Table of Contents

Staff Consultation Times ................................................................... 1

Module Coordinators ........................................................................ 2

Double Honours Semester 1 Outline ................................................. 3

Interviews with External Examiner .................................................... 3

BI422 General Methodology Lectures ............................................... 4

Continual Assessment & Practical Module Descriptors ...................... 4

Schedule of Advanced Practicals/Professional Modules (BI426) ........ 5

Lecture Module Descriptors .............................................................. 11

Staff Research Interests .................................................................... 15

Writing a 4th Year Dissertation: Essential Information ....................... 20

Departmental Plagiarism Policy ........................................................ 24

Guidelines for Literature Project (BI424) ........................................... 26

• BI424 Literature Project list ..................................................... 26

Guidelines for Laboratory Project (BI428) ......................................... 29

• BI428 Laboratory Project list ................................................... 32 • Plagiarism and the Research Thesis ......................................... 36

Literature & Research Project Deadlines ........................................... 37

Alltech Young Scientist Award Programme 2015 ............................... 38

Biochemical Calculations ................................................................... 39

Examination Assessment Scale .......................................................... 40

Lab Safety ......................................................................................... 41

Notification of Absence ..................................................................... 43

Sample Forms:

• Guidelines for Module Registration ......................................... 46 • Declaration of Originality ........................................................ 47 • Cover Sheet ............................................................................. 48 • Notification of Absence ........................................................... 49

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MAYNOOTH UNIVERSITY DEPARTMENT OF BIOLOGY Information for Fourth Year Double Honours Students 2014 - 2015

Please read this manual carefully and keep it safely so that you can refer to it during the year. The Biology staff extends a warm welcome back to all Fourth Years; we hope you will enjoy your final year with us and gain valuable skills and knowledge.

AIMS OF THE BIOLOGY DEPARTMENT To enhance students’ knowledge and understanding of important concepts in the Biological Sciences and to develop their analytical, practical and communication skills and appreciation of environmental and other bioethical issues.

STAFF CONSULTATION TIMES Teaching Staff Room E-mail Consultation Time Dr. Özgür Bayram (OB) 2.31 ozgur.bayram@nuim.ie Tuesday 11.00-13.00 Dr. Marion Butler (MB) B3.18 marion.butler@nuim.ie Tuesday 10.00-12.00 Dr. Jim Carolan (JC) 2.29 james.carolan@nuim.ie Monday 11.00-14.00 Prof. Phil Dix (PD) B2.15 phil.dix@nuim.ie Monday 14.00-16.00 Dr. Paul Dowling (PDo) F6 paul.dowling@nuim.ie Tuesday 11.00-13.00 Prof. Sean Doyle (SD) 1.24* sean.doyle@nuim.ie Tuesday 10.00-11.30 Dr. David Fitzpatrick (DF) 1.26* david.fitzpatrick@nuim.ie Monday 14.30-16.00 Dr. Emmanuelle Graciet (EG) B1.25 emmanuelle.graciet@nuim.ie Friday 10.00-12.00 Dr. Christine Griffin (CG) 2.36 christine.griffin@nuim.ie Monday 14.00-16.00 Dr. Gary Jones (GJ) 2.35 gary.jones@nuim.ie Tuesday 14.30-16.00 Dr. Kevin Kavanagh (KK) 2.39 kevin.kavanagh@nuim.ie Mon & Wed 14.00-16.00 Dr. Gemma Kinsella (GK) B2.16 gemma.kinsella@nuim.ie Tuesday 11.00-13.00 Prof. James McInerney (JMcI) F7 james.o.mcinerney@nuim.ie Tuesday 14.30-15.30 Dr. Conor Meade (CM) 2.34 conor.v.meade@nuim.ie Monday 12.00-13.00 Dr. Sinead Miggin (SM) B3.14 sinead.miggin@nuim.ie Tuesday 11.00-13.00 Prof. Paul Moynagh (PM) B1.21 paul.moynagh@nuim.ie Monday 14.00-16.00 (Head of Department) Dr. Noel Murphy (NM) B3.17 noel.murphy@nuim.ie Tuesday 12.00-14.00 Dr. Jackie Nugent (JN) B1.23 jackie.nugent@nuim.ie Monday 10.00-12.00 Dr. Shirley O’Dea (SO’D) B2.19 shirley.odea@nuim.ie Monday 11.00-13.00 Prof. Kay Ohlendieck (KO) 2.33 kay.ohlendieck@nuim.ie Monday 14.00-15.00 Ms. Teresa Redmond (TR) 1.21* teresa.redmond@nuim.ie During practical classes Dr. Martina Schroeder (MS) B2.18 martina.schroeder@nuim.ie Monday 15.00-16:30 Dr. Fiona Walsh (FW) B1.24 fiona.walsh@nuim.ie Thursday 09.30-11.00

*=Located on ground floor Callan Building; F=Located in Foyer, 1st floor Callan Building; B=Biosciences & Electronic Engineering Building

The times when staff are normally available for consultation are given above. Appointments for other times must be arranged with individual lecturers. Administrative Staff Offices are open daily: 10am-12.45pm; 2-4pm Biology Office (room 2.41): Ms. Jean Burbridge (jean.burbridge@nuim.ie) /Ms Eimear Ryan (eimear.m.ryan@nuim.ie) Departmental Administrator (room 2.40): Ms. Terry Roche (terry.roche@nuim.ie)

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Programme Coordinators: OMNIBUS SCIENCE: Dr. Jackie Nugent BIOTECHNOLOGY: Prof. Sean Doyle SCIENCE EDUCATION: Dr. Jackie Nugent BIOLOGICAL & BIOMEDICAL SCIENCE: Dr. Kevin Kavanagh MATURE STUDENT COORDINATOR: Dr. Christine Griffin POSTGRADUATE COORDINATOR: Dr. Gary Jones MSC IN IMMUNOLOGY & GLOBAL HEALTH: Dr. Noel Murphy For urgent matters the Programme Coordinators and/or Head of Department may be contacted in their rooms at any time. Please contact Jean/Eimear to make an appointment. 4th Year Committee: The members will be James McInerney and Paul Moynagh and 3 elected fourth year students (2 single honours and 1 double honours student). The committee will discuss problems and matters of interest. If you have issues which you would like to be considered you should tell your representative. James McInerney will be responsible for Group 1 (Literature Project and professional modules). Paul Moynagh will be responsible for Group 2 (Research Project). Please direct any queries concerning your course to the appropriate group head. Module Coordinators:

CODE NAME Coordinator e-mail address BI401 Environmental Field Studies Conor Meade conor.v.meade@nuim.ie BI403 Plant Biotechnology Phil Dix phil.dix@nuim.ie

BI405 Advanced Immunology Marion Butler marion.butler@nuim.ie BI406 Behavioural Ecology Christine Griffin christine.griffin@nuim.ie

