Senior Freshman

Senior Freshman Modules

• BY2201: Cell Structure and Function
  
• BY2202: Vertebrate Form and Function
• BY2203: Metabolism
  
• BY2204: Evolution
• BY2205: Microbiology
  
• BY2206: Ecosystem Biology and Global Change
  
• BY2207: Behaviour
  
• BY2208: Genetics
  
• BY2209: Infection and Immunity
  
• BY2210: Plant and Animal Bioresources

 

 

 

BY2201: Cell Structure and Function

 

Module coordinator:

• Dr Emma Creagh (ecreagh@tcd.ie) School of Biochemistry and Immunology

 

Other contributors:

• Dr Colm Cunningham (colm.cunningham@tcd.ie) School of Biochemistry and Immunology
• Dr Tim Mantle (tmantle@tcd.ie) School of Biochemistry and Immunology
• Dr Daniela Zisterer (dzistrer@tcd.ie) School of Biochemistry and Immunology

 

Module organisation and description:

click here for module organisation and description (PDF - 33KB)

 

Timetable:

click here for BY2201 timetable (PDF - 29KB)

 

Lecture notes:

click here for lecture notes (School of Biochemistry and Immunology website)

 

Practicals:

• Dr Glynis Robinson (robinsog@tcd.ie) School of Biochemistry and Immunology
• Dr Audrey Carroll (aucarrol@tcd.ie) School of Biochemistry and Immunology

 

Recommended text/reading:

Berg, Jeremy M., Tymoczko, John L. and Stryer, Lubert.  2011.  Biochemistry (7th edition)
Publisher - Palgrave Macmillan, Basingstoke
 ISBN 978-1-4292-76351, c.€63.00
(Hamilton Counter Reserve - 14 copies - 574.192 L592*6;15 - 6;65)
(Hamilton Lending - 54 copies - S-LEN 574.192 L592*6;1 - 6;14)

click here for textbook companion website

Devlin, T.M. (ed.).  2010.  Textbook of Biochemistry with Clinical Correlations (7th edition)
PublisherJohn Wiley & Sons,
ISBN 978-0-470-28173-4, c.€59.00 (hardcover)
ISBN 978-0-470-60976-7, c.€38.00 (e-book)

Assessments/examinations:

The allocation of marks for assessment of BY2201 will be as follows:

• Pre-practical assessments - 10 %
• Post-practical assessments (Write-ups and Proteomics theme) - 20 %
• End of year examination of lecture material (Choice of 2 from 5 essays) - 70 %

(Note: Marks awarded for post-practical assessment is subdivided into a quarter for technical competency - awarded during laboratory sessions - and three-quarters for work handed in after laboratory.)

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BY2202: Vertebrate Form and Function

 

Module coordinator:

• Dr Áine Kelly (aikelly@tcd.ie) Department of Physiology, School of Medicine

 

Other contributors:

• Prof. Tom Connor (connort@tcd.ie) Department of Physiology, School of Medicine
• Prof. Kumlesh Dev (devk@tcd.ie) Department of Physiology, School of Medicine
• Dr Neil Docherty (dochertn@tcd.ie) Department of Physiology, School of Medicine
• Prof. Peter Wilson (pwil@eircom.net) Department of Zoology, School of Natural Sciences
• Dr Michael Wride (wridem@tcd.ie)  Department of Zoology, School of Natural Sciences

 

Module organisation and description:

click here for module organisation and description (PDF- 33kb)

 

Timetable:

click here for BY2202 timetable (PDF - 29kb)

 

Lecture notes:

Dr Wride's lecture notes:

 

Practicals:

 

Recommended text/reading

Sherwood, Lauralee.  2007.  Human Physiology: From Cells to Systems (6th edition)
publisher - Thomson Brooks/Cole, Belmont, CA
ISBN   0495014850 / 0495109347 (International student edition)
(Hamilton Counter Reserve - 8 copies - 612 M98*5;27 - 5;34)
(Hamilton Lending - 2 copies - S-LEN 612 M98*5;5 - 5;6)
or
Stanfield, Cindy L. and Germann, William J.  2008.  Principles of human physiology (3rd edition)
publisher - Pearson/Benjamin Cummings, San Francisco, CA
ISBN  9780321454287 / 0321454286 / 0321455061 (package)
(Hamilton Counter Reserve - 6 copies -  612 P23*2;14 - 2;19)
(Hamilton Lending - 4 copies - S-LEN 612 P23*2 - 2;3)

