School of Biology current student

Information for current students at the School of Biology

Biology Online Module Handbook

BL2309 Applied Molecular Biology

(BL2309 online module handbook version 122)

cover image

image: Applied Molecular Biology ⠂¬ €œ A Powerful Box of Tools

Techniques in molecular biology represent a powerful box of tools that are used to address a wide variety of modern research questions across a broad range of biological disciplines including; ecology, biotechnology, cell biology, medicine, conservation biology, infectious disease, evolution, genetics and synthetic biology. Key molecular biology techniques will be introduced in the context of case studies that will provide examples of how molecular biology techniques are being used in cutting edge research to address real-life questions and problems that impact health, food security, the environment and the economy.*

Credits: 15*

Semester: 2

Module Organiser
Dr Simon Young
say2@st-andrews.ac.uk
01334 463417
Pre-requisite Modules:
Before taking this module you must pass BL1101 and pass BL1102*
Anti-requisite Modules:
*
Post-requisite Modules:
*
Additional Module Information:


Biology Teaching Office:
Level 2, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST

Email: bioteach@st-andrews.ac.uk      Phone: +44 (0)1334 46 3602 or 3566

BL2309: Timetable

Legend (not all modules have every event type):
lecture
tutorial
workshop
practical
other

Semester 2: Week 1

DATE & TIMEVENUESTAFFEVENT
Thursday
18-01-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Simon Young
-
Lecture L1: Introduction to module
2023-4_BL2309_L1
Friday
19-01-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Jacqueline Nairn
-
Lecture L2: Topic 1: The era of omics I
2023-4_BL2309_L2

Semester 2: Week 2

DATE & TIMEVENUESTAFFEVENT
Wednesday
24-01-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Jacqueline Nairn
-
Lecture L3: Introduction to practical 1
2023-4_BL2309_L3
Thursday
25-01-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Jacqueline Nairn
-
Lecture L4: Topic 1: The era of omics II
2023-4_BL2309_L4
Thursday
25-01-2024
14:00 to 17:00
Medical and Biological Sciences Building
Biology teaching lab 143
Dr Jacqueline Nairn
-
Practical P1: Practial 1: A proteomic study of an ancient protein with a timely application
2023-4_BL2309_P1
Please bring your laptop
Friday
26-01-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Jacqueline Nairn
-
Lecture L5: Topic 1: The era of omics III
2023-4_BL2309_L5
Friday
26-01-2024
14:00 to 17:00
Medical and Biological Sciences Building
Biology teaching lab 143
Dr Jacqueline Nairn
-
Practical P2: Practial 1: A proteomic study of an ancient protein with a timely application
2023-4_BL2309_P2
Please bring your laptop

Semester 2: Week 3

DATE & TIMEVENUESTAFFEVENT
Thursday
01-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Prof Dave Ferrier
-
Lecture L6: Topic 2: Molecular evolution and comparative genomics I
2023-4_BL2309_L6
Friday
02-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Prof Dave Ferrier
-
Lecture L7: Topic 2: Molecular evolution and comparative genomics II
2023-4_BL2309_L7

Semester 2: Week 4

DATE & TIMEVENUESTAFFEVENT
Wednesday
07-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Prof Dave Ferrier
-
Lecture L8: Introduction to practical 2
2023-4_BL2309_L8
Thursday
08-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Prof Dave Ferrier
-
Lecture L9: Topic 2: Molecular evolution and comparative genomics III
2023-4_BL2309_L9
Thursday
08-02-2024
14:00 to 17:00
Biomolecular Sciences Building
BMS Teaching lab level 2
Prof Dave Ferrier
-
Practical P3: Practical 2: Gene family evolution
2023-4_BL2309_P3
Assessed practical - Please bring your laptop
Friday
09-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Jacqueline Nairn
-
Tutorial T1: Feedback for Practical 1
2023-4_BL2309_T1
Friday
09-02-2024
14:00 to 17:00
Biomolecular Sciences Building
BMS Teaching lab level 2
Prof Dave Ferrier
-
Practical P4: Practical 2: Gene family evolution
2023-4_BL2309_P4
Assessed practical - Please bring your laptop

