module consists of a series of lectures on a wide range of modern research
techniques, including stem cell and tissue engineering, use of bioluminescent intracellular probes,
electrophysiology, gene expression analysis, proteomic approaches, etc. These lectures are
complemented by tutorials designed to develop the fundamental skills required for laboratory research,
including data handling, generation of Figures, scientific writing and preparation of poster and oral
presentations.
Frontiers in Biomedical Sciences
In this part of the module, the emphasis is on how state-of-the-art research techniques are used to
advance knowledge in specific biomedical research areas and on modern methods/approaches
employed in the diagnosis of disease and the treatment of patients. Lectures on these topics are
complemented by tutorials and journal clubs designed to develop analytical and critical thinking skills.
Both the Techniques and Frontiers modules are enhanced by Seminars and Biomedical Review
Lectures within the Institute of Translational Medicine. Eminent scientists from throughout the UK
contribute to this by presenting their research on a variety of topics. Seminars take place weekly during
term time; Biomedical Review Lectures take place periodically on Thursdays from 5-6pm. It is
important that MRes students attend both Seminars and Biomedical Review Lectures to broaden their
knowledge and range of learning experiences. Seminars are organized by the individual Departments
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within the Institute and are advertised regularly via email. Attendance at certain Departmental Seminars
may be recommended by strand convenors to enhance awareness of research that is particularly relevant
to individual MRes strands.
Finally, strand-specific activities are an important part of the Techniques and Frontiers modules, as
they facilitate awareness of the science associated with particular research strands.
Students will be assessed on one short review based on the Techniques module, one short
review based on the Frontiers module, and a referees report based on a journal club.
C) Transferable Skills
Training in this module is on-going throughout the year and is delivered by staff involved with the
program and the University via central provisions. It includes training in research techniques and the
development of personal and professional transferable skills. Topics include research philosophy,
principles and ethics, managing research progress, data analysis and presentation, health and safety,
scientific and technical writing, patent law, exploitation of research, team work skills, time and resource
management, communication skills, self-assessment skills and leadership skills. In addition, there is a
weekly “English conversation” session run by The English Language Unit to improve communication
skills for students with English as a second language. Important and innovative parts of the
transferable skills module include the “IP and Commercialization” and “Writing a PhD Studentship”
workshops and debates for public understanding of science (science & society). At the end of the
module you will need to prepare a Portfolio of Assessment commentary as part of the transferable
skills training. Finally, you will attend a Demonstrator Training session as part of the transferable skills
training. Further information on the 3 assessed components of the module is given below (detailed
information can be found later in this handbook):
The IP and Commercialization Workshop will raise awareness of the issues associated with, and
necessary for, successful commercialisation of academic research. Intellectual property is a key
component for business success. You will learn about the types and importance of intellectual property
and how to search for patent information on the Web. The routes available for creating value from
basic research will be described. There will be a comparison of the licensing and spin-out routes,
together with detail of the business planning process and the role of the technology transfer office. You
will be working as a group to prepare a written business plan for potential commercialisation of
research. In addition, you will be required to present your idea as a „pitch‟ to a panel of judges in a
similar way to the popular television programme “Dragon‟s Den”.
The “Writing a PhD Studentship” workshop will enable students to create a coherent and feasible
research proposal for a scientific project to continue studying for a PhD, and to present this in a form
suitable for external scrutiny.
The Portfolio of Assessment Commentary will enable students to evaluate and reflect on the aims
and objectives of the individual programme components, as well as their own achievements. Students
will be required to assemble a professional-looking portfolio that documents their progression through
the programme in a form suitable for external scrutiny.
Students will be assessed on the business plan and presentation given in the IP and
Commercialisation component, on the PhD Studentship application, and on the Portfolio of
Assessment Commentary.
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3.3 Timetable and Deadlines
Research
Projects
October - July
(10am - 5.30 pm
Monday-Friday)
Research Project 1
(3 October – 9 December)
Oral/poster presentations:
6 January 2012
Project report deadline:
9 January 2012
Research Project 2
(9 January – 16 March)
Oral/poster presentations:
30 March 2012
Project report deadline:
10 April 2012
Research Project 3
(10 th April – 15 th June)
Oral/poster presentations:
29 June 2012
Project report deadline:
2 July 2012
Techniques and Frontiers
Modules
October - June
(9 am - 10 am
Monday-Thursday)
Techniques In Biomedical Sciences
Short review deadline:
30 January 2012
Frontiers In Biomedical
Sciences
Short review deadline:
15 May 2012
Journal Clubs
Referee‟s report deadline:
11 June 2012
Biostatistics workshop
October 2011
(date to be confirmed)
Seminars and Biomedical Review
Lectures
(dates to be announced)
Transferable Skills,
University &
Graduate School Courses
October - August
Prospective Licensee Training
Course
26-28 September 2011
University Demonstrator Training
Workshop
6 th October 2011
IP and Commercialization Workshop
July 2012
(dates to be confirmed)
Writing a PhD Studentship
Workshop
2 July 12.00-2.00pm
Application deadline
10 Aug 2012
Submission of portfolio
by 17 August 2012
English Conversation Classes
Fridays 9-10am
Please note: Students need to be resident in Liverpool until 18 August 2012 except timetabled
holidays.
Timetabled holidays: 17 December 2011 – 2 January 2012
31 March 2012 – 9 April 2012
18 August 2012 – 9 September 2012 (Inclusive)
Students MUST attend a viva with the MRes external examiner in order to be awarded an MRes
degree. The specific date for your viva will be set nearer the time but you must be available in
Liverpool from 10 - 14 September 2012, when vivas will be held.
English Conversation Classes are compulsory for students with English as a second
language.
20

3.4 Quick Overview of Daily Activities
Days English
Classes
Monday
Tuesday
Wednesday
Thursday
Friday
Techniques, Seminar Research
Frontiers
Project
9-10am All day
9-10am All day
9-10am All day
9-10am 5-6pm
(Biomed Review)
All day
9-10am All day
Event Location
Techniques/Frontiers lectures Physiology Seminar Room
Techniques/Frontiers strand specific activities Venues to be confirmed later
English Conversation Classes Venue to be confirmed later
Biomedical Review Seminars Sherrington Lecture Theatre
21

3.5 Schedule of Techniques, Frontiers and Transferable Skills sessions
Semester 1 (Techniques and Transferable Skills)
Time: 9 a.m. Monday-Thursday
Venue: Physiology Seminar Room (except for strand specific activities and seminars)
Date Presenter Session
03.10.11 Prof. Alan Morgan Introduction to module
04.10.11 Prof. Alan Morgan Science skills (basic lab skills)
05.10.11 Dr. Jeff Barclay Science skills (literature and database searching)
06.10.11 Prof. Rod Dimaline Quantitative Analysis of Gene Expression
10.10.11 Strand convenor Strand-specific activity
11.10.11 Dr. Andrew Owen Real time polymerase chain reaction (PCR).
12.10.11 Dr. Steve Royle Science skills (organisation/record keeping)
13.10.11 Dr. Ted Burdyga Confocal imaging of smooth muscles in situ
17.10.11 TBA Strand-specific activity
18.10.11 Dr. Bettina Wilm Transgenic Techniques
19.10.11 Dr. Ian Prior Science skills (Making Publication Quality Figures)
20.10.11 Dr. Lee Haynes Applications of GFP and its variants in cell biology
24.10.11 TBA Strand-specific activity
25.10.11 Dr. Jean Sathish Flow cytometry – principles and applications
26.10.11 Prof. Alan Morgan Workshop: preparing for debates
27.10.11 Prof. Alexei Tepikin Optical Techniques
31.10.11 TBA Strand-specific activity
01.11.11 Dr. Diana Moss Production and use of recombinant proteins in cell and
developmental biology
02.11.11 Dr. Jeff Barclay Genetics and invertebrate model organisms in
biomedical sciences
03.11.11 Dr. Ian Prior Electron Microscopy for Bioscience
07.11.11 TBA Strand-specific activity
08.11.11 Dr. Geoff Edwards Lecture
09.11.11 Students Debate 1 (animal research)
10.11.11 Dr. Eithne Costello-Goldring Science Skills (writing project reports)
14.11.11 TBA Strand-specific activity
15.11.11 Dr. John Quayle In vitro techniques used to study arterial function
16.11.11 Prof. Alan Morgan Science skills (publishing in journals)
17.11.11 Dr Marta van der Hoek Lecture (handling clinical trial data)
21.11.11 TBA Strand-specific activity
22.11.11 Prof. John Quinn Nurturing Nature: How Polymorphic Variation Helps
Shape The Individual
23.11.11 Students Debate 2 (human stem cell research)
24.11.11 Dr. Chris Goldring Fine-tuning the expression of proteins in cell and
animal models
28.11.11 TBA Strand-specific activity
29.11.11 Dr. Neil Kitteringham Proteomics in biomedical research
30.11.11 Dr. Jeff Barclay Science skills (poster presentations)
01.12.11 Prof. Chris Sanderson An introduction to molecular cartography
05.12.11 Strand convenor Strand-specific activity
06.12.11 Prof. Alan Morgan Science skills (oral presentations)
07.12.11 Prof. Alan Morgan Q&A/feedback/information session
22

Frontiers in Biomedical Sciences (semester 2)
Time: 9 a.m. Monday-Thursday
Date Presenter Session
09.01.12 Strand convenor Strand-specific activity
(All strands submit project 1)
10.01.12 Prof. Alan Morgan Introduction to module and journal clubs
11.01.12 Prof. Alan Morgan Molecular mechanisms of ageing
12.01.12 Prof. Bob Burgoyne Calcium sensor proteins in the regulation of neuronal
function
16.01.12 Prof. Alan Morgan Journal club demonstration (all strands)
17.01.12 Prof. Bob Burgoyne Journal club demonstration (all strands)
18.01.12 Dr Graeme Sills Lecture
19.01.12 Prof. Mike Clague Lecture
23.01.12 Students Debate 3 (medically assisted suicide)
24.01.12 Prof. Mike Clague Journal club demonstration (all strands)
25.01.12 Dr. Dominic Williams Lecture
26.01.12 Prof. David Edgar Stem cells and induced pluripotent cells
30.01.12 Dr. Dominic Williams Journal club (Drug Safety)/SSA
(All strands submit short review 1)
31.01.12 Prof. David Edgar Journal club (Stem cell)/SSA
01.02.12 Dr. Steve Royle Clathrin-mediated endocytosis: a complex web of
interactions.
02.02.12 Prof. Andrea Varro Biomarkers, cancer microenvironment and upper GI
carcinogenesis
06.02.12 Dr. Steve Royle Journal club (Cell Mol Physiol)/SSA
07.02.12 Prof. Andrea Varro Journal club (Gastro)/SSA
08.02.12 Prof Saye Khoo Lecture
09.02.12 Prof. Susan Wray Lecture
13.02.12 Prof Saye Khoo Journal club (Pharmacology)/SSA
14.02.12 Prof. Susan Wray Journal club (Cell Mol Physiol)/SSA
15.02.12 Dr. Barry Campbell Lecture
16.02.12 Dr. Toni Plagge Lecture
20.02.12 Students Debate 4 (topic chosen by students)
21.02.12 Dr. Toni Plagge Journal club (IMB)/SSA
22.02.12 Dr. Ana Alfirevic Pharmacogenetics
23.02.12 Dr. Dean Naisbitt Lecture
27.02.12 Dr. Ana Alfirevic Journal club (Pharmacology)/SSA
28.02.12 Dr. Dean Naisbitt Journal club (Drug Safety)/SSA
29.02.12 Dr Patricia Murray Lecture
01.03.12 Prof. Ross Sibson „Normal‟ Alternative Splicing and Disease
05.03.12 Dr Patricia Murray Journal club (Stem cell)/SSA
06.03.12 Prof. Ross Sibson Journal club (Cancer)/SSA
07.03.12 Dr. Dharani Hapangama Lecture
08.03.12 Prof. Mark Pritchard Why do some people develop cancers of the
gastrointestinal tract?
12.03.12 Dr. Dharani Hapangama Journal club (Stem cell)/SSA
13.03.12 Prof. Mark Pritchard Journal club (Gastro)/SSA
14.03.12 Dr Joe Slupsky Pathogenetic role of PKCbetaII in chronic
lymphocytic leukaemia
15.03.12 Dr. Sylvie Urbe Lecture
23

Frontiers in Biomedical Sciences (semester 3)
Time: 9 a.m. Monday-Thursday
Date Presenter Session
10.04.12 Dr. Sylvie Urbe Journal club (Cell Mol Physiol)/SSA
(All strands submit project 2)
11.04.12 Dr. Judy Coulson Transcription in cancer: regulating the regulators
12.04.12 Dr. Laiche Djouhri Role of Primary Afferent Dorsal Root Ganglion
(DRG) Neurons in Chronic Pain
16.04.12 Dr. Judy Coulson Journal club (Cell Mol Physiol)/SSA
17.04.12 Dr. Laiche Djouhri Journal club (IMB)/SSA
18.04.12 Dr. Lugang Yu Circulating galectin-3 and cancer metastasis
19.04.12 Dr. Silvia Mora Lecture
23.04.12 Dr. Lugang Yu Journal club (Gastro)/SSA
24.04.12 Dr. Silvia Mora Journal club (Stem cell)/SSA
25.04.12 Dr. Michael Cross Lecture
26.04.12 Dr. Tim Green Obtaining and using structural information:
30.04.12 Dr. Michael Cross Journal club (Drug Safety)/SSA
01.05.12 Dr. Tim Green Journal club (Pharmacology)/SSA
02.05.12 Dr. Carlos Rubbi Lecture
03.05.12 Prof Soraya Shirazi-Beechey Glucose sensing and signalling; regulation of intestinal
glucose transport
07.05.12 NONE BANK HOLIDAY
08.05.12 Dr. Carlos Rubbi Journal club (Cancer)/SSA
09.05.12 Dr. Andrew Owen Lecture
10.05.12 Dr. Helen Wallace Airway Disease in Cystic Fibrosis: Diagnosis and the
Search for Improved Therapies‟
14.05.12 Dr. Andrew Owen Journal club (Pharmacology)/SSA
(All strands submit short review 2)
15.05.12 Dr. Helen Wallace Journal club (Stem cell)/SSA
16.05.12 Dr. Swamy Thippeswamy Lecture
17.05.12 Students Debate 5 (topic chosen by students)
21.05.12 Dr. Swamy Thippeswamy Journal club (IMB)/SSA
22.05.12 Dr. John Jenkins Proteomic Approaches: Colon Cancer Biomarkers
23.05.12 Dr. David Criddle Mitochondrial dysfunction in acute pancreatitis
24.05.12 Dr. Eithne Costello-Goldring Lecture
28.05.12 Dr. John Jenkins Journal club (Gastro)/SSA
29.05.12 Dr. Eithne Costello-Goldring Journal club (Cancer)/SSA
30.05.12 Dr. David Criddle Journal club (Cell Mol Physiology)/SSA
04.06.12 NONE BANK HOLIDAY
05.06.12 NONE BANK HOLIDAY
06.06.12 Students Debate 6 (topic chosen by students)
07.06.12 Prof. Alan Morgan Module review/information session
11.06.12 Strand convenor Strand-specific activity
(All strands submit referees report)
02.07.12 Strand convenor Strand-specific activity
(All strands submit project 3)
24

Section 4
Assessment
4.1 Overview of Assessment
The accreditation for a Research Masters Degree is regulated by The University of Liverpool
Ordinances and Regulations.
The award of MRes requires that a minimum of 180 credits be obtained. In order to be eligible for the
award of an MRes, candidates must achieve a minimum mark of 50% in each of the 3 modules
(Research projects, Techniques and Frontiers in Biomedical Sciences, Transferable Skills). However,
where the average of the total marks in all modules is 50% or above, a mark in the range 40-49% may
be deemed compensatable.
Candidates who fail to satisfy the examiners in a module assessment shall be permitted to re-present
the failed work on one further occasion only, at a time specified by the examiners.
4.1.1 Late submission of work
Please note that the standard University penalty for late submission of written work applies; 5%
of the total marks available for the assessment will be deducted from the final mark for each
day after the submission date up to maximum of seven days. Work received after seven days
will receive a mark of zero.
4.1.2 Marking of submitted work
We aim to assess all written work within three working weeks after submission.
4.1.3 Mitigating Circumstances
When awarding degrees, the Board of Examiners will take into consideration any mitigating
circumstances that may have adversely affected a candidate‟s performance providing these
have been notified in writing to the Programme Director. Where illness is involved a medical
certificate should be supplied. Rules and regulations can be downloaded from the University
website.
Please note that the appropriate application form needs to be filled out to be eligible for
consideration. A copy of the mitigating circumstances form can be found at the back of this
handbook.
4.1.4. External Examiner
The External Examiner(s) will oversee course assessment procedures and assess annually the
quality and relevance of the subjects taught. The External Examiner(s) will conduct a viva voce
examination on the research elements of all candidates. Attendance at the viva is a prerequisite
for obtaining the MRes degree.
25

4.1.5 Award of Distinction
A distinction will be awarded to MRes candidates who obtain an overall mark of 70% or over
AND achieve marks of 70% or over in at least 2 out of the 3 assignments in each of the three
assessed components of the course. In other words, a distinction will be awarded if the
following conditions are met:
� Average mark of 70% or over for the 3 Research Project reports AND 70% or over in at
least 2 out of these 3 assignments
� Average mark of 70% or over for the 3 Techniques & Frontiers in Biomedical Sciences
assignments AND 70% or over in at least 2 out of these 3 assignments
� Average mark of 70% or over for the 3 Transferable Skills assignments AND 70% or over
in at least 2 out of these 3 assignments
For example, a student who obtained the following marks would not be awarded for a distinction
despite obtaining 70% overall, because they had two marks of less than 70% in the
Techniques/Frontiers component:
Research Projects Techniques/Frontiers Transferable Skills
1 2 3 Review 1 Review 2 Referee Portfolio Studentship Business
100% 100% 100% 100% 100% 100% 100% 100% 100% Total Mark %
70 71 71 65 66 80 80 72 70 70
4.1.6 Progression to PhD
Progression to PhD of MRes graduates is subject to obtaining 65% or above in the Research
Projects and is also subject to the discretion of the supervisor.
4.2 Role of the External Examiner
The external examiner has the important task of checking and validating the marks and degree
recommendations of the Board of Examiners for the MRes. This process is carried out at several
levels.
� The external examiner views all marks from taught modules, and examples of in-course
assessment work, including communication skills exercises.
� The external examiner is also sent copies of student‟s portfolio to assess.
� The external examiner is sent a list of all marks for each module.
� The external examiner shall viva all students for around 20-30 minutes. The focus of the viva will
be the student‟s research projects and its assessment in the portfolio. The Strand Convenor is
also present throughout the viva process.
� The external examiner performs a significant role at the final Examiners Board meeting. The
external examiner might comment at this meeting on each student‟s performance and on the
course in general.
26

� The external examiner writes an annual report on the course and on the assessment process.
There will be several external examiners representing research expertises in the main strands of the
Degree Program.
The vivas will take place in September (10-14 September 2012) and attendance at the viva is
prerequisite for obtaining the degree.
27

4.3 Plagiarism or Collusion
Cases of suspected plagiarism or collusion will be considered by the Board of Examiners. If the Board
of Examiners decides that collusion or plagiarism have taken place, the Board shall have the discretion
to award the marks [if any] which it thinks appropriate in the light of the gravity and extent of the
offence. A talk on plagiarism and how to avoid it will be given as part of the compulsory induction
activities. Below are highlighted examples of definitions of plagiarism and collusion for your attention.
An extract from The University Code of Practice on Assessment on these issues is copied for your
information in full below. All students must read this section and be aware and observe these rules in
regard of all written work submitted for assessment. The plagiarism form should be signed for all
written work (a copy of this form can be found at the back of this handbook).
Plagiarism includes:
The representation of the work, written or otherwise, of any other person, including another student, or any
institution, as the candidate’s own. Examples of plagiarism may be any of the following forms:
i the verbatim copying of another‟s work without acknowledgement;
ii the close paraphrasing of another‟s work by simply changing a few words or altering the order
of presentation, without acknowledgement.
Iii unacknowledged quotation of phrases from another‟s work;
iv the deliberate and detailed presentation of another‟s concept as one‟s own.
It is also very important to avoid self-plagiarism, i.e. re-using text, data or images that have been
previously submitted for assessment. In other words, you are expressly forbidden from copying any
such material from one of your written assignments to another. Any cases of suspected self-plagiarism
will be investigated and dealt with as for other forms of plagiarism, as detailed below.
Collusion includes:
The conscious collaboration, without official approval, between two or more students in the preparation
and production of work which is ultimately submitted by each in an identical, or substantially similar
form and/or is represented by each to be the product of his or her individual efforts. Collusion also
occurs where there is unauthorized co-operation between a student and another person in the
preparation and reproduction of work which is presented as the student‟s own.
Extract on Plagiarism and collusion taken from the University Code of Practice on Assessment.
Submission of other work for formal assessment
1. A dissertation, thesis, essay, project or any other work which is not undertaken in an examination
room under supervision, but which is submitted by a student for formal assessment during his
course of study must be written by the candidate himself and in his own words except for
quotations from published and unpublished sources which shall be clearly indicated and
acknowledged as such. The incorporation of material without acknowledgement will be treated as
plagiarism, subject to the custom and usage of the subject. The source of any photograph, map or
other illustration shall also be indicated as shall the source, published or unpublished, of any
material not resulting from the candidates own experimentation, observation or specimencollecting.
28

2. A candidate shall not be permitted to incorporate material which has been submitted in support of a
successful application for a degree of this or any other university or any other approved degreeawarding
body except for the purpose of drawing attention, for reference purposes only, to such
material, including calculations or the results of experimental work. Where such material is
incorporated, the fact shall be recorded together with the title of the thesis or other work, the date of
the award of the degree and the name of the university of other degree-awarding body making the
award.
3. The conscious collaboration, without official approval, between two or more students in the
preparation and production of work which is ultimately submitted for assessment by each in an
identical, or substantially similar form, and/or, is represented by each to be the product of his or her
individual efforts, is not permitted. No student is permitted to enter into unauthorized cooperation
with another person in the preparation and production of work which is presented for assessment of
the student‟s own.
4. Except when special provisions are made, a dissertation, thesis, essay, project or any other work
which is not undertaken in an examination room, shall remain in the ownership of the university
irrespective of whether or not such work has been returned to the candidate. Marks awarded at
any stage of the academic year shall be provisional, pending confirmation at the final meeting of
the Board of Examiners.
Candidate shall be required to re-submit any provisionally-marked work for further inspection when
required to do so by any member of the Board of Examiners.
5. Except when prevented by illness or by other sufficient cause, the marks of any student who fails to
submit work by the prescribed date shall be subject to penalty deduction in accordance with a scale
determined by the Head of Department. It shall be the duty of Heads of Departments to ensure
that students are notified of due submission dates and the penalty scale to be applied in the case of
late submission.
6a. Work submitted for assessment (Instructional Courses)
Where an Examiner suspects a candidate of reproducing, in a University test, work of another
person or persons without acknowledgement, he shall report the matter to the Chairman of the
Board of Examiners, who shall as soon as possible investigate (or arrange an investigation of) the
circumstances, with a view to ascertaining whether there is a case to be considered by the Board of
Examiners. For this purpose, the Chairman of the Board of Examiners (or his nominated
representative) shall inform the candidate of the matter under investigation and invite the candidate
to provide an explanation of the circumstances. The candidate shall be afforded an opportunity to
make any representations he may with to make to the Chairman of the Board of Examiners (or his
nominated representative). The Chairman of the Board of Examiners (or his nominated
representative) shall consider any representations made by the candidate and report his findings to
the Board of Examiners. If the Board of Examiners, decides that plagiarism has taken place, the
Board shall have the discretion to award the marks (if any) which it thinks appropriate in the light of
the gravity and extent of the plagiarism involved. The marks (if any) thus awarded shall be treated
in the same way and have the same consequences are regards the assessment of the candidate‟s
overall performance as a similar mark awarded to other candidates.
If, in the opinion of the Board of Examiners, the gravity of proven plagiarism or collusion calls into
question of the propriety of (i) deeming the Candidate to have been successful in the examination,
or if (ii) recommending an award in accordance with the total accumulated marks, the Chairman of
the
Board of Examiners, in consultation with the appropriate Dean of Faculty, shall submit a report and
recommendation, the consideration of the Senate Committee for the Award of Decrees, Diplomas
29

and Certificates. Following consideration of such report and recommendation, the Senate
Committee for the award of Degrees, Diplomas and Certificates shall have the power to determine
that accordance with the circumstances, either (i) the degree classification be modified, (ii) the
degree be awarded without honours, (iii) the candidate be failed and no award be made, or (iv) the
matter be referred for further review by the Board of Examiners.
6b Work submitted for assessment (Higher Degrees by Research)
Where the panel of Examiners suspect a candidate of reproducing, in a dissertation or thesis, work
of another person or persons without acknowledgement, they shall afford the candidate an
opportunity to make any representation he may wish to make. Following consideration of such
representation, the panel of Examiners shall have the discretion to recommend the award of the
degree or otherwise, in the light of the gravity and extent of the plagiarism involved.
7. Where an Examiner suspects (i) unauthorized collaboration between two or more students or (ii)
unauthorized co-operation with another person, the procedure for suspected plagiarism as
determined in clause 6(a) of these regulations shall be followed.
4.4 Plagiarism form
A plagiarism form must be submitted with every piece of work you submit. A copy of this form can be
found at the back of this handbook, and you can use copies of the form for this purpose.
4.5 Procedure for requesting a deadline extension
In cases where you are unable to meet assessment deadlines, for example due to illness, you must
request an extension to the deadline from your Strand Convenor, who will decide whether or not to
grant your request.
30

Section 5
Research Projects
Students will undertake three research projects, comprising 10 weeks of lab work followed by 2 weeks
in which to write a project report and prepare an oral or poster presentation. During the course of the
project, all students will be encouraged to suggest experiments, design experimental protocols, as well
as being taught subject specific techniques and advanced knowledge transferable skills. The research
projects will include at least three different research techniques to enhance experimental training skills.
Students will have regular (usually daily) contact with supervisors and other laboratory members for
advice and guidance during the 10 weeks in the lab. Time will be allowed to undertake the necessary
literature searches during the 10-week experimental period, and a further 2 weeks is to be spent out of
the lab in order to write a project report and make an oral or a poster presentation to the Institute at the
end of each project. Supervisors will provide advice on which results should be included in the project
report, the presentation of Figures, the interpretation of results and the overall structuring of the project
report. However, supervisors are not permitted to comment on written draft reports. Supervisors are
also expected to provide advice on the preparation of the oral and poster presentations. Students will
be assessed on their project report, their presentation and their general performance in the lab.
Further information on these assessments is provided later in this Section.
5.1 Laboratory safety and working hours
You need to read carefully and obey all the instructions regarding safety that have been given to you
before commencing experimental work in the laboratory. You are normally be expected to work in the
lab between 10.00am-5.30pm, Monday to Fridays, although flexibility is required depending on the type
of experiments undertaken after discussion with supervisor. A supervisor who is frequently away from
the laboratory is expected to allocate a post doc or a experienced PhD student to help with your day to
day supervision. Work outside these hours, including at weekends, is only permitted if either
your supervisor or a suitably qualified person approved by your supervisor is present. The out
of hours work book must be signed on entering and leaving the building stating the name of the person
who is supervising you.You are not expected or advised to work in the lab longer than the 10
weeks allocated for your project, in order to allow you enough time to complete your writing and
prepare your talk or poster by the end of your project placement.
If for any reason you need to be absent (e.g. other meetings, courses, illness, etc) you should inform
your supervisor as soon as possible, at the latest by 9.30am on the day that you will be away from the
lab, by calling or emailing them. You must provide information on when and why you will be absent,
and ask him/her to make arrangements for any ongoing experiments that you cannot complete that
day. You should also call or email your strand convenor to formally report your absence.
Working with human subjects and/or human material
Supervisors have a responsibility to ensure that all work involving human subjects is covered by
appropriate Ethics Comittee Permission. They should also ensure that students conducting research
projects involving human subjects and/or material understand the permission given for their work, and
in writing their dissertation, they make a clear statement of the Ethics Comittee Approval for the work.
Working with animals
Supervisors have a responsibility to ensure that the appropriate Home Office Authority (both personal
and project licence) are in place before working with experimental animal is started. They should also
ensure that students conducting research projects involving experimental animals understand the
permission given for their work, and in writing their dissertation, they make a clear statement of the
Home Office Approval for the work.
31