BI407 Tumour Biology Marion Butler marion.butler@nuim.ie

BI409 Organelle Genome Evolution Jackie Nugent jackie.nugent@nuim.ie BI410 Plant Developmental Biology Jackie Nugent jackie.nugent@nuim.ie

BI411 Bioethics & Biotechnology Sean Doyle sean.doyle@nuim.ie

BI422 Research Methodology 1 Gary Jones gary.jones@nuim.ie

BI424 Literature Project 1 James McInerney james.o.mcinerney@nuim.ie BI426 Advanced Practicals/ProfessionalModules1 Fiona Walsh fiona.walsh@nuim.ie

BI428 Laboratory Project 1 Paul Moynagh paul.moynagh@nuim.ie

BI435 Molecular Ecology and Biogeography Conor Meade conor.v.meade@nuim.ie BI436 Medical Mycology Kevin Kavanagh kevin.kavanagh@nuim.ie BI437 Neuromuscular Biology Kay Ohlendieck kay.ohlendieck@nuim.ie BI439 Antibiotics: Discovery, Modes of Action &

Resistance Fiona Walsh fiona.walsh@nuim.ie

BI440 Control of Protein Activity Emmanuelle Graciet emmanuelle.graciet@nuim.ie BI441 Fungal & Bacterial Secondary Metabolism Ozgur Bayram ozgur.bayram@nuim.ie BI442 Human Genetics James McInerney james.o.mcinerney@nuim.ie BI443 Clinical Proteomics: Discovery, Validation &

Medical Utility Paul Dowling paul.dowling@nuim.ie

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DOUBLE HONOURS SEMESTER 1 OUTLINE: BI422 Research methodology 2 (2.5 credits) BI424 Literature project 2 (5 credits)* AND BI426 Advanced practicals/Professional modules 2 (2.5 credits) OR BI428 Laboratory Project 2* (7.5 credits) LECTURE MODULES (5 credits each) One, Two or Three lecture modules from: BI401 Environmental Biology Field Course (not offered this year) CM/CG BI403 Plant Biotechnology PD BI405 Advanced Immunology MB/MM or BI441 Fungal & Bacterial Secondary Metabolism OB BI407 Tumour Biology MB or BI443 Clinical Proteomics: Discovery, Validation & Medical Utility PDo BI409 Organelle Genome Evolution JN BI411 Bioethics & Biotechnology MD/SD *Some Double Honours Chemistry students may take these in Semester 2, only if their Chemistry projects take place in Semester 1. DOUBLE HONOURS SEMESTER 2 OUTLINE: BI426 Advanced practicals/Professional modules 2 (2.5 credits) (continued) LECTURE MODULES (5 credits each) One, Two or Three lecture modules from: BI406 Behavioural Ecology CG BI410 Plant Development JN BI435 Molecular Ecology And Biogeography CM BI436 Medical Mycology KK or BI439 Antibiotics: Discovery, Modes of Action & Resistance FW BI437 Neuromuscular Biology KO or BI440 Control of Protein Activity EG BI442 Human Genetics JMcI Fourth Year Interviews with External Examiner: Please note: The external examiner, interviews several students each year. Please ensure that you remain available to attend for interview, which usually takes place after the Summer Exams (between 9-13 June). If you have particular difficulty about being available at that time please discuss the matter with Professor Moynagh. Sets of previous exam papers may be used as a guide to the types of question which might be set, but you are reminded that courses are continually evolving and the content may not remain the same from one year to the next. Copies of past papers are available from the Library Exam Paper Database: (web address: https://www.maynoothuniversity.ie/library/exam-papers)

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CONTINUAL ASSESSMENT & PRACTICAL MODULE DESCRIPTORS BI422 Research Methodology 2 Schedule (11 x 1hr lectures; 5 x 2 or 3 hour practicals as below)

-2.5 credit COMPULSORY module DATE TIME PLACE TITLE GIVEN BY Tues 23 Sept 1pm JH2 Laboratory Safety Lecture 1* A. Power Tues 23 Sept 4-5pm Teaching Lab 1 Research Instrumentation Lecture

Series 1 N. Gavin

Wed 24 Sept 11am Hall F Laboratory Safety Lecture 2* A. Power Wed 24 Sept 2-4pm Teaching Lab 1 Intro to Lab Techniques J.Nugent Thurs 25 Sept 3-5pm Teaching Lab 1 Basic Microbiological Techniques K.Kavanagh Thurs 25 Sept 5pm TH1 Options with your degree (incl.

introduction to career planning, postgrad study & employment)

E. Strain

Fri 26 Sept 9am JH4 Plagiarism/Turnitin C.Meade Fri 26 Sept 10am JH4 Thesis Writing 1 P.Moynagh Mon 29 Sept 3-5pm Teaching Lab 1 Molecular Biology Techniques 1 G. Jones Tues 30 Sept 1pm JH2 Accessing Information Postgraduate

Study F. Brady

Tues 30 Sept 2-5pm Computer Sci, Lab 4 (Callan Bldg. -Rm 1.105)

Introduction to Excel L. McNamara

Tues 30 Sept 5pm JH7 Postgraduate Study M.Schroeder Wed 1 Oct 11am Hall F GM Induction A.Power Wed 1 Oct 2-4pm Teaching Lab 1 Molecular Biology Techniques 2 G. Jones Wed 1 Oct 4-4.30

pm Teaching Lab 1 Intro to Lab Techniques

Questionnaire K.Kavanagh/ J.Nugent

Thurs 2 Oct 5pm TH1 How to write a Science CV** E. Strain Mon 6 Oct 2-5pm Teaching Lab 1 Basic Biochemical Techniques 1 N. Murphy Wed 8 Oct 2-4pm Teaching Lab 1 Research Instrumentation Lecture

Series: 2&3 N. Gavin/ N. Irani

*Students must pass the LABORATORY SAFETY EXAM before they can begin BI426 or BI428. This will be a Moodle based exam; arrangements for this exam will be discussed at one of the Laboratory Safety lectures above. **There will be a CV assignment at the end of the Career Module which the department will keep on file. Academic staff will refer to this document when preparing any references you may request during the year. BI424 Literature Project 2 A 6 week independent literature project. The topics will be set by the Academic staff of the Department. They will collectively cover a wide range of biological disciplines, and where possible the student will have an element of choice on the subject area. Individual topics will have a narrow enough focus to ensure a survey of the primary literature is appropriate. Projects will be assessed based on thesis write-up (80%) and an oral presentation (20%) of the research topic.