Other support material:

Campbell, Neil A.  2008.  Biology (8th edition)
publisher - Pearson/Benjamin Cummings, San Francisco, CA
ISBN   9780321536167 / 0321536169
(Hamilton Counter Reserve - 12 copies -  574 M84*7;25 - 7;36)
(Hamilton Lending - 25 copies - S-LEN 574 M84*7 - 7;24)
and
Gilbert, Scott F.  2006.  Developmental biology (8th edition)
publisher - Sinauer Associates, Sunderland, Mass.
ISBN   087893250x
(Hamilton Counter Reserve - 5 copies -  574.3 M81*7;14 - 7;18)
(Hamilton Lending - 18 copies - S-LEN 574.3 M81*7 - 7;13, 7;19 - 7;22)

Assessments/examinations:

The in-course assessment is based on the 5 practical classes associated with this module and is worth 25% of the overall mark for this module.  Students are required to submit a completed data sheet at the end of each practical, or to comlete the required exercises and have the Lab Manual assessed and signed by a lecturer or demonstrator at the end of each class.

The end of year written exam is worth 75% of the module marks and consists of one 90 min paper.  Students are required to answer one essay from a choice of 3, plus 5 compulsory short-answer questions. Students should allow 40min for the essay question and 10 min for each of the short answer questions.

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BY2203: Metabolism

 

Module coordinator

• Dr Emma Creagh (ecreagh@tcd.ie) School of Biochemistry and Immunology

 

Other contributors:

• Dr Anne Molloy (amolloy@tcd.ie) School of Biochemistry and Immunology
• Dr Derek Nolan (denolan@tcd.ie) School of Biochemistry and Immunology
• Dr Richard Porter (rkporter@tcd.ie) School of Biochemistry and Immunology

 

Module organisation and description:

click here for module organisation and description (PDF- 33kb)

 

Timetable:

click here for BY2203 timetable (PDF - 29KB)

 

Lecture notes:

click here for lecture notes (School of Biochemistry and Immunology website)

 

Practicals:

• Dr Glynis Robinson (robinsog@tcd.ie) School of Biochemistry and Immunology
• Dr Audrey Carroll (aucarrol@tcd.ie) School of Biochemistry and Immunology

 

Recommended text/reading:

Berg, Jeremy M., Tymoczko, John L. and Stryer, Lubert.  2011.  Biochemistry (7th edition)
Publisher - Palgrave Macmillan, Basingstoke
 ISBN 978-1-4292-76351, c.€63.00
(Hamilton Counter Reserve - 14 copies - 574.192 L592*6;15 - 6;65)
(Hamilton Lending - 54 copies - S-LEN 574.192 L592*6;1 - 6;14)

click here for textbook companion website

Devlin, T.M. (ed.).  2010.  Textbook of Biochemistry with Clinical Correlations (7th edition)
Publisher - John Wiley & Sons,
ISBN 978-0-470-28173-4, c.€59.00 (hardcover)
ISBN 978-0-470-60976-7, c.€38.00 (e-book)

 

Assessments/examinations

The allocation of marks for assessment of BY2203 will be as follows:

• Pre-Practical Exams - 10 %
  
• Post-practical assessments (Write-ups) - 20 %
  
• End of year examination of lecture material (Choice of 2 from 5 essays) - 750%

End of year examination of lecture material (Choice of 2 from 5 essays) - 70 %

(Note: Marks awarded for post-practical assessment is subdivided into a quarter for technical competency - awarded during laboratory sessions - and three-quarters for work handed in after laboratory.) 