Laboratory books are the property of Liverpool University and are to be handed to the supervisor at the
end of the project placement.
5.2 Preparation of Research Project Reports
These notes are intended to help you in the preparation of the report describing your project. You will
also be given a lecture on how to prepare a good project report as part of the Techniques in
Biomedical Sciences lecture series. Your project should be prepared in the format of a research paper
recently published in the Journal of Biological Chemistry. Please consult a recent issue of this
journal to check on the appropriate style to adopt. It is expected that your report will be produced to
“publication quality”, which means that you should pay close attention to spelling, punctuation and
grammar, as well as scientific content. You should also take care with the quality of figures, clarity of
legends, and citation of references. An example of a project report is given at the end of this Section
for you to refer to. Your paper should be single spaced, in font size 12 and must be no more than 4000
words in length (excluding references). Marks will be deducted proportionally for exceeding this limit
(for example, 4400 words = 10% over the limit = 10% deducted), down to a minimum cap set at 50%
for the assignment. Figures and tables should be embedded in the text, in a similar style to papers
published in the Journal of Biological Chemistry. The report should be produced on a computer using
appropriate word processing and graphic packages. Please attach a front cover sheet to your report
stating your name, your student number, the title of the report, the name of your supervisor, the name
of your internal assessor (2nd marker) if known, and the word count of your report. A template cover
sheet is supplied at the end of this Section for this purpose. You should submit three copies of
your final project report; one to your supervisor, one to your internal assessor, and one to your strand
convenor. You also need to submit an electronic copy of the final version via Turnitin. These files need
to be able to be uploaded onto Turnitin with all Figures included so where necessary your files will
need to be compressed. Deadlines for submission of the project reports and dates of the oral/poster
presentations are given in Section 3.3.
The report must conform to the following style:
1. Abstract. This is a concise summary of the work. It should deal with the reasons why the work
was performed, the methods used, the results obtained, and the major conclusions reached.
This section must not exceed 250 words.
2. Introduction. This should describe the background to the relevant scientific literature and the
work performed. The hypothesis to be tested should be explained, and the major aims should
be specified. The length of this section should not exceed 2 pages.
3. Methods. The description of methods should be adequate for a competent worker in the area
to follow and repeat your experiments. You should however be concise; again recent papers in
your field of study should provide a guide for you.
4. Results. This section should consist of text which describes the experimental data obtained
and where appropriate describes the rationale that links one experiment to the next. The text
should be cross-referenced to the relevant figure or table. Is it not necessary to reproduce the
same material in tables and figures. This section must not take the form of a diary of your
experimental observations in the laboratory, nor need every single experimental observation be
recorded. Instead, you must take responsibility for collating the data, and whatever statistical
analysis are appropriate, and presenting your findings in a way that makes it possible for the reader
to understand your major conclusions. Each figure should have an explanatory legend that
enables the reader to understand how the experiment was performed. Figures and tables should
be inserted into the main body of the text as close as possible to the relevant section.
32

5. Discussion. This section should focus on the interpretation of your results, and set them in the
context of current knowledge in the field. It should not be necessary to repeat your description
of the experimental data, but you will want to summarise your main findings and explain how
they are meaningful.
6. References. Again, this should follow the Journal of Biological Chemistry style. It is strongly
recommended that you use reference organising software (such as EndNote) to construct
your references, which will ensure that you use the correct Journal of Biological
Chemistry style. References in the text should be cited as a number in the order in which they
appear. The reference list should be correspondingly numbered, and references listed in order
of their citation in the text.
7. Footnotes. Abbreviations and acronyms used in the text must be defined immediately after the
first use of the abbreviation. In addition, a complete list of all abbreviations used should
also be cited in a single Footnote section (see a recent Journal of Biological Chemistry
paper for how Abbreviations Footnotes are presented). The abbreviations of some important
biochemical compounds, e.g. ATP, NADH, DNA, and amino acids in proteins, need not be
defined.
5.3 Preparation of Oral and Poster Presentations
You will be required to make a presentation for each of your Research projects. This will comprise 2
poster presentations and 1 oral presentation. The dates of these presentation sessions are given in
Section 3.3, but the scheduling of oral/poster presentations for individual strands will be announced
nearer the time. You will be given instructions on how to prepare good oral and poster presentations as
part of the Science Skills series in the Techniques in Biomedical Sciences module. You will also be
given advice and assistance from your supervisor in preparing your presentations. The cost of
printing your poster will be provided by your supervisor.
33

5.4 Assessment of Research Projects
For each research project, students will be assessed on their project report, their presentation and on
their general performance in the lab. Assessment of the project report will be conducted by the
supervisor (1 st marker) and an internal assessor (2 nd marker). Continual assessment of performance in
the lab is provided by the supervisor alone. Assessment of the presentation is by 2 independent
markers. The 3 research projects combined contribute 60% of the total marks available for the MRes.
An explanation of how marks are awarded for these individual assessments and how they are
combined to give the final mark is given below:
Supervisor and Internal Assessor
Mark 1: Awarded for the project report; this will reflect scientific quality of the dissertation, its originality,
clarity and thoroughness; the internal assessor will also base his/her mark on a short informal mini-viva
(project discussion).
Supervisor
Mark 2: This will be a continual assessment mark awarded for assessment of the student‟s conduct during
the project taking into account organization, initiative, effort and performance in the lab.
Two Internal Assessors
Mark 3: Awarded for oral/ poster presentation.
Supervisor and Internal Assessor
Supervisor
Mark 1 - Project report, 40%
Mark 2 - Continual Assessment, 10%
Internal Assessors Mark 3 - Oral/poster Presentation, 10%
Total = 60%
The average of the marks for the three Research Projects will contribute 60% of the total
MRes mark (marks for Project 1 + 2 + 3 divided by 3).
Details of the assessment criteria used and the assessment forms that will be used by markers
are given on the on the pages that follow.
34

5.4.1 Assessment Form for research MRes in project Biomedical reports Sciences
Project Write Up Assessment Form
Student:
Rotation:
Project Title:
Supervisor:
Second marker:
Moderator:
Please complete this form WITH A TICK AS APPROPRIATE when marking the M.Res write ups, and return it, with
the dissertation to your strand convenor. INDICATION OF POTENTIAL DEGREE CLASS BY MARK ATTAINED
(Distinction 70-100); (Merit 60-69); (Pass 50-59); (Fail

5.4.2 Specific Criteria for assessment of research project reports
Distinction Level 100% - 90%
90% - 80%
80% - 70%
Pass Level 69% - 65%
64% - 60%
59% - 55%
54% - 50%
Fail Level 49% - 45%
44% - 40%
39% - 35%
34% - 10%
0%
Outstanding. No (or virtually no – use scaling) better result
conceivable at Masters level. Factually correct and
complete, with extensive evidence of critical thinking.
Evidence of extensive research of relevant literature. Very
logical structure, very well written and presented. Clear
evidence of original thought and cogent scientific argument.
Excellent. Clear evidence of achievement on a scale
reserved for exceptionally high quality work at Masters level.
Essentially correct and complete, with evidence of critical
thinking and excellent use of relevant literature. Logical
structure, well written and presented, displaying varying
degrees (use scaling) of original thought and cogent
scientific argument.
Very Good. Content essentially without any major flaws,
very well explained with clear evidence of a high level of
scientific competence, and mature, critical scientific
judgement in discussing the extent to which the objectives of
the research have been achieved.
Good. Well explained, showing good evidence of critical
scientific judgement.
Quite Good. Well explained, with good understanding and
some evidence of critical scientific judgement
Fairly Good. A generally sound project with a good or quite
good level of understanding, evidence of sound scientific
competence and judgement.
Adequate. Showing some progress but with some
deficiencies in one or more aspects of theoretical and/or
experimental approach, knowledge of the literature, scientific
competence and judgement.
A poor dissertation with an overall superficial approach.
Essentially an incomplete report with major omissions in
several areas and evidence of a poor understanding of the
project‟s aims, methods and outcomes.
A poor project with superficial approach and more errors
and/or omissions and/or evidence of a deficiency of effort
and/or poor understanding.
A marked deficiency in content of understanding and
application.
Even more marked deficiencies in content (on a variable
scale) of understanding and application and presentation.
A complete absence of relevant content.
36

5.4.3 Specific Criteria for continual assessment
Distinction
Level
100% - 90%
90% - 80%
80% - 70%
Pass Level 69% - 65%
64% - 60%
59% - 55%
54% - 50%
Fail Level 49% - 45%
44% - 40%
39% - 35%
34% - 10%
0%
Outstanding. Student highly motivated and capable of
working independently on all aspects of project. As good
as can be expected at Masters level. No room for
improvement in project (design), execution and
motivation.
Excellent. Student able to (design) and execute project
work independently with the minimum of assistance.
Varying degrees of competence depending on task (use
scaling).
Very Good. Student able to generate high quality data
and/or identify and answer important questions, mostly
at the first attempt.
Good. Student able to (design) and execute project
work with initial help, showing good evidence of scientific
judgement. Occasionally requiring additional assistance.
Quite Good. Student able to (design) and execute
project work with initial help, showing some evidence
independent of critical scientific judgement. Student
requiring additional assistance more frequently, but still
able to work independently.
Fairly Good. Well motivated student able to (design)
and execute project work only with significant help.
Adequate. Student needing considerable initial help
and has encountered a few deficiencies in
motivation/application and in reporting and analysing
data.
Quite Poor. Student requiring constant help to (design)
and execute project work and analyze data. Student
less inclined to seek necessary help.
Poor. Student requiring constant help to (design) and
execute project work and analyze data and produces
results/questions of variable quality.
Student requires considerable help to design and
execute project work. Produces data/work of poor
quality and is unable to analyze data. Poor motivation
Student displays inability to carry out project work and
low or no motivation (use scaling)
Complete inability or willingness to do project work and
no motivation.
37

5.4.4 Assessment Form for oral presentations
Presentation, grammar & readability Guide Mark %
Very good structure. Slides clear, and well matched to
talk itself.
Excellent communication with audience. Very confident
delivery.
Perfect timing and pace.
Good talk structure, with informative slides showing wellselected
content.
Good communication with audience. Confident delivery.
Timing and pace acceptable.
Room for improvement in the talk structure and content
of the slides.
Limited contact with audience. Lack of confidence in
delivery.
Problems with timing and/or pace.
> 70%
60 – 69%
50 – 59%
Structure and/or content of slides poor. 40 – 49%
Little or no communication with audience. Delivery hard
to follow.
Talk badly timed (i.e. very brief, or had to be stopped
mid-way).
Unsatisfactory < 40%
Scientific content Guide Mark %
Excellent understanding of the topic and interpretation of
the science.
Answers to questions were rational and confident.
Good understanding of the topic and interpretation of the
science.
Answered most questions well.
Covered the basic concepts fairly well. Provided some
interpretation of the science.
Problems with answering some (more complex)
questions.
Very limited understanding of the topic. Little or no
interpretation of the science
Had difficultly answering even basic questions.
> 70%
60 – 69%
50 – 59%
40 – 49%
Unsatisfactory < 40%
General comments (if applicable)
5.4.5 Assessment Form for poster presentations
Overall Mark %
38

Presentation, grammar & readability Guide Mark
%
Presented in a logical and very easy to follow format. Excellent use of
language with no or very few grammatical/spelling errors.
Excellent quality figures and tables, with clear and informative legends.
Presented in a clear, easy to follow style with good use of English. Few
grammatical or spelling errors.
Figures, tables and associated legends well presented.
Some issues with style and format that make it somewhat difficult to
follow in parts. Several grammatical and/or spelling errors.
Figures, tables and legends reasonable, but clarity and/or content could
be improved.
Significant issues with style and format. Difficult to read and follow.
Numerous problems with grammar and spelling.
Figures, tables and/or legends are not well presented, or are absent.
>70%
60 – 69%
50 – 59%
40 – 49%
Unsatisfactory < 40%
Scientific content Guide Mark
%
Background: Excellent introduction to topic. Very clear project aims. > 70%
Results: Data presented extremely clearly and logically. Interpretation
faultless.
Verbal Presentation: Explained the project impecably. Answers to
questions were rational and confident.
Background: Good introduction of the topic and project aims. 60 – 69%
Data: Very clear presentation of data. Few problems of interpretation.
Verbal Presentation: Explained the project competantly. Answered
most questions well.
Background: Introduced basic concepts and aims. 50 – 59%
Data: Data reasonably well presentated, but gaps and/or errors in
interpretation.
Verbal Presentation: Explained the project fairly well. Problems with
answering more complex questions.
Background: Poor description of background and aims. 40 – 49%
Data: Significant issues with both presentation and analysis of the data.
Verbal Presentation: Explanation of project poor; had difficultly
answering even basic questions.
Unsatisfactory < 40%
General comments (if applicable)
Overall Mark %
39

5.5 Submitting your Research Project Report
You must adhere to the following instructions:
1. Use the example in section 5.6 to create a front sheet for each of your project reports;
2. Submit one hard copy to your supervisor;
3. Submit one hard copy to your internal assessor (allocated to you by your Strand
Convenor);
4. Submit one hard copy to your Strand Convenor;
5. You must also submit an electronic copy via Turnitin which includes all figures.
40

5.6 Front sheet for all Research Project Report submissions (example)
Research Project Report [Insert number]
TITLE OF YOUR RESEARCH
PROJECT REPORT
Joe Bloggs
Student I.D. 200700000
Supervisor: [Insert name]
Internal Assessor: [Insert name]
Strand: [Insert name of your strand]
Word Count: [Insert word count]
41

5.7 Example of a Research Project Report (see following pages)
42

Design of a Hypothesis-Driven Screen for Regulators of Neurodegenerative Diseases
Author name
Physiological Laboratory, School of Translational Medicine, University of Liverpool, Crown St,
Liverpool, L69 3BX, U.K.
The discovery of the fundamental role of a
synaptic chaperone unit, cysteine string
protein (CSP), in neurotransmission and
neuroprotection, and the growing evidence
that it may be subverted in multiple human
neurodegenerative diseases (NDs) have
increased the urgency for further study of this
protein. Genetic suppressor and enhancer
screenings using model organisms have
facilitated the dissection of essential genetic
contributors to NDs. In this study, we have
implemented a targeted gene approach
utilising the previous published literature of
C. elegans, S. cerevisiae and in D.
melanogaster to manually curate a set of 618
unique worm genetic modifiers. Subsequent
bioinformatic selection of candidate genes
with established adult neuronal expression
and non-RNAi lethal phenotypes revealed a
final set of 47 modifier genes that can be
harnessed for in-depth analyses of gene
networks regulating CSP. Comparative
analysis of modifiers from diverse screens
provided insights into the distinct molecular
pathways mediating multiple NDs, while
scrutiny of the modifier gene set we compiled
further revealed 25 modifiers that are
consistently shared between multiple screens,
and of those, genetic regulators of protein
homeostasis, stress responsiveness and ageing
are common to most disease proteins.
Furthermore, fluorescence confocal imaging
of transgenic C. elegans lines confirmed the
GFP localisations of six neuronal promoters
which are applicable as means of probing and
validating positive genetic modifiers of CSP
KO-induced neurodegeneration in future
assays. Accordingly, our study provides a
basis for further characterisation of the
pathways by which evolutionarily conserved
CSP exerts its effects and identification of the
regulators of this pathway that could become
potential targets for future therapeutic
intervention.
INTRODUCTION
Despite major advances, debilitating
neurodegenerative disorders (NDs) including
Alzheimer‟s disease (AD), Parkinson‟s disease
(PD), and polyglutamine (polyQ) diseases as
exemplified by Huntington‟s disease (HD) and
related ataxias afflict millions worldwide and
remains a significant and unresolved global
health burden facing the ageing populations.
Essentially, most of these disorders are
associated with the unifying theme of
accumulation of toxic, misfolded protein
aggregates, inclusion bodies, necrotic or
apoptotic neurodegenerative changes,
progressive neuronal loss and eventual neuronal
dysfunction and death (1-3).
There is growing evidence that the cellular
protein quality control system is an underlying
common denominator of these diseases. One
such component which has recently received
considerable attention is cysteine-string protein
(CSP). CSP is a neuroprotective synaptic
chaperone protein with an essential
physiological role in the maintenance of
exocytotic release of neurotransmitter, hormones
and enzyme precursors and in preventing a
geing-induced presynaptic neurodegeneration
(4). The similar neurodegenerative phenotypes
of CSP mutants i.e. severely diminished
locomotion, reduced cholinergic
neurotransmission and increased mortality
observed in Drosophila and mammals, and more
recently in Caenorhabditis elegans with deleted
dnj-14 that encodes the sole CSP orthologue
(DNJ-14) suggests that perturbations in CSP
activity in different models have similar
significant consequences for the nervous system.
In support of this premise is the emerging
picture that CSP may be implicated in some
human NDs such as HD, PD and AD and may
play a central role in protecting against protein
misfolding and expression of toxicity in neurons
(5). CSP was found to functionally overlap in
vivo with the PD protein, α-synuclein, for
preventing neurodegeneration (6). The profound
43

neurodegeneration and lethality in CSP mutant
flies and mice can be ameliorated by transgenic
overexpression of normal α-synuclein (6-8) and
exacerbated in α-synuclein knock-out mice.
Similarly, it was also suggested that CSP binds
to mutant huntingtin (Htt), but not to normal Htt.
The sequestration and subsequent depletion of
CSP by expanded polyQ stretches eliminates the
robust inhibition of N-type Ca 2+ channels
promoted by CSP (9). This would be a
prominent mechanism contributing to
accelerated neurodegeneration due to lack of
CSP availability for neuroprotection. However,
the mechanistic insight into why CSP absence
results in neurodegeneration and how this may
be alleviated by α-synuclein remain largely
obscure.
In theory, one way to characterise the
evolutionarily conserved pathway through which
CSP functions and gain insight into how CSP
may be of physiological or pathological
importance for preventing neurodegeneration is
to identify genetic modifiers, which are genes
that modulate the manifestations of
neurodegenerative disease-induced primary
mutations (3). Genetic modifiers are classified as
suppressors or enhancers by conferring either
neuroprotection or enhancement of
neurodegeneration. Their isolations and analysis
of the underlying pathophysiology could lead to
the identification of proteins whose expression
has the potential to modulate CSP activity and in
particular protect from neurodegeneration in
CSP‟s absence, and elucidate the molecular
mechanisms and genetic susceptibility of
multiple NDs.
The employment of a plethora of powerful
model organisms with shorter generation times
such as C. elegans, S. cerevisiae and D.
melanogaster, has not only expedited screening
of potential genetic modifiers of the late-onset
cellular and behaviour phenotypes, but also
facilitated high-throughput testing of hypotheses
to illuminate a prospective cellular cause of
protein-misfolding diseases like HD, PD,
Amyotrophic Lateral Sclerosis (ALS) and AD or
neuroprotective mechanisms against underlying
functional aspects of neurodegeneration (1,10).
Screening can be performed by molecular,
genetic and chemical manipulations of gene
function, i.e. using mutagenesis (deletion
libraries, transposon based insertion), transgenic
overexpression of exogenous human misfolding
disease-related proteins, or RNA interference
(RNAi)-mediated knockdown to determine the
loss- or gain-of-function phenotypes (11).
Previous genome-wide screens have used C.
elegans to develop multiple tissue-specific
transgenic models manifesting pathological
phenotypes that faithfully recapitulate many
salient cellular and molecular pathologies of
complex neurodegenerative disease processes
based on muscular or neuronal expression of
aggregation-prone proteins such as mutant tau,
superoxide dismutase (SOD1) and α-synuclein
proteins, polyQ constructs, Htt fragment and
toxic amyloid beta 1-42 (Aβ1-42), and identified
modifiers and cellular processes of α-synuclein
inclusion formation (12), α-synuclein and Htt
misfolding-induced toxicity (13), tau-induced
pathology (14), presenilin function (15), polyQ
(16) and mutant SOD1 aggregation (17).
However, whole genome RNAi screening of
genetic modifiers of neurodegeneration or
protein aggregation in worms lacks efficiency in
identifying positive hits (12,14,16). An
alternative way to identify potential modifier
genes in a specific pathway is to perform a
targeted screen (a candidate approach/reverse
genetic, hypothesis-driven approach) based on
hypothesis generated by screens in lower model
organisms or existing knowledge of disease
mechanisms and pathways (10,18).
In view of this, we adopted a targeted gene
approach to mine and integrate multiple
heterogeneous data accumulated in previous
RNAi knockdown and mutagenesis studies in
model organisms, and selected a small number
of worm genetic disease modifiers which fit both
adult neuronal expression and non-RNAi
lethality criteria. Comparative analysis of
diverse genetic modifier screens indicates that
the pathological processes underlying multiple
neurodegenetive diseases are largely distinct.
Upon closer look, common classes of modifier
genes from our candidate list that act on
pathology of most disease proteins are those
involved in genetic regulation of protein
homeostasis, stress responsiveness and cellular
ageing. Furthermore, we subjected six transgenic
44

lines containing either pan-neuronal or discrete
neuronal promoters to confocal microscopy and
three-dimensional (3D) reconstructions and
verified the accuracy of the reported GFP
localisations in targeted neuronal types, as
revealed by the location of the fluorescent GFP
reporter.
EXPERIMENTAL PROCEDURES
Data Mining — Published literature was
manually curated to compile a collection of
experimentally delineated genetic modifiers of
protein aggregation, misfolding and
neurodegeneration in C. elegans, S. cerevisiae
and D. melanogaster (Table 1). PDF files
containing full lists of modifiers in the online
supplemental materials were converted and
imported into Microsoft Excel (version 2007;
Microsoft, Redmond, WA) by PDF2XL
Software (Cogniview). Individual worm
orthologues of yeast and fly modifier genes were
identified by consulting the Princeton Protein
Orthology Database (P-POD)
[http://ortholog.princeton.edu/findorthofamily.ht
ml], Saccharomyces Genome Database (SGD)
[http://www.yeastgenome.org] and FlyBase
[http://flybase.org/]. To extract genetic modifiers
with known expression in adult neurons that also
non-RNAi lethal, the list of modifiers was
further refined by conducting search queries in
bioinformatic interfaces such as WormBase
[WormBase Web site, available at
www.wormbase.org, release version WS224,
April, 2011], Biomart [http://www.biomart.org/],
and most predominantly GExplore 1.1
[http://genome.sfu.ca/gexplore/]. First, a list of
all adult neuronal genes within the genome of C.
elegans was obtained by searching within
GExplore for genes belonging to the expression
pattern “neuron, nerve, nervous system” and life
stage “adult”. The candidate list was then
checked using available RNAi phenotypic data
provided by GExplore and Wormbase to
specifically exclude modifiers for which existing
RNAi experimental data indicate to have elicited
severe deleterious phenotypes due to the
potential for non-specific effects from knocking
down well known important housekeeping
genes. All C. elegans genes were filtered for the
RNAi phenotype “lethal” under GExplore
Phenotype search field. For data analyses, all
annotations returned were imported into
Microsoft Excel and were processed manually
for subsequent categorisations. Each genetic
modifier was then cross-compared with these
GExplore data using the Microsoft Excel
VLOOKUP function to identify those which fit
our exact criteria. As an additional test of the
validity of the data, all the non-RNAi lethal
genetic modifiers with adult neuronal expression
were searched within GExplore Combined
Search Interface. Note: Preselected modifier
gene sets, data downloaded from GExplore 1.1
and all data analyses performed are not
appended. Please contact the author for any
additional supporting data.
Nematode culture — C. elegans provided by
the Caenorhabditis Genetics Center (CGC) were
grown and maintained on seeded nematode
growth medium (NGM) agar plates at 20°C. Six
transgenic lines used for confocal microscopy
were kindly provided by Dr. James R. Johnson:
N2;Ex[Prab-3::EGFP], N2;Ex[Pdat-1::GFP] and
RM2754;Ex[Pgcy-8::GFP] carry the GFP reporter
alone without an experimental modify transgene;
PS3551;Ex[Punc-17::hsf-1 + Punc-17::GFP],
PS3551;Ex[Pglr-1::hsf-1 + Pglr-1::GFP] and
PS3551;Ex[Posm-6::hsf-1 + Posm-6::GFP] carry
both the GFP reporter as well as the full length
hsf-1 rescuing construct.
Fluorescence Confocal Microscopy and 3D
Image and Animation Processing — Before the
procedure, young adult worms, four days posthatch
from individual GFP expressing lines were
cleansed of adhering bacteria by transferring to
an unseeded NGM plate, and were allowed to
crawl for 5 minutes. Microscopy of living
animals was performed by mounting the worms
on cover glass (22X40 mm, VWR International,
PA) in a 5μl drop of PEG/glycerol. PEG/glycerol
mounting medium is a blend of equal percentage
(20:20) of PEG 20000 and glycerol in PBS
which immobilises the nematode (personal
communication). Slides were rapidly sealed with
a clean glass coverslip (13 mm, VWR
International, PA). All fluorescence images were
acquired on a Leica TCS-SP-MP AOBS laser
45

Reference
Model
Organism
Number of
Genetic Modifiers
Uncovered
scanning confocal microscope (Leica
Microsystems, Heidelberg, Germany) using a
20X Plan Apo dry objective for imaging the
entire worm, and a LEICA DM IRB E laserscanning
confocal microscope (Leica
Microsystems AG, Wetzlar, Germany) with a
1.3 numerical aperture 63X Plan Apo oilimmersion
objective for high resolution imaging
of the head region of worms. Fluorochromes
were excited using an argon laser source at 488
nm. For high quality 3D reconstruction,
optimised sections of Z stacks were scanned
with a line average of 4-8. 3D data stacks of
confocal images and animations are shown as
maximum-intensity projections generated by
Leica Confocal Software, and were exported as
TIFF and AVI files respectively.
Number in
C. elegans
Nollen (16) C .elegans 186 186
Wang (17) C .elegans 81 81
van Ham (12) C .elegans 80 82*
Kraemer (14) C .elegans 75 75
Hamamichi (20) C .elegans 20 20
Kuwahara (21) C .elegans 11 11
Bates (22) C .elegans 6 6
Parker (13) C .elegans 4 4
Cohen (23) C .elegans 2 2
Kraemer (24) C .elegans 2 2
Guthrie (25) C .elegans 2 2
Yamanaka (26) C .elegans 2 2
Faber (27) C .elegans 1 1
Willingham (28) S. cerevisiae 138 41 (61)**
Yeger-Lotem (29) S. cerevisiae 77 20 (25)**
Giorgini (30) S. cerevisiae 28 5
Cooper (31) S. cerevisiae 22 7
Gitler (32) S. cerevisiae 6 1
Blard (33) D. melanogaster 30 14 (15)**
Kaltenbach (34) D. melanogaster 27 34 (50)**
Branco (35) D. melanogaster 24 20 (21)**
Shulman (36) D. melanogaster 24 10
Bilen (37) D. melanogaster 18 17 (24)**
Fernandez-Funez (38) D. melanogaster 18 11 (12)**
Kazemi-Esfarjani (39) D. melanogaster 2 1
Auluck (40) D. melanogaster 1 1
Total 887 656
RESULTS
(12,13,16,17,19-40)
TABLE 1: Candidate modifier
genes gleaned from literature.
For each published study, the
model organism used, the
number of experimentally
verified genetic modifiers and the
number of genetic modifiers
found in C. elegans are indicated.
We identified 887 genetic
modifiers in total, of which 656
C. elegans modifiers were
collected. Note these numbers
also encompass genes that have
appeared multiple times in
various screens. Additional
orthologues of a modifier gene
(*). Number of modifiers if
taking into account of the
multiple C. elegans orthologues
found for that particular gene
(**).
A smaller than expected bioinformatically
prioritised target gene set was obtained — We
first compiled a candidate list of hitherto
experimentally verified genetic disease
modifiers in C. elegans by assessing available
literature. To identify additional conserved
modifier genes and to further extend our target
gene set, worm orthologues of modifiers that
were uncovered via genome-wide screens for
effectors of neurodegeneration in S. cerevisiae
and in D. melanogaster were also incorporated
(Table 1). As a further stricture in the analysis,
we selected for modifier genes based on their
respective expression pattern and RNAi
phenotypes [obtained from (41,42)] to retrieve
only those with known expression in adult
neurons that are also non-RNAi lethal. We
specifically excluded modifiers that have been
46