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BI426 Advanced Practicals/Professional Modules 2 IMPORTANT: CHECK THE TIMES AGAINST YOUR SECOND SUBJECT SCHEDULE AS SOME PRACTICAL/PROFESSIONAL MODULE TIMES MAY CLASH. One advanced practical (1 x 9 hour labs) from: SEMESTER 1: Lab Times: Mondays 3-6pm; Wednesdays 2-5pm; Thursdays 2-5pm -Chemical Cross-linking analysis of an oligomeric protein from skeletal muscle: 13-17 Oct, Lab 3 -Applied Medical Mycology: 20-24 Oct, Lab 3 (Mon 3-6; Tues 3-5; Wed 3-4.30; Thurs 3-4) -Plant Biotechnology (can only be taken with BI403): 3-7 November, Lab 3 -Clinical Applications 1: 17-21 November, Lab 3 -Molecular Cloning: 8-12 December, Lab 2; Mon 3-6; Tues 2-5; Wednesday 2-5, Thurs 2-5 SEMESTER 2: Lab Times VARIOUS: -Immunology: Assessment of Antibody response by ELISA & Detection of Proteins by Western Blotting: 9-

13 Feb Lab 2; Mon 2-5pm, Tues 2-5pm, Wed 2-5pm -Clinical Applications 2: 16-20 February, Lab 3; Mon 2-5pm; Wed 2-5pm; Thurs 2-5pm -Mammalian Cell Culture: 2-5pm Tues 24 Feb; 3-6pm Wed 25 Feb, 2-5pm Tues 4 Mar, Lab 3 -Comparative Genomics of Pathogenic Bacteria: 9-13 March, Computer Science Lab; Mon 2-5pm; Wed 2-

5pm; Thurs 2-5pm -Behaviour Observation: 13-17 April, Lab 2; Mon 2-5pm; Tues 2-5pm; Wed 2-5pm

Two professional modules (2 x 8 hours lectures/computer labs) from: SEMESTER 1: Mondays 3-4pm APT; Wednesdays 3-5pm SLT; Thursdays 3-4pm Hall F -Scientific Communication (various from Media Studies Dept.) weeks 4-5 (Semester 1) 13-24 Oct -Management of Information Security (TDowling) weeks 7-8 (Semester 1) 3-14 Nov: (Wednesdays 3-6pm; Thursdays 3-4pm Hall F -Personal effectiveness (PHehir) weeks 10-11 (Semester 1) 24 Nov-4 Dec SEMESTER 2: VARIOUS: -End User computing weeks 4-5 (Semester 2) 23 Feb-2 Apr: Mondays 3-4pm JH5; Wednesdays 2-4pm

Long Corridor; Thursdays 3-4pm Hall F -Patenting and Licensing of Biological Products (SD/NM) weeks 8-9 (Semester 2) 23 March - 3 April:

Mondays 3-4pm JH5; Wednesdays 3-5pm SLT; Thursdays 3-4pm Hall F Advanced Practical Descriptions: SEMESTER 1 Applied Medical Mycology (Dr. Kevin Kavanagh) A number of yeasts have been implicated in superficial and systemic diseases in humans. In general the superficial diseases (oral candidosis, 'Thrush', cutaneous infection) can be effectively treated with either azole or polyene drugs and under most circumstances are not life threatening. However, systemic diseases occur in severely debilitated individuals and are potentially fatal. Treatment may be protracted and often fails to arrest the dissemination of the yeast. The ability to differentiate yeasts is critically important since it facilitates treatment and allows the tracking of yeasts implicated in recurring bouts of superficial disease. In this practical we shall examine means of morphologically distinguishing between pathogenic yeast species and of discriminating between them on the basis of their altered susceptibilities to antifungal agents. Restriction Fragment Length Polymorphisms may be used to differentiate between the main fungal pathogens and this technique will be used in conjunction with the variations evident in the whole cell protein banding pattern to identify and distinguish yeast strains. At the end of this practical the student will be familiar with the main techniques used to rapidly identify the most common yeast pathogens of humans and the reasons why identification is important for patient recovery.

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Clinical Applications 1 (Dr. Jim Carolan) limited to 20 Central to the diagnosis and subsequent treatment of disease is biomarker discovery, involving the identification of molecules (usually proteins) that are more or less abundant in samples taken from patients with and without a disease. The most commonly used biomarkers are those that are found in the fluid fractions of our body such as saliva, urine or blood as their identification generally involves non-invasive and rapid procedures. Samples are screened for the presence or quantity of the biomarker protein and thus give the clinician an idea of whether the patient is suffering from a disease and the stage of disease progression. Although biomarker screening involves focusing on one or two individual proteins, their initial discovery require high throughput analysis of thousands of proteins (e.g. the blood serum proteome) to find those that are consistently different or diagnostic for a disease.

One of the most commonly used methods for high throughput proteome characterisation is 2 Dimensional Electrophoresis (2DE). During these practicals you will conduct 2DE and LC-MS/MS on samples representing serum obtained from patient’s that have been diagnosed with ovarian cancer. By comparing the 2D profiles of sufferers and non sufferers it is anticipated that differentially expressed proteins will be identified; proteins which could represent novel biomarkers for ovarian cancer. Differentially expressed protein spots will be excised and identified using mass spectrometry. The techniques and experience you obtain during these practicals will be valuable to those interested in immunology, clinical research, drug discovery, proteomics and mass spectrometry. NOTE: Clinical Applications 1 and Clinical Applications 2 (Semester 2) are linked, and as such it is recommended that students take both advanced practicals where possible. Molecular Cloning (Dr. Gary Jones) This practical will incorporate some of the basic techniques used in cloning experiments. If one wished to analyse a particular gene for its sequence and expression pattern one would first clone the gene. This involves ligating fragments of the total genomic DNA into a vector such as a plasmid. The mixture would be transformed into competent cells, usually of E. coli, in order to separate the thousands of different fragments and to screen the transformed colonies for that one which contains the gene of interest. This practical incorporates some of these techniques. You will be provided with a plasmid called pBluescript as well as a recombinant pBluescript plasmid which contains an insert in the multiple cloning site. You will prepare competent cells of E. coli, transform them with the cloning vector and the recombinant plasmid and plate the transformation mix on selective medium. The plates also contain a substrate which allows you to distinguish between transformants which contain the cloning vector, which are blue and transformants which contain the recombinant plasmid, which grow as white colonies. Once the colonies have grown you will lyse the cells to release the DNA and then determine whether you have the correct insert using the polymerase chain reaction (PCR) followed by electrophoresis of your PCR product. Plant Biotechnology (Dr. Jackie Nugent) offered to students taking BI403 only The purpose of these experiments is to provide familiarity with some of the most widely used procedures for genetic transformation of plants (i.e. the introduction, integration and expression of foreign genes in plants) and with some basic molecular and biochemical techniques commonly used to characterise transformed plants. Two methods of generating transgenic plants are routinely used in plant Biotechnology labs: Agrobacterium-mediated gene transfer and transformation by microprojectile bombardment using a “gene gun”. Participants in this course will characterise transgenic plants that have been generated by Agrobacterium mediated transformation. Characterisation of the transformed plants will be carried out by, marker gene assay, the polymerase chain reaction (PCR) and detection of proteins by Western Blotting. In addition students will initiate plant transformation experiments using the "gene gun". SEMESTER 2 Behavioural Observation (Dr. Christine Griffin) limited to 30 This course introduces students to methods for sampling and recording animal behaviour. You will learn how to categorize behavioural events and record them using pen-and-paper and/or computer-based methods. Using these skills, you will then devise, carry out and analyse the results of an experiment