Semester 2: Week 5

DATE & TIMEVENUESTAFFEVENT
Thursday
15-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B

-
Other O1: Reading Day
2023-4_BL2309_O1
Feel free to use the lecture theatre to study
Friday
16-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Simon Young
-
Tutorial T2: Mid term Q&A
2023-4_BL2309_T2

Semester 2: Week 6

DATE & TIMEVENUESTAFFEVENT
Wednesday
21-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Natalie Pilakouta
-
Lecture L10: Topic 3: Molecular tools in ecology I
2023-4_BL2309_L10
Thursday
22-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Natalie Pilakouta
-
Lecture L11: Topic 3: Molecular tools in ecology II
2023-4_BL2309_L11
Thursday
22-02-2024
14:00 to 17:00
Medical and Biological Sciences Building
Biology teaching lab 143
Dr Natalie Pilakouta
-
Practical P5: Practical 3: The genetic basis of fitness in the wild: a case study
2023-4_BL2309_P5
Please bring your laptop
Friday
23-02-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Natalie Pilakouta
-
Lecture L12: Topic 3: Molecular tools in ecology III
2023-4_BL2309_L12
Friday
23-02-2024
14:00 to 17:00
Medical and Biological Sciences Building
Biology teaching lab 143
Dr Natalie Pilakouta
-
Practical P6: Practical 3: The genetic basis of fitness in the wild: a case study
2023-4_BL2309_P6
Please bring your laptop

Spring Break: 26-Feb-2024 to 01-Mar-2024

Semester 2: Week 7

DATE & TIMEVENUESTAFFEVENT
Thursday
07-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Prof Dave Ferrier
-
Tutorial T3: Feedback for practical 2
2023-4_BL2309_T3
Friday
08-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Simon Young
-
Lecture L13: Topic 4: Molecular tools in infectious disease I
2023-4_BL2309_L13

Semester 2: Week 8

DATE & TIMEVENUESTAFFEVENT
Wednesday
13-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Simon Young
-
Lecture L14: Topic 4: Molecular tools in infectious disease II
2023-4_BL2309_L14
Thursday
14-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Simon Young
-
Lecture L15: Introduction to practical 4
2023-4_BL2309_L15
Thursday
14-03-2024
14:00 to 17:00
Medical and Biological Sciences Building
Biology teaching lab 143
Dr Simon Young
-
Practical P7: Practical 4: Emerging disease outbreak
2023-4_BL2309_P7
Assessed practical - Please bring your laptop
Friday
15-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Simon Young
-
Lecture L16: Topic 4: Molecular tools in infectious disease III
2023-4_BL2309_L16
Friday
15-03-2024
14:00 to 17:00
Medical and Biological Sciences Building
Biology teaching lab 143
Dr Simon Young
-
Practical P8: Practical 4: Emerging disease outbreak
2023-4_BL2309_P8
Assessed practical - Please bring your laptop

Semester 2: Week 9

DATE & TIMEVENUESTAFFEVENT
Thursday
21-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr V Anne Smith
-
Lecture L17: Topic 5: Synthetic Biology I
2023-4_BL2309_L17
Friday
22-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr V Anne Smith
-
Lecture L18: Topic 5: Synthetic Biology II
2023-4_BL2309_L18