Total
Expression in
Adult
Neurons
experimentally proven as essential for worm
survival and development due to the potential for
non-specific, off-target effects and false positive
results (20). As shown in both Table 2 and
Figure.1, a total number of 618 unique worm
genetic modifiers were collected. Within this
dataset, 21% (132/618) are adult neuronal; 46%
(287/618) are non-RNAi lethal. Applying both
criteria together, only 8% (47/618) of all unique
modifier genes we extracted correspond to genes
that are currently known to be both adult
neuronal and non-RNAi lethal, which are listed
in Table 3. 91% of the modifiers within this
specific set have clear human orthologues and
function in a variety of basal cellular processes.
94% of all modifier genes collected are also
represented in the two available RNAi feeding
libraries.
Given that CSP has presynaptic localisation
and defective presynaptic transmission has
recently been implicated as an early mechanism
preceding neurodegeneration (43), we
subsequently compared our candidate modifier
set with a set of 2072 candidate genes previously
screened for genes involved in the C. elegans
neuromuscular junction (44), with the aim of
providing confidence in the shortlist of testable
targets generated and enriching for modifier
RNAi Lethal Non-RNAi Lethal
Expression in Adult Neurons
& Non-RNAi Lethal
Genetic
Modifiers 618 132 331 287 47
Availability in
RNAi library
580 130 314 266 44
Overlap with
Sieburth
Screen 108 33 51 57 9
TABLE 2: Refinement of candidate modifier genes. The table summarises the findings following selection
of the target modifier gene set based on their respective expression pattern and RNAi phenotypes which are
available from GExplore and WormBase (WS224). Our stringent selection criteria preferentially include
modifier genes with known expression in adult neurons and non-lethal phenotypes arising from existing RNAi
experiments. The majority of the RNAi clones for our modifiers are available in both Vidal and Ahringer
RNAi feeding libraries. To gain increased confidence in our candidate gene set, we also compared our
modifier set to a published list of 2072 C. elegans genes reported by Sieburth et al. which includes genes that
influence synaptic function. 108 overlapping genes were identified to be present in both gene lists. Note that
the total number of modifier genes in Table 2 is less than the number represented in Table 1, because the
complete list of candidate genes collected in Table 1 also include ones that have appeared in multiple screens
and were subsequently discounted so that the data displayed in Table 2 contains only the unique worm genetic
modifiers.
FIGURE 1: Venn Diagram analysis of genetic
modifier set. Analysed data in adjacent Table 2 were
used to generate the Venn diagram and are
represented as colour-coded circles. A total of 618
unique worm modifiers were collected. Of these, 132
(21%) are adult neuronal genes (green). After
removing modifiers which existing RNAi
experimental data indicate as RNAi lethal positives
(red), 287 (46%) non-RNAi lethal modifiers (light
blue) were subjected to further analysis and we have
an end list of 47 genes (8%) that are both adult
neuronal and non-RNAi lethal (yellow intersecting
region). Comparison with C. elegans genes reported
by Sieburth et al. (44) are also shown.
genes known to influence presynaptic function
when targeting the respective genetic modifier in
the future by genetic and/or chemical means. Of
the 2072 candidate genes that were subjected to
47

Functional Category Genetic screen Gene name
Chaperone/quality
control
Protein
turnover/degradation/
UPS
Neurotransmission and
signalling
CGC
Name
Description
Animal
Model
Human
orthologues
Wang (17) F08H9.4 - heat shock protein (HSP) of the HSP16 class worm HSPB6 Vidal
Kraemer (14),
Branco (35)
Wang (17), Yeger-
Lotem (29)
T09B4.10 chn-1
F55B12.3 sel-10
mammalian carboxyl-terminus of Hsc70 interacting
protein
F-box and WD-repeat-containing protein of CDC4/CUL-
1 family of E2-E3 ubiquitin ligases
RNAi
library
worm, fly STUB1 CHIP Ahringer
worm,
yeast
FBXW7 Vidal
Guthrie (25) Y61A9LA.8 sut-2 nuclear polyadenylated RNA binding protein yeast ZC3H14
Not
available
Bilen (37) T05H10.1 - putative ubiquitin-specific protease fly USP47 Ahringer
Bilen (37) T26A5.5 - F-box protein JEMMA fly FBXL19 Vidal
Kaltenbach (34) K09A9.6 - aspartyl beta-hydroxylase fly ASPHD2 Ahringer
Kraemer (14) F47G6.1 dyb-1 ZZ type zinc finger worm DTNA Vidal
Parker (13) T04D1.3 unc-57 endophilin A, required for synaptic vesicle endocytosis worm SH3GL2 Vidal
Kaltenbach (34) Y22F5A.3 ric-4 intracellular protein transport, neurotransmitter secretion fly SNAP-25 Vidal
Signal transduction Hamamichi (20) EEED8.9 pink-1 BRPK/PTEN-induced protein kinase worm PINK1 Ahringer
Wang (17) T25F10.2 dbl-1
a member of the transforming growth factor beta
(TGFbeta) superfamily
worm BMP4 Vidal
Yeger-Lotem (29) M04C9.5 dyf-5 a putative MAP kinase yeast MAK/ICK Ahringer
Willingham (28) K11E8.1 unc-43 type II calcium/calmodulin-dependent protein kinase yeast CaMKII Vidal
Willingham (28) K07A9.2 cmk-1 Ca 2+ /calmodulin-dependent protein kinase I yeast CaMK1 Vidal
Branco (35) B0334.8 age-1 functions in an insulin-like signalling (ILS) pathway fly PI3K Ahringer
Shulman (36) W08G11.4 pptr-1 Serine/threonine protein phosphatase 2A fly PP2A
Not
available
Transcription cofactor
van Ham (12),
Branco (35)
R11A8.4 sir-2.1 NAD-dependent deacetylase sirtuin-1 worm, fly SIRT1 Ahringer
Cohen (23) R13H8.1 daf-16 sole C. elegans forkhead box O (FOXO) homologue worm FOXO4 Vidal
Giorgini (30) H21P03.1 mbf-1 transcription factor MBF1 yeast EDF1 Vidal
Bilen (37) C04G6.3 pld-1 phospholipase D1 fly PLD1 Vidal
Branco (35) F02E9.4 sin-3 SIN3 family of histone deacetylase subunits fly SIN3 Vidal
ECM/Cytoskeletal
organisation
Kaltenbach (34) F39C12.2 add-1 cytoskeletal protein alpha-adducin fly ADD1 Vidal
Kaltenbach (34) K05B2.3 ifa-4 a nonessential intermediate filament protein fly IFB-1 Vidal
Kaltenbach (34) R05D3.7 unc-116 kinesin-1 heavy chain ortholog fly KIF5 Ahringer
Enzymes Kraemer (14) F47G4.7 smd-1 S-adenosylmethionine decarboxylase worm AMD1 Vidal
Willingham (28) C06E7.1 sams-3 S-adenosylmethionine synthetase yeast MAT1A Vidal
Willingham (28) F44E7.2 - p-nitrophenyl phosphatase yeast PDXP Vidal
Willingham (28) Y56A3A.13 nft-1 carbon-nitrogen hydrolase yeast FHIT Vidal
Redox/oxidative stress Wang (17) C30H7.2 -
human thioredoxin domain-containing protein 4
precursor
worm ERP44 Vidal
Branco (35) K08F4.7 gst-4 a putative glutathione-requiring prostaglandin D synthase fly GSTA3 Vidal
Branco (35) F35E8.8 gst-38 unclassified fly GSTA4 Vidal
Voltage-gated ion
channels
Kaltenbach (34) C50C3.9 unc-36 alpha2/delta subunit of a voltage-gated calcium channel fly CACNA2D3 Vidal
Kaltenbach (34) R05G6.7 - porin/voltage-dependent anion-selective channel protein fly VDAC2 Vidal
Transport ATPase Yeger-Lotem (29) ZK256.1 pmr-1 a Golgi P-type ATPase Ca 2+ /Mn 2+ -pump yeast ATP2C1
Not
available
Dopamine metabolism Wang (17) T23G5.5 dat-1 a plasma membrane dopamine transporter worm SLC6A2/A3 Vidal
Lipid metabolism van Ham (12) C28C12.7 spp-10 sphingolipid metabolism/lysosomal worm PSAP Vidal
RNA metabolism Bilen (37) M88.5 - IGF-II mRNA-binding protein IMP fly IGF2BP2 Vidal
Carbohydrate
metabolism
Kaltenbach (34) K11H3.1 gpdh-2 glycerol 3-phosphate dehydrogenases fly GPD1L Vidal
Trehalose
biosynthesis
Yeger-Lotem (29) T05A12.2 tre-2 putative trehalases of unknown function yeast TREH Vidal
Yeger-Lotem (29) W05E10.4 tre-3 putative trehalases of unknown function yeast TREH Vidal
Unclassified Kraemer (14) C04B4.2 - unclassified worm None Vidal
Kraemer (14) R74.3 xbp-1 unclassified worm None Vidal
Kraemer (14) R13A1.8 glb-23 unclassified worm None Vidal
Faber (27) F52C9.8 pqe-1 unclassified worm REXO1 Vidal
Willingham (28) F08C6.3 tag-197 unclassified yeast VPS52 Vidal
Kaltenbach (34) Y55F3AM.14 - unclassified fly None Vidal
TABLE 3: Set of 47 modifier genes with known adult neuronal expression and non-RNAi lethality. Manual
analysis of modifier genes compiled identified a list of 47 genes out of the 618 unique genetic modifiers for further
dissection. For each genetic screen, assigned functional category, C. elegans gene name, CGC approved name,
available description, model organism used and human orthologue are shown. RNAi feeding library coverage of our
modifier genes is also indicated. Three modifiers that are common to multile screens are highlighted in red, while the
nine modifiers that overlapped with genes reported by Sieburth et al. are highlighted in orange. Four modifier genes
are nematode specific and six genes remain uncharacterised. UPS: Ubiquitin-proteasome system, ECM: Extracellular
matrix.
48

Biological process Ce Sc Dm Ce Sc Dm Ce Sc Dm Ce
RNA binding and processing
Synaptic transmission
Vesicle transport/ER Golgi
Protein folding
Protein degradation /UPS/Autophagy
Transcriptional regulation
Apoptosis
Translation
Lipid metabolism
Mitochondrial energy metabolism
General signalling
Oxidative stress
Signal transduction
Extracellular matrix
Cytoskeletal organisation
DNA replication/repair
Polyglutamine α-synuclein Tau SOD
classes of genes
that are specifically
= mentioned in
original literature
TABLE 5: Classes of modifier genes common to multiple disease proteins in small model organisms. This table is
a complete listing, restricted to our 618 unique modifier genes that have been identified in multiple screens of the
associated animal models. The common genes shared among different screens function in a variety of cellular
processes, including protein folding (hsf-1, hsp-1, dnj-13), UPS (chn-1, ubc-8) and transcriptional cofactor (sir-2.1)
Overlapping genes are categorised according to their roles; the degree of overlap between specific models of
neurodegeneration and protein misfolding, the overall times the modifiers appeared in screens of a particular model, 49
and the pathology of disease proteins they act on are also illustrated.
=
=
classes of genes
mentioned, but found
only 1 or 2 genes in
that respective class
either no genes in that
specific class were
found or mentioned in
the original publication
Ce = Caenorhabditis elegans
Sc
=
Worm screens that
utilised neuronal
expression system to
drive exogenous
neurodegenerative
proteins
= Saccharomyces cerevisiae
Screen 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
Dm = Drosophila melanogaster
TABLE 4: Functional profiling of genetic modifiers identified in diverse screens. Comparative analysis of worm
modifiers of polyQ, tau, SOD and α-synuclein aggregation, yeast modifiers of misfolded α-synuclein and Htt toxicity
and fly modifiers of misfolded tau and polyQ toxicity from diverse screens reveals that the modifier genes identified in
most screens function in a wide variety of biological processes. The molecular mechanisms mediating neuronal toxicity
in tauopathies, synucleopathy and polyQ diseases appear to be largely distinct due to the lack of overlap exists between
the underlying causative pathways. A larger proportion of the neurodegeneration studies using C. elegans have focused
more on overexpression of either wild-type or mutant forms of α-synuclein and polyQ constructs in comparison with
other aggregation prone disease proteins. The functional class of vesicle trafficking appears specifically enriched in αsynuclein
screens, whereas protein degradation and transcriptional regulation are more enriched in polyQ screens.
Screen numbers correspond to the following publications: 1 Nollen et al., 2004 (16); 2 Faber et al., 2002 (27); 3 Bates et
al., 2006 (22); 4 Willingham et al., 2003 (28); 5 Giorgini et al., 2005 (30); 6 Branco et al., 2008 (35); 7 Bilen et al., 2007
(37); 8 Kaltenbach et al., 2007 (34); 9 Fernandez-Funez et al., 2000 (38); 10 Kazemi-Esfarjani et al., 2000 (39); 11 van Ham
et al., 2008 (12); 12 Kuwahara et al., 2008 (21); 13 Hamamichi et al., 2007 (20); 14 Willingham et al., 2003 (28); 15 Cooper
et al., 2006 (31); 16 Yeger-Lotem et al., 2009 (29); 17 Gitler et al., 2009 (32); 18 Auluck et al., 2002 (40); 19 Kraemer et al.,
2006 (14); 20 Kraemer et al., 2007 (24); 21 Guthrie et al., 2009 (25); 22 Blard et al., 2007 (33); 23 Shulman et al., 2003 (36);
and 24 Wang et al., 2009 (17).
Overlapping classes of genes
Degree of overlap
and models used
Disease proteins
Heat shock transcription factor 3 X worm tau, SOD and Aβ1-42 Molecular chaperones 4 X worm, 11 X fly α-synuclein, polyQ and tau
Ubiquitin-proteasome system (UPS)
1 X worm, 1 X yeast,
5 X fly
α-synuclein, polyQ and tau
Transcriptional cofactor 3 X worm,11 X fly α-synuclein, polyQ and tau
Kinases and phospatases 2 X worm, 2 X fly tau and SOD
Nucleoporin 2 X fly polyQ ans tau
Transport ATPase
2 X worm, 3 X yeast,
1 X fly
α-synuclein and polyQ
SNARE protein 2 X yeast α-synuclein
GTPase activator protein 2 X yeast α-synuclein
Putative cargo transport protein ERV29 1 X worm, 2 X yeast α-synuclein
Acyl-CoA oxidase 1 X yeast, 1 X fly α-synuclein and polyQ

RNAi-mediated knockdown in Sieburth et al.
(44), 185 positive genes were identified in their
subsequent multi-tiered drug screens for
assessing C. elegans exocytosis. In comparing
these genes to our list of 618 modifiers, we
observed limited overlap, since only 108 genes
were common to both candidate gene sets (Table
2, Fig. 1). Among these overlapping modifier
genes, only 21 modifiers overlapped with
Sieburth et al. positive hits.
Molecular mechanisms mediating
neurodegenerative processes in tauopathies,
synucleopathies and polyQ diseases are largely
distinct — The majority of the experimentally
delineated modifiers identified fall into distinct
functional categories. In order to discern whether
their cellular mechanisms underlying the
pathology are common to several or all disease
proteins, or whether some specialise in
mediating pathology of particular disease
proteins, models from diverse modifier screens
expressing different aggregation-prone proteins
using either RNAi or biochemical approaches
were compared (Table 4). Ideally, we are
looking for modifier genes that may have a
widespread rather than disease-specific role in
neurodegeneration. However, there appears to be
little overlap between the modifier genes pulled
out from most worm, yeast and fly screens,
thereby highlighting that the molecular steps
preceding the pathology of various disease
protein are superficially very different.
Functional classes of modifier genes such as
vesicle trafficking are found exclusively for αsynuclein
pathologies in all of yeast as well as C.
elegans α-synuclein screens, whereas those
associated with RNA metabolism, protein
folding and degradation, and transcriptional
regulation appear to influence the pathology of
various disease proteins, but are more
specifically enriched in polyQ aggregation and
toxicity screens (Table 4), hence accentuating
the importance of these evolutionarily conserved
molecular processes as integral pathways
affected by respective disease proteins.
Positive genes that are consistently shared
between various datasets are involved in cellular
protein quality control and ageing — To further
ascertain if specific modifiers within a common
class of genes act on the pathology of different
or same disease proteins, we focused on the
overlapping genes within our candidate modifier
gene set and identified 25 modifiers that are
consistently shared between multiple screens
(Table 5). In support of the above functional
class comparison, modifier genes involved in
protein folding, degradation and cellular ageing
appear to be potent regulators of multiple
neurodegenerative disorders. Heat shock
transcription factor (hsf-1), a critical
evolutionarily conserved principal regulator of
chaperone gene expression was found in three C
.elegans screens for modifiers of tau, SOD and
Aβ1-42, indicating that this may be a modifier
common to these misfolding disease proteins.
Stress responsive and neuroprotective molecular
chaperones, such as hsp-1 and dnj-13 and UPS
components i.e. chn-1 and ubc-8, appear to
specialise in mediating degradation of αsynuclein,
tau and polyQ disease proteins; while
activation and depletion of genetic regulator of
lifespan sir-2.1 have been shown to either
pharmacologically or genetically ameliorate the
polyQ-induced toxicity, and accelerate agedependent
aggregation of α-synuclein
respectively.
Selected C. elegans neuronal promoters
correctly represent their endogenous gene
expression — Modifier genes we selected could
be examined in a subsequent RNAi screen to
identify the positive candidate hits. To further
explore possible effects of RNAi silencing and
overexpression of positive genes on dnj-14 -/- -
induced age-dependent neurodegeneration,
appropriate C. elegans neuronal promoters
would need to be selected in order to incorporate
targeted transgene expression of a positive gene
and gain insights into its role in neuronal
subtype survival, vulnerability and function.
Direct visual screens for neurodegeneration
have become feasible as neuronal loss can be
reliably assayed in live worms by monitoring the
morphological and degenerative changes of all
or a discrete subset of neurons labelled with
green fluorescent protein (GFP) reporter (45,46).
However, it remains possible that some of the
localisation patterns reported do not accurately
reflect the localisation of the corresponding
endogenously expressed proteins (3,44). Here,
we subjected 6 transgenic lines containing either
50

A
P rab-3::EGFP
B
P unc-17::GFP
FIGURE 2: Localisation of GFP
expression in transgenic C. elegans is
confirmed by fluorescent reporter
constructs in extrachromosomal arrays.
Fluorescence microscopy of whole body
(A,B;C-F: left panels) or magnified 3D
confocal reconstruction of neuronal
architecture in the head region (C-F: right
panels). A, The pan-neuronal localisation
of enhanced GFP (EGFP) expression is
consistent with the expected rab-3
promoter driven expression pattern in all
worm neurons. B, Punc-17::GFP labels most
regions of the nervous system,
predominantly cholinergic motor neuronal
processes. C, The dat-1 promoter labels all
eight dopamine (DA) neurons: six anterior
neurons in the head and two posterior
deirid neurons (PDEs, thick arrow). 3D
C
P dat-1::GFP
D
P osm-6::GFP
E
P glr-1::GFP
F
P gcy-8::GFP
confocal reconstruction of the magnified head region (right), detailing the six anterior-most DA neurons: four cephalic
CEP neurons (asterisks) project dendrites (thin arrows) to the tip of the nose and two anterior deirid ADE neurons (arrow
head) extend ciliated processes posteriorly. The CEP dendritic processes of another worm are also visible. D, Posm-6::GFP
selectively labels all 60 ciliated sensory neurons. E, The glr-1 promoter drives expression of the GFP in the ventral cord
interneurons, motorneurons and nerve ring. F, gcy-8::GFP localises exclusively to one thermo-sensory AFD pair (dashed
arrow). 3D confocal reconstruction (right) shows that the AFD dendrites extend anteriorly to the tip of the nose. The
sensory endings of both neurons are positioned at the tip of the dendrites (double asterisks). All animals imaged are
young adults, four days post-hatch. They include transgenic N2 and RM2754 lines overexpressing GFP reporter alone (A,
C and F) or together with HSF-1 in the targeted neurons of PS3551 strain, a hsf-1 mutant (B,D,E). All 3D confocal
reconstructions shown are maximal projections of z-stacks. Anterior to the left (C,E,F: right panesl); Anterior to the right
(D, right panel). Scale bars: A,B;C-F: left panels, 100 μm; C-F: right panels, 10 μm. Representative images of at least 5
worms from each transgenic line are shown.
*
*
51

pan-neuronal or discrete neuronal promoters to
confocal microscopy and 3D reconstructions and
verified the accuracy of their GFP localisations.
We observed in N2;Ex[Prab-3::EGFP] transgenic
line, that the rab-3 reporter for synaptic vesicle
does indeed drive the expected pan-neuronal
enhanced GFP (EGFP) expression in the nerve
ring, axons of ventral and dorsal nerve cords,
neuronal cell bodies, dendrites of sensory
neurons as well as outgrowth of motor neuron
commissures that connect ventral and dorsal
cord (Fig. 2A). The unc-17 promoter is active in
most regions of the nervous system, including
nerve ring, dorsal and ventral nerve cord and
pharyngeal nervous system. GFP expression
pattern observed correspond exactly to the
expected localisation of unc-17 (Fig. 2B).
C. elegans haemarphrodites have precisely
eight dopaminergic (DA) neurons and their
anatomic locations can be readily visualised with
an endogenous dopamine–specifc transporter
promoter (Pdat-1) which drive transgene
expression exclusively in all DA neurons (Fig.
2C). Expression of osm-6 gene is limited to 60
ciliated sensory neurons, where it has a role in
transducing chemo- and mechanosensory
stimuli. GFP is easily detected in the complex
neuronal process bundles that extend to the tip of
the nose of the worm (Fig. 2D). glr-1 encodes an
AMPA-type ionotropic glutamate receptor
subunit. Expression of GFP is limited to four of
the five pairs of command interneurons of the
motor circuit, as well as several classes of motor
neurons, ventral nerve cord and nerve ring (Fig.
2E). gcy-8 encodes a receptor-type guanylyl
cyclase and is expressed exclusively to a pair of
AFD thermosensory neurons that regulate
thermotaxis (Fig. 2F).
DISCUSSION
The candidate gene strategy described herein
is in keeping with the recent preselected screens
(20,21) which unlike previous genome-wide
screens, pooled genes that were preselected
based on their established role in neuronal
function or for their predicted role in
neurodegeneration (47). We have mined and
refined genetic modifiers of three well-studied
model organisms to produce a tractable list of 47
C. elegans candidates practical for detailed
future investigation by genetic and/or chemical
means with low false-negative rate, that could
contribute to the identification of proteins whose
expression has the potential to modulate CSP
activity and in particular protect from
neurodegeneration in CSPs absence. For several
reasons, we believe that our target gene set is
likely to be an underestimate of the true
conservation among all disease modifier genes.
Firstly, the present approach differs from
previous genome-wide screening for genetic
modifiers. Although this focused strategy may
enhance our ability to identify functionally
relevant effectors or enrich for certain groups or
categories of genes, the selection of genetic
modifiers in our study was based on prior
knowledge and will therefore consist of only
biased, preselected subsets which are likely to
miss many important genes, gene families, or
novel pathways, that may be potential effectors
of protein misfolding and neuroprotection in C.
elegans, which would otherwise be identified by
genome-wide screening (12,20). Secondly,
before the discovery of neuronal RNAi
hypersensitive strains such as eri-1, rrf-3, lin-35,
eri-1;lin-15B, and sid-1 transgenic TU3311
strains, RNAi resistance in WT C. elegans
postmitotic neurons was a stumbling block for
interrogating neuronal gene function with
confidence. In order to overcome the potential
problems caused by the neuronal intractability of
this species, many research groups performed
genetic modifier RNAi screens by
overexpressing human proteins in non-neuronal
cells i.e. body wall muscles and intestine cells in
order to rapidly pre-screen potential modifiers
(12,15,20,48,49). Muscle cells may be large and
easy to score, and certain models may also
express certain postsynaptic receptors that
receive synaptic signals from neurons, but given
that processes such as threshold for pathology
relevant to neurons are likely very different to
muscle cells, expression in muscle is not a
suitable model. This could not only lead to
identification of regulators not expressed in
neurons (i.e. muscle-specific), but certain
neuronal tissue-specific genes that affect
neurodegeneration and the actual site where the
misfolded proteins in question cause disease,
52

may have also been missed (11,47,50). Thirdly,
within WormBase, most of the modifier genes
are annotated with more than one RNAi
phenotype. Amongst all the RNAi lethal genes
we excluded, some are definitive essential genes
with 100% lethality reported in all prior studies,
whereas others may be false-negative or lowconfidence
lethal that were automatically
eliminated from our set because of a single
RNAi experiment. The strong penetrance
reported by one RNAi assay may not genuinely
reflect the phenotypic outcome and should be
interpreted cautiously (51). RNAi in C. elegans
is known to yield varied efficacy on all tissues
due to inherent variability in the level of target
mRNA knock-down for different genes and
tissues, resulting in different phenotypes in
RNAi screens. As such, some potential „hits‟
may have been overlooked because the genes
may not be knocked down far enough to result in
a phenotype, leading to insufficient or incorrect
annotation of RNAi phenotypes (11,12,16,50).
With regard to the specificity and confidence of
this subset, there is not a strong consensus
between the candidates we collected and the
Sieburth et al. (44) data, suggesting that our
target genes lack enrichment for synaptic
function. Most genes pulled-out by Sieburth et
al. that are expressed in neurons are also
expressed outside the nervous system, which
could explain why our modifier might not be
enriched among the positives of their screen.
In general, a large proportion of the modifiers
that have been robustly demonstrated to alter the
toxicity and aggregation phenotypes screened in
animal models have diverse cellular functions
that act either directly (components of protein
folding and ubiquitin-proteasome system) or
indirectly (signal transduction pathway
components, cytoskeletal proteins and
transcription factors) in cellular protein quality
control and different ageing pathways. Recent
genetic screens have further expanded the range
of modifiers to include additional classes of
modifiers, some are clearly novel and are at
present not well explained i.e. RNAi metabolism
(12,16,50,52), but possess potentially broad
significance to neurodegeneration.
It was striking to see that the pathology and
functional deficits of each of the NDs can be
induced or influenced by alterations of a
multitude of disease-protein-specific molecular
processes. Components of the vesiculartrafficking
machinery specifically modify αsynuclein
toxicity and aggregation, but are rarely
found as modifiers of polyQ and tau toxicity and
aggregation. This indicates that the α-synuclein
misfolding and toxicity may be more sensitive to
perturbations in this specific biological process
than the underlying common denominator of
polyQ diseases, the cellular protein quality
control system. However, this does not wean the
magnitude of protein folding and degradation in
pathological processes associated with αsynuclein
toxicity and accumulation since
several of them such as Hsp70 are known to alter
α-synuclein toxicity in a fly α-synuclein
overexpression model (40). It is possible that
vesicle trafficking may be more important as an
early stage effect related to the initiation of αsynuclein
pathology than the typical protein
aggregation modifiers (12).
As suggested previously, the technical
differences between the screens could also
confound making direct comparisons between
studies. Considering the many variables in each
of the genetic modifier screens conducted,
including different model organisms and
transgenic constructs, different modes of gene
targeting and scoring criteria for different
phenotypes, insufficient congruence even
between screens that have a similar scope is not
entirely surprising. Furthermore, genetic screens
to date have only implicated a limited number of
tau, SOD and Aβ1-42 toxicity modifier genes, in
comparison with those identified for α-synuclein
and polyQ.
Given that components of ubiquitindegradation
systems were found to co-localise
with aggregated proteins and various molecular
chaperone in the brain of patients (47), and
integration of stress response and ageing has
recently been demonstrated to facilitate agerelated
failures in proteostasis (53), it is not
surprising to find that hsf-1, hsp-1 and sir-2.1
play pivotal roles in ameliorating the onset,
development and progression of protein
misfolding, aggregation and toxicity associated
with expression of different disease proteins in
models of multiple NDs (53).
53