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testing a hypothesis about how certain animals behave. The course material includes video recordings (primarily of birds and chimpanzees), and observations of live animals (such as insects) in the lab. Clinical Applications 2 (Dr. Jim Carolan) limited to 20 students The successful treatment of disease depends on early detection which in many cases involves screening patient samples for specific diagnostic biomarkers. These biomarkers are usually proteins that vary significantly in quantity during the disease. Mor et al., (2005) identified a number of biomarkers associated with ovarian cancer (OVCA). One of these proteins, prolactin, was shown to be consistently higher in abundance in patients with OVCA. Subsequently prolactin has been used in clinical situations as a pre-screen for OVCA and to monitor the success treatment in patients with OVCA. In the following set of Advanced Practicals the presence and progression of ovarian cancer will be investigated using antibodies for prolactin. Students will initially assess patient serum samples for the presence of elevated prolactin (compared to a negative control) and then evaluate the success of different cancer treatments. The presence of prolactin will also be confirmed using mass spectrometry based proteomics.

Over the course of these practicals you will be introduced to many of the core methods used to study proteins, including protein extraction and quantification, SDS PAGE, Western Blotting and ELISA. These techniques and the experience you obtain during these practicals will be valuable to those interested in immunology, clinical research, drug discovery and proteomics. Comparative Genomics of Pathogenic Bacteria (Dr. David Fitzpatrick) limited to 18 Genomics is defined as the study of an organisms complete genome sequence. The first complete genome to be sequenced was the bacterium Haemophilus influenzae in 1995 at a cost of millions of dollars. Today more than 1,300 bacterial genomes have been sequenced. With the advent of next generation sequencing technologies the costs of sequencing a bacterial genome are decreasing rapidly and it is now possible to sequence a complete bacterial genome for approximately two thousand dollars. This practical will examine next generation sequence techniques and use computational approaches to assemble a bacterial genome from the raw sequence reads. Once we have an assembly we will computationally locate genes and perform a partial annotation by comparing them to a database of genes with known functions. When annotated we can determine if our bacterial genome contains any genes normally associated with disease. Finally we will use comparative genomics to compare the genomic sequence of a pathogenic bacterium to a non-pathogenic bacterium in an attempt to determine putative virulence factors. Immunology: Assessment of Antibody response by ELISA and Detection of Proteins by Western Blotting (Dr. M. Schroeder). The immune system responds to proteins on infectious organisms and in vaccines, by mounting cellular and humoral immune responses to foreign antigens. Antigens are simply short amino acid sequences that are recognized as foreign, or non-self, in the host organism. B cells produce antibodies that can bind to almost any antigen and these can be detected in serum or mucosal secretions of immune individuals. The immunoglobulin molecules (antibodies) in the serum can be detected by a variety of techniques, including enzyme-linked immunoassay (ELISA). The ELISA is based on the principle that the protein antigen binds to plastic on the wells of an assay plate and when the serum is added the antibodies specific for that antigen will selectively bind to the antigen (other antibodies in the serum specific for another antigens will not bind and can be washed away). The bound antibody can be detected by using a second antibody raised against the immunoglobulin of the species from which the serum was obtained (e.g. anti-mouse IgG) coupled to an enzyme, which coverts a colourless substrate to a coloured product, which can be detected by measurement of absorbance.

The ability of antibodies to bind to other proteins, coupled with the ability of the immune system to generate endless antibody variants all with their own antigenic specificity, make antibodies the perfect tools with which to identify almost any protein. These characteristics are taken advantage of in Western blotting where antibodies raised against a specific protein (e.g. a HIV protein) can be used to detect the presence of this protein in a complex protein mixture that may contain thousands of other proteins. Western blotting is a technique where complex mixtures of proteins that have been separated by electrophoresis and blotted onto a solid support (e.g. PVDF, nitrocellulose) are probed for the presence of

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the protein of interest using an antibody raised against that protein. The bound antibody is subsequently detected by a method similar to that described for the ELISA procedure above Mammalian Cell Culture (Dr. G. Kinsella) Cells that previously grew in humans or animals (in vivo) can be modified to grow (culture) in glass or plastic vessels in the laboratory (in vitro). Cultured mammalian cells are used widely and extensively as an alternative to using animals in research. Whole animals are highly complex and contain many different cell types with diverse and interacting activities. Cell cultures (for example lung epithelial cells, skin cells, bone cells etc.) reduce this complexity and enable more specific questions to be addressed in a simplified context. In addition, cell culture reduces the numbers of animals required to address scientific questions.

Specific growth conditions must be maintained in order to keep the cells alive outside the body and a number of special skills are required to preserve the structure, function, behavior and biology of the cells. The conditions and skills include: using specialised growth media, storing the cells at 37°C and importantly, using ‘aseptic’ technique to prevent microbial contamination and death of the cultures which lack the immune defense system present in the full organism. This course describes the basic skills required to maintain and preserve cell cultures: aseptic technique, medium characteristics, passaging, freezing and storage, recovering frozen stocks, and counting viable cells. Students will then use these skills to carry out experiments to study factors that affect the growth and structure of lung cells. Professional Module Descriptors: Science and the Media in Ireland: Structure, Process and Practical Engagement (Media Studies) How ‘science’ tells its story in the complex and dynamic environment of 21st century mass media This course seeks to respond to a demand from students for a module based on how science is framed and presented in traditional mass media of print and television news and current affairs; how science is represented and stereotyped in popular culture, such as films, advertisements, and TV programme series and how ‘new media’, including the emergence of specialist science blogs and general social media outlets such as Facebook and Twitter, are affecting the way in which science is communicated. both among scientists themselves and throughout the broader public sphere. Over the course of eight lectures this module seeks to impart basic knowledge of science communication processes to meet the needs of Department of Biology undergraduate students as an aspect of their professional development and to enhance their future career prospects. International experience suggests that students derive most benefit from practically –oriented science communication course materials. The module seeks to secure an appropriate balance between theoretical and practical instruction, by combining practical examples and workshop experience of how science communications works in real-life settings with a contextual appreciation of the ideas and concepts that underpin those practices. With an emphasis on engagement opportunities, this course introduces students to the processes whereby expert and specialist information is disseminated and represented across media platforms generally, including traditional print, public and private broadcasting and new media, both in an Irish context and within a broader international framework. Course Content: Lecture 1 – Science in the Public Sphere: Examines how the media frame science stories and the various roles assigned to scientists in media representation as advocates, or providers of expert opinion, or independent engagement with the public on science matters. Lectures 2-3 – Workshop 1 The Science Communications Toolkit: Discussion of media processes and how to construct and disseminate science information to the media; practical exercise in press release and interviews preparation. Lecture 4 - Cultural Representation of Science: Science stereotypes in film and TV drama; use of science information for advertising; use of pop-culture science icons in media Lecture 5 – Science and Contentious Politics: Case study of media representation of controversial science issue