Semester 2: Week 10

DATE & TIMEVENUESTAFFEVENT
Wednesday
27-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Frances der Weduwen
-
Lecture L19: Introduction to Practical 5
2023-4_BL2309_L19
Thursday
28-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Jens Tilsner
-
Lecture L20: Topic 6: Genetically modified crops I
2023-4_BL2309_L20
Thursday
28-03-2024
14:00 to 17:00
Medical and Biological Sciences Building
Biology teaching lab 143
Dr Frances der Weduwen
-
Practical P9: Practical 5: mini-iGEM competition
2023-4_BL2309_P9
Please bring your laptop
Friday
29-03-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Jens Tilsner
-
Lecture L21: Topic 6: Genetically modified crops II
2023-4_BL2309_L21
Friday
29-03-2024
14:00 to 17:00
Medical and Biological Sciences Building
Biology teaching lab 143
Dr Frances der Weduwen
-
Practical P10: Practical 5: mini-iGEM competition
2023-4_BL2309_P10
Please bring your laptop

Semester 2: Week 11

DATE & TIMEVENUESTAFFEVENT
Thursday
04-04-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Simon Young
-
Tutorial T4: Feedback for Practical 4
2023-4_BL2309_T4
Friday
05-04-2024
10:00 to 11:00
Mathematical Institute
Lecture theatre B
Dr Simon Young
jn37;dekf;np84;vas1;jt58
Tutorial T5: Module summary & feedback
2023-4_BL2309_T5
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL2309: Assessment

2-hour Written Examination = 50%, Coursework = 50%*

The following related information applies to all Biology modules:

School of Biology Marking Criteria: See JH booklet info (st-andrews.ac.uk) 
Late submission of continuous assessment work:

All late submissions of coursework that do not require electronic submission should be made via the Biology Teaching Office, Level 2, BMS Building, North Haugh.
Exam details: See School of Biology UG Handbook JH booklet info (st-andrews.ac.uk)  : All Biology exams will be conducted online for 2022-23.
Exam timetable: See Timetables - Exams - University of St Andrews (st-andrews.ac.uk) 
Expected attendance: See JH booklet info (st-andrews.ac.uk)  for detailed attendance requirements.
Good Academic Practice & Avoiding Academic Misconduct: See JH booklet info (st-andrews.ac.uk)
University Student Handbook: University Student Handbook
School and University regulations in the School and University Undergraduate Handbook relating to absence reporting, penalties and rules for late submission of work, extensions for coursework, return of coursework, S-coding, good academic practice and Academic Alerts.: JH booklet info (st-andrews.ac.uk)
University Student Handbook
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

Who to ask

(Information in this section applies to all Biology Modules)

Before contacting staff, students should check the content of the Biology Undergraduate Handbook, the module handbook and specific task instructions.

Questions about Contact
General teaching matters Biology Teaching Office ( bioteach@st-andrews.ac.uk )
Rescheduled or cancelled events Check your University email
Lecture or practical content The lecturer who presented the material
Completing assessed practical assignments The lecturer who set the assignment
Completing assessments Module Organiser (Dr Simon Young say2@st-andrews.ac.uk)
Marking on continuous assessment The Demonstrator or Module Organiser (Dr Simon Young say2@st-andrews.ac.uk)
Marking on exams Module Organiser (Dr Simon Young say2@st-andrews.ac.uk)
Rearranging practical days
Module Organiser (Dr Simon Young say2@st-andrews.ac.uk)
Absence and/or extensions Module Organiser (Dr Simon Young say2@st-andrews.ac.uk)

and the Biology Teaching Office ( bioteach@st-andrews.ac.uk )

Difficulties with academic progress which impact more than one module:

Year Coordinator

See School of Biology UG Handbook for list:
JH booklet info (st-andrews.ac.uk)

Overall performance, progress or future directions:

Advisor of Studies

Disability:

Disability Coordinator ( biodisabilities@st-andrews.ac.uk )

For advice and support on any issue e.g. academic, financial, international, personal or health matters, or if you are unsure of who to go to for help:

Advice & Support Centre

Address: 79 North Street, St Andrews

Email: theasc@st-andrews.ac.uk

Web: https://www.standrews.ac.uk/ask-a-question/

Tel: 01334 462020

University assistance with urgent matters out of office hours:

Tel: 01334 476161

Web: https://www.st-andrews.ac.uk/students/advice/counselling/incrisis/

Biology Teaching Office:

We are happy to hear from you about teaching matters. The School of Biology Teaching Office is open Monday to Friday 09.00 - 13.00 and 14.00 - 17.00. School of Biology staff will respond to your emails during these hours. Our team will provide a response to you within three working days.