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BY2204: Evolution

 

Module coordinator:

• Dr Trevor Hodkinson (hodkinst@tcd.ie) Department of Botany, School of Natural Sciences

 

Other contributers:

• Dr Nicola Marples (nmarples@tcd.ie) Department of Zoology, School of Natural Sciences
• Prof. Aoife McLysaght (aoife.maclysaght@tcd.ie) Department of Genetics, School of Genetics and Microbiology

 

Module organisation and description:

click here for module organisation and description (PDF - 33kb)

 

Timetable:

click here for BY2204 timetable (PDF - 29kb)

 

Lecture notes:

Dr Marples' Lecture Notes:
Lecture 1: Darwinism and pre-Darwinian thinking (PDF - 7.9Mb)
Lecture 3: Fossils and the Origin of Diversity (PDF -5.9Mb)
Lecture 7: What is a Species and How do they arise?(PDF - 4.9Mb)
Lecture 9: Coevolution and Mimicry(PDF - 3.9Mb)
Lecture 14: Evolution of Sex and Sexual Selection (PDF - 3.6Mb)
Lecture 15: Kin Selection and Cooperation(PDF - 2.6Mb)
Lecture 17: Altruism (PDF - 2.2Mb)

Prof. McLysaght's Lecture Notes:

Dr Hodkinson's Lecture Notes:
Lecture 8: Speciation in Plants (PDF - 22.5Mb)
Lecture 11: Global Change, Extinctions and Evolution (PDF - 9.2Mb)
Lecture 16: Endosymbiosis (PDF - 4.5Mb)

 

Practicals:

 

Recommended text/reading:

Freeman, Scott and Herron, John C. 2007.  Evolutionary Analysis (4th edition)
publisher - Pearson/Benjamin Cummings, San Francisco, CA
ISBN   0132275848 / 9780132275842   c.€100.00
(Hamilton Counter Reserve - 5 copies (3rd edition, 2004) - 575 P43;16 - 20)
(Hamilton Lending - 15 copies (3rd edition, 2004) - S-LEN 575 P43;1 - 15)

Skelton, Peter (ed.)  1993.  Evolution: a biological and palaeontological approach
publisher - Addison-Wesley, Wokingham
ISBN  0201544237 (out of print)
(Hamilton Counter Reserve - 8 copies -  575 N3, 3;2, 3;11 - 13, 3;21 - 23)
(Hamilton Lending - 11 copies S-LEN 575 N3;3 - 4, 3;14 - 20, 3;24 - 25)

Ridley, Mark.  2003.  Evolution (3rd edition)
publisher - Wiley-Blackwell, Malden, MA, Oxford
ISBN  9781405103459   c.€51.00
(Hamilton Lending - 2 copies S-LEN 575 N33*2;1 - 2)

Other support material:

Campbell, Neil A.  2008.  Biology (8th edition)
publisher - Pearson/Benjamin Cummings, San Francisco, CA
ISBN   9780321536167 / 0321536169
(Hamilton Counter Reserve - 12 copies -  574 M84*7;25 - 7;36)
(Hamilton Lending - 25 copies S-LEN 574 M84*7 - 7;24)

Gould, Stephen Jay.  1980.  The Panda's Thumb
publisher - W.W. Norton, NY / Penguin, Harmondsworth
ISBN   780393308198 (1992 reprint)  c.€12.50
(Santry Stacks - 2 copies -  SHL-52-139 and PB-45-517)

Assessments/examinations:

The in-course assessment associated with this module is worth 25% of the overall mark.  Students are required to submit their final reports to the Science Course Office on Monday, 15 November 2010, between 09.00 and 16.00.  Penalties for late submission will be:

• Up to 16.00 on Tuesday, 16 November - 10%
• Up to 16.00 on Friday, 19 November - 25%
• Any later - 100%

The end of year written exam is worth 75% of the module marks and consists of one 90min paper.  Students are required to answer one essay from a choice of 3, plus 5 compulsory short-answer questions. Students should allow 40 min for the essay question and 10 min for each of the short answer questions.