Despite its apparent neuronal simplicity, C.
elegans has different neuronal classes, including
motor neurons, sensory neurons, and
interneurons (3). Certain neurodegenerative
disorders such as HD have been reported to
confer differential vulnerability of specific
neuronal populations which lead to distinct
clinical phenotypes (54). This can therefore be
reproduced in C. elegans as neurons manifesting
neurodegeneration are characterised by
distinctive loss of neuron soma and breakdown
of neurites (45). Screens have used pan-neuronal
promoters (1,17,19) as well as neuronal specific
promoters (21,55,56) to direct expression of
aggregation-prone proteins such as mutant
SOD1, tau, α-synuclein, polyQ constructs, and
Htt fragment in targeted C. elegans neurons to
mimic the selective neuronal vulnerability and
pathology observed in higher organisms. In
particular, dat-1 promoter has been well
established as a valid means of probing αsynuclein-age-dependent
neurodegeneration in
multiple studies (45,46,57,58). The six neuronal
promoters we selected direct GFP expression
exclusively in targeted neurons, and are
therefore feasible for future fluorescence
imaging of transgenic worms to gain insights
into the roles of positive genetic modifiers in
neuronal subtype vulnerability and CSP KOinduced
neurodegeneration.
Taken together, modifier genes identified in
disparate models are clearly pertinent to many
aspects of neurological phenotype expression,
though most have a disease-specific role in
certain disease proteins rather than a general role
affecting every disease protein. The small
number of candidates isolated in this study
which modulate phenotypic consequences,
directly or indirectly, provides a basis for more
detailed molecular analyses. A hypothesis-driven
RNAi screen would be performed and to
maximise neuronal RNAi efficacy, we would
create a dnj-14; rrf-3 double mutant by crossing,
with the latter strain being recently reported as a
mutant most sensitised to neuronal RNAi (59).
This would reveal conserved genes and
pathways that are important for CSP loss of
function defects or alternatively independent
factors that regulate neurodegeneration. With
either outcome, they are vital for future
development of neuroprotective therapeutic
strategies.
Acknowledgments....
References
1. Brignull, H. R., Morley, J. F., and Morimoto,
R. I. (2007) Adv Exp Med Biol 594, 167-189
2. Caldwell, G. A., and Caldwell, K. A. (2008)
Dis Model Mech 1, 32-36
3. Voisine, C., and Hart, A. C. (2004) Methods
Mol Biol 277, 141-160
4. Zinsmaier, K. E., and Imad, M. (2011)
Cysteine-String Protein‟s Role at Synapses.
in Folding for the Synapse (Wyttenbach, A.,
and O'Connor, V. eds.), Springer US. pp
145-176
5. Johnson, J. N., Ahrendt, E., and Braun, J. E.
A. (2010) Biochem Cell Biol 88, 157-165
6. Chandra, S., Gallardo, G., Fernandez-
Chacon, R., Schluter, O. M., and Sudhof, T.
C. (2005) Cell 123, 383-396
7. Fernández-Chacón, R., Wölfel, M.,
Nishimune, H., Tabares, L., Schmitz, F.,
Castellano-Muñoz, M., Rosenmund, C.,
Montesinos, M. L., Sanes, J. R.,
Schneggenburger, R., and Südhof, T. C.
(2004) Neuron 42, 237-251
8. Zinsmaier, K., Eberle, K., Buchner, E.,
Walter, N., and Benzer, S. (1994) Science
263, 977-980
9. Miller, L. C., Swayne, L. A., Chen, L., Feng,
Z.-P., Wacker, J. L., Muchowski, P. J.,
Zamponi, G. W., and Braun, J. E. A. (2003)
J Biol Chem 278, 53072-53081
10. Kearney, J. A. (2011) Current Opinion in
Genetics & Development 21, 349-353
11. Johnson, J. R., Jenn, R. C., Barclay, J. W.,
Burgoyne, R. D., and Morgan, A. (2010)
Biochem Soc Trans 38, 559-563
12. van Ham, T. J., Thijssen, K. L., Breitling, R.,
Hofstra, R. M. W., Plasterk, R. H. A., and
Nollen, E. A. A. (2008) PLoS Genet 4,
e1000027
13. Parker, J. A., Metzler, M., Georgiou, J.,
Mage, M., Roder, J. C., Rose, A. M.,
Hayden, M. R., and Neri, C. (2007) J
Neurosci 27, 11056-11064
14. Kraemer, B. C., Burgess, J. K., Chen, J. H.,
Thomas, J. H., and Schellenberg, G. D.
(2006) Hum Mol Genet 15, 1483-1496
54

15. Link, C. D. (1995) Proc Natl Acad Sci U S A
92, 9368-9372
16. Nollen, E. A. A., Garcia, S. M., van Haaften,
G., Kim, S., Chavez, A., Morimoto, R. I.,
and Plasterk, R. H. A. (2004) Proc Natl Acad
Sci U S A 101, 6403-6408
17. Wang, J., Farr, G. W., Hall, D. H., Li, F.,
Furtak, K., Dreier, L., and Horwich, A. L.
(2009) PLoS Genet 5, e1000350
18. Ni, Z., and Lee, S. S. (2010) Brief Funct
Genomics 9, 53-64
19. Kraemer, B. C., Zhang, B., Leverenz, J. B.,
Thomas, J. H., Trojanowski, J. Q., and
Schellenberg, G. D. (2003) Proc Natl Acad
Sci U S A 100, 9980-9985
20. Hamamichi, S., Rivas, R. N., Knight, A. L.,
Cao, S., Caldwell, K. A., and Caldwell, G. A.
(2008) Proc Natl Acad Sci U S A 105, 728-
733
21. Kuwahara, T., Koyama, A., Koyama, S.,
Yoshina, S., Ren, C.-H., Kato, T., Mitani, S.,
and Iwatsubo, T. (2008) Hum Mol Genet 17,
2997-3009
22. Bates, E. A., Victor, M., Jones, A. K., Shi,
Y., and Hart, A. C. (2006) J Neurosci 26,
2830-2838
23. Cohen, E., Bieschke, J., Perciavalle, R. M.,
Kelly, J. W., and Dillin, A. (2006) Science
313, 1604-1610
24. Kraemer, B. C., and Schellenberg, G. D.
(2007) Hum Mol Genet 16, 1959-1971
25. Guthrie, C. R., Schellenberg, G. D., and
Kraemer, B. C. (2009) Hum Mol Genet 18,
1825-1838
26. Yamanaka, K., Okubo, Y., Suzaki, T., and
Ogura, T. (2004) J Struct Biol 146, 242-250
27. Faber, P. W., Voisine, C., King, D. C., Bates,
E. A., and Hart, A. C. (2002) Proc Natl Acad
Sci U S A 99, 17131-17136
28. Willingham, S., Outeiro, T. F., DeVit, M. J.,
Lindquist, S. L., and Muchowski, P. J.
(2003) Science 302, 1769-1772
29. Yeger-Lotem, E., Riva, L., Su, L. J., Gitler,
A. D., Cashikar, A. G., King, O. D., Auluck,
P. K., Geddie, M. L., Valastyan, J. S.,
Karger, D. R., Lindquist, S., and Fraenkel, E.
(2009) Nat Genet 41, 316-323
30. Giorgini, F., Guidetti, P., Nguyen, Q.,
Bennett, S. C., and Muchowski, P. J. (2005)
Nat Genet 37, 526-531
31. Cooper, A. A., Gitler, A. D., Cashikar, A.,
Haynes, C. M., Hill, K. J., Bhullar, B., Liu,
K., Xu, K., Strathearn, K. E., Liu, F., Cao, S.,
Caldwell, K. A., Caldwell, G. A.,
Marsischky, G., Kolodner, R. D., Labaer, J.,
Rochet, J. C., Bonini, N. M., and Lindquist,
S. (2006) Science 313, 324-328
32. Gitler, A. D., Chesi, A., Geddie, M. L.,
Strathearn, K. E., Hamamichi, S., Hill, K. J.,
Caldwell, K. A., Caldwell, G. A., Cooper, A.
A., Rochet, J.-C., and Lindquist, S. (2009)
Nat Genet 41, 308-315
33. Blard, O., Feuillette, S., Bou, J., Chaumette,
B., Frebourg, T., Campion, D., and
Lecourtois, M. (2007) Hum Mol Genet 16,
555-566
34. Kaltenbach, L. S., Romero, E., Becklin, R.
R., Chettier, R., Bell, R., Phansalkar, A.,
Strand, A., Torcassi, C., Savage, J., Hurlburt,
A., Cha, G. H., Ukani, L., Chepanoske, C.
L., Zhen, Y., Sahasrabudhe, S., Olson, J.,
Kurschner, C., Ellerby, L. M., Peltier, J. M.,
Botas, J., and Hughes, R. E. (2007) PLoS
Genet 3, e82
35. Branco, J., Al-Ramahi, I., Ukani, L., Pérez,
A. M., Fernandez-Funez, P., Rincón-Limas,
D., and Botas, J. (2008) Hum Mol Genet 17,
376-390
36. Shulman, J. M., and Feany, M. B. (2003)
Genetics 165, 1233-1242
37. Bilen, J., and Bonini, N. M. (2007) PLoS
Genet 3, 1950-1964
38. Fernandez-Funez, P., Nino-Rosales, M. L.,
de Gouyon, B., She, W.-C., Luchak, J. M.,
Martinez, P., Turiegano, E., Benito, J.,
Capovilla, M., Skinner, P. J., McCall, A.,
Canal, I., Orr, H. T., Zoghbi, H. Y., and
Botas, J. (2000) Nature 408, 101-106
39. Kazemi-Esfarjani, P., and Benzer, S. (2000)
Science 287, 1837-1840
40. Auluck, P. K., Chan, H. Y. E., Trojanowski,
J. Q., Lee, V. M.-Y., and Bonini, N. M.
(2002) Science 295, 865-868
41. GExplore 1.1 (2011) Available at:
http://genome.sfu.ca/gexplore/. Accessed 1 st
May - 3 rd June 2011.
42. WormBase web site release WS224 (2011)
Available at: http://www.wormbase.org.
Accessed 13th May 2011.
43. Zhang, C., Wu, B., Beglopoulos, V., Wines-
Samuelson, M., Zhang, D., Dragatsis, I.,
Sudhof, T. C., and Shen, J. (2009) Nature
460, 632-636
44. Sieburth, D., Ch'ng, Q., Dybbs, M.,
Tavazoie, M., Kennedy, S., Wang, D.,
Dupuy, D., Rual, J.-F., Hill, D. E., Vidal, M.,
Ruvkun, G., and Kaplan, J. M. (2005) Nature
436, 510-517
45. Yao, C., El Khoury, R., Wang, W., Byrd, T.
A., Pehek, E. A., Thacker, C., Zhu, X.,
55

Smith, M. A., Wilson-Delfosse, A. L., and
Chen, S. G. (2010) Neurobiol Dis 40, 73-81
46. Nass, R., and Nichols, C. D. (2007)
Invertebrates as Powerful Genetic Models
for Human Neurodegenerative Diseases. in
Handbook of Contemporary
Neuropharmacology, John Wiley & Sons,
Inc. pp
47. van Ham, T. J., Breitling, R., Swertz, M. A.,
and Nollen, E. A. A. (2009) EMBO
Molecular Medicine 1, 360-370
48. Harrington, A. J., Knight, A. L., Caldwell, G.
A., and Caldwell, K. A. (2011) Methods 53,
220-225
49. Mohri-Shiomi, A., and Garsin, D. A. (2008)
J Biol Chem 283, 194-201
50. Teschendorf, D., and Link, C. (2009) Mol
Neurodegener 4, 1-13
51. Fernandez, A. G., Gunsalus, K. C., Huang,
J., Chuang, L.-S., Ying, N., Liang, H.-l.,
Tang, C., Schetter, A. J., Zegar, C., Rual, J.-
F., Hill, D. E., Reinke, V., Vidal, M., and
Piano, F. (2005) Genome Res 15, 250-259
52. Williams, A. J., and Paulson, H. L. (2008)
Trends Neurosci 31, 521-528
53. Voisine, C., Pedersen, J. S., and Morimoto,
R. I. (2010) Neurobiol Dis 40, 12-20
54. Khurana, V., and Lindquist, S. (2010) Nat
Rev Neurosci 11, 436-449
55. Faber, P. W., Alter, J. R., MacDonald, M. E.,
and Hart, A. C. (1999) Proc Natl Acad Sci U
S A 96, 179-184
56. Parker, J. A., Connolly, J. B., Wellington, C.,
Hayden, M., Dausset, J., and Neri, C. (2001)
Proc Natl Acad Sci U S A 98, 13318-13323
57. Cao, S., Gelwix, C. C., Caldwell, K. A., and
Caldwell, G. A. (2005) J Neurosci 25, 3801-
3812
58. Kuwahara, T., Koyama, A., Gengyo-Ando,
K., Masuda, M., Kowa, H., Tsunoda, M.,
Mitani, S., and Iwatsubo, T. (2006) J Biol
Chem 281, 334-340
59. Zhuang, J. J., and Hunter, C. P. (2011)
Genetics
56

Section 6
Techniques and Frontiers in Biomedical Sciences
Techniques in Biomedical Sciences
This part of the module consists of a series of lectures on a wide range of modern research
techniques, including stem cell and tissue engineering, use of bioluminescent intracellular
probes, electrophysiology, gene expression analysis, proteomic approaches, etc. These
lectures are complemented by tutorials designed to develop the fundamental skills required
for laboratory research, including data handling, generation of Figures, scientific writing and
preparation of poster and oral presentations.
Frontiers in Biomedical Sciences
In this part of the module, the emphasis is on how state-of-the-art research techniques are
used to advance knowledge in specific biomedical research areas and on modern
methods/approaches employed in the diagnosis of disease and the treatment of patients.
Lectures on these topics are complemented by tutorials and journal clubs designed to
develop analytical and critical thinking skills.
Both the Techniques and Frontiers modules are enhanced by Seminars and Biomedical
Review Lectures within the Institute of Translational Medicine. Eminent scientists from
throughout the UK contribute to this by presenting their research on a variety of topics.
Seminars take place weekly; Biomedical Review Lectures take place periodically on
Thursdays from 5-6pm. It is important that MRes students attend both Seminars and
Biomedical Review Lectures to broaden their knowledge and range of learning experiences.
Seminars are organized by the individual Departments within the Institute and are advertised
regularly via email. Attendance at certain Departmental seminars may be recommended by
strand convenors to enhance awareness of research that is particularly relevant to individual
MRes strands.
Finally, strand-specific activities are an important part of the Techniques and Frontiers
modules, as they facilitate awareness of the science associated with particular research
strands.
Students will be assessed on one short review based on the Techniques module, one
short review based on the Frontiers module, and a referees report based on a journal
club.
6.1 Preparation of Short Reviews and Referees Reports
Short Reviews
Students should make every effort to ensure that their work is presented in good English,
and is clearly written. The sources used to prepare the review should be listed at the end, in
full, and cited at the appropriate point in the text; citations and bibliography should appear in
Physiological Reviews style. Any material - text or figures - that is taken verbatim from
other sources must be fully identified. In the case of text, it is essential to use quotation
marks (“....”) to identify such material in order to avoid accusations of plagiarism (which is a
serious academic offence). Any schematic diagrams, cartoons etc used as Figures should,
wherever possible, be created by yourself using appropriate graphics packages, rather than
by copying and pasting from published (and hence copyright protected) literature. The
University policy with regard to plagiarism is explained in this handbook.
A good review should include: (a) an opening statement that introduces the subject, sets it in
the context of published work, and attracts the attention of the reader. (b) In the main part of
the review, the major theme, should be developed and critically discussed. Points should be
made systematically using paragraph headings if appropriate and avoiding repetition. The
57

text should include citations to the relevant literature, which should be described and
discussed in sufficient detail for the review to stand on its own as a piece of scientific writing.
(c) A final concluding statement may take the form of an overview, summary or outline of
prospects for future work (or all three).
Short reviews should be no more than 2,500 words (excluding references). Marks will be
deducted proportionally for exceeding this limit (for example, 2,750 words = 10% over the
limit = 10% deducted), down to a minimum cap set at 50% for the assignment. Short reviews
should include up to 30 citations to peer-reviewed papers. It will often be the case that many
more papers have been consulted; the process of selecting the most appropriate literature
citations is therefore a matter of judgement and this will be reflected in the quality of the final
product. Three copies of the short review should be submitted in printed form (i.e. produced
on a word-processor): one for the lecturer giving the topic and two to your strand convenor.
You also need to submit an electronic copy of the final version (including any Figures) via
Turnitin. Please attach a front cover sheet to your report stating your name, the title of your
review, your student number, the name of the lecturer giving the topic, the title of the report,
and the word count. A template cover sheet is supplied at the end of this Section for
this purpose.
Short review 1
Choose a technique that was discussed in the lecture course “Techniques in Biomedical
Sciences”. This should not be connected to the main method used in your first project, and
should not be a lecture given by your strand convenor. It is essential that you contact the
lecturer of your chosen Techniques lecture well in advance of the deadline to check
that they are available to assess your review and to get advice on the content of the
planned short review. Once the chosen lecturer has agreed to mark your short review,
you should immediately contact your strand convenor to inform them of the
arrangement. Prepare a short review style article discussing the principles on which the
technique is based, any practical problems in applying the technique, and the importance of
the technique in modern Biomedical Sciences.
Short review 2
Choose a topic covered in “Frontiers in Biomedical Sciences”. This should not be connected
to the main method used in your first project, and should not be a lecture given by your
strand convenor. It is essential that you contact the lecturer of your chosen Techniques
lecture well in advance of the deadline to check that they are available to assess your
review and to get advice on the content of the planned short review. Once the chosen
lecturer has agreed to mark your short review, you should immediately contact your
strand convenor to inform them of the arrangement. Prepare a short review style article
discussing the importance of the subject, its topicality, and why or how recent progress has
been made.
Journal Club
The idea behind a journal club is to provide insights into how to critically analyse papers and
allow an appreciation of recent advances. Our journal club will be organised as follows: one
strand will be allocated to each paper. The paper will be chosen by the presenter of the
preceding lecture. An electronic copy will be made available (or a reference to the paper
given) at the lecture. The paper will be chosen to illustrate some important technical aspects
or novel biological findings, or to highlight problems with the data/interpretations in the
paper. Excessively long papers should preferably be avoided. All participating students will
be expected to read the paper and prepare a brief summary, as a series of bullet points, of
the major issues. These will be helpful for the discussions of the paper and should be
emailed to the chairperson in advance of each journal club.
58

Referee’s report
A paper that was discussed at a Journal Club should provide the basis for this submission.
Your strand convenor will inform you which journal club is to be chosen for this nearer the
time. After the Journal Club, you should produce a written account in the style of an
extended referee‟s report. Guidance on how to construct referees‟ reports will be given by
the Programme Director in the Science Skills session on Scientific Publishing and also in the
introductory lecture to the Frontiers module, and these can be used to provide the basis for
the written account. Your referees report should be no more than 1000 words and the word
count should be indicated. Marks will be deducted proportionally for exceeding this limit (for
example, 1100 words = 10% over the limit = 10% deducted), down to a minimum cap set at
50% for the assignment. The referee‟s report should be submitted to the lecturer giving the
topic and the Strand Convenor in printed form (i.e. produced on a word-processor) and a
copy of the refereed paper should be attached. You also need to submit an electronic copy
of the final version via Turnitin. Please attach a front cover sheet to your report stating your
name, your student number, the name of the lecturer giving the topic, the title of the report,
and the word count. A template cover sheet is supplied at the end of this Section for
this purpose.
6.2 Assessment
Each short review will contribute 8%, and the referee‟s report 4% of the total marks.
Therefore, the Techniques and Frontiers modules contribute 20% of the total marks
available for the MRes.
Both short reviews and referees reports will be double marked by the person who gave the
lecture or journal club and a 2 nd internal assessor (usually the strand convenor). The mark
awarded will be the average of these two marks.
Please note that the standard university penalty for late submission of written work applies (see
earlier, under overview of assessment).
Details of the assessment criteria used and the assessment forms that will be used by markers
are given on the on the pages that follow, as are examples of a short review and a referee‟s
report.
59

6.2.1 Assessment Form for short reviews
MRes in Biomedical Sciences
Short Review Assessment Form
Student:
Rotation:
Project Title:
Supervisor (lecturer):
Moderator:
Please complete this form when marking the M.Res write ups, and return it, with the SHORT REVIEW to your
strand convenor. INDICATION OF POTENTIAL DEGREE CLASS BY MARK ATTAINED (Distinction 70-100); (Merit 60-
69); (Pass 50-59); (Fail

6.2.2 Specific marking criteria for assessments of short reviews
Distinction Level 100% - 90%
90% - 80%
80% - 70%
Pass Level 69% - 65%
64% - 60%
59% - 55%
54% - 50%
Fail Level 49% - 45%
44% - 40%
39% - 35%
34% - 10%
0%
Outstanding. No (or virtually no – use scaling) better
result conceivable at Masters level. Comprehensive.
Factually correct, with extensive evidence of critical
thinking. Evidence of extensive research of relevant
literature. Very logical structure, very well written and
presented. Clear evidence of original thought and
cogent scientific argument.
Excellent. Clear evidence of achievement on a scale
reserved for exceptionally high quality work at Masters
level. Essentially correct and complete, with evidence of
critical thinking and excellent use of relevant literature.
Logical structure, well written and presented, displaying
varying degrees (use scaling) of original thought and
cogent scientific argument.
Very Good. Content essentially without any major
flaws, very well explained with clear evidence of a high
level of scientific competence, and mature, critical
scientific judgement.
Good. Well explained, showing good evidence of
critical scientific judgement.
Quite Good. A well explained report, with good
understanding and some evidence of critical scientific
judgement
Fairly Good. A generally sound report with a good or
quite good level of understanding, evidence of sound
scientific competence and judgement.
Adequate. Showing some progress but with some
deficiencies in one or more aspects of knowledge of the
literature and scientific judgement.
A poor report with an overall superficial approach.
Essentially an incomplete report with major omissions in
several areas and evidence of a poor understanding.
A poor report with an overall superficial approach and
more errors and/or omissions and/or evidence of a
deficiency of effort and/or poor understanding.
A marked deficiency in content of understanding and
application.
Even more marked deficiencies in content (on a variable
scale) of understanding and application and
presentation.
A complete absence of relevant content.
61

6.2.3 Assessment Form for referees’ reports
62

6.2.4 Specific marking criteria for assessments of referees’ reports
Distinction Level 100% - 90%
90% - 80%
80% - 70%
Pass Level 69% - 65%
64% - 60%
59% - 55%
54% - 50%
Fail Level 49% - 45%
44% - 40%
39% - 35%
34% - 10%
0%
Outstanding. No better result conceivable at Masters
level. Extensive evidence of critical thinking and cogent
scientific argument. Evidence of reading around the
subsect of the paper reviewed
Excellent. Essentially correct and complete, with
evidence of critical thinking and excellent use of the
paper reviewed. Logical structure, well written and
presented, displaying a cogent scientific argument.
Very Good. Content essentially without any major
flaws, very well explained with clear evidence of a high
level of scientific competence, and mature, critical
scientific judgement.
Good. Well explained, showing good evidence of
critical scientific judgement.
Quite Good. A well explained review, with good
understanding and some evidence of critical scientific
judgement.
Fairly Good. A generally sound review with a good or
quite good level of understanding, evidence of sound
scientific competence and judgement.
Adequate. Showing some progress but with some
deficiencies in one or more aspects of understanding of
the paper and scientific judgement.
A poor report with an overall superficial approach.
Essentially an incomplete report with major omissions in
several areas and evidence of a poor understanding.
A poor report with an overall superficial approach and
more errors, omissions and evidence of a deficiency of
effort and poor understanding.
A marked deficiency in content of understanding the
paper and the task set.
Even more marked deficiencies in content of
understanding and application.
A complete absence of relevant work presented.
63

6.3 Front sheet for referee’s report and short review submissions
(example)
Short Review [Insert number] or Referee’s Report
TITLE OF YOUR REVIEW
OR REPORT
Joe Bloggs
Student I.D. 200700000
Lecturer (who gave the Techniques/Frontiers lecture): [Insert name]
Strand: [Insert name of your strand]
Word Count: [Insert word count]
64

6.4 Example of a short review
Galectin-3 – a cancerous jack-of-all-trades
Author name
Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool,
Crown Street, Liverpool L69 3BX, UK
Galectin-3 is a member of a family of animal lectins that bind β-galactosides. It is involved in a vast
range of biological processes and its expression has been related to cancer progression and
metastasis. Galectin-3 exerts different functions depending on its cellular localisation and binding
partners. It has been implicated in regulation of cell growth, proliferation, cellular transformation,
immune reactions and spreading of cancer metastases, to name a few. This review summarises
the diversity of its functions with particular emphasis on its role in cancer pathogenesis and
metastasis.
INTRODUCTION
Lectins are carbohydrate-binding proteins that serve as a link between glycan recognition and
cellular responses (56). One of lectin families comprises galectins – multifunctional animal proteins
that share highly conserved carbohydrate recognition domains (CRDs), which bind to β-galactoside
(6). To date, 15 members of this family have been isolated and classified into subgroups depending
on their structure and the number of CRDs (63). Prototypical galectins (galectin-1, -2, -5, -7, -10, -11,
-13, -14 and -15) contain one CRD, whereas the tandem-repeat galectins (galectin-4, -6, -8, -9 and -
12) have two CRDs separated by a linker region in a single polypetide chain. Galectin-3, in turn, is the
exclusive member of the chimera-type subgroup and it contains a CRD connected to an extended
non-lectin N-terminal domain.
Galectin-3 is probably the best-studied animal lectin and since its discovery in 1982 (22, 14)
the diversity of its functions in physiological and pathological processes seems to expand
continuously. It is involved in growth and apoptosis regulation, proliferation, cell-cell adhesion,
angiogenesis and regulation of immune response, just to mention a few. Similarly to some other
galectins, galectin-3 is ubiquitously expressed in mammalian tissues and is often deregulated in
human cancers (63). The plethora of tumours in which it is overexpressed, makes it a promising
therapeutic target. Moreover, galectin-3 is now often used as a prognostic marker for certain
cancers.
Thorough understanding of the cellular mechanisms that involve galectins-3 is pivotal to
delineate the complexity of transformation and tumour metastasis, as well as the many physiological
processes, in which this particular lectin is implicated. This review will present a comprehensive
summary of the multitude of tasks performed by galectin-3 and will focus on its role in cancer
development and progression.
GENERAL CHARACTERISTICS
Structural properties
Galectin-3 was first characterised as a 32kDa antigen called Mac-2 expressed on the surface of
murine macrophages (22). It was also previously known as CBP-35, HL-29, RL-29, IgEBP, hL-31 and
LBP, as a result of its isolation from different species (14). Its structure remains highly conserved
across animal kingdom and is unique in the whole galectin family (13). It comprises a CRD and an
unusual flexible N-terminal domain (ND) (Fig.1) of about 110-130 amino acids, depending on species
of origin. The ND consists of 7-14 repeats of a
65