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Lectures 6-7 – Workshop 2: Popularity of Science Blogs and their endless variation; practical exercise in blog construction on group topics of choice Lecture 8 – Future Direction in Science Communication: Focus on expanding range of options for communicating science in the public sphere; post-graduate training and further skills development opportunities Voluntary Media Site Visit: Students are offered the opportunity to engage, as a voluntary supplement to their course work, in a specially organised media site visit. Depending on numbers interested in such an opportunity, options may include, for example, a visit to RTE live studio discussion programme, local radio station or ‘new media’ news organization. Assessments are designed to measure learning outcomes in respect of science communication processes and understanding of underlying concepts and ideas. Options include: (1) Constructing a press release (500 words; 40% mark) and related essay on communications plan (1000 words; 60% mark) on a recently published science paper of choice. (2) Writing a blog entry, with appropriate illustrations, on subject matter of choice( 500 words; 40% mark) and related essay on rationale for topic selection and further dissemination opportunities envisaged on media outlets ( 1,000 words; 60% mark). (3) Essay on cultural representation of science issue/ role of scientists in film or TV drama series of choice, including discussion of science communications concepts and ideas explored in lectures (1500 words). (4) Essay on case study of choice on science controversy and how science information is framed in media representation of the issues at stake. (1500 words) All assignments must include bibliography and in-text citations using Harvard Style Referencing. Management of Information Security (T. Dowling, Claude Shannon Institute) Computers and the internet are here to stay. Organizations are becoming more aware of the need to defend themselves in this environment. This process needs to be organized and managed (due to image and also legislation), taken away computer gurus and given to decision makers. This introduction is a survival guide for anyone who wishes to become more secure in this increasingly insecure world. The objectives of this course are to describe how to manage and defend information in an organisation. The focus is on managers not computer science and no coding will be expected for the course. The course falls into four main categories Core: The cryptographic techniques that can protect information. What are they and how can they be of use to you? Technical: The systems that can be used to protect information. If you ever wondered how safe your facebook or PC password is, how someone can see the web page you are looking at or how someone can recover deleted files then this will be of interest. Legal: What are your responsibilities when handling client information? What is legal and not legal when using security tools.. What is social engineering and why is it so successful? Management: What assets should a manager protect? How do you assess and manage risk? How do you develop and implement useful security policies? How to you minimize the effect of attacks? How do you recover from disasters? How do you develop multilevel security? How do you know when a techie is talking B%^&*£T?

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Personal Effectiveness (P. Hehir, Adult Education Consultant) This course will consider three broad areas - time management; presentation skills and interpersonal skills. People who are successful in their business, professional and private lives are usually very efficient at deciding which of the many tasks they have to do are the most important (and in doing them!). As part of this course we will look at ways to make best use of the time available so that routine tasks are accomplished quickly and sufficient time is left available for non-urgent but important tasks such as strategic planning, networking, learning new skills etc. Research scientists, as well as people working in business/industry/banking/journalism etc., are often required to make oral presentations on their work or to present technical information at meetings. So good communication skills are a very valuable asset. In this course we will try to get a better understanding of what it is that makes a good presenter and a good presentation and students will have the opportunity to practice their presentation skills. Lastly the course will consider the area of interpersonal skills - how to work effectively and harmoniously with other people - colleagues, team members, subordinates & superiors. Patenting Evaluation and Licensing of Biological Products (S.Doyle,N.Murphy) Following discovery of a new biological product or process in the laboratory, the first step to commercialization is to establish intellectual property rights by submitting a patent application. This involves a thorough search of existing patents in the area and close scrutiny of submitted material, including supporting experimental data, by national and international patent agencies. Once a patent has been issued the next step is to seek an industrial partner or raise the finance to scale up production and begin the process of evaluation prior to licensure. The transition of a biological product (e.g. vaccine or blood product) from laboratory to the market place requires evaluation in humans in clinical trials and approval by regulatory authorities. Biological products are evaluated in a sequence of clinical trials, which provide increasingly stringent tests on safety and efficacy. Successful completion of three phases of clinical trials is normally required prior to licensure, after which further observational studies are undertaken to monitor performance in the field. The World Health Organization (WHO) establishes minimal requirement for biological products, which form the basis for assuring acceptability of products globally. In general they specify the need for appropriate starting materials, including seed pools; strict adherence to established protocols; tests for purity, potency, and safety at specific steps during production; and the keeping of proper records. These requirements provide guidelines for those responsible for production and control procedures and national regulatory Authorities, such as the Federal Drug Administration (FDA) in the US or the Irish Medicines Board usually adopt them. Each product has to be approved by the local regulatory authority prior to marketing in that country. End User Computing The World Wide Web is the fastest growing communication medium on earth. This growth has created huge demand for new designers specialising in web design. In this course, you will be planning, designing and launching a complete website with creative interfaces, strong graphic images and functional website organisation. The course focuses on the development of your design skills and creativity rather than simply concentrating on software programming. The technical issues, of web design, will be sufficiently covered when and where they impact upon the design process. Topics covered include raw HTML coding, Design and Visual Logic Principles, Javascript programming, Website Navigation Structures Cascading Style Sheets. Students will be required to submit a compulsory project to build a complete website demonstrating their newly acquired web design skills. BI428 Laboratory Project 2 A 6 week independent laboratory research project. Students undertake a research project under the guidance of a supervisor. Students may be provided with a reading list but are expected to perform a literature search to familiarise themselves with the topic assigned. Over the period of the project students must become competent in the techniques and equipment relevant to the project. The module is assessed based on student performance in the lab (20%), a 10-minute oral presentation of research findings (15%), and on thesis write-up (65%).