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BY2205: Microbiology 

 

Module coordinator:

• Prof. Charles Dorman (cjdorman@tcd.ie) Department of Microbiology, School of Genetics and Microbiology

Other contributers:

• Prof. Ursula Bond (ubond@tcd.ie)Department of Microbiology, School of Genetics and Microbiology
• Prof. Tim Foster (tfoster@tcd.ie) Department of Microbiology, School of Genetics and Microbiology
• Prof. Joan Geoghegan (geoghejo@tcd.ie) Department of Microbiology, School of Genetics and Microbiology
• Prof. Kim Roberts (kroberts@tcd.ie) Department of Microbiology, School of Genetics and Microbiology
• Prof. Ronnie Russell (rrussell@tcd.ie) Department of Microbiology, School of Genetics and Microbiology

Module organisation and description:

click here for module organisation and description (PDF - 33kb)

Timetable:

click here for BY2205 timetable (PDF - 29kb)

Lecture notes:

Prof. Bond's Lecture Notes: Cell and Molecular Biology of Yeasts

Prof. Dorman's Lecture Notes: Bacterial and Phage Genetic Switches

Prof. Foster's Lecture Notes:
Prof Foster's lecture notes appear in two formats - 4 b/w slides per page (suitable for printing off before the lectures) and 2 larger, colour slides per page (providing clearer detail of images)

Prof. Russell's Lecture Notes: Defense and Immunity in a Microbial Environment

Practicals:

Lab Session 1 (25.01.12)
Introductory and Support Material (PDF - 21.8MB)

Lab Session 2 (01.02.12)
Introductory and Support Material (PDF - 17.4MB)

Lab Session 3 (08.02.12)
Introductory and Support Material (PDF - 25.3MB)

Lab Session 4 (15.02.12)
Introductory and Support Material (PDF - 16.1MB)

Lab Session 5 (22.02.12)
Introductory and Support Material (PDF - 38.8MB)

Web Galleries:

Gallery 1
Amoeboid protozoa (PDF - 2Mb)
Candida (PDF - 2Mb)
Ciliates (PDF - 3Mb)
Dimorphic fungi (PDF - 1.2Mb)
Filamentous fungi (PDF - 4.8Mb)
Flagellates (PDF - 1.9Mb)
Plasmodium falciparum (PDF - 1.1Mb)
Protozoal cysts (PDF - 2.2Mb)
Saccharomyces (PDF - 2.6Mb)
Schizosaccharomyces (PDF - 1.1Mb)
Trypanasomatid flagellates (PDF - 2.8Mb)

Gallery 2
Bacterial capsules (PDF - 831kb)
Bacterial cell walls (PDF - 729kb)
Bacterial endospores (PDF - 1Mb)
Bacterial fimbriae adherence (PDF - 2.2Mb)
Bacterial flagella (PDF - 594kb)
Bacterial intracellular structures (PDF - 971kb)
Gram stains (PDF - 1.9Mb)
Specifically stained bacteria (PDF - 2.2Mb)

Gallery 3
Oral streptococci lactobacilli (PDF - 1.7Mb)
Staphylococcus species (PDF - 1.7Mb)

Recommended text/reading:

Assessments/examinations:

Practical MCQ Exam
Sample questions (PDF - 188kb)

 

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BY2206: Ecosystem Biology and Global Change

 

Module coordinator:

• Prof. Fraser Mitchell

Other contributers:

• Prof. Jim Wilson

Module organisation and description:

 

Timetable:

click here for BY2206 timetable (PDF - 45kb)

Lecture notes:

Prof. Mitchell's Lecture Notes:

Prof. Wilson's Lecture Notes:

Practicals:

 

Recommended text/reading:

 

Assessments/examinations:

 

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BY2207: Behaviour

 

Module coordinator:

• Dr Nicola Marples (nmarples@tcd.ie) Department of Zoology, School of Natural Sciences

Other contributers:

• Dr Andrew Jackson (a.jackson@tcd.ie) Department of Zoology, School of Natural Sciences
• Dr Alice Witney (awitney@tcd.ie) Department of Physiology, School of Medicine
• Prof Peter Wilson (pwil@eircom.net) Department of Zoology, School of Natural Sciences
• Dr Mike Wride (wridem@tcd.ie) Department of Zoology, School of Natural Sciences

Module organisation and description:

click here for module organisation and description (PDF - 33kb)

Timetable:

click here for BY2207 timetable (PDF - 61kb)

Lecture notes:

Dr Marples' Lecture Notes:
Lecture 1: The Fathers of Ethology (PDF - 7.2Mb)
Lecture 2: Types of Learning (PDF -6.2Mb)
Lecture 3: Memories are made of this (PDF - 5Mb)
Lecture 4: Finding your way about - colour (PDF - 25.6Mb) black/white (5.7Mb)
Lecture 5: Cultural Transmission - Part 1 (PDF - 8Mb)
Lecture 6: Cultural Transmission - Part 2: Imitation (PDF - 10Mb)
Lecture 7: Play (PDF - 7.1MB)
Lecture 8: Intentionality and Theory of Mind (PDF - 8.6Mb)

Dr Wride's Lecture Notes:
Lecture 1: Genetics and Behaviour 1 (PDF - 717kb)
Lecture 2: Genetics and Behaviour 2 (PDF -623kb)
Lecture 2 notes 1: Genetics and Human Behaviour (PDF - 147kb)
Lecture 2 notes 2: Twin and Combination studies (PDF - 165kb)
Lecture 3: Physiology and Behaviour 1 (PDF - 1.2Mb)
Lecture 4: Physiology and Behaviour 2 (PDF - 877kb)
Lecture 5: Parasite altered Behaviour (PDF - 1Mb)

Ms Loxton's Lecture Notes:
Lecture 1: Parasites and Animal Behaviour (PDF - 2.2Mb)

Dr Jackson's Lecture Notes:
Lecture 1: Collective Behaviour - 09.02.12 (PPT - 7.9Mb)

Practicals:

Recommended text/reading:

Assessments/examinations:

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BY2208: Genetics

 

Module coordinator:

• Dr Kevin Mitchell (kevin.mitchell@tcd.ie) Smurfit Institute of Genetics, School of Genetics and Microbiology

Other contributers:

• Prof. David McConnell (david.mcconnell@tcd.ie) Smurfit Institute of Genetics, School of Genetics and Microbiology
• Prof. Mani Ramaswami (ramaswam@tcd.ie) Smurfit Institute of Genetics, School of Genetics and Microbiology
• Prof. Dan Bradley (dbradley@tcd.ie) Smurfit Institute of Genetics, School of Genetics and Microbiology
• Prof. Ken Wolfe (khwolfe@tcd.ie) Smurfit Institute of Genetics, School of Genetics and Microbiology
• Prof. Seamus Martin (martinsj@tcd.ie) Smurfit Institute of Genetics, School of Genetics and Microbiology
• Dr Adrian Bracken (adrian.bracken@tcd.ie) Smurfit Institute of Genetics, School of Genetics and Microbiology
• Dr Frank Wellmer (wellmerf@tcd.ie) Smurfit Institute of Genetics, School of Genetics and Microbiology

Module organisation and description:

click here for module organisation and description (PDF - 33kb)

Timetable:

click here for BY2208 timetable (PDF - 45kb)

Lecture notes:

Prof Bradley's Lecture Notes: Genetic Analysis
Lectures - part 1 (PDF - 5.4Mb)
Lectures - part 2 (PDF - 2.6Mb)
Recommended Reading (PDF - 25kb)

Prof. Martin's Lecture Notes: The Genetic Basis of Cancer
Lectures (PDF - 4.6Mb)

Prof McConnell's Lecture Notes: The Central Dogma
Lecture 1 part 1: DNA Structure (PDF - 7.2Mb)
Lecture 1 part 2: DNA Structure (PDF - 3.6Mb)
Lecture 1 part 3: DNA Replication (PDF - 3.1Mb)
Lecture 1 part 4: DNA Replication (PDF - 1.5Mb)
Lecture 2: DNA Replication (PDF -2Mb)
Lecture 3: RNA Synthesis(PDF - 7.3Mb)
Lecture 4 part 1: Protein Synthesis (PDF - 3.2Mb)
Lecture 4 part 2: Protein Synthesis (PDF - 5.7Mb)

Dr Mitchell's Lecture Notes: Regulation of Gene Expression
Lecture 1 (PDF - 2.5Mb)
Lecture 2 (PDF - 3.6Mb)
Lecture 3 (PDF - 2.7Mb)
Lecture 4 (PDF - 1.8Mb)

Prof Ramaswami's Lecture Notes: Cracking the Code
Lecture 1 (PDF - 2.2Mb)
Lecture 2: A Molecular Genetics Toolbox - 1 (PDF - 1.9Mb)