FIG. 1. A schematic representation of monomeric (left) and pentameric (right) structures of galectin-
3. The carbohydrate-binding domain consists of about 130 amino acid residues, the proline-,
glycine- and tyrosine-rich repeats of N-terminal domain contain about 100 residues and the small Nterminal
domain of galectin-3 contains about 30 residues. Adapted from (6).
nine amino acid sequence: Pro-Gly-Ala-Tyr-Pro-Gly and 3 extra amino acids (8, 14). It is also referred
to (as) a collagen-like ND, due to its homology to collagen α1 (II) chain (49).
The ND is essential for multimerisation of galectin-3 and is sensitive to proteolysis by MMP-2
and MMP-9 matrix metalloproteinases (37, 45). Moreover, it is indispensable for the activity of
galectin-3 (54) and it has been demonstrated that it takes part in carbohydrate-binding via its Tyr102
residue (5). The first 12 amino acids of the ND, referred to as small ND, are necessary for galectin-3
secretion as well as its nuclear localization (20, 40) and the highly conserved Ser6 is responsible for
the anti-apoptotic activity (65), which will be discussed later.
The C-terminal CRD of galectin-3 contains approximately 130 amino acids that form a
globular structure comprising five- and six-stranded β-sheets arranged in a β-sandwich (54), similar
to galectin-1 and -2. The CRD constitutes the galectin activity, as it creates the entire carbohydrate
binding site (25, 46, 54). It contains a NWGR (Asp-Trp-Gly-Arg) motif, which is essential for binding βgalactosides
(2, 13) as well as for homodimerisation (61). This motif is also present in the B-cell
lymphoma 2 (Bcl2) family members of apoptosis regulators and it has been confirmed to be
responsible for the anti-apoptotic activity of galectin-3 (62).
Both lactose (Lac) and N-acetyllactosamine (LacNAc) are specifically recognised by the CRD
of galectin-3, which has a 5-times higher binding affinity for the latter (3, 53, 54). What is more, the
ND of galectin-3 seems to contribute to its increased affinity for larger oligosaccharides (extended
Lac or LacNAc), as compared to other galectins (21). It has been demonstrated that binding of
carbohydrate ligands results in a conformational change of galectin-3 (3) and it can be modulated by
phosphorylation of Ser6 (39). Furthermore, the multiple interacting partners of galectin-3 also
encompass many intracellular proteins that are recognised in a carbohydrate-independent manner
(15, 41, 48, 57, 58).
Multimerisation and cellular localisation
As mentioned before, oligomerisation of galectin-3 is accredited to both the CRD and the ND (37,
61), but the formation of pentamers (Fig.1) occurs only via the NDs in the presence of multivalent
carbohydrate ligands (1). In solution, however, galectin-3 has been shown to primarily occur as a
monomer (42).
Extracellularly, galectin-3 can be found in the extracellular matrix (ECM) and in biological
fluids (14) and its multimers form lattice-like structures by cross-linking glycoconjugates on the cell
surface (1, 9). This brings about cell-cell associations or bridging of cells to extracellular matrix
proteins and, hence, results in triggering of downstream signalling (35, 44, 63), as discussed later.
Galectin-3 does not contain endoplasmic reticulum (ER) translocation signal sequence, and,
66

therefore, it is not secreted via the classical ER/Golgi pathway, but by the not fully understood
process of ectocytosis, which is dependent on the ND (27, 40).
Intracellularly, galectin-3 is present in both the cytoplasm and nucleus, depending on the cell
proliferation status and a range of factors, such as cell type and the stage of tumour progression
(14). For some cancer types, there is a general shift from nucleus to the cytoplasm, where galectin-3
can interact with a multitude of its binding partners (4, 52). The translocation from the nucleus
involves the nuclear export signal (NES) contained within the CRD (60), whereas the nuclear import
might be attributed to the ND (20), but there is some evidence for the implication of the CRD in this
process (19).
Physiological functions
The different cellular localisations of galectin-3 imply its vast range of functions in normal and
pathological conditions. Extracellular galectin-3 has been shown to be involved in cell adhesion via
glycan-dependent interactions with integrins: α1β1 and α subunit of αMβ1 (14). Besides, it mediates
cell adhesion by associating with glycosylated cell surface and ECM proteins, such as collagen IV,
elastin, fibronectin and laminin. In this way, extracellular galectin-3 plays important role in autocrine
and paracrine signalling.
Galectin-3 has a particular function in immune response. For example, it stimulates
production of superoxide and induces production of interleukin-1 by monocytes, resulting in
increased inflammation (29, 34). Among its other effects, galectin-3 enhances phagocytosis of
neutrophils (16) and oxidative response of immune cells (17).
Besides, extracellular activity of galectin-3 is involved in morphogenesis of endothelial cells
and angiogenesis (43). At high concentration, its function is also associated with chemoattraction
and an increased Ca 2+ influx in monocytes, whereas at low concentration galectin-3 promotes
chemokinesis (14). It also participates in endocytosis of modified low density lipoproteins and
advanced glycation end products.
Functions of galectin-3 inside the cell are better described than for other galectins (63). In
the cytoplasm, galectin-3 binds to Bcl-2 and inhibits cell apoptosis (62). What is more, it has also
been demonstrated that it interacts with a death receptor CD95 (APO-1/Fas), as well as with nucling
and Alix/AIP1 – proteins involved in apoptosis regulation (14). Moreover, cytosolic galectin-3 exhibits
important effects on cell survival, differentiation and proliferation. To substantiate these multiple
functions, it has been shown that galectin-3 interacts with activated GTP-bound K-Ras (15, 55) and it
affects Akt signaling (33, 47).
On the other hand, nuclear galectin-3, like galectin-1, regulates splicing of pre-mRNA and
takes part in spliceosome assembly (14, 63). Its interaction with pre-mRNA may occur indirectly via
complexes including its nuclear binding partner Gemin4. In nucleus, galectin-3 has also been shown
to regulate gene transcription by enhancing transcription factor association with Spi1 and CRE
elements in gene promoter sequences, e.g. to induce cyclin D1 expression (14). Also, intranuclear
galectin-3 seems to regulate Wnt pathway signalling.
Certainly, this myriad of functions exhibited by galectin-3 is a result of juxtaposition of its
unique characteristics: the atypical ND, the diverse cellular localisations and wide tissue distribution
(14, 21). Galectin-3 has been found widely expressed in human tissues, including immune cells,
epithelial cells of many organs as well as respiratory and gastrointestinal tracts and in some sensory
neurons (14, 26). However, during early stages of human embryogenesis, galectin-3 shows a more
specific expression pattern, mainly in the epithelia, kidney, chondrocytes and the liver (14). Yet,
galectin-3 knock-out mice remain viable and display no obvious abnormalities (13), which indicates
that galectin-3 functions may be redundant. Conversely, galectin-3 overexpression is a predominant
feature of many cancers and, therefore, the insights into its functions in physiological processes are
of great importance in elucidating its role in these pathological states (14, 63).
ROLE IN TUMOUR DEVELOPMENT
Galectin-3 overepression has been shown to be associated with tumourigenesis and increased
metastatic potential of transformed cells (14, 63). Its role in cancer pathogenesis encompasses
67

egulation of a diverse range of cancer-related processes: transformation, cell survival, proliferation,
inhibition of apoptosis and spreading of metastasis (Fig.2, Fig.3). In majority of tumours galectin-3
expression is enhanced and its cellular distribution is altered (14). Its intracellular localisation is
mainly cytoplasmic and is related to its anti-apoptotic activity (62). In turn, extracellular galectin-3 is
associated with dissemination of metastatic cells (63). The following sections will compile the various
functions of galectin-3 in different stages and aspects of cancer development and metastasis, with
particular emphasis on its binding partners.
FIG. 2. A simplified representation of the many roles of galectin-3 in cancer pathogenesis – for
further details refer to text.
68

FIG. 3. The diversity of galectin-3 functions in cancer progression and metastasis – only few main
processes in which galectin-3 is involved could be depicted this figure. Galectin-3 has a crucial role in
cellular transformation, inhibition of apoptosis and possibly in cell cycle regulation. During
metastasis, galectin-3 is engaged in several distinct processes, which include cell-cell and cell-matrix
adhesions and angiogenesis. Adapted from (35).
Initiation of transformation
Substantial evidence is accumulating regarding the role of galectin-3 in neoplastic transformation
(15, 23, 35, 66). In highly malignant human breast carcinoma cells, suppression of galectin-3 resulted
69

in reversion of the altered cell morphology as well as in loss of anchorage- and serum-independent
growth (23). Moreover, it led to inhibition of tumour growth in immunologically suppressed mice.
Likewise, inhibition of galectin-3 by antisense cDNA in human thyroid papillary carcinoma cell line
led to suppression of anchorage-independent growth (66). What is more, transfection of galectin-3
cDNA into normal thyroid follicular cells resulted in altered gene expression, loss of contact
inhibition and serum-independent growth (59). These results suggest that the maintenance of the
transformed phenotype in malignant breast and thyroid cells is dependent on high levels of galectin-
3 expression.
The molecular mechanisms behind galectin-3 function in transformation initiation may
involve interactions with oncogenic K-Ras4B (15). Galectin-3 selectively promotes Ras-dependent
phosphatidylinositol 3-kinase (PI3-K) and Raf-1 activation and attenuates ERK that results in altered
transcriptional outcomes. Hence, galectin-3 might be necessary for Ras anchorage to the plasma
membrane and for Ras-dependent cell transformation.
The tumourigenic potential of galectin-3 may also involve interactions with β-catenin that
subsequently result in enhanced expression of cyclin D and c-MYC (58, 63). Nuclear localisation of
galectin-3 may also imply its role in regulation of gene transcription and, indeed, it has been shown
to interact with transcription factors involved in activation of cyclin D1 expression and possibly
expression of cyclin A, E, p27/KIP1 and p21/CIP1 (14). In this way galectin-3 might be involved in
regulation of the cell cycle. Also, it has been demonstrated that galectin-3 bind to the thyroidspecific
transcriptiona factor 1 (TTF-1) in human papillary thyroid cancer cells, and, hence
contributes to cell proliferation (48).
Inhibition of apoptosis
Regulation of apoptosis is probably the best studied function of galectin-3 related to cancer
progression (35). Galectin-3 bears high sequence homology to anti-apoptotic Bcl-2 (2, 62), to which
it binds in vitro. Point mutations within the homologous NWGR motif lead to the attenuation of the
anti-apoptotic activity of galectin-3. Following apoptotic stimuli, overexpressed galectin-3 has been
shown to translocate to the mitochondria, where it protects the cell from the production of reactive
oxygen species, blocks the alteration of mitochondrial membrane potential and inhibits cytochrome
c release (38, 67).
Interestingly, cytoplasmic galectin-3 interactcs with synexin in human breast epithelial cells
(67). This calcium-dependent and phospholipid-binding protein is responsible for the translocation
of galectin-3 to the mitochondria and is essential for its anti-apoptotic activity. Furthermore,
phosphorylation of galectin-3 at serine6 by casein kinase I is indispensable for its export from the
nucleus and activation of the mitogen activated protein kinase (MAPK) pathway, and, hence, it is
essential for anti-apoptotic activity of galectin-3 (35). Besides, galectin-3 is capable of preventing
anoikis – a type of apoptosis induced by loss of cell-ECM interactions – of human breast carcinoma
cells, possibly due to mediating cell cycle arrest (31). On the other hand, inhibition of apoptosis in
human bladder carcinoma cells by galectin-3 seems to be mediated via Akt signalling (47).
Conversely, in human prostate cancer cell line galectin-3 plays a dual role in apoptosis
regulation (11). In the cytosol it exhibits anti-apoptotic activity, whereas in the nucleus it promotes
apoptosis. Moreover, extracellular galectin-3 also exerts a pro-apoptotic effect, presumably by
binding to cell surface glycoproteins (35). Taken together, the effects of galectin-3 on the regulation
of apoptosis are complex and depend on its cellular localisation. In oncogenesis, however, its role is
predominatly anti-apoptotic and it might be regulated by upstream p53 pathway (63).
ROLE IN METASTASIS
Neoplastic metastases are the result of increased tumour cell motility, alteration of cell adhesion,
angiogenesis and immune response evasion (35). There is substantial evidence that galectin-3 is
implicated in all of these pathological processes; thus, understanding of its function is imperative in
elucidating the mechanisms of tumour invasiveness and dissemination through biological fluids. Yet,
overexpression of galectin-3 in some cancer types appears to be a potential diagnostic marker for
their malignancy. For instance, high levels of galectin-3 expression could be predictive for high
70

invasiveness of a neuroendocrine tumour pheochromocytoma (51), epithelial ovarian carcinoma
(31), primary cutaneous melanoma (10), thyroid cancer (12), colorectactal cancer (7) and pituitary
tumours (50), to name a few. Henceforth, the importance of galectin-3 in cancer prognosis seems to
be invaluable and its role in different aspects of metastasis will be discussed below.
Angiogenesis
Formation of new blood vessels from pre-existing vessels – angiogenesis – is considered to be a
crucial process in tumour invasiveness (35). New blood vessels supply oxygen and the essential
nutrients to tumour cells and serve as a link between primary and secondary tumour sites. The role
of galectin-3 in angiogenesis has been extensively documented and it appears that it might be
connected to induction of endothelial cells morphogenesis and their increased motility (43).
In fact, in vivo mice studies revealed that exogenous galectin-3 induces formation of new
capillaries surrounding the transplanted human breast tumour (43). The mechanism by which
galectin-3 exhibits this angiogenic activity may involve formation of complexes containing α3β1
integrin and a transmembrane proteoglycan NG2 (18). Also, it may be a result of galectin-3dependent
clustering of αvβ integrin and activation of focal adhesion kinase that leads to
modulation of vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF)mediated
angiogenesis (36). Finally, galectin-3 could mediated vascularisation via binding to
aminopeptidase N/CD13 - the endothelial cell surface enzyme involved in early steps of angiogenesis
(64).
Cell adhesion
Loss of cell-cell and cell-matrix adhesion is linked to initiation of tumour metastases (35). As a result,
cancer cells detach from the primary tumour site and start migration to secondary sites. Indeed,
galectin-3, as well as galectins -1 and -8, inhibits cancer cell-ECM proteins adhesion possibly via
disruption of normal interactions that consequently leads to escape of cancer cells from their
primary tumour site (44).
On the contrary, galectin-3 can promote cell adhesion thanks to its multivalent properties
(35). In this way, galectin-3 could augment homotypic adhesion of tumour cell and could enhance
tumour-endothelial cells adhesion at secondary tumour sites, therefore, promoting metastasis. For
example, highly invasive human breast carcinoma cells show enhanced galectin-3-dependent
adhesion to endothelial cells (30). This process may involve galectin-3 binding to Mgat5-modified Nglycans
on the tumour cell surface and triggering α5β1 integrin translocation to fibrillar adhesions
(32). Some potential galectin-3 cell adhesion ligands in human colon carcinoma include laminin and
lysosome-associated membrane glycoproteins. Also, cross-linking and preventing of endocytosis of
epidermal growth factor receptor (EGFR) or transforming growth factor-β receptor (TGFβR) by
galectin-3 cell-surface lattices may affect cell growth and receptor density and, hence, could result in
increased invasiveness of tumour cells (7).
Tumour cell spreading
Circulating galectin-3 has been detected at a 5-fold higher concentration in the bloodstream of
patients with colorectal cancer as compared to healthy individuals (28). Increased levels of galectin-3
in blood circulation could be prognostic for metastatic potential of colorectal tumours (7). In the
bloodstream, galectin-3 has been shown to bind to the oncofoetal Thomsen-Friedenreich
(galactoseβ1,3N-acetylgalactosamineα, TF) antigen present on MUC1 – a glycosylated
transmembrane mucin highly expressed in many cancers (68). This interaction triggers polarisation
and redistribution of MUC1 on the cell surface and subsequent exposure of smaller cell adhesion
molecules. As a result, there is increased cancer cell adhesion to vascular endothelial cells and
increased homotypic interactions between transformed cells. The latter effect leads to formation of
cancer cell aggregates (emboli) that survive longer in blood circulation and, hence, allow tumour cell
spreading to sites distant from the primary tumour.
Furthermore, overexpressed galectin-3 in human breast carcinoma cells contributes to the
remodelling of the cytoskeletal microfilaments, which are involved in cell spreading (35). Finally,
71

ecause galectin-3 binds to and stimulates expression of integrins, which take part in cell migration,
it may also regulate tumour invasion by activating integrins.
Importantly, galectin-3 can suppress immune response and consequently may aid tumour
cells in evasion of the immune surveillance (35). Unfortunately, due to space restrictions, it is
beyond the scope of this review to describe the complexity of immune reactions regulated by
galectin-3. In short, galectin-3 is responsible for T-cell apoptosis and cross-linking of T-cell receptors
(TCRs) that results in TCR-dependent signal inhibition. Also, it is capable of reducing IL5 production
and inhibiting B lymphocyte differentiation (35).
CONCLUSION AND PERSPECTIVES
Galectin-3 is a multi-talented lectin that mediates a myriad of physiological processes. Its implication
in cancer pathogenesis is obvious and is associated with a multitude of protein-protein and proteinglycan
interactions. Galectin-3 is a promising therapeutic target, as its inhibition by the CRD-specific
ligands has been shown to be effective in reducing lung and liver metastases in melanoma and
sarcoma mouse models, respectively (7). However, future studies are necessary for developing
clinically significant therapeutics.
Clearly, galectin-3 is a potential diagnostic and prognostic biomarker in several cancers.
However, care should be taken in interpretation of the results, as they may not always reflect the
correct outcome of tumour progression/diagnosis (14). Moreover, many of the aforementioned
interactions of galectin-3 with its binding partners/ligands have been investigated only in vitro and
there is no data regarding binding affinities of its intracellular ligands (7); therefore, it is important
not to over-interpret galectin-3 function at physiological levels.
Much remains to be learned about the role of galectin-3 in cancer progression and
metastasis, as well as in non-pathological processes. The mechanistic detail of its action at different
cellular locations might be crucial in understanding tumourigenesis and developing better anticancer
therapies. Additionally, galectin-3 has been shown to be involved in other disease conditions,
such as diabetes, atherosclerosis and inflammation (63), and, hence, it may also be a promising
therapeutic target for these pathological states.
REFERENCES
1. Ahmad N, Gabius HJ, Andre S, Kaltner H, Sabesan S, Roy R, Liu B, Macaluso F, Brewer CF.
Galectin-3 precipitates as a pentamer with synthetic multivalent carbohydrates and forms
heterogeneous cross-linked complexes. J. Biol. Chem. 279: 10841–10847, 2004.
2. Akahani S, Nangia-Makker P, Inohara H, Kim HR & Raz A. Galectin-3: a novel antiapoptotic
molecule with a functional BH1 (NWGR) domain of Bcl-2 family. Cancer Res. 57: 5272–5276,
1997.
3. Agrwal N, Sun Q, Wang SY, Wang JL. Carbohydrate-binding protein 35. I. Properties of the
recombinant polypeptide and the individuality of the domains. J. Biol. Chem. 268: 14932–
14939, 1993.
4. Andre S, Kojima S, Yamazaki N, Fink C, Kaltner H, Kayser K, Gabius HJ. Galectin-1 and -3 and
their ligands in tumour biology. Non-uniform properties in cell surface presentation and
modulation of adhesion to matrix glycoproteins for various tumor cell lines, in
biodistribution of free and liposome-bound galectins and in their expression by breast and
colorectal carcinomas with/without metastatic propensity. J. Cencer Res. Clin Oncol 125:
461-474, 1999.
5. Barboni EA, Bawumia S, Henrick K, Hughes RC. Molecular modeling and mutagenesis
studies of the N-terminal domains of galectin-3: evidence for participation with the Cterminal
carbohydrate recognition domain in oligosaccharide binding. Glycobiology 10:
1201–1208, 2000.
6. Barondes SH, Castronovo V, Cooper DN, Cummings RD, Drickamer K, Feizi T, Gitt MA,
Hirabayashi J, Hughes C, Kasai K, Leffler H, Liu F-T, Lotan R, Mercurio AM, Monsigny M,
72

Pillai S, Poirer F, Raz A, Rigby PWJ, Rini JM, Wang JL. Galectins: a family of animal betagalactoside-binding
lectins. Cell 76: 597–598, 1994.
7. Barrow H, Rhodes JM, Yu L-G. The role of galectins in colorectal cancer progression. Int J
Cancer 129: 1-8, 2011.
8. Birdsall B, Feeney J, Burdett IDJ, Bawumia S, Barboni EAM and Hughes RC. NMR solution
studies of hamster galectin-3 and electron microscopic visualization of surface-adsorbed
complexes: evidence for interactions between the N- and C-terminal domains. Biochemistry
40: 4859–4866, 2001.
9. Brewer CF, Miceli MC & Baum LG. Clusters, bundles, arrays and lattices: novel mechanisms
for lectin-saccharide-mediated cellular interactions. Curr. Opin. Struct. Biol. 12: 616–623,
2002.
10. Buljan M, Situm M, Tomas D, Milošević M, Krušlin B. Prognostic value of galectin-3 in
primary cutaneous melanoma. J Eur Acad Dermatol Venereol. 2010 (ahead of print)
11. Califice S, Castronovo V, Bracke M & van Den Brule F. Dual activities of galectin-3 in human
prostate cancer: tumor suppression of nuclear galectin-3 vs tumor promotion of cytoplasmic
galectin-3. Oncogene 23: 7527–7536, 2004.
12. Cheng S, Serra S, Mercado M, Ezzat S, Asa SL. A high-throughput proteomic approach
provides distinct signatures for thyroid cancer behavior. Clin Cancer Res. 17(8): 2385-2394,
2011.
13. Colnot C, Fowlis D, Ripoche MA, Bouchaert I, and Poirier F. Embryonic implantation in
galectin 1/galectin 3 double mutant mice. Dev. Dyn. 211: 306–313, 1998.
14. Dumic J, Dabelic S, Flögel M. Galectin-3: an open-ended story. Biochim Biophys
Acta. 1760(4): 616-635, 2006.
15. Elad-Sfadia G, Haklai R, Ballan E. & Kloog Y. Galectin-3 augments K-Ras activation and
triggers a Ras signal that attenuates ERK but not phosphoinositide 3-kinase activity. J. Biol.
Chem. 279: 34922–34930, 2004.
16. Fernandez GC, Ilarregui JM, Rubel CJ, Toscano MA, Gomez SA, Beigier Bompadre M, Isturiz
MA, Rabinovich GA, Palermo MS. Galectin-3 and soluble fibrinogen act in concert to
modulate neutrophil activation and survival: involvement of alternative MAPK pathways.
Glycobiology 15: 519–527, 2005.
17. Feuk-Lagerstedt E, Jordan ET, Leffler H, Dahlgren C, Karlsson A. Identification of CD66a and
CD66b as the major galectin-3 receptor candidates in human neutrophils. J. Immunol. 163:
5592–5598, 1999.
18. Fukushi J, Makagiansar IT, Stallcup WB. NG2 proteoglycan promotes endothelial cell
motility and angiogenesis via engagement of galectin-3 and alpha3beta1 integrin. Mol. Biol.
Cell 15: 3580–3590, 2004.
19. Gaudin JC, Mehul B, Hughes RC. Nuclear localisation of wild type and mutant galectin-3 in
transfected cells. Biol. Cell 92: 49–58, 2000.
20. Gong HC, Honjo Y, Nangia-Makker P, Hogan V, Mazurak N, Bresalier RS, Raz A. The NH2
terminus of galectin-3 governs cellular compartmentalization and functions in cancer cells.
Cancer Res. 59: 6239–6245, 1999.
21. Hirabayashi J, Hashidate T, Arata Y, Nishi N, Nakamura T, Hirashima M, Urashima T, Oka T,
Futai M, Muller WEG, Yagi F and Kasai K. Oligosaccharide specificity of galectins: a search by
frontal affinity chromatography. Biochim. Biophys. Acta 1572: 232–254, 2002.
22. Ho MK, Springer TA. Mac-2, a novel 32,000 Mr mouse macrophage subpopulation-specific
antigen defined by monoclonal antibodies, J. Immunol. 128: 1221–1228, 1982.
23. Honjo Y, Nangia-Makker P, Inohara H & Raz A. Downregulation of galectin-3 suppresses
tumorigenicity of human breast carcinoma cells. Clin. Cancer Res. 7: 661–668, 2001.
24. Houzelstein D, Goncalves IR, Fadden AJ, Sidhu SS, Cooper DN, Drickamer K, Leffler H,
Poirier F. Phylogenetic analysis of the vertebrate galectin family. Mol. Biol. Evol. 21: 1177–
1187, 2004.
25. Hsu DK, Zuberi RI, Liu F-T. Biochemical and biophysical characterization of human
recombinant IgE-binding protein, an S-type animal lectin. J. Biol. Chem. 267: 14167–14174,
1992.
73