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LECTURE MODULES (SEE http://www.nuim.ie/courses/?Target=CS&Mode=SEARCH FOR FULL MODULE DESCRIPTIONS) BI401 Environmental Field Studies (CM/CG) (not offered this year) Students who have satisfactorily participated in the 8-day out-of-term field course (The Fourth Year Biology Away-Week) will follow a course of prescribed reading on field course topics and global environmental change before taking the examination in this module. (There will be no class time outside of the field course). The required reading list will be announced after the completion of the field course. This will vary year-to-year, partly with the field course content. BI403 Plant Biotechnology (PD) In the first half of the course, the commercial use of tissue culture methods for rapid clonal population of crop plants is followed by a consideration of the potential for producing valuable chemicals in cell cultures, and the potential for mutation breeding at the cell level. The remainder of the course looks at the procedures for genetic transformation of crops, examines the relative merits of nuclear vs.plastid transformation, and reviews the progress in relation to a range of traits including herbicide, pest, stress and disease resistance, improved nutritional and storage quality of foods, and the production of valuable pharmaceuticals. The different methods for transforming crop plants are explained, including infection with modified pathogens such as Agrobacterium tumefaciens, and direct DNA delivery methods such as particle bombardment (the “gene gun”), and chemically or electrically induced uptake into protoplasts. The importance of regulation of gene activity, and stability of the transgene are considered, alongside ethical and safety concerns about exploiting the technology. Particular traits, which can be tackled by this approach, are evaluated as a number of case histories. Foremost among these are those which have already led to a marketed product, e.g. tomatoes with a long storage life, cotton resistant to boll weevil, and herbicide resistant soybean. A number of other characters are under development in this rapidly moving field, and new case histories will be introduced every year. BI405 Advanced Immunology (MB/MS) This module will provide the students with a detailed understanding of the immune system, including the signalling pathways and effector molecules that mediate immune effector functions. Topics covered include: Innate Immunity, Pattern recognition receptor signalling, the Major Histocompatibility complex, antigen processing and –presentation, T and B cell activation, Immune effector mechanisms, Cell migration and Inflammation, Transplantation immunology, the immune response to viruses and viral immune evasion. Assessment: Total marks 100%. 70% for two hour written examination at the end of the semester, 30% continuous assessment: Moodle based assessment 10%; MCQ 20%. Pass standard: 40% overall with minimum 30% in written exam and 40% in continuous assessment. BI406 Behavioural Ecology (CG) This module will enable students to develop an understanding of the adaptive value of behaviours to animals and how these behaviours evolve. The first part of the course deals with parasites and insects, covering topics such as the role of behaviour in parasite transmission; altered behaviour of parasitised animals (parasite manipulation and alternative explanations), and insect plant relationships (the importance of plant chemicals for insects, how insect feding preferences may change over evolutionary time or in the lifetime of an individual, and signalling by plants to attract predators and parasitoids). The secod part of the course deals has a boader focus and includes topics such as optimal foraging, sexual selection and parental behaviour. BI407 Tumour Biology (MB) The course is lecture based with prescribed additional reading and self directed private study. The course examines the question “What is Cancer?” To answer this, the following topics are explored: Control of the Cell division cycle; Cyclins and cyclin dependent kinases; Oncogenes, Tumour suppressor genes; DNA and RNA tumour viruses; Familial cancers; a detailed study of the role of the Rb gene; P53 as the guardian of the genome; Cell death; Positive and negative induction of apoptosis; the execution phase of apoptosis;

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beyond the molecular biology of cancer; how the body resists neoplasia; tumour progression; Angiogenesis, how diagnosis is made; the major therapeutic interventions (existing therapies and new therapies). Assessment: Total marks 100% 75% for two hour written examination at the end of the semester, 25% continuous assessment: Moodle based assessments (5%), 1 MCQ 20%. Pass standard: 40% overall with minimum 30% in written exam and 40% in continuous assessment. BI409 Organelle Genome Evolution (JN) The course is lecture based with prescribed additional reading and recommendations for self-directed study. Topics covered include: origin and function of organelles. Animal and plant mitochondrial genomes: structure, gene content, mode of evolution. The impact of mitochondrial DNA on tracing human evolution. The significance of mitochondrial DNA in human disease. The impact of lateral and horizontal gene transfer events on plant mitochondrial genome evolution. The plant plastid genome: structure, gene content, mode of evolution. The impact of gene transfer events on plastid genome evolution. Assessment: Total marks 100%: 80% for two hour written examination at the end of the semester, 20% for continuous assessment. Pass standard: 40% overall with minimum 30% in written exam and 40% in continuous assessment. BI410 Plant Developmental Biology (JN) The course is lecture based with prescribed additional reading and recommendations for self-directed study. Topics may vary from year to year but typically include: meristems and their importance for plant development, how meristem architecture is established and maintained; leaf development and pattern; changes in meristem identity; how flower pattern is established, how flower shape is established. An evolutionary approach to aspects of plant development is emphasized as much as possible. On successful completion of the module, students should be able to:

• Discuss current views on the molecular and genetic factors that regulate aspects of plant development e.g. meristem architecture, leaf development, meristem identity, flower development.

• Explain how developmental models established for model species can contribute to our understanding of how plant diversity has been generated.

• Evaluate recent primary literature relevant to enhancing their understanding of this subject. • Take personal responsibility for their learning.

Assessment: Total marks 100%: 80% for two hour written examination at the end of the semester, 20% for continuous assessment. Pass standard: 40% overall with minimum 30% in written exam and 40% in continuous assessment. BI411 Bioethics & Biotechnology (MD/SD) Module Content: How ethicists work; basic Western ethical ideas including classical and preference utilitarianism, Kant and deontological theory, rights approaches, virtue ethics, feminist thought, the void; application to issues in biology, biotechnology, medicine and environment. Current cases histories with stakeholder analyses: these may include genetic engineering, cloning, patenting of biological material. Detailed knowledge of relevant biotechnological science will form a central part of the bioethics component of this module. Fungi are amazing reservoirs of bioactive molecules, such as penicillin and statins, which are used to treat human diseases. Collectively, these molecules are known as natural products (NP) or secondary metabolites (SM) and are made by fungi, and bacteria, using processes known as non-ribosomal peptide synthesis or polyketide synthesis. This course will provide the student with a thorough understanding of these biosynthetic processes at the molecular and proteomic level. This topic is of special relevance as many microbial genome mining programmes are identifying ever more genes involved in NP biosynthesis. Consequently, research in this area is beginning to reveal a range of new molecules with biomedical potential. BI435 Molecular Ecology And Biogeography. (CM) Topics covered include: DNA polymorphism and molecular markers, particularly microsatellites and Amplified Fragment Length Polymorphisms (AFLPs); Sexual recombination, allele inheritance and natural selection; Statistical methods and bioinformatics tools for analyzing gene flow and inferring historical biogeographic relationships: Wright’s indices, pairwise dis/similarity and hierarchical clustering; Gene flow between crops and wild plants; The risks and hazards of gene-flow from GM crops; Plate-tectonics, climate