Biology Teaching Office (Level 2), University of St Andrews, Biomolecular Sciences Building, North Haugh, St Andrews, Fife KY16 9ST

Email: bioteach@st-andrews.ac.uk

Tel: 01334 46 3602 or 3566

BL2309: Contributing Staff

Dr Simon Young
(Module Organiser)

Associate Lecturer (Education focused)say2@st-andrews.ac.uk
Dr Frances der WeduwenAssociate Lecturer (Education Focused)fe9@st-andrews.ac.uk
Prof Dave FerrierReader in Biology and Deputy Director of the Scottish Oceans Institutedekf@st-andrews.ac.uk
Dr Jacqueline NairnSenior Lecturer jn37@st-andrews.ac.uk
Dr Natalie PilakoutaLecturernp84@st-andrews.ac.uk
Dr V Anne SmithSenior Lecturervas1@st-andrews.ac.uk
Dr Jens TilsnerLecturerjt58@st-andrews.ac.uk
Dr Simon Young
(Module Organiser)
Associate Lecturer (Education focused)say2@st-andrews.ac.uk
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL2309: Learning Outcomes

Students completing module BL2309 successfully should be able to:

  • Identify a range of key techniques that are commonly used in molecular biology.
  • Describe the concepts behind key molecular biology techniques, which generally require the manipulation of DNA, RNA, protein or lipid.
  • Discuss examples of how molecular biology techniques are used to address current questions and problems across a broad range of biological disciplines.
  • Learn about the large scale omic approaches in biology with the integrated experimental design and data analysis
  • Gain an understanding of molecular evolution and the application of comparative genomics
  • Understand the molecular basis of evolution in ecology
  • Describe the appplication of molecular tools to the detection, control and treatment of viral diseases
  • Understand the molecular tools and techniques utilised in synthetic biology
  • Be aware of the fundamental techniques used to genetically modify crops
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL2309: Acquired Skills

Practical Skills

  • Database interogation
  • Mendelian genetics

Transferable Skills

  • Group discussion - participating
  • Short group presentation on given topic (up to 15 min)
  • Short group presentation on project idea (up to 15 min)
  • Short individual presentation on given topic (up to 15 min)
  • Short informal presentation (using PowerPoint or not)
  • "Short" practical write-up (e.g. completed worksheet)
  • Critically evaluating sources/information
  • Finding information on the web
  • Finding literature
  • Searching databases
  • Ethical considerations
  • Online learning
  • Problem-solving questions
  • Biodiversity analysis
  • Calculations/equations
  • Concentrations
  • Data analysis
  • Data analysis (depending on project)
  • Data presentation
  • Descriptive statistics
  • Draw a line of best fit
  • Genetic Drift
  • Linear regression
  • Logarithms
  • Phylogenetic analysis
  • Powers of ten
  • Produce graphs/figures
  • Produce tables
  • Use Excel
  • Use other data analysis software
  • Sustainability Related Skills
  • Generate class dataset
  • Working in large groups
  • Working in pairs/small groups
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

Policies

(Information in this section applies to all Biology Modules)

  • The procedures and regulations followed by the School of Biology are outlined in the University Handbook and in the School of Biology UG handbook  JH booklet info (st-andrews.ac.uk) 
  • All coursework associated with the module must be completed and submitted by its due date.
  • Specific School regulations relating to absence reporting, penalties and rules for late submission of work, extensions for coursework, return of coursework, S-coding, Good Academic Practice and Academic Alert are stated in the School of Biology UG hand book JH booklet info (st-andrews.ac.uk)  and students are required to carefully read these regulations.
  • Students are also referred to the University Handbook, available at: http://www.st-andrews.ac.uk/studenthandbook/