26. Hughes RC. The galectin family of mammalian carbohydrate-binding molecules. Biochem.
Soc. Transact. 25: 1194–1198, 1997.
27. Hughes R.C. Secretion of the galectin family of mammalian carbohydrate-binding proteins.
Biochim. Biophys. Acta 1473: 172–185, 1999.
28. Iurisci I, Tinari N, Natoli C, Angelucci D, Cianchetti E, Iacobelli S. Concentrations of galectin-
3 in the sera of normal controls and cancer patients. Clin Cancer Res 6: 1389-1393, 2000.
29. Jeng KC, Frigeri LG, Liu FT. An endogenous lectin, galectin-3 (epsilon BP/Mac-2), potentiates
IL-1 production by human monocytes. Immunol. Lett. 42: 113–116, 1994.
30. Khaldoyanidi SK, Glinsky VV, Sikora L, Glinskii AB, Mossine VV, Quinn TP, Glinsky
GV, Sriramarao P. MDA-MB-435 human breast carcinoma cell homo- and heterotypic
adhesion under flow conditions is mediated in part by Thomsen-Friedenreich antigengalectin-3
interactions. J. Biol. Chem. 278: 4127–4134, 2003.
31. Kim MK, Sung CO, Do IG, Jeon HK, Song TJ, Park HS, Lee YY, Kim BG, Lee JW, Bae DS.
Overexpression of Galectin-3 and its clinical significance in ovarian carcinoma. Int J Clin
Oncol. 2011 (ahead of print)
32. Lagana A, Goetz JG, Cheung P, Raz A, Dennis JW, Nabi IR. Galectin binding to Mgat5modified
N-glycans regulates fibronectin matrix remodeling in tumor cells. Mol Cell Biol.
26(8): 3181-3193, 2006.
33. Lee YJ, Song YK, Song JJ, Siervo-Sassi RR, Kim HR, Li L, Spitz DR, Lokshin A, Kim JH.
Reconstitution of galectin-3 alters glutathione content and potentiates TRAIL-induced
cytotoxicity by dephosphorylation of Akt. Exp. Cell Res. 288: 21–34, 2003.
34. Liu FT, Hsu DK, Zuberi RI, Kuwabara I, Chi EY, Henderson WR Jr. Expression and function of
galectin-3, a beta-galactoside-binding lectin, in human monocytes and macrophages. Am. J.
Pathol. 147: 1016–1028, 1995.
35. Liu FT, Rabinovich GA. Galectins as modulators of tumour progression. Nat Rev Cancer.
5(1): 29-41, 2005.
36. Markowska AI, Liu FT, Panjwani N. Galectin-3 is an important mediator of VEGF- and bFGFmediated
angiogenic response. J Exp Med. 207(9): 1981-1993, 2010.
37. Massa SM, Cooper DN, Leffler H, Barondes SH. L-29, an endogenous lectin, binds to
glycoconjugate ligands with positive cooperativity, Biochemistry 32 260–267, 1993.
38. Matarrese P, Tinari N, Semeraro ML, Natoli C, Iacobelli S, Malorni W. Galectin-3
overexpression protects from cell damage and death by influencing mitochondrial
homeostasis. FEBS Lett. 473: 311–315, 2000.
39. Mazurek N, Conklin J, Byrd JC, Raz A, Bresalier RS. Phosphorylation of the beta-galactosidebinding
protein galectin-3 modulates binding to its ligands. J. Biol. Chem. 275: 36311–36315,
2000.
40. Menon RP, Hughes RC. Determinants in the N-terminal domains of galectin-3 for secretion
by a novel pathway circumventing the endoplasmic reticulum–Golgi complex. Eur. J.
Biochem. 264: 569–576, 1999.
41. Menon RP, Strom M, Hughes RC. Interaction of a novel cysteine and histidine-rich
cytoplasmic protein with galectin-3 in a carbohydrate-independent manner. FEBS Lett. 470:
227–231, 2000.
42. Morris S, Ahmad N, André S, Kaltner H, Gabius HJ, Brenowitz M, Brewer F. Quaternary
solution structures of galectins-1, -3, and -7. Glycobiology 14(3): 293-300, 2004.
43. Nangia-Makker P, Honjo Y, Sarvis R, Akahani S, Hogan V, Pienta KJ, Raz A. Galectin-3
induces endothelial cell morphogenesis and angiogenesis. Am. J. Pathol. 156: 899–909,
2000.
44. Ochieng J, Furtak V & Lukyanov P. Extracellular functions of galectin-3. Glycoconj. J. 19:
527–535 (2004).
45. Ochieng J, Green B, Evans S, James O, Warfield P. Modulation of the biological functions of
galectin-3 by matrix metalloproteinases. Biochim. Biophys. Acta 1379: 97–106, 1998.
46. Ochieng J, Platt D, Tait L, Hogan V, Raz T, Carmi P, Raz A. Structure–function relationship of
a recombinant human galactosidebinding protein. Biochemistry 32: 4455–4460, 1993.
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47. Oka N, Nakahara S, Takenaka Y, Fukumori T, Hogan V, Kanayama HO, Yanagawa T, Raz A.
Galectin-3 inhibits tumor necrosis factor-related apoptosis-inducing ligand-induced
apoptosis by activating Akt in human bladder carcinoma cells. Cancer Res. 65: 7546–7553,
2005.
48. Paron I, Scaloni A, Pines A, Bachi A, Liu F-T, Puppin C, Pandolfi M, Ledda L, Di Loreto C,
Damante G, Tell G. Nuclear localization of Galectin-3 in transformed thyroid cells: a role in
transcriptional regulation. Biochem. Biophys. Res. Commun. 302: 545–553, 2003.
49. Raz A, Pazerini G, Carmi P. Identification of the metastasis-associated, galactoside-binding
lectin as a chimeric gene product with homology to an IgE-binding protein. Cancer Res. 49:
3489–3493, 1989.
50. Righi A, Jin L, Zhang S, Stilling G, Scheithauer BW, Kovacs K, Lloyd RV. Identification and
consequences of galectin-3 expression in pituitary tumors. Mol Cell Endocrinol. 326(1-2): 8-
14, 2010.
51. Saffar H, Sanii S, Heshmat R, Haghpanah V, Larijani B, Rajabiani A, Azimi S and Tavangar
SM. Expression of galectin-3, nm-23, and cyclooxygenase-2 could potentially discriminate
between benign and malignant pheochromocytoma. Am. J. Clin. Pathol. 135 (3): 454-460,
2011.
52. Sanjuan X, Fernandez PL, Castells A, Castronovo V, van den Brule F, Liu FT, Cardesa A,
Campo E. Differential expression of galectin-3 and galectin-1 in colorectal cancer
progression. Gastroenterology 113: 1906-1915, 1997.
53. Sato S, Hughes RC. Binding specificity of a baby hamster kidney lectin for H type I and II
chains, polylactosamine glycans, and appropriately glycosylated forms of laminin and
fibronectin. J. Biol. Chem. 267: 6983–6990, 1992.
54. Seetharaman J, Kanigsberg A, Slaaby R, Leffler H, Barondes SH, Rini JM. X-ray crystal
structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution. J.
Biol. Chem. 273: 13047–13052, 1998.
55. Shalom-Feuerstein R, Cooks T, Raz A, Kloog Y. Galectin-3 regulates a molecular switch from
N-Ras to K-Ras usage in human breast carcinoma cells. Cancer Res. 65: 7292–7300, 2005.
56. Sharon N. Lectins: carbohydrate-specific reagents and biological recognition molecules. J
Biol Chem. 282(5):2753-2764, 2007.
57. Shimura T, Takenaka Y, Fukumori T, Tsutsumi S, Okada K, Hogan V, Kikuchi A, Kuwano H,
Raz A. Implication of galectin-3 in Wnt signaling. Cancer Res. 65: 3535–3537, 2005.
58. Shimura T, Takenaka Y, Tsutsumi S, Hogan V, Kikuchi A, Raz A. Galectin-3, a novel binding
partner of beta-catenin. Cancer Res. 64: 6363–6367, 2004.
59. Takenaka Y, Inohara H, Yoshii T, Oshima K, Nakahara S, Akahani S, Honjo Y, Yamamoto
Y, Raz A, Kubo T. Malignant transformation of thyroid follicular cells by galectin-3. Cancer
Lett. 195: 111–119, 2003.
60. Tsay YG, Lin NY, Voss PG, Patterson RJ, Wang JL. Export of galectin-3 from nuclei of
digitonin-permeabilized mouse 3T3 fibroblasts. Exp.Cell Res. 252: 250–261, 1999.
61. Yang R-Y, Hill PN, Hsu DK, Liu F-T. Role of the carboxylterminal lectin domain in selfassociation
of galectin-3. Biochemistry 37: 4086–4092, 1998.
62. Yang R-Y, Hsu DK & Liu F-T. Expression of galectin-3 modulates T-cell growth and apoptosis.
PNAS 93: 6737–6742, 1996.
63. Yang R-Y, Rabinovich GA, Liu F-T. Galectins: structure, function and therapeutic potential.
Expert Rev Mol Med. 10: e17, 2008.
64. Yang E, Shim JS, Woo HJ, Kim KW, Kwon HJ. Aminopeptidase N/CD13 induces angiogenesis
through interaction with a pro-angiogenic protein, galectin-3. Biochem Biophys Res
Commun. 363(2): 336-341, 2007.
65. Yoshii T, Fukumori T, Honjo Y, Inohara H, Kim HR, Raz A. Galectin-3 phosphorylation is
required for its anti-apoptotic function and cell cycle arrest. J. Biol. Chem. 277: 6852–6857,
2002.
66. Yoshii T, Inohara H, Takenaka Y, Honjo Y, Akahani S, Nomura T, Raz A, Kubo T. Galectin-3
maintains the transformed phenotype of thyroid papillary carcinoma cells. Int. J. Oncol. 18:
787–792, 2001.
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67. Yu F, Finley RL Jr, Raz A & Kim HR. Galectin-3 translocates to the perinuclear membranes
and inhibits cytochrome c release from the mitochondria. A role for synexin in galectin-3
translocation. J. Biol. Chem. 277: 15819–15827, 2002.
68. Yu LG, Andrews N, Zhao Q, McKean D, Williams JF, Connor LJ, Gerasimenko OV, Hilkens
J, Hirabayashi J, Kasai K, Rhodes JM. Galectin-3 interaction with Thomsen-Friedenreich
disaccharide on cancer-associated MUC1 causes increased cancer cell endothelial adhesion.
J Biol Chem. 282(1): 773-781, 2007.
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6.5 Example of a Referee’s Report
Deubiquitylase HAUSP stabilizes REST and promotes maintenance of neural progenitor
cells
Zhi Huang, Qiulian Wu, Olga A. Guryanova, Lin Cheng, Weinian Shou, Jeremy N. Rich and
Shideng Bao
The authors identify previously unknown regulatory mechanism of stabilisation of the
repressor element 1-silencing transcription factor (REST). REST is responsible for maintenance of
neuronal stem/progenitor cells (NPCs) and is a key silencing factor of neuronal and non-neuronal
genes. Deregulation of REST expression is implicated in neurodegenerative diseases and neural
tumours and the authors recognise the importance of stringent regulation of REST levels in lineage
commitment and self-renewal.
It has been previously demonstrated that β-TrCP is an E3 ligase that targets REST for
degradation via the ubiquitin-proteasome pathway (UPS) during neuronal differentiation. The authors
reasoned that there must be a counterbalancing mechanism for USP-driven REST degradation and
they performed a screen to look for potential REST deubiquitylases. They identified the herpes virusassociated
ubiquitin-specific protesase (HAUSP) (also known as USP7), which expression levels
decrease concordantly with REST upon retinoic acid (RA)-induced differentiation of NPCs. In turn,
expression levels of β-TrCP gradually increase. This is demonstrated by both immunoblotting and
immunofluorescence.
Further experiments show that HAUSP antagonises β-TrCP and acts as a deubiquitylase
(DUB) to stabilise REST. The authors utilise a variety of methods to substantiate their results. They
demonstrate that HAUSP knockdown by shRNA in NPCs specifically decreases REST protein levels
as well as results in neuronal differentiation and disruption of self-renewal that can be rescued by
ectopic expression of REST. Moreover, using real-time PCR (rtPCR), the authors show that the
knockdown does not affect REST mRNA levels. In turn, immunoprecipitation experiments with
REST- or ubiquitin-specific antibodies show that HAUSP knockdown leads to increased
polyubiquitination of REST. Conversely, overexpression of HAUSP results in increased REST
protein levels and decreased polyubiquitynation.
In vitro and in vivo deubiquitynation assays that utilise catalytically inactive mutant HAUSP
(Mt-HAUSP) further substantiate the specificity of HAUSP as a direct deubiquitylase of REST. Also,
overexpression of HAUSP, but not Mt-HAUSP, rescues the neuronal differentiation phenotype
induced by the knockdown, which was demonstrated by immunostaining, immunoprecipitation and
Western blotting. Finally, the authors identify a consensus binding site of human REST (310-PYSS-
313) that is required for HAUSP-dependent deubiquitynation of REST. This is confirmed by
immunoprecipitation which reveals that mutant REST (S313A) is not deubiquitynated by HAUSP. In
addition, RA-induced neuronal differentiation results in increased ubiquitylation of REST, whereas
double-knockdown of β-TrCP and HAUSP leads to intermediate levels of REST ubiquitination.
Taken together, these data validate that REST protein levels are controlled by opposing roles of β-
TrCP and HAUSP and the authors propose a „Ying-Yang‟ model of deubiquitination and
ubiquitination as post-translational mechanisms that regulate REST protein levels and NPC
differentiation.
General comments:
The article demonstrates that deubiquitylase HAUSP plays essential role in the maintenance of
neuronal progenitor cells. The various methods used by the authors provide solid arguments to claim
that HAUSP is a critical factor in positive regulation of REST and indeed it acts directly on REST as
its specific deubiquitylase to counteract β-TrCP-dependent ubiquitylation. Certainly, these results give
important insights into the regulation of neuronal lineage commitment and, hence, could significantly
aid in elucidating the causes of pathological states, such as neurodegenerative diseases and brain
cancers. Also, the authors are aware of the potential use of deubiquitylase HAUSP as a therapeutic
target and as an invaluable tool in regenerative medicine. The article is well-written and sounds
convincing; however, the data presented does not fully explain or validate some of the conclusions
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drawn by the authors. Therefore, to substantiate their final conclusions, I recommend the following
changes before submission of the paper:
Major points:
1) Figure 2 – immunoblotting experiments use CoREST as a negative control to show that
HAUSP knockdown specifically reduces REST protein levels. Although CoREST is a
primary co-factor of REST, the authors do not show whether HAUSP knockdown affects the
levels of other factors in the repressor complex with REST, such as HDAC-1 and -2
(Abrajano , J.J. et al.). It would be good to confirm whether these protein levels remain
unchanged to validate whether HAUSP specifically affects REST.
2) Figure 4 – similarly to Figure 2, CoREST is used as a negative control for rtPCR to check
whether mRNA levels of REST are affected by HAUSP knockdown. The authors should also
investigate mRNA levels of other REST co-factors and possibly other transcription factors
involved in NPC differentiation.
3) Figure S4d – the authors argue that „forced expression of flag-HAUSP (...) increased REST
protein levels‟. This is not convincing as immunoblotting does not actually show any
significant increase in protein levels.
4) Figure 5e – in vitro deubiquitylation assay utilises proteins that were overexpressed in 293T
cells and subsequently purified. This means that there is a potential risk of co-purifying other
DUBs and/or other factors or scaffold proteins that could affect REST polyubiquitination
status. The result might be particularly dubious if WT-HAUSP, but not Mt-HAUSP was
contaminated, but this could be checked by mass spectrometry or protein sequencing.
5) Figure 7 – the authors claim to identify a consensus HAUSP binding sequence in REST, but
fail to show a direct loss of interaction between HAUSP and mutant REST. Although
decreased deubiquitination of REST(S313A) is demonstrated, immunoprecipitation of
HAUSP and immunoblotting with mutant REST would be crucial to validate the authors‟
conclusions.
6) Figure 8 – the concept of direct modulation of REST protein levels and, hence, lineage
commitment and self-renewal, by β-TrCP and HAUSP as presented in the „Ying-Yang‟ model
is very simplified. The authors fail to discuss other potential factors involved in this
regulation, only with a brief mention of TRF2. Certainly, REST is a critical factor in
regulating NPC differentiation, but other factors are also implicated. For example, RAinduced
differentiation results in activation of LIF (Asano, H. et al). Finally, authors do not
show how β-TrCP and HAUSP antagonise each other at the molecular level and whether
modulation of REST protein levels is phosphorylation-dependent, as β-TrCP requires a
phosphodegron for ubiquitination (Westbrook, T.F. et al.).
Minor points
1) Figure 1 – the authors show protein levels of HAUSP, β-TrCP, REST and TUJ1 by
immunoblotting during NPC differentiation and the results are confirmed by immunostaining
of all proteins, but β-TrCP. It would be nice to include β-TrCP in this experiment and also to
be consistent with the cell line used, as the authors sometimes utilise 15167 and sometimes
ENStemA NPCs.
2) Figure 3e – immunoblot shows protein levels of ectopically expressed Flag-REST after
HAUSP knockdown; it would be good to see also total REST levels.
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3) Figure 7b – immunoblot shows incomplete disruption of deubiquitylation of REST(S313A)
(lane 4) as compared to control not overexpressing HAUSP (lane 2) – this is not discussed in
text.
4) Figure S6: a –REST is almost completely degraded in differentiated cells (lane 2), although a
proteasomal inhibitor is used. b – REST ubiquitination in cells overexpressing HAUSP is
only slightly reduced (lane 1) as compared to control (lane 2). These results are not explained.
5) Most of the immunoprecipitation experiments do not include input REST levels (Figure 5c, e,
f, Figure 6d, Figure 7b, c, d, Figure S4c and Figure S6), so it is hard to assess the relevancy of
the results of deubiquitination assays.
6) Figure 1, 3 and 6 – apart from TUJ1, it would be nice to use antibodies against other neuronal
markers to substantiate the results.
References
1. Abrajano JJ, Qureshi IA, Gokhan S, Zheng D, Bergman A, Mehler MF. REST and CoREST
modulate neuronal subtype specification, maturation and maintenance. PLoS One. (2009)
4(12):e7936.
2. Asano H, Aonuma M, Sanosaka T, Kohyama J, Namihira M, Nakashima K. Astrocyte
differentiation of neural precursor cells is enhanced by retinoic acid through a change in
epigenetic modification. Stem Cells. (2009) 27(11):2744-52.
3. Westbrook TF, Hu G, Ang XL, Mulligan P, Pavlova NN, Liang A, Leng Y, Maehr R, Shi Y,
Harper JW, Elledge SJ. SCF β-TRCP controls oncogenic transformation and neural
differentiation through REST degradation. Nature (2008) 452, 370-374.
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Section 7
Transferable Skills
Training in this module is on-going throughout the year and is delivered by staff involved with
the program and the University via central provisions. It includes training in research
techniques and the development of personal and professional transferable skills.
Assessment of this module is via three assignments: the business plan and presentation
given in the IP and Commercialisation component (8% of the marks), the PhD Studentship
application (10% of the marks), and the Portfolio of Assessment Commentary (2% of the
marks). Altogether, these 3 assignments contribute 20% of the total marks available for the
MRes. Further information on the 3 assessed components of the module is given on the
pages that follow.
PhD Studentship Applications are assessed by two independent markers. The Portfolio of
Assessment Commentary will be evaluated by the course director. The Business Proposal
will be assessed by a panel representing members from the Management School, Business
Gateway and the Programme Director.
Please note the standard University penalty for late submission of written work applies (see
under overview of assessment).
7.1 Intellectual Property and Commercialization
The IP and Commercialization Workshop will raise awareness of the issues associated
with, and necessary for, successful commercialisation of academic research. Intellectual
property is a key component for business success. You will learn about the types and
importance of intellectual property and how to search for patent information on the Web. The
routes available for creating value from basic research will be described. There will be a
comparison of the licensing and spin-out routes, together with detail of the business planning
process and the role of the technology transfer office. You will be working as a group to
prepare a written business plan for potential commercialisation of research. In addition, you
will be required to present your idea as a „pitch‟ to a panel of judges in a similar way to the
popular television programme “Dragon‟s Den”. Marks will be awarded to each group by the
judging panel based on both the business plan and the presentation.
7.2 Writing a PhD Studentship
The “Writing a PhD Studentship” workshop will enable students to create a coherent and
feasible research proposal for a scientific project to continue studying for a PhD, and to
present this in a form suitable for external scrutiny. An overview of the material covered in
this workshop is given below.
Aims:
- To improve your understanding of the concepts of hypothesis testing and
experimental planning.
- To practice the skills required for producing a scientific proposal in writing.
Learning outcomes:
On completion of this assignment, you will have improved your ability to:
- formulate testable hypotheses
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- explain the rationale and design of experiments to test specific hypotheses
- write a scientific proposal in a structured way.
How is this relevant to me?
- In your later career you may need to think analytically about new experiments, and
may need to explain your thinking in writing.
- Almost all scientific activity that occurs in the outside world (and almost all new
scientific activity in Universities) is based on written proposals that justify the work to
be done.
- In some cases, your future salary (or that of your colleagues) may even depend on
the ability to write a convincing proposal describing what you intend to do.
Examples of types of proposal
Deciding what experiments are worth doing, how to design them to produce useful data, and
then how to explain these processes to other people, is central to all modern scientific
activity. The same generic approach is used at many different levels, including Ph.D.
projects proposal you will need write as part of your transferable skill task, and proposals for
grants that provide the salary for a post-doctoral researcher or a research fellow. The same
general principles also apply to the formulation of proposals for large projects in industry
designed to produce new products (eg drug discovery and development), and for big
international research projects that might involve the collaboration of many different research
groups.
The elements of a scientific proposal
The general questions that provide the basis for any scientific proposal are:
(a) What is already known about the specific topic ? This component often takes the
form of a review of previous studies in the area.
(b) What are the gaps in present knowledge ? A critical analysis of previous work in the
field may identify unanswered questions, or there may be conflicting data that need
to be explained and reconciled. Developments in one field, including new types of
technology, may suggest new applications in another field, or new ways of looking at
specific questions in other fields.
(c) What specific hypothesis will provide the basis for the proposed experiments ? The
concept of hypothesis-testing lies at the foundation of much of modern science. A
section below deals with this in more detail.
(d) What experimental plan will be followed ? For a proposal to be convincing, it needs to
be clear what types of experiment are to be done and how; what problems are
anticipated, and what strategies are available to overcome these problems ? There
are often several different types of experiment that can be done to address a specific
question, so it is useful to ask what is the rationale for a particular approach. Can
multiple lines of evidence be brought to a support a particular conclusion ? If so what
are they ?
(e) What outcomes are anticipated ? Any problems that are anticipated with data
interpretation should be identified. Virtually all experimental work costs money: will
the financial backer be able to use the outcomes of the experiment, will there by
value for money ?
Hypothesis testing
The definition of a hypothesis that most scientists would recognise goes something like this:
a supposition made as the basis for experiment without assumption of its truth. A typical
example in physiology might take the form “substance X plays a role in regulating process
Y”. Several obvious lines of experiment to test the hypothesis might include measuring the
activity of Y after removing substance X, after over-stimulation by X, and after blocking the
effects of X. It may be possible to do these experiments both in vivo (for example in
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experimental animals) and in vitro (for example in cell lines). Depending on the outcomes,
the data would be said to be either consistent with the hypothesis (in which case one might
then ask about the relevant mechanisms), or they are inconsistent in which case the
hypothesis should be rejected (and an alternative one developed).
There are some major scientific projects that are not strongly based on hypothesis. An
example would be the sequencing of the human genome which has sometimes been called
“hypothesis-generating” activity. In general, however, most modern science is based on the
formulation of specific testable hypotheses. The generation of hypotheses is one of the most
important parts of any scientific plan.
Good hypotheses are sometimes also described as “useful”. In turn, useful hypotheses
generally possess most if not all of the following: they take account of existing knowledge
and indicate ways in which this knowledge could be extended (if correct), and they provide
the basis for designing specific experiments (ie tests of the hypothesis) that should yield
clear-cut answers one way or the other. They may also provide a way of unifying disparate
sets of observations.
Writing a proposal
The proposal you are asked to complete in this assignment is for a PhD studentship and
should have the following sections: Summary, Background, Hypothesis, Specific aims &
objectives, Experimental plan, Outcomes, & Sources of information (ie references etc). In
addition, you are required to write a short summary of the proposal for both scientific and lay
audiences. Each section should address a distinct set of points.
Summary: this should provide a brief overview of the entire proposal. The lay summary
should avoid the use of technical terms and jargon that would not be familar to the average
lay person.
Background: existing knowledge should be reviewed (and sources referenced at the end of
the proposal). If there are pilot data, or preliminary experimental findings available (see
below), these can be described at the end of this section. The objective in writing this section
should be the identification of worthwhile new experiments. You would like to reader to
recognise you‟re your proposed experiments are exactly the right ones to do next.
Hypothesis: The workshop will provide help in formulating hypotheses and in distinguishing
between useful and inappropriate hypotheses. A specific hypothesis can be quite brief (one
or two sentences) but may represent a lot of hard thinking.
Aims and objectives. These can be quite briefly expressed. In effect they should translate
the hypothesis into specific questions that your intended experiments will answer.
Experimental plan: at least in part this section may be written in the future tense since it
should describe what you intend to do. It might help you to think in terms of three subsections;
(1) The first part of the plan should outline the general strategy to be followed, and
may explain why other strategies are rejected. If you have pilot data, or other reasons for
supposing that a particular strategy will be successful, this should be explained. (2) You may
already have an idea of the specific experimental protocols that you propose to use: if so,
explain this – but consider also, what will happen if things don‟t go exactly according to plan?
What priorities will govern your decisions in this case. . If the experimental methods are not yet worked out in detail, explain
how you will go about optimising the methods to yield useful data. What criteria will be
applied to evaluating any data from optimisation experiments. Depending on the specific
experiments, you may need to define the number of observations required to yield useful
conclusions; in addition, you should already consider what statistical methods will be applied
to the analysis of the data. (3) For many complex projects it is useful to provide a time-line,
or milestones; these are generally regarded as useful tools for project management. Ask
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yourself, should some projected tasks be completed before others, or by specific times
within the project as a whole? If so, how is this incorporated into the experimental plan? In
the real world, time and money are always limited: what resources will you need to achieve
your objectives in an efficient and cost-effective way.
Outcomes: Briefly summarise how, if everything works well, you will have achieved your
objectives (and how a financial backer will have obtained value for money).
Justification for support requested: Briefly describe how the funds requested will be spent,
breaking down consumables funds to give an idea of how much individual parts of the
experimental plan will cost.
References: cite any sources of information quoted in the application. The application
typically should include up to 25 citations to peer-reviewed papers.
Not more than 2,000 words should be used to describe the research proposal (excluding
the scientific and lay summaries, and excluding references). Each section should be written
in good English (not note form or bullet points). Make sure you also choose an informative
title. A template for you to enter the application on will be provided for the application
nearer the time and an example PhD Studentship application is given in section 7.3.
7.3 Portfolio of Assessment Commentary
The Portfolio of Assessment Commentary will enable students to evaluate and reflect on
the aims and objectives of the individual programme components, as well as their own
achievements. Students will be required to assemble a professional-looking portfolio that
documents their progression through the programme in a form suitable for external scrutiny.
Please note that completion of the portfolio self-assessment and participation in the English
conversation sessions for oversees students are obligatory for completion of the program.
7.3.1 Portfolio Contents
Your portfolio should include the following:
1. The three Research Project Reports.
2. Project presentations (poster presentations should be printed on an A4 paper).
3. The 2 Short Reviews.
4. The Referee‟s Report, including the refereed paper.
6. The Business Plan and presentation.
7. The PhD studentship application.
8. the Portfolio self-assessment commentary.
Your portfolio will be viewed by the main External Examiner and therefore should look
professional and presentable.
7.3.2 Portfolio Self-Assessment (Commentary)
Students need to assess:
1. The Research Projects.
2. The Techniques in Biomedical Sciences component.
3. The Frontiers in Biomedical Sciences component.
4. The Transferable Skills component.
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Profile for a portfolio self-assessment:
1. Describe the work to be assessed.
2. Give the aim of the assignment.
3. Describe your learning objectives.
4. Critically evaluate your achievements.
5. What are the learning outcomes?
It is essential to use the same template for each item of work using the same headings
(description, aims, learning objectives, achievements, learning outcomes; ~ one paragraph
for each). A template for this purpose will be provided by the Programme Director.
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7.4 Assessment form for MRes PhD in Biomedical Studentship Sciences application
Grant Application Assessment Form
Student:
Project Title:
Marker 1:
Moderator:
Please complete this form when marking the M.Res write ups, and return it, with the grant application to your
strand convenor. INDICATION OF POTENTIAL DEGREE CLASS BY MARK ATTAINED (Distinction 70-100); (Merit 60-
69); (Pass 50-59); (Fail

7.5 Marking criteria for assessment of PhD Studentship application
Distinction Level 100% - 90%
90% - 80%
80% - 70%
Pass Level 69% - 65%
64% - 60%
59% - 55%
54% - 50%
Fail Level 49% - 45%
44% - 40%
39% - 35%
34% - 10%
0%
Outstanding. No better result conceivable at Masters
level. Extensive evidence of critical thinking and cogent
scientific argument. Evidence of reading around the
topic. Excellent experimental design.
Excellent. Essentially correct and complete, with
evidence of critical thinking and excellent use of the
literature. Logical structure, well written and presented,
displaying a cogent scientific argument. Very good
experimental design.
Very Good. Content essentially without any major
flaws, very well explained with clear evidence of a high
level of scientific competence. Good experimental
design.
Good. Well explained, showing good evidence of
critical scientific judgement. Good experimental design.
Quite Good. A well explained application, with good
understanding and some evidence of critical scientific
judgment. Satisfactory experimental design.
Fairly Good. A generally sound review with a good or
quite good level of understanding, evidence of sound
scientific competence and judgment.
Adequate. Showing some progress but with some
deficiencies in one or more aspects of understanding of
the paper and scientific judgment.
A poor application with an overall superficial approach.
Essentially an incomplete application with major
omissions in several areas and evidence of a poor
understanding.
A poor application with an overall superficial approach
and more errors, omissions and evidence of a deficiency
of effort and poor understanding.
A marked deficiency in content of understanding of the
work proposed and the task set.
Even more marked deficiencies in content of
understanding and application.
A complete absence of relevant work presented.
86