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cycles and glaciation; Historical biogeography and tracing migration using nuclear, mitochondrial and chloroplast DNA markers; The postglacial colonization of Europe by animals and plants: dispersal waves, hybridization zones and extinction events; Population structure of tropical rainforest plants; Conservation genetics of endangered mammals; The biogeographic impact of continent collisions – recent invasions in Tropical Central America and Southeast Asia. BI436 Medical Mycology (KK) Fungal pathogens are a major cause of superficial and systemic disease in immuncompromised (e.g. HIV+ patients) and immunodeficient (e.g. transplant recipients) patients and may contribute to over 4% of hospital-based deaths. The diagnosis and treatment of fungal infections can be difficult and there is a limited range of effective anti-fungal agents currently in use. This module will examine the molecular and cellular mechanisms employed by fungal pathogens to colonise and disseminate within the host, and to evade the immune response. Specific sections will examine the biology of the yeast Candida albicans and its ability to colonise mucosal surfaces. The role of toxins in the pathogenesis of Aspergillus fumigatus, a pulmonary pathogen, will be discussed. The emergence of ‘new’ fungal pathogens will be studied and the factors that have lead to their emergence will be characterized. Other areas to be studied include means of diagnosing fungal infections, treatment options, mode of action of antifungal agents, and the immune response to fungal infection. BI437 Neuromuscular Biology (KO). This advanced module focuses on the molecular and cellular mechanisms of normal skeletal muscle functions, as well as the molecular pathogenesis of selected neuromuscular disorders. Specific sections will be concerned with the biochemistry, physiology, cell biology and ultrastructure of skeletal muscle fibres, focusing on the molecular mechanisms underlying development, differentation, fibre transitons and metabolic adaptations to changed functional demands. The diagnosis of muscle diseases and pathobiochemical aspects of major neuromuscular pathologies will be examined, including a discussion of disorders related to myasthenia gravis, myotonia, motor neuron disease, malignant hyperthermia, x-linked inherited muscular dystrophy, disuse atrophy and sarcopenia of old age. Cell biological and biochemical research tools in the study of the molecular pathogenesis of genetic, autoimmune and pharmacogenetic muscle disorders are described. The potential sites for genetic and cell biological interventions at different stages of the neuromuscular disease process will be discussed. BI439 Antibiotics: Discovery, Modes of Action & Resistance (FW). The series of lectures would start with a short introduction into how the antibiotics that we use today were discovered and developed over the past century. This would incorporate the discovery of the first antibiotics all the way to the use of screening genomes for the ‘next big thing’, to explaining that most pharmaceutical companies have abandoned their R & D in this area. The next section would introduce the students to the different classes of antibiotics, how they differ and how they interact with the bacteria to inhibit their growth or kill them. This section would also give a brief introduction to the pharmacodynamics and pharmacokinetics that are necessary for the antibiotic to function in the body. The following lectures would be a discussion of the different mechanisms of resistance and emerging resistance problems and epidemics of resistance currently of concern. The techniques used to measure antibiotic susceptibility or resistance in hospital laboratories and the molecular methods that we can now use would be described to highlight how a combination of phenotypic and molecular tools can aid the understanding of resistance. There will also be a section on the origins of antibiotic resistance and how resistance mechanisms may have entered into the human food chain or other possible routes of transmission to human pathogens and the importance of human waste in the propagation of resistance in the water supply and environment. The module would encompass human, agricultural and environmental antibiotic use and resistance to discuss the problem from a One Health perspective. Lecture content (two lectures for each topic):

1. Antibiotic history and discovery from 20th to 21st century. 2. Antibiotic classes, mode of action and bacterial inhibition or killing. 3. Pharmacokinetics and pharmacodynamics of antibiotics. 4. Mechanisms of antibiotic resistance. 5. Emerging antibiotic resistance problems and epidemics worldwide. 6. Measuring antibiotic resistance in a hospital laboratory. 7. Molecular methods used to detect the emergence and spread of resistance. 8. Origins and transfer of antibiotic resistance prior to the pathogen.

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BI440 Control of Protein Activity (EG). Proteins are fundamental cellular components that regulate practically all processes in the cell. The control of their activity and abundance is essential for their physiological function and therefore needs to be tightly regulated. This course focuses on the cellular mechanisms leading to the control of protein activity and abundance and describes how changes in protein function affect biological processes (e.g. transcription, developmental programs, immunity…). Topics covered include: basic notions of protein structure; changes in protein activity through protein-protein interactions; control of protein activity by ligand binding; regulation of protein activity and localization by different types of covalent modifications; role of signaling cascades involving kinases; control of protein stability by the ubiquitin/proteasome system. These topics will be introduced and illustrated using examples from a wide range of research areas, as well as from different organisms such as bacteria, yeast, plants and animals. BI441 Fungal & Bacterial Secondary Metabolism (OB). Fungal and bacterial secondary metabolites have great potential due to their potent physiological influences on cellular functions such as antibiotics, antivirals, antifungals, antiapoptotics, cytotoxics, immunosuppressives, and deadly mycotoxins. Therefore, they are extremely important for medical, biotechnological and chemical applications. The focus of this advanced module is the fungal and bacterial secondary metabolites and the control of their production by genetic and epigenetic factors. Specific sections found in this module will be connected with chemical biology, genetics, epigenetics and fungal molecular biology. The major classes of microbial natural products and their biosynthetic pathways will be introduced. Potential impact of the bioactive metabolites in biotechnology, medicine and chemical biology will be discussed in depth. The term “gene clusters” will be introduced by analogy to prokaryotic operons. Control of gene clusters in fungi at the chromatin and epigenetic level will be examined by examples of histone modifications. Cellular signaling elements (MAPK, PKA, PKC) regulating the biosynthesis of fungal secondary metabolites will be analyzed. BI442 Human Genetics. (JMcI) Understanding the biological basis of being human involves, in part, an understanding of our genetics. In this module, we will study the history of the human genome, the structure of the human genome and variation in the human genome. We will study how a person’s genetic makeup has a huge impact on their current and future health. We will also look at the history of the human genome from the time of separation of the human lineage from the rest of the great apes until today. We will compare Human, Denisovan, Neanderthal and Chimpanzee genomes, analyse introgression of non-human DNA into the human lineage and we will study the effects of these introgressions. We will look at genetic haplotypes and gain an understanding of what these mean for human health and how they can be studied. We will discuss what, if anything is meant by “race” in the human genetic context and we will discuss human genetic variation more broadly. Finally, we will look at signatures of natural selection in the human genome. BI443 Clinical Proteomics: Discovery, Validation & Medical Utility (PDo). This advanced module focuses on the field of clinical proteomics, which can be divided into the analysis of body fluids and tissues. Soluble biomarkers will be discussed, which are found in biofluids including blood, urine and saliva, are considered indicator biomolecules that assist in detecting diseased conditions at an early stage, make discrimination between different diseases, and are useful for monitoring progression and response to specific therapeutic strategies. Established clinical biomarkers such as carcinoembryonic antigen (CEA) will be discussed and problems associated with their diagnostic utilities will be addressed. Expression of tissue-based proteins (up-regulation or down-regulation) in various pathological conditions will be explored with emphasis on metabolic and signalling pathways as potential therapeutic targets for treatment of disease. The relationship between biomarkers and therapeutic targets will be examined and the role of companion diagnostics in this area assessed. Underpinning clinical proteomics are the recent developments in quantitative mass-spectrometry, array-based high-throughput protein microarrays and novel fractionation technologies, which will be examined in detail. The role of other "omic" methodologies that are complementary and synergistic to clinical proteomics will be reviewed, specifically looking at metabolomics as an example. Assessment 80% 2hr written exam; 20% MCQ's (2 MCQ's at 10% each)