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Practicals:

Lab Sessions 1/2 (21-28.01.13)
Introductory Notes - B/W (PDF - 4.5Mb) Colour (PDF - 5.1Mb)

Lab Session 3 (04.02.13)
Introductory Notes - B/W (PDF - 2.9Mb) Colour (PDF - 7.1Mb)

Lab Session 4 (11.02.13)
Introductory Notes - Colour (PDF - 1.4Mb)

Lab Session 5 (18.02.13)
Introductory Notes - Colour (PDF - 692kb)

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Recommended text/reading:

Assessments/examinations:

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BY2209: Infection and Immunity

 

Module coordinator:

• Dr Angus Bell (abell@tcd.ie) Department of Microbiology, School of Genetics and Microbiology

Other contributers:

• Prof. Jay Hinton (jay.hinton@tcd.ie) Department of Microbiology, School of Genetics and Microbiology
• Prof. Cliona O'Farrelly (ofarrecl@tcd.ie) School of Biochemistry and Immunology
• Prof. Kingston Mills (kingston.mills@tcd.ie) Division of Immunology, School of Biochemistry and Immunology
• Prof. Dan Bradley (daniel.bradley@tcd.ie) Department of Genetics, School of Genetics and Microbiology

Module organisation and description:

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Timetable:

click here for BY2209 timetable(PDF - 66kb)

Lecture notes:

Prof. Hinton's Lecture Notes:
Lecture 1 - Infectious diseases in the 21st century (PDF - 6.1Mb)
Lecture 2 - How pathogens make us ill (PDF - 4.7)

Prof. O'Farrelly's Lecture Notes:
Lecture 1 - Overview of Immunology (PDF - 2.9Mb)
Lecture 2 - Cells, Organs and Molecules of the Immune System (PDF - 2.2Mb)
Lecture 3 - Innate Immunity (PDF - 1.9Mb)
Lecture 4 - Adaptive Immunity (PDF - 3.3Mb)

Prof. Mill's Lecture Notes:
Lectures 1 and 2 - Adaptive Immunity (PDF - 6.5Mb)

Prof. Bradley's Lecture Notes
Part 1 (PDF - 4Mb)
Part 2 (PDF - 5.4Mb)

Dr Bell's Lecture Notes
Biology, pathogenesis and treatment of malaria (PDF - 1Mb)

Practicals:

Recommended text/reading:

Assessments/examinations:

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BY2210: Animal and Plant Bioresources

 

Module coordinator:

• Dr Trevor Hodkinson (hodkinst@tcd.ie) Department of Botany, School of Natural Sciences

Other contributers:

• Prof. Nick Gray (nfgray@tcd.ie) Department of Botany, School of Natural Sciences
• Dr Daniel Kelly (daniel.kelly@tcd.ie) Department of Botany, School of Natural Sciences

Module organisation and description:

click here for module organisation and description (PDF - 250kb)

Timetable:

click here for BY2210 timetable (PDF - 49kb)

Lecture notes:

Dr Hodkinson's Lecture Notes:
Lecture 1: Introduction to Bioresources (PDF - 4.7Mb)
Lecture 2: Biodiversity and Bioprospecting (PDF - 31.2Mb)
Lecture 3: Medicinal Drug Products (PDF - 27.8)
Lecture 4: Genetic Resources 1 (PDF - 17.5Mb)
Lecture 5: Genetic Resources 2 (PDF - 14.8Mb)
Lecture 6: Biotechnology 1 (PDF - 13.1Mb)
Lecture 7: Biotechnology 2 (PDF - 5.5Mb)
Lecture 8: GMOs (PDF - 6.9)
Lecture 9: Agricultural Bioresources (PDF - 12.8Mb)
Lecture 10: Agricultural Productivity, Sustainability and Climate Change (PDF - 12.4Mb)

Dr Kelly's Lecture Notes:
Lecture 15: Dispersal 1 (PDF - 19.9Mb)
Lecture 16: Dispersal 2 (PDF - 21Mb)
Lecture 17: Pollination (PDF - 16.7Mb)

Practicals:

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Recommended text/reading:

Recommended Reading for BY2210 (2011/12) (PDF - 66kb)

Assessments/examinations:

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