7.6 Example PhD Studentship application
1. APPLICANT (Please include full name, title, department and affiliation)
Your name and details here
2. TITLE OF RESEARCH PROJECT (no more than 220 characters)
Using Caenorhabditis elegans to Fight Human Neurodegenerative Diseases
3. SUMMARY OF RESEARCH
a) For scientifically qualified assessors (no more than 200 words)
In spite of exciting progress, the molecular determinants involved in the aetiology and
susceptibility of various chronic age-related neurodegenerative disorders (NDs) such as
Alzheimer‟s disease (AD), Parkinson‟s disease (PD), Huntington‟s disease (HD), and
amyotrophic lateral sclerosis (ALS), remain mechanistically undefined. Numerous genetic
and pharmacological screens have been conducted in Caenorhabditis elegans disease
models to unravel candidate genes and /or specific cellular pathways pertinent to multiple
neurodegenerative cascades and successfully identified and validated many neuroprotective
factors. The overall aim of this project is to elucidate critical cellular mediators of
neuropathology and neuron vulnerability by exploiting the experimental attributes of C.
elegans and integrating genetic and pharmacological evaluation of a set of experimentally-
delineated genetic modifiers. Multiple transgenic, non-transgenic and toxicant C. elegans ND
models will be generated and optimised by examining their pathological phenotypes. The
bioinformatically prioritised modifiers will then be characterised and validated by phenocopy
using a reverse genetic approach by applying RNA interference (RNAi). In addition, a
chemical reverse genetic screen will be performed to illuminate neuroprotective compounds‟
molecular targets, mechanism of action and affected molecular pathways.
For lay readers (no more than 200 words)
The biological underpinnings of a diverse spectrum of progressive neurological disorders
have remained elusive. Large-scale screens have been performed in model organisms to
isolate genes that either rescue or exacerbate the manifestations of neurodegenerative
disorders (NDs), which in turn yield valuable insights into mediators of disease within cells
and reveal targets for potential therapies. This project will utilise microscopic nematode
roundworm, Caenorhabditis elegans to elucidate the incompletely understood disease
mechanisms and genetic susceptibility of multiple NDs. Worms are used because of their
facile genetics and strikingly similar neuronal mechanisms to the humans. Worms will be
87

manipulated to simulate the cardinal features of several NDs by inserting human disease
proteins, removing or depleting worm version of the disease proteins and administering toxic
compounds, and the animals will be observed for any effects. A collection of previously
identified C. elegans genes already known to influence the severity of dysfunction will be
suppressed in a subsequent screen to discern how they work. In addition, a set of drugs
known to alleviate some disease symptoms will also be applied to reveal their mechanism of
action. Ultimately, the project aims to expand our knowledge of the mechanisms of NDs.
4. RESEARCH QUESTION
a) What is your research question/hypothesis (no more than 100 words)
This project will address the following fundamental questions:
1. What are the conserved genetic and molecular pathways underlying
neurodegenerative diseases?
2. How do genetic modifiers and pharmacological reagents contribute to
neurodegeneration and neuroprotection?
3. Through what mechanisms do therapeutic candidates mediate their neuroprotective
effects?
4. Do modifier genes have a widespread or disease-specific role in neurodegeneration?
5. Are pathogenic mechanism shared between several or all NDs, irrespective of the
specific disease?
6. Which types of neurons are most vulnerable to alterations of modifier genes?
b) Why is it important? (no more than 250 words)
Neurodegenerative diseases (NDs) pose a tremendous economical and societal burden to
our rapidly ageing populations. Though toxic functions of specific disease proteins have
been ascribed following the identification of many predisposition genes, the lack of
mechanistic insights into why and how these genes contribute or influence the aetiology and
progression of the NDs has severe repercussions for treatment of these crippling diseases
since effective therapeutic agents with disease-modifying or preventive properties remain
acutely deficient and development of new drugs continues to be a challenging job. Definitive
insights into the complex mechanistic connections between specific cellular pathways and
specific misfolded protein pathologies are likely to explain the conundrums and facilitate the
development of new disease biomarkers and promising disease-modifying neuroprotective
therapies for timely intervention.
5. DETAILS OF RESEARCH PROJECT: Summarise under the following headings:-
88

a) Aims and objectives of the project
b) Work which has led up to the project
c) Detailed experimental plan of investigation
d) Outcomes
e) Contingency plans
f) Timetable and milestones
NO MORE THAN 2,000 WORDS SHOULD BE USED TO DESCRIBE THE
RESEARCH PROJECT (PLEASE INCLUDE A WORD COUNT)
a) Aims and objectives of the project
This project aims to use a combined application of appropriate genetic and toxicant
Caenorhabditis elegans (C. elegans) neurodegenerative diseases (NDs) models to unravel
the incompletely understood key molecular pathways, disease mechanisms and genetic
susceptibility of multiple NDs. The main focus of the investigation is the genetic and
pharmacological characterisation of modifier genes involved in neuropathology and neuron
vulnerability, which contribute toward the identification of putative novel targets and
therapeutic leads.
b) Work which has led up to the project
Essentially, the majority of neurodegenerative disorders (NDs) are characterised by the
mechanistic unifying theme of aggregation, accumulation and deposition of prominent intra-
or extracellular toxic proteinaceous inclusions in a particular population of neurons (1) where
subsequent necrotic or apoptotic neurodegeneration results in irreversible neuronal loss,
synaptic impairments and eventual neuronal death. The use of Caenorhabditis elegans (C.
elegans) as a primary platform to probe the poorly defined disease mechanisms of several
major NDs and a more rapid means towards novel gene and drug discovery has escalated
over the last decade, since worms are amenable to high-throughput genetic, genomic,
proteomic, and drug screening approaches. Indeed, a multitude of informative, tissue-
specific C. elegans ND models have been developed manifesting abnormal behavioural or
pathological phenotypes that partially recapitulate the salient cellular, molecular and
pathological aspects of complex ND processes (Table 1), to explore the dynamics of
aggregate formation, cellular malfunctions, genetic and environmental susceptibility factors
and putative neuroprotective genes and compounds against disease-protein toxicity (2). As
shown in Figure 1, these models can be subjected to medium or high-throughput genome-
wide forward and reverse genetic screens to identify genetic modifiers, which are essential
physiologic determinants of aggregation and toxicity and yield new potential therapeutic
targets or models for the given disease, as well as low-throughput chemical screens that
directly explore effective lead compounds that rescue the phenotype to identify
89

pharmacological treatments that block neurodegeneration. Targets identified in several
disease models (Table 1) using RNAi screening and microarray analysis have already
advanced to the stage of drug validation for efficacy in mammalian system (3-5).
Substantial evidence implicates that while genetic regulators of protein homeostasis, stress
responsiveness and ageing, including molecular chaperones and components of the
ubiquitin-degradation systems, are common to most disease proteins, the onset,
development and progression of each of the NDs can be induced or influenced by alterations
of a multitude of disease-protein-specific molecular processes (6). All C. elegans and yeast
α-synuclein screens identified components of the vesicular-trafficking machinery to
specifically modify α-synuclein toxicity and aggregation, but are rarely found as modifiers of
polyglutamine (polyQ) and tau toxicity and aggregation, whereas those associated with RNA
metabolism, protein folding and degradation, and transcriptional regulation appear to
influence the pathology of various disease proteins, but are specifically enriched in polyQ
aggregation and toxicity screens including those that have since been validated in other
model organisms and mammals. It also remains unclear which populations of neurons are
most susceptible to the loss of modifier genes when combined with ectopic-overexpression
of aggregation-prone proteins.
Though genome-wide screening in C. elegans may facilitate the identification of all possible
effectors of protein misfolding and neuroprotection, this approach is limited by its inefficiency
in detecting positive hits (2,7,8), due to inclusion of large gene sets that are not necessarily
unique which in turn result in some redundancy, as well as important house-keeping genes
that give rise to non-specific, off-target effects and false positive results. Few screens have
recently used a more focused strategy - a candidate approach/hypothesis-driven approach
to reveal potential modifier genes in a specific pathway based on hypothesis generated by
screens in lower model organisms or existing knowledge of disease mechanisms and
pathways (9,10).
Preliminary work in this laboratory adopted a candidate approach to mine the literature and
compile a collection of experimentally delineated genetic modifiers of protein aggregation,
misfolding and toxicity in C. elegans. Using online databases WormBase
(www.wormbase.org) and GExplore (http://genome.sfu.ca/gexplore/), modifier genes were
further selected for to retrieve only those with known expression in adult neurons that are
also non-RNAi lethal (Table 2) which form the basis for a hypothesis-driven RNAi screen and
subsequent in-depth analyses and mechanistic dissection. Our recent work also used
fluorescence confocal imaging of transgenic C. elegans lines to confirm the promoter
specificity of six neuronal promoters (Fig. 2) which are applicable as means of probing the
role of positive genetic modifiers in the survival, vulnerability and function of specific sets of
neurons and their subsequent validations.
90

TABLE 1. Summary of all available C. elegans neurodegeneration models. Worms are subjected
to molecular, genetic and chemical manipulations to initiate the neurodegenerative cascade.
Corresponding pathological phenotypes and identified drug compounds that confer neuroprotection
are indicated. Models highlighted in beige are most suitable for this project. Human diseases: AD,
Alzheimer‟s disease; HD, Huntington‟s disease; PD, Parkinson‟s disease; ALS, Amyotrophic lateral
sclerosis; SMA, Spinal muscular atrophy
91

Method of
disease model
generation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Molecular
manipulation
Neurodegenerative
diseases
AD P unc-54::Aβ - constitutive muscle
myo-3::Aβ 1-42 - inducible muscle
P unc-54::Aβ 1-42 - constitutive muscle
Transgene expression Phenotype Drug References
Uncoordinated (Unc), paralysis, amyloid formation Ginkgo biloba extract EGb 761 and
Ginkgolide A (12)
Soya isoflavone glycitein (35)
Reserpine (48)
Thioflavin T; curcumin (21)
92
Link et al (15)
AD P snb-1::Aβ 1-42 - inducible pan-neuronal Paralysis Wu et al (12)
AD P aex-3::tau – pan-neuronal Unc, tau phosphorylation and aggregation,
neurodegeneration
- Kraemer et al(16)
AD P mec-7::tau – mechanosensory neurons Mec, tau phosphorylation, neurodegeneration - Miyasaka et al (17)
AD P rgef-1:: PHP tau- pan-neuronal Unc, decreased lifespan, defective neuronal
development
- Brandt et al (18)
HD P myo-3::polyQ–GFP – inducible muscle Paralysis, age-dependent polyQ aggregation - Caldwell et al (41)
HD P unc-54::polyQ–GFP - constitutive muscle Motility defect - Wang et al (19)
Saytal et al (20)
HD P unc-54::DRPLAP::GFP- constitutive muscle - - Yamanaka et al (36)
HD P mec-3::polyQ–GFP - mechanosensory neurons Mec, axon morphology abnormalities Resveratrol Parker et al (37)
HD P osm-10::polyQ–GFP - chemosensory neurons polyQ aggregation, ASH neuron degeneration,
nose-touch defective
Lithium chloride; mithramycin (23) Faber et al (42)
HD P rgef-1::polyQ–GFP - pan-neuronal Unc, motility defects, paralysis - Brignull et al (22)
HD pqe-1(rt13); Htn-Q150(rtIs11) Accelerated neurodegeneration - Voisine et al (23)
HD pha-1(e2123); Htn-Q150(rtIs11) ASH neuronal death Trichostatin (38) Voisine et al (23)
PD P aex-3::α-syn WT and A53T - pan-neuronal Unc, DA dendritic abnormalities, reduced motor
movement
- Lakso et al (24)
Springer et al (25)
PD P snb-1::α-syn WT - pan-neuronal Mitochondrial stress - Ved et al (26)
PD P unc-119::α-syn A53T- pan-neuronal Mitochondrial stress - Ved et al (26)
PD P unc-51 ::α-syn WT,A30P and A53T - pan-neuronal Motor/developmental defects, endocytosis defects - Kuwahara et al (27)
PD P dat-1 ::α-syn WT, A30P, A53T, A56P and A76P –
DA neurons
DA neurodegeneration, α-syn accumulation in DA
neurons, reduced DA levels, altered DA neuronal
activity
Acetaminophen (39)
Bromocriptine, Quinpirole (3)
Lakso et al (24)
Settivari et al (32)
Cao et al (31)
Kuwahara et al (27)
Karpinar et al (40)
PD P acr-2::α-syn WT and A53T – motor neurons Reduced motor movement - Lakso et al (24)
PD P mec-7::α-syn WT and A53T - mechanosensory
neurons
Impaired touch response - Kuwahara et al (27)
PD P unc-54 ::α-syn::GFP - constitutive muscle α-syn misfolding and accumulation - Hamamichi et al (10)
Van Ham et al (2)
PD P snb-1::LRRK2 WT, R1441C, G2019S – panneuronal
PD eri-1 (mg366);P dat-1 ::α-syn WT,
eri-1 (mg366);P dat-1 ::α-syn A53T
eri-1 (mg366);P dat-1 ::α-syn A30P
Mitochondrial stress, reduced DA levels, DA
degeneration
PD pdr-1(lg103); α-syn A53T Highly penetrant, temperature sensitive lethality,
early larval arrest phenotype
ALS P myo-3::SOD-1
hsp-16::SOD-1 - body wall muscle or inducible
ALS P snb-1::SOD-1 WT, G85R, H46R/H48Q – YFP –
pan-neuronal
- Saha et al (28)
Unc, growth retardation (Gro) - Kuwahara et al (27)
- Kuwahara et al (27)
Paraquat hypersensitivity - Oeda et al (43)
Locomotory defects, intra-neuronal aggregation,
abnormal processes and synaptic function
- Wang et al (44)
Mutant/RNAi AD sel-12 or hop-1 Egg laying defective (Egl) - Lakowski et al (45)
Mutant/RNAi HD pqe-1(rt13) Accelerated neurodegeneration - Voisine et al (23)
Mutant/RNAi HD pha-1(e2123) ASH neuronal death - Voisine et al (23)
Mutant/RNAi PD lrk-1 (km17), (km41), (tm1898) and (RNAi) Mitochondrial stress, ER stress sensitive - Saha et al (28)
Mutant/RNAi PD pdr-1 (lg103), (XY1046, Parkin KO3) and (RNAi) Mitochondrial stress, ER stress sensitive,
decreased life span
Mutant/RNAi PD pink-1 (tm1779) Oxidative stress sensitive, neurite outgrowth
defects, mitochondrial cristae defects
- Samann et al (29)
Springer et al (25)
Ved et al (26)
- Samann et al (29)
Mutant/RNAi PD catp-6 (RNAi) α-syn misfolding - Gitler et al (46)
Mutant/RNAi PD djr-1.1 (RNAi) Mitochondrial stress - Ved et al (26)
Mutant/RNAi SMA smn-1 (ok355) Neuromuscular function deficits - Briese et al (47)
Chemical treatment PD P dat-1::GFP subjected to 6-hydroxydopamine (6-
OHDA)
Chemical treatment PD N2 , P dat-1::GFP, P dat-1::α-syn subjected to
Manganese (Mn 2+ )
DA neurodegeneration - Nass et al (30)
Cao et al (31)
Oxidative stress, mitochondrial stress, enhanced
DA neurodegeneration, reduced DA levels
- Settivari et al (32)
Chemical treatment PD N2, P cat-2::GFP subjected to MPTP and MPP + DA neurodegeneration, motility defects, lethality Lisuride, apomorphine, Rottlerin (33) Braungart et al. (33)
Chemical treatment PD pink-1 (tm1779) subjected to Paraquat Oxidative stress - Samann et al (29)
Chemical treatment PD pdr-1 (XY1046), P snb-1::α-syn WT, P unc-119::α-syn
A53T, N2, lrk-1 (km17), P snb-1::LRRK2 WT,
R1441C, G2019S subjected to Rotenone
Chemical treatment PD P dat-1::GFP subjected to Streptomyces
venezuelae secondary metabolite
Mitochondrial stress, reduced viability - Ved et al (26)
Saha et al (28)
DA neurodegeneration - Caldwell et al (34)

WormBase C. elegans
genome
RNAi screen
(reverse genetics)
suppressor
enhancer
Feeding worms
with individual
RNAi clones
Confirmation of
RNAi clones
Genetic screen
(forward genetics)
suppressor
enhancer
EMS
Mutagenesis
Phenotype analysis
Positive hits identified
Gene mapping
Hits prioritisation
Hits validation
Pharmacological intervention in worms
if successful
Mammalian assays and identification
of human orthologues
Drug Validation
genetic
complementation
and sequencing of
mutant alleles
Disease
C. elegans disease model
Functional C. elegans assay
Recapitulation of phenotypes in worms
Pharmacological screen
Screening goal
drug sensitivity
drug resistance
Determine optimal drug
concentrations
Distribution of compounds
Confirmation of drug efficacy
Exclude drug effects on
growth/development and
aging pathway
Secondary analyses in multiple worm models
Tissue-specific expression
of mutant disease gene;
mutation/RNAi;
compound-induced
Expression profiling Epistatic analysis
gene expression
changes
miRNA microarray
Quantitative real-time
PCR
Target analysis
mechanisms of
disease
Pharmacological
intervention
FIGURE 1. Schematic diagram of the various screening routes for the identification of genetic or
pharmacological targets of a C. elegans disease model
93

Functional Category Gene name CGC
Name
Chaperone/quality
control
Protein
turnover/degradation/
UPS
Neurotransmission and
signalling
Signal transduction
Transcription cofactor
ECM/Cytoskeletal
organisation
Enzymes
Redox/oxidative stress
Voltage-gated ion
channels
Description
Human
orthologues
RNAi
library
F08H9.4 - heat shock protein (HSP) of the HSP16 class HSPB6 Vidal
T09B4.10 chn-1 mammalian carboxyl-terminus of Hsc70 interacting protein STUB1 CHIP Ahringer
F55B12.3 sel-10
F-box and WD-repeat-containing protein of CDC4/CUL-1
family of E2-E3 ubiquitin ligases
FBXW7 Vidal
Y61A9LA.8 sut-2 Nuclear polyadenylated RNA binding protein ZC3H14
Not
available
T05H10.1 - Putative ubiquitin-specific protease USP47 Ahringer
T26A5.5 - F-box protein JEMMA FBXL19 Vidal
K09A9.6 - Aspartyl beta-hydroxylase ASPHD2 Ahringer
F47G6.1 dyb-1 ZZ type zinc finger DTNA Vidal
T04D1.3 unc-57 endophilin A, required for synaptic vesicle endocytosis SH3GL2 Vidal
Y22F5A.3 ric-4 Intracellular protein transport, neurotransmitter secretion SNAP-25 Vidal
EEED8.9 pink-1 BRPK/PTEN-induced protein kinase PINK1 Ahringer
T25F10.2 dbl-1
a member of the transforming growth factor beta
(TGFbeta) superfamily
BMP4 Vidal
M04C9.5 dyf-5 a putative MAP kinase MAK/ICK Ahringer
K11E8.1 unc-43 type II calcium/calmodulin-dependent protein kinase CaMKII Vidal
K07A9.2 cmk-1 Ca 2+ /calmodulin-dependent protein kinase I CaMK1 Vidal
B0334.8 age-1 functions in an insulin-like signalling (ILS) pathway PI3K Ahringer
W08G11.4 pptr-1 Serine/threonine protein phosphatase 2A PP2A
Not
available
R11A8.4 sir-2.1 NAD-dependent deacetylase sirtuin-1 SIRT1 Ahringer
R13H8.1 daf-16 sole C. elegans forkhead box O (FOXO) homologue FOXO4 Vidal
H21P03.1 mbf-1 Transcription factor MBF1 EDF1 Vidal
C04G6.3 pld-1 Phospholipase D1 PLD1 Vidal
F02E9.4 sin-3 SIN3 family of histone deacetylase subunits SIN3 Vidal
F39C12.2 add-1 cytoskeletal protein alpha-adducin ADD1 Vidal
K05B2.3 ifa-4 a nonessential intermediate filament protein IFB-1 Vidal
R05D3.7 unc-116 kinesin-1 heavy chain ortholog KIF5 Ahringer
F47G4.7 smd-1 S-Adenosylmethionine decarboxylase AMD1 Vidal
C06E7.1 sams-3 S-adenosylmethionine synthetase MAT1A Vidal
F44E7.2 - p-Nitrophenyl phosphatase PDXP Vidal
Y56A3A.13 nft-1 Carbon-nitrogen hydrolase FHIT Vidal
C30H7.2 - human thioredoxin domain-containing protein 4 precursor ERP44 Vidal
K08F4.7 gst-4 a putative glutathione-requiring prostaglandin D synthase GSTA3 Vidal
F35E8.8 gst-38 unclassified GSTA4 Vidal
C50C3.9 unc-36 alpha2/delta subunit of a voltage-gated calcium channel CACNA2D3 Vidal
R05G6.7 - Porin/voltage-dependent anion-selective channel protein VDAC2 Vidal
Transport ATPase ZK256.1 pmr-1 a Golgi P-type ATPase Ca 2+ /Mn 2+ -pump ATP2C1
Not
available
Dopamine metabolism T23G5.5 dat-1 a plasma membrane dopamine transporter SLC6A2/A3 Vidal
Lipid metabolism C28C12.7 spp-10 sphingolipid metabolism/lysosomal PSAP Vidal
RNA metabolism M88.5 - IGF-II mRNA-binding protein IMP IGF2BP2 Vidal
Carbohydrate
metabolism
K11H3.1 gpdh-2 glycerol 3-phosphate dehydrogenases GPD1L Vidal
Trehalose
biosynthesis
Unclassified
T05A12.2 tre-2 putative trehalases of unknown function TREH Vidal
W05E10.4 tre-3 putative trehalases of unknown function TREH Vidal
C04B4.2 - unclassified None Vidal
R74.3 xbp-1 unclassified None Vidal
R13A1.8 glb-23 unclassified None Vidal
F52C9.8 pqe-1 unclassified REXO1 Vidal
F08C6.3 tag-197 unclassified VPS52 Vidal
Y55F3AM.14 - unclassified None Vidal
TABLE 2: Set of 47 modifier genes with known adult neuronal expression and non-RNAi lethality.
Assigned functional category, C. elegans gene name, CGC approved name, available description and
human orthologue are shown. RNAi feeding library coverage of the modifier genes is also indicated. Four
modifier genes are nematode specific and six genes remain uncharacterised. UPS: ubiquitin-proteasome
system, ECM: extracellular matrix.
94

P rab-3::EGFP
P unc-17::GFP
E
P dat-1::GFP
P osm-6::GFP
FIGURE 2: Promoter specificity of
transgenic C. elegans is confirmed by Pglr-1::GFP fluorescent reporter constructs in
extrachromosomal arrays. Fluorescence
microscopy of whole body (A,B;C-F left
F
panels) or magnified 3D confocal
reconstruction of neuronal architecture in
the head region (C-F right panels). A, The
pan-neuronal localisation of enhanced
GFP (EGFP) expression is consistent with
the expected rab-3 promoter driven
expression pattern in all worm neurons. B,
Punc-17::GFP labels most regions of the
nervous system, predominantly cholinergic
motor neuronal processes. C, The dat-1
promoter labels all 8 dopaminergic (DA)
neurons: six anterior neurons in the head
and two posterior deirid neurons (PDEs,
thick arrow). 3D confocal reconstruction of
Pgcy-8::GFP the magnified head region (right), detailing the six anterior-most DA neurons: four cephalic CEP neurons (asterisks)
project dendrites (thin arrows) to the tip of the nose and two anterior deirid ADE neurons (arrow head) extend ciliated
processes posteriorly. The CEP dendritic processes of another worm are also visible. D, Posm-6::GFP selectively labels all
60 ciliated sensory neurons. E, The glr-1 promoter drives expression of the GFP in the ventral cord interneurons,
motorneurons and nerve ring. F, gcy-8::GFP localises exclusively to one thermo-sensory AFD pair (dashed arrow). 3D
confocal reconstruction (right) shows that the AFD dendrites extend anteriorly to the tip of the nose. The sensory endings
of both neurons are positioned at the tip of the dendrites (double asterisks). All animals imaged are young adults, four
days post-hatch. They include transgenic N2 and RM2754 lines overexpressing GFP reporter alone (A, C and F) or
together with HSF-1 in the targeted neurons of PS3551 strain, a hsf-1 mutant (B,D,E). All 3D confocal reconstructions
shown are maximal projections of z-stacks. Anterior to the left (C,E,F right panels); Anterior to the right (D, right panel).
Scale bars: A,B;C-F: left panels, 100 μm; C-F right panels, 10 μm. Representative images of at least 5 worms from each
transgenic line are shown.
*
*
95

c) Detailed experimental plan of investigation
Since the availability of a reliable disease model that recreates the molecular characteristics
and associated major pathological hallmarks of neurodegenerative disorders (NDs), with a
pronounced, measurable phenotype is the prerequisite for targets screening (5,11), this
project will commence by generating and characterising multiple transgenic, non–transgenic
and pharmacological disease models (Table 1, highlighted in beige) to choose the optimal
models. Mutant models will be requested from the C. elegans mutant collection at the
Caenorhabditis elegans Genetic Center, while standard transformation technique of
microinjection will be used to generate transgenic models overexpressing a variety of wild-
type and toxic gain-of-function aggregation-prone proteins under different promoters.
Neuronal expression models will be favoured over muscle expression strains. The transgene
will be chromosomally integrated by subsequent treatment with long-wave UV using a UV
cross-linker. Immunohistochemistry, single-worm PCR and Western blotting will be
performed to verify the expression of transgenes in transgenic lines. Two Parkinson‟s
disease (PD) pharmacological models will also be generated by exposing transgenic
backgrounds to Parkinsonism-inducing neurotoxins which will be purchased from Sigma (St
Louis, MO). Among the behavioural assays that have been well established in C. elegans to
assess neuronal toxicity-evoked phenotypic abnormalities (including thrashing/swimming,
body bend, paralysis, pharyngeal pumping, and egg-laying) (12), this project will focus on
locomotion and aldicarb (paralysis) assays to characterise and optimise disease models in
comparison with wild-types (WT). These assays examine motor impairments and defective
exocytosis rate respectively, and can be applied generically to majority of the models. The
food-sensing assay which is exclusive to PD transgenic, mutant and compound intoxicated
models with enhanced dopaminergic (DA) neuron degeneration will be performed to
determine aberrant basal slowing behavioural phenotype since C. elegans food-sensing
behaviour is mediated exclusively through an intact DA neural circuitry. Typically 20-30 age-
synchronised worms per strain will be evaluated at all developmental stages and statistical
significance will be determined by a t-test for single strains and one-way ANOVA for multiple
strains. Disease models with prominent phenotypic deviations from control strains will be
selected.
Next a selective RNAi genetic modifier screen will be carried out in which bioinformatically
prioritised modifiers retrieved from disparate datasets of previous genome-wide analyses
(Table 2) will be specifically knocked down in the chosen disease models to characterise
their function and the pathways through which they act. This laboratory has the published
RNAi feeding libraries, which together cover 95% of expressed worm genes. To circumvent
RNAi resistance in WT C. elegans postmitotic neurons and to maximise RNAi efficacy, RNAi
hypersensitive rrf-3 (mg373) strain which has recently been reported as a mutant most
sensitised to neuronal RNAi (13) will be injected with transgene constructs of the chosen
96

models together with a green fluorescent protein (GFP) reporter, while models that were
generated by mutagenesis will be crossed onto the rrf-3 background to construct the new
double transgenic models. Synchronised larvae will be grown to young adults on agar plates
containing the dsRNA-expressing bacterial culture that will target a specific C. elegans
modifer gene (and one empty vector control per experiment), and then transferred to fresh
RNAi plates containing FUdR (to prevent progeny growth) every five days. The initial round
of screening will be carried out based on examining locomotion at adult day 0, 2, 5, 7 and 9.
These days have been selected to enable detection of either amelioration or exacerbation of
the model-specific phenotypes. Knock-down rate of the target gene will be confirmed by
reverse transcriptase polymerase chain reaction (RT-PCR) and Western blot analysis. After
initial screening, positive hits will be re-tested three times to verify the initial findings and
determine reproducibility. A neurodegeneration assay which has more direct implications for
NDs will also be performed using the six validated pan-neuronal and discrete neuronal
promoters (Fig. 2) to directly assess age-dependent neuronal loss during the lifetime of the
worms, and identify particular classes of neurons that are most vulnerable to the loss of
modifier genes when combined with disease protein overexpression. However, this project
aims to use methods for culturing C. elegans neurons to facilitate accurate quantitative
evaluation of cumulative neurodegenerative changes in distinct C. elegans neuronal classes
(14), as opposed to conventional neurodegeneration assays in whole nematode studies
which have many considerable challenges i.e. living-worm microscopy, following neuronal
loss in the same worm consecutively that would require repetitive worm recoveries etc.
Following dissociation from early embryos, cultured embryonic C. elegans cells are plated on
culture dish surfaces covered with peanut lectin where they adhere and subsequently
differentiate into neurons. Rate of degeneration will be determined by following GFP-labeled
neurons over time which can undergo further manipulation to provide a means for discerning
cellular mechanisms associated with ND (14). These molecular regulators will be validated
further by overexpressing the proteins in WT and additional worm models before entry into
secondary analyses.
It is conceivable that neuroprotective compounds mitigate the behavioural deficits and delay
degenerative phenotype through unexplored pathways parallel, upstream or downstream of
targets. Therefore, this project will aim to further identify the therapeutic targets and
pathways involved in neuroprotective compounds‟ efficacy, and illuminate their mechanism
of action. A collection of twelve chemicals (Table1) i.e. antioxidants, kinase inhibitors,
dopamine D2 receptor agonists and amyloid-binding compounds (Sigma) that have been
previously identified to confer neuroprotection will be tested in a chemical reverse genetics
screen.
Synchronised larvae of disease models expressing GFP in the targeted neurons will be
incubated with and without solubilised drugs for three days in 24-well plates. Each well will
contain a bacteria culture from the RNAi library expressing dsRNA to a C. elegans modifier
97

gene (12 wells per bacteria), followed by addition of individual or a combination of
compounds per well. The presence or absence of GFP fluorescence will be evaluated in
each well to determine neuronal survival prior to replating on solid media for further
behaviour assays for confirmation. Wells that contain a weak or absent fluorescent signal
would indicate that the modifier is involved in suppression of the compound‟s
neuroprotective effects. Significance will be determined using a Fisher‟s exact test which is
appropriate for small sample sizes.
d) Outcomes
These investigations will help to reveal conserved molecular and therapeutic mechanisms
which contribute not only to the molecular understanding of human NDs but also eventually
to the development of effective therapeutic preventions and interventions for those who are
at genetic risk or are affected clinically.
e) Contingency plans
Project progression may be temporarily slowed by some unexpected events, or potential
difficulties in the operations. In such a case, efforts will be made to tackle the bottleneck as
detailed below:
Difficulties to integrate transgene in the germ-line of the animals.
The difficulty with transgene expression in the C. elegans germ-line resides in
uncharacterised repression mechanisms of this organism and has long been a problem. In
the event that no satisfactory transgene expression can be obtained by conventional
microinjection, double transgenic models will be created by genetic crossing. Alternatively,
this problem can also be circumvented by the new Mos1 techniques developed by
Jorgensen Lab.
RNAi knock-down rate cannot be confirmed by PCR
GFP reporter will be used as an alternate to confirm reduced gene expression. Strains with
GFP-labelled neurons will have gradual loss of fluorescence if RNAi have successfully
suppressed gene expressions. Technical challenges of RNAi-based phenotypic analysis
arise from the inherent limitations of RNA (i.e., neuronal intractability, inherent variability in
the level of target mRNA knock-down for different genes, possibility of off-target effects). If
this proves too difficult, alternative “loss of function” experiments can be validated with a
forward genetic screen using knockout mutants.
98

Milestone 1. Characterise and optimise
neurodegenerative models
Milestone 2. RNAi screens
Year 1 Year 2 Year 3
Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4
Generation of transgenic strains
Screen and select
Milestone 3. Suppressor chemical screens Obtain
Potential difficuties and contingency plans
Genetic crossing
Forward genetic screens
f) Timetable and milestones
Word count: 1990
References:
Generate RNAi sensitive Identification of positive hits
double transgenic models Validation of positive hits
Screen and examine
(12,15-48)
1. Bonini, N. M., and Fortini, M. E. (2003) Annu Rev Neurosci 26, 627-656
2. van Ham, T. J., Thijssen, K. L., Breitling, R., Hofstra, R. M. W., Plasterk, R. H. A., and Nollen, E.
A. A. (2008) PLoS Genet 4, e1000027
3. Marvanova, M., and Nichols, C. D. (2007) J Mol Neurosci 31, 127-137
4. Nass, R., Hahn, M. K., Jessen, T., McDonald, P. W., Carvelli, L., and Blakely, R. D. (2005) J
Neurochem 94, 774-785
5. Harrington, A. J., Hamamichi, S., Caldwell, G. A., and Caldwell, K. A. (2010) Dev Dynam 239,
1282-1295
6. van Ham, T. J., Breitling, R., Swertz, M. A., and Nollen, E. A. A. (2009) EMBO Molecular
Medicine 1, 360-370
7. Kraemer, B. C., Burgess, J. K., Chen, J. H., Thomas, J. H., and Schellenberg, G. D. (2006) Hum
Mol Genet 15, 1483-1496
8. Nollen, E. A. A., Garcia, S. M., van Haaften, G., Kim, S., Chavez, A., Morimoto, R. I., and
Plasterk, R. H. A. (2004) Proc Natl Acad Sci U S A 101, 6403-6408
9. Kuwahara, T., Koyama, A., Koyama, S., Yoshina, S., Ren, C.-H., Kato, T., Mitani, S., and
Iwatsubo, T. (2008) Hum Mol Genet 17, 2997-3009
10. Hamamichi, S., Rivas, R. N., Knight, A. L., Cao, S., Caldwell, K. A., and Caldwell, G. A. (2008)
Proc Natl Acad Sci U S A 105, 728-733
11. Artal-Sanz, M., de Jong, L., and Tavernarakis, N. (2006) Biotechnol J 1, 1405-1418
12. Wu, Y., Wu, Z., Butko, P., Christen, Y., Lambert, M. P., Klein, W. L., Link, C. D., and Luo, Y.
(2006) J Neurosci 26, 13102-13113
13. Zhuang, J. J., and Hunter, C. P. (2011) Genetics
14. Tucci, M. L., Caldwell, G. A., and Caldwell, K. A. (2011) Cell Culture to Investigate Neurotoxicity
and Neurodegeneration Utilizing Caenorhabditis elegans. pp 129-143
15. Link, C. D. (1995) Proc Natl Acad Sci U S A 92, 9368-9372
16. Kraemer, B. C., Zhang, B., Leverenz, J. B., Thomas, J. H., Trojanowski, J. Q., and Schellenberg,
G. D. (2003) Proc Natl Acad Sci U S A 100, 9980-9985
17. Miyasaka, T., Ding, Z., Gengyo-Ando, K., Oue, M., Yamaguchi, H., Mitani, S., and Ihara, Y.
(2005) Neurobiol Dis 20, 372-383
18. Brandt, R., Gergou, A., Wacker, I., Fath, T., and Hutter, H. (2009) Neurobiol Aging 30, 22-33
19. Wang, H., Lim, P. J., Yin, C., Rieckher, M., Vogel, B. E., and Monteiro, M. J. (2006) Human
Molecular Genetics 15, 1025-1041
20. Satyal, S. H., Schmidt, E., Kitagawa, K., Sondheimer, N., Lindquist, S., Kramer, J. M., and
Morimoto, R. I. (2000) Proc Natl Acad Sci U S A 97, 5750-5755
21. Alavez, S., Vantipalli, M. C., Zucker, D. J., Klang, I. M., and Lithgow, G. J. (2011) Nature 472,
226-229
22. Brignull, H. R., Moore, F. E., Tang, S. J., and Morimoto, R. I. (2006) J Neurosci 26, 7597-7606
23. Voisine, C., Varma, H., Walker, N., Bates, E. A., Stockwell, B. R., and Hart, A. C. (2007) PLoS
One 2, e504
24. Lakso, M., Vartiainen, S., Moilanen, A. M., Sirvio, J., Thomas, J. H., Nass, R., Blakely, R. D., and
Wong, G. (2003) J Neurochem 86, 165-172
25. Springer, W., Hoppe, T., Schmidt, E., and Baumeister, R. (2005) Hum Mol Genet 14, 3407-3423
99

26. Ved, R., Saha, S., Westlund, B., Perier, C., Burnam, L., Sluder, A., Hoener, M., Rodrigues, C. M.,
Alfonso, A., Steer, C., Liu, L., Przedborski, S., and Wolozin, B. (2005) J Biol Chem 280, 42655-
42668
27. Kuwahara, T., Koyama, A., Gengyo-Ando, K., Masuda, M., Kowa, H., Tsunoda, M., Mitani, S.,
and Iwatsubo, T. (2006) J Biol Chem 281, 334-340
28. Saha, S., Guillily, M. D., Ferree, A., Lanceta, J., Chan, D., Ghosh, J., Hsu, C. H., Segal, L.,
Raghavan, K., Matsumoto, K., Hisamoto, N., Kuwahara, T., Iwatsubo, T., Moore, L., Goldstein,
L., Cookson, M., and Wolozin, B. (2009) J Neurosci 29, 9210-9218
29. Sämann, J., Hegermann, J., von Gromoff, E., Eimer, S., Baumeister, R., and Schmidt, E. (2009)
J Biol Chem 284, 16482-16491
30. Nass, R., Miller, D. M., and Blakely, R. D. (2001) Parkinsonism & Related Disorders 7, 185-191
31. Cao, S., Gelwix, C. C., Caldwell, K. A., and Caldwell, G. A. (2005) J Neurosci 25, 3801-3812
32. Settivari, R., LeVora, J., and Nass, R. (2009) J. Biol. Chem., M109.051409
33. Braungart, E., Gerlach, M., Riederer, P., Baumeister, R., and Hoener, M. C. (2004)
Neurodegener Dis 1, 175-183
34. Caldwell, K. A., Tucci, M. L., Armagost, J., Hodges, T. W., Chen, J., Memon, S. B., Blalock, J. E.,
DeLeon, S. M., Findlay, R. H., Ruan, Q., Webber, P. J., Standaert, D. G., Olson, J. B., and
Caldwell, G. A. (2009) PLoS One 4, e7227
35. Gutierrez-Zepeda, A., Santell, R., Wu, Z., Brown, M., Wu, Y., Khan, I., Link, C. D., Zhao, B., and
Luo, Y. (2005) BMC Neurosci 6, 54
36. Yamanaka, K., Okubo, Y., Suzaki, T., and Ogura, T. (2004) J Struct Biol 146, 242-250
37. Parker, J. A., Arango, M., Abderrahmane, S., Lambert, E., Tourette, C., Catoire, H., and Neri, C.
(2005) Nat Genet 37, 349-350
38. Bates, E. A., Victor, M., Jones, A. K., Shi, Y., and Hart, A. C. (2006) J Neurosci 26, 2830-2838
39. Locke, C. J., Fox, S. A., Caldwell, G. A., and Caldwell, K. A. (2008) Neurosci Lett 439, 129-133
40. Karpinar, D. P., Balija, M. B., Kugler, S., Opazo, F., Rezaei-Ghaleh, N., Wender, N., Kim, H. Y.,
Taschenberger, G., Falkenburger, B. H., Heise, H., Kumar, A., Riedel, D., Fichtner, L., Voigt, A.,
Braus, G. H., Giller, K., Becker, S., Herzig, A., Baldus, M., Jackle, H., Eimer, S., Schulz, J. B.,
Griesinger, C., and Zweckstetter, M. (2009) EMBO J 28, 3256-3268
41. Caldwell, G. A., Cao, S., Sexton, E. G., Gelwix, C. C., Bevel, J. P., and Caldwell, K. A. (2003)
Hum Mol Genet 12, 307-319
42. Faber, P. W., Alter, J. R., MacDonald, M. E., and Hart, A. C. (1999) Proc Natl Acad Sci U S A 96,
179-184
43. Oeda, T., Shimohama, S., Kitagawa, N., Kohno, R., Imura, T., Shibasaki, H., and Ishii, N. (2001)
Hum Mol Genet 10, 2013-2023
44. Wang, J., Farr, G. W., Hall, D. H., Li, F., Furtak, K., Dreier, L., and Horwich, A. L. (2009) PLoS
Genet 5, e1000350
45. Lakowski, B., Eimer, S., Göbel, C., Böttcher, A., Wagler, B., and Baumeister, R. (2003)
Development 130, 2117-2128
46. Gitler, A. D., Bevis, B. J., Shorter, J., Strathearn, K. E., Hamamichi, S., Su, L. J., Caldwell, K. A.,
Caldwell, G. A., Rochet, J. C., McCaffery, J. M., Barlowe, C., and Lindquist, S. (2008) Proc Natl
Acad Sci U S A 105, 145-150
47. Briese, M., Esmaeili, B., Fraboulet, S., Burt, E. C., Christodoulou, S., Towers, P. R., Davies, K.
E., and Sattelle, D. B. (2009) Hum Mol Genet 18, 97-104
48. Arya, U., Dwivedi, H., and Subramaniam, J. R. (2009) Exp Gerontol 44, 462-466
100

6. SUMMARY OF FINANCIAL SUPPORT REQUESTED
STIPEND
ANIMALS
Specify the funds required for staff, animals, consumables and travel in the Table below.
CONSUMABLES
TRAVEL
YEAR 1 YEAR 2 YEAR 3
£13590 £13590 £13590
- - -
£10,000 £10,000 £10,000
£1000 £1000 £1000
TOTAL £24590 £24590 £24590
7. JUSTIFICATION OF FINANCIAL SUPPORT REQUESTED
In this section, justify the funds requested for animals, consumables and travel (no more than
200 words).
The applicant will be working full time and participating in the experimental design,
application and analysis. She has gained experience working with C. elegans in our
laboratory during three 10-week Masters-level rotation projects.
The requested funding will cover the purchase for project-specific consumables such as
routine chemicals and labware, the molecular biology techniques outlined above e.g.
microinjections, primary culture of embryonic neurons, as well as obtaining knockout
mutants. The collection of drug compounds required for chemical screening costs around
£5000 if to be purchased from Sigma, therefore contributes to a significant portion of the total
costs. In addition, there are also charges relating to use of communal facilities (i.e. confocal
microscope). Finally, funds requested will cover travel expenses to attend and present
research findings at relevant conferences.
101

7.7 Demonstrator Training Workshop
Practical Based Teaching
Overview:
This session will help postgraduate students to consider in more depth how their role in a practical
class complements that of the lecturer and how they can take responsibility for helping the
students to get the most from the practical class.
Aim:
To help participants plan and teach a practical class.
Objectives:
Following the session the participants will be able to:
� define the purpose of practical-based teaching and discuss their role within it
� discuss the interactions between teaching assistants and other members of staff and
students
� prepare themselves prior to a practical class
� identify the skills necessary to operate effectively as a teacher within practical sessions
� understand the range of skills that practical classes can help students to develop
� explore the ways in which language and attitude can affect communication
� critically evaluate a number of incidents occurring in practical classes, and identify
appropriate courses of action
� consider how to ensure reliability in marking assessments.
102

Section 8
Attendance Monitoring & Absence Reporting
Attendance Monitoring
Attendance at all scheduled activities in the MRes course is compulsory and will be monitored
carefully. Any student who fails to attend such scheduled activities will be contacted by their strand
convenor and required to explain their absence. Penalties for unauthorised absence will depend on
the frequency of the absenteeism, and range from prevention of the award of a distinction, through
loss of marks from the affected module, to suspension or termination of studies.
Experience has shown us that students who are absent from scheduled activities are often having
either academic or personal problems. We therefore monitor attendance closely to identify
problems as early as possible. The University also has a responsibility to report international
students with poor attendance to the UK Border Agency (UKBA) and this could lead to visa
problems.
Students will be asked to scan their student ID card at each scheduled activity to register their
attendance. It is therefore important that students always carry their ID cards with them. If students
forget their card, there is a temporary paper register available for signing. Students must scan their
card or sign the register BEFORE the lecture commences. Students who arrive after the lecture
has begun will not be able to scan/sign in and will be marked as absent. To avoid this, we request
that students arrive 10 minutes before the scheduled start time (e.g., at 8.50 am for lectures
starting at 9.00 am).
NOTE: Your door access card does not contain you student ID student. Because of this, if you
scan this card instead of your student ID card, you will be marked as absent.
If a scheduled activity is missed for good reason (e.g. illness, family circumstances, medical
appointment) students should complete an absence form (see below). Their attendance records
will then be amended accordingly.
Students whose attendance fails to meet the required standard will be contacted by their strand
convenor and required to explain their absence.
Absence Reporting
If for any reason you need to be absent (e.g. other meetings, courses, illness, etc) you should
inform your supervisor and strand convenor as soon as possible, at the latest by 9.30am on
the day that you will be away from the lab, by telephoning or emailing them. You must provide
information on when and why you will be absent, and ask him/her to make arrangements for any
ongoing experiments that you cannot complete that day. You should also email the Programme
Administrator to formally report your absence.
If your absence is for 5 consecutive days or less, then you should use the Self-Certificates as
detailed below (see items 1 and 2 below). Absences of longer than 5 consecutive days will require
a Medical Certificate authorised by a medical practitioner (see item 3 below). Each of these three
forms can be found in the Appendix at the back of this handbook.
1. Self-Certificate of Absence caused by ILLNESS
103

This can be used for a period of 5 consecutive days and does not require the signature of a
medical practitioner. It should be submitted no later than 5 days after the last day of
absence.
a. Thoroughly complete the Self-Certificate of Absence caused by ILLNESS form.
b. Obtain your supervisor‟s signature.
c. Obtain your strand convenor‟s authorisation.
d. Submit the form to the Programme Administrator.
2. Self-Certificate of Absence caused by OTHER REASONS (i.e. attending meetings, hospital
appointments, interviews).
The form should be submitted no later than 5 days after the last day of absence.
a. Thoroughly complete the Self-Certificate of Absence caused by OTHER REASONS
form.
b. Obtain your supervisor‟s signature.
c. Obtain your strand convenor‟s authorisation.
d. Submit the form to the Programme Administrator.
3. Absence due to Illness – VERIFIED BY A MEDICAL CERTIFICATE
This form and accompanying medical certificate should be submitted no later than 5 days
after the last day of absence.
a. Thoroughly complete the Absence due to Illness – VERIFIED BY A MEDICAL
PRACTICTIONER form.
b. Obtain your supervisor‟s signature.
c. Obtain your strand convenor‟s authorisation.
d. Submit the form and medical certificate to the Programme Administrator.
Mitigating Circumstances
if you feel that your performance has been adversely affected by circumstances beyond your
control, such as illness etc, and wish this to be taken into account, you must fill out the appropriate
form in this handbook. This form must be submitted to the Programme Administrator as soon as
possible after the event and should be accompanied by all relevant documentation.
104

Section 9
Student Feedback and Representation
Feedback on assignments will be given by strand convenors in the first instance. Students will also
be able to meet with individual markers for additional feedback on assignments, if desired. We aim
to mark all written assignments and provide feedback with 3 weeks of submission.
There will be a Staff-Student Consultative Committee (SSCC), which will operate in accordance
with the University Code of Practice and Guidelines. It will meet once per semester (3 times per
year), around the middle of each semester. In addition, there is student representation on the
Board of Studies. Students will be elected to serve on both forums.
Staff-Student Consultative Committee (SSCC)
Constitution
Elected MRes student representing each of the main strands
One MRes student from the previous year
MRes Programme Director
Strand Convenors
MRes Programme Administrator
Institute Director of Postgraduate Studies
Institute Senior Postgraduate Research Administrator
Head of Institute
Senior Institute Administrator
Representative from the University Guild of Students
The SSCC will report to the Board of Studies for the Programme.
Board of Studies
Constitution
Elected MRes students representing each of the main strands
One MRes student from the previous year
MRes Programme Director
Strand Convenors
MRes Programme Administrator
Institute Director of Postgraduate Studies
Institute Senior Postgraduate Research Administrator
Head of Institute
Senior Institute Administrator
Terms of Reference
(i) All aspects of curriculum delivery;
(ii) Resources provided for teaching and learning;
(iii) Matters of general relevance and interest to the course.
105

Section 10
APPENDIX
The following pages contain useful additional forms and information.
A signed copy of the plagiarism form should be attached to all submitted written assignments
(Research Project reports, Short Reviews, Referees Report, PhD studentship application).
A copy of the appropriate absence reporting form, signed by you, your supervisor and your strand
convenor, should be submitted to the Programme Secretary to formally report any absences.
The mitigating circumstances form should be copied, completed and submitted to the Programme
Administrator if you feel that your performance has been adversely affected by circumstances
beyond your control such as illness etc and wish this to be taken into account. This form must be
submitted as soon as possible after the event and should be accompanied by relevant
documentation.
The campus map shows the location of the various University buildings on campus.
106

DECLARATION ON PLAGIARISM AND COLLUSION
NAME……………………………………….STUDENT NUMBER………………………………....
MODULE TITLE/CODE……………………………………………………………………………
TITLE OF WORK…………………………………………………………………….……………
This form should be completed by the student and appended to any piece of work that is submitted for
summative assessment.
Section 8.1 of the University‟s Code of Practice on Assessment provides the following definition of
plagiarism:
“Plagiarism occurs when a student misrepresents, as his/her own work, the work, written or otherwise, of any
other person (including another student) or of any institution. Examples of forms of plagiarism include: the
verbatim (word for word) copying of another‟s work without appropriate and correctly presented
acknowledgement; the close paraphrasing of another‟s work by simply changing a few words or altering the
order of presentation, without appropriate and correctly presented acknowledgement; unacknowledged
quotation of phrases from another‟s work; the deliberate and detailed presentation of another‟s concept as
one‟s own.”
“Another‟s work” covers all material, including, for example, written work, diagrams, designs, charts, musical
compositions and pictures, from all sources, including, for example, the internet, journals, textbooks and
essays.
You must also avoid self-plagiarism, i.e. re-using text, data or images that you have previously submitted for
assessment. In other words, you are expressly forbidden from copying any such material from one of your
written assignments to another.
Section 8.1 of the University‟s Code of Practice on Assessment provides the following definition of collusion:
“Collusion occurs when, unless with official approval (e.g. in the case of group projects), two or more
students consciously collaborate in the preparation and production of work which is ultimately submitted by
each in an identical, or substantially similar, form and/or is represented by each to be the product of his or
her individual efforts. Collusion also occurs where there is unauthorised co-operation between a student and
another person in the preparation and production of work which is presented as the student‟s own.”
Further information on plagiarism and collusion can be found in departmental/programme handbooks.
Students found to have committed plagiarism or to have colluded in the production of work for assessment
are liable to receive a mark of zero for the assessment concerned. Subsequent offences will attract more
severe penalties, including possible termination of studies.
STUDENT DECLARATION
I confirm that I have read and understood the above definitions of plagiarism, self-plagiarism and collusion. I
confirm that I have not committed plagiarism when completing the attached piece of work, nor have I
colluded with any other student in the preparation and production of this work.
SIGNATURE………………………………………………………DATE…………………………………..
107

ACTIVITY
MRes in Biomedical Sciences and Translational Medicine
Name (in full):
Student I.D.:
Strand Name:
Student Self-Certificate of Absence caused by ILLNESS
PLEASE TICK BELOW THE ACTIVITIES YOU HAVE MISSED FROM EACH DAY OF YOUR ABSENCE:
TYPE OF
ACTIVITY
Day 1
of absence
Day 2
of absence
Day 3
of absence
Day 4
of absence
Day 5
of absence
Lecture
�
Strand
Specific
Activity
�
Science
Skills
�
Journal
Club
�
Debate
�
Lab
Work
�
English
Class
�
Other
(specify
below)
ASSESSMENT(S) AFFECTED (TICK AS APPROPRIATE): my absence prevented my attendance at, or
affected my submission of, the following assessed work.
�
Research
Project
Report
submission
Research
Project Oral
or Poster
presentation
Short
Review
submission
Referee’s
Report
Submission
IP &
Comm.
Workshop
Business
Plan
PhD
Studentship
Application
submission
Final
Portfolio
submission
108

STUDENT:
I certify that I was absent from the University through illness during the period:
Date from:
My attendance resumed on:
The reason for illness was:
Student Signature:
HOW TO SUBMIT THIS FORM:
1. Ask your Supervisor to sign this form (below).
2. Ask your Strand Convenor to sign this form (below).
3. Take the fully completed form to Mrs Helen Barclay, Physiology Building. This must be done within 5
days of your last day of absence.
SUPERVISORS SIGNATURE:
Supervisor’s Name:
Signature:
STRAND CONVENOR’S AUTHORISATION:
Strand Convenor’s
Name:
Signature:
FOR OFFICE USE ONLY:
Date:
Absence: 1 day [ ] 2 days [ ] 3 days [ ] 4 days [ ] 5 days [ ] more than 5 days
[ ]
Number of self-certificates submitted: 1 [ ] 2 [ ] 3 [ ] 4 [ ] more than 4 [ ]
109

ACTIVITY
MRes in Biomedical Sciences and Translational Medicine
Name (in full):
Student I.D.:
Strand Name:
Student Self-Certificate of Absence caused by OTHER REASONS
PLEASE TICK BELOW THE ACTIVITIES YOU HAVE MISSED FROM EACH DAY OF YOUR ABSENCE:
TYPE OF
ACTIVITY
Day 1
of absence
Day 2
of absence
Day 3
of absence
Day 4
of absence
Day 5
of absence
Lecture
�
Strand
Specific
Activity
�
Science
Skills
�
Journal
Club
�
Debate
�
Lab
Work
�
English
Class
�
Other
(specify
below)
ASSESSMENT(S) AFFECTED (TICK AS APPROPRIATE): my absence prevented my attendance at, or
affected my submission of, the following assessed work.
�
Research
Project
Report
submission
Research
Project Oral
or Poster
presentation
Short
Review
submission
Referee’s
Report
Submission
IP &
Comm.
Workshop
Business
Plan
PhD
Studentship
Application
submission
Final
Portfolio
submission
110

STUDENT:
I certify that I was absent from the University during the period:
Date from:
My attendance resumed on:
The reason(s) for my absence were:
Student Signature:
ATTACH EVIDENCE CONFIRMING THE REASONS FOR ABSENCE WHERE AVAILABLE
HOW TO SUBMIT THIS FORM:
1. Ask your Supervisor to sign this form (below).
2. Ask your Strand Convenor to sign this form (below).
3. Take the fully completed form to Mrs Helen Barclay, Physiology Building. This must be done within 5
days of your last day of absence.
SUPERVISORS SIGNATURE:
Supervisor’s Name:
Signature:
STRAND CONVENOR’S AUTHORISATION:
Strand Convenor’s
Name:
Signature:
FOR OFFICE USE ONLY:
Date:
Absence: 1 day [ ] 2 days [ ] 3 days [ ] 4 days [ ] 5 days [ ] more than 5 days
[ ]
Number of self-certificates submitted: 1 [ ] 2 [ ] 3 [ ] 4 [ ] more than 4 [ ]
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ACTIVITY
MRes in Biomedical Sciences and Translational Medicine
Student Name:
Student I.D.:
Strand Name:
Absence due to Illness – VERIFIED BY A MEDICAL CERTIFICATE
Students are to complete this form each time they submit a medical certificate
or letter received from a doctor or hospital
PLEASE TICK BELOW THE ACTIVITIES YOU HAVE MISSED FROM EACH DAY OF YOUR ABSENCE:
TYPE OF
ACTIVITY
Day 1
of absence
Day 2
of absence
Day 3
of absence
Day 4
of absence
Day 5
of absence
Lecture
�
Strand
Specific
Activity
�
Science
Skills
�
Journal
Club
�
Debate
�
Lab
Work
�
English
Class
�
Other
(specify
below)
ASSESSMENT(S) AFFECTED (TICK AS APPROPRIATE): my absence prevented my attendance at, or
affected my submission of, the following assessed work.
�
Research
Project
Report
submission
Research
Project Oral
or Poster
presentation
Short
Review
submission
Referee’s
Report
Submission
IP &
Comm.
Workshop
Business
Plan
PhD
Studentship
Application
submission
Final
Portfolio
submission
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STUDENT:
I certify that I was absent from the University through illness during the period:
Date from:
My attendance resumed on:
Student Signature:
HOW TO SUBMIT THIS FORM:
1. Ask your Supervisor to sign this form (below).
2. Ask your Strand Convenor to sign this form (below).
3. Take the fully completed form AND MEDICAL CERTIFICATE to Mrs Helen Barclay, Physiology Building.
This must be done within 5 days of your last day of absence.
SUPERVISORS SIGNATURE:
Supervisor’s Name:
Signature:
STRAND CONVENOR’S AUTHORISATION:
Strand Convenor’s
Name:
Signature:
FOR OFFICE USE ONLY:
Date:
Absence: 1 day [ ] 2 days [ ] 3 days [ ] 4 days [ ] 5 days [ ] more than 5 days
[ ]
Number submitted: 1 [ ] 2 [ ] 3 [ ] 4 [ ] more than 4 [ ]
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Application for Consideration of Mitigating Circumstances
Full name: …………………………………………………………………………….
Registration number: …………………………………………………………………
Programme of study: ...……………………………………………………………….
Year of study: …………………
Modules affected by mitigating circumstances
Module Code Module Name Assessment missed/affected
Details of mitigating circumstances
Please provide a description of the mitigating circumstances that may have affected your
performance in the above modules, including the time period over which these circumstances
occurred. Please state what aspect(s) of the assessment you feel have been affected.
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Supporting documentation
Please list all the documentation provided in support of your claim. The documentation should be
stapled to this form. Medical claims should be supported by a medical note, other claims should be
supported by appropriate documentation (for example, police reports, insurance reports).
Student declaration
I confirm that all the information contained in this statement is accurate and complete to the best of
my knowledge. I consent to the information being used by the Mitigating Circumstances
Committee, and understand that the information will be treated in the strictest confidence.
Signature of student:…………………………………………. Date:…………………
FOR USE BY THE CHAIR OF THE MITIGATING CIRCUMSTANCES COMMITTEE ONLY
I recommend that the following action be taken in respect of this claim:
Signature of Chair:……………………………………………………………………...
Date: …………………………………………
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