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DEPARTMENT OF BIOLOGY STAFF RESEARCH INTERESTS Title

Name & Qualifications

Key Words

Research Interests

Lecturer O. Bayram, MSc PhD

Secondary metabolism, Mycotoxins, Fungal development, Cell signaling, Epigenetics, Gene expression, Protein-protein interactions

Fungal secondary metabolites (SM), including food contaminating mycotoxins (e.g. aflatoxin, sterigmatocystin, fumonisins), antibiotics (e.g. penicillin, cephalosporin) and many other pharmaceuticals have great influence on human activities on earth. Secondary metabolite genes are mostly clustered in the subtelomeric regions of eukaryotic chromosomes. Many SM gene clusters are silenced by facultative heterochromatin and activated upon environmental signals, including light, pH, temperature, organismic interactions, and nutritional conditions during development of the fungus. Our laboratory focuses on understanding of the molecular control mechanisms of SM production and development in the model system Aspergillus nidulans as well as in Aspergillus flavus that produces aflatoxins. Fungal development and secondary metabolite production is coordinated by the regulatory protein complexes. In this context, we are interested in two questions: (I) How are the gene clusters turned on and off at the epigenetic level by the regulatory proteins? (II) What kind of signals are important for the activation of gene clusters? While approaching to these questions, we use genetical, biochemical, cell biological methods, including gene disruption, epitope tagging, overexpression, protein enrichment, protein-protein interactions.

Lecturer M.P. Butler BSc PhD

Innate & Adaptive Immunity, Toll-like Receptor Signalling, Neurodegenerative Disease, lymphomas

My research interest is probing at the molecular level key signaling events that ultimately lead to an effective immune response to pathogen. Specifically my research focuses on gaining insight into the complexity of Toll-like receptor (TLR) signaling, the activation of these receptors which is now recognized to be central to pathogen elimination. TLRs are expressed by cells from both the innate and adaptive immunity, including dendritic cells, macrophages and B cells. My research interests include defining the functional role of key TLR signalling molecules at the molecular level. Current research in the lab is addressing the role of signalling molecules in autoimmune diseases including Multiple Sclerosis and Rheumatoid Arthritis.

Lecturer J.C. Carolan B.A (Mod) PhD

Proteomics, Mass Spectrometry, Genomics, Molecular Biology

Research in the lab focuses on understanding interactions between organisms particularly parasites/ pests and their plant or animal hosts. We adopt an integrative approach, employing genomic, proteomic and transcriptomic methods. Numerous interactions have been studied including those between bacterial symbionts and insects, insects and plants, nematodes and their bumblebee hosts and fish and their ectoparasites. Currently the majority of the research conducted in the lab involves the economically important plant pest, the aphid and the key ecological pollinator, the bumblebee. Our laboratory is also involved in a number of insect genome and DNA Barcoding projects.

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Title Name & Qualifications

Key Words Research Interests

Professor P.J. Dix BSc PhD

Plant biotechnology and cell genetics

Plant Cell Genetics, Tissue Culture and Biotechnology, with a strong emphasis on the chloroplast. Current or recent studies have involved genetic engineering of plastids for pharmaceutical protein (eg. HIV and TB antigens) production, or modified starch, fatty acid and amino acid (cystine, methionine) metabolisism, improved abiotic stress tolerance through manipulating reactive oxygen species (ROS) scavenging systems, or fatty acid desaturation, and the role of peroxidases in plants. A recent interest is in the use of the chloroplast thylakoid as a production platform for human membrane proteins. A skilled tissue culture laboratory, we also seek to extend transformation (especially plastid transformation) technology to “difficult” species like perennial ryegrass and oilseed rape.

Lecturer P. Dowling BSc, PhD

Oncoproteomics, Biomarkers, Detection, Biofluids, Mass Spectrometry

Oncoproteomics-preparing for the challenges ahead: Oncoproteomics, the application of proteomics technologies in oncology, particularly their structures and functions, has evolved quiet considerably over the past decade or so. Modern proteomics workflows and platforms have considerably added to our ability to dig deeper into the proteome and have allowed researchers to analyse a new protein population previously found to be inaccessible. Proteomics is broadly broken down into two areas. The first area is focused on quantifying the expression levels of proteins between different groups, for instance looking for biomarkers from patients with a particular cancer that will allow for early detection/ monitoring/treatment of that disease. The second area focuses on functional proteomics, generating information on where the proteins are localized to, what other proteins they interact with and if they contain any post-translational modifications that are important to their function. Answers to these questions will culminate in the identification of many disease-related biomarkers and potential new drug targets.

Professor S. Doyle BSc PhD

Disease diagnosis, Aspergillus fumigatus, proteomics, nonribosomal peptide synthesis, oxidative stress, immunoassays and immunochemistry

The primary objective of our research is to apply functional genomic and proteomic strategies to the identification of novel protein function in the human pathogen. This strategy enables identification of new disease biomarkers and potential drug targets. Our extensive immunochemical and molecular expertise also facilitates the ongoing development of novel antibody and nucleic acid detection systems, which are of both biomedical and commercial importance.

Lecturer D.A. Fitzpatrick BSc PhD

Computational Biology, Genome evolution, Phylogenomics, Candida, Fungi, Metabolic pathways, Genome sequencing.

The research of this laboratory focuses on the evolution of unicellular microorganisms especially fungal species. We use comparative genomic techniques on completely sequenced Candida genomes to identify species-specific metabolic pathways that may be associated with virulence. The frequency of horizontal gene transfer and gene order within the Candida genus are also primary research objectives. We are also interested in sequencing and annotating medically/biotechnological important fungal strains.

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Title Name & Qualifications

Key Words Research Interests

Professor J. Findlay BSc PhD

Integral membrane proteins, structure and activity, G-protein coupled receptors, Retinol binding protein receptor, Membrane proteins and human dysfunction, Drug discovery, Proteomics

Our research activities centre around understanding the structure, organisation, interactions and mechanisms of action of integral membrane proteins with an emphasis on G-protein coupled receptors, the retinol binding protein receptor and ion channels. The experimental approaches used include protein expression, engineering, purification and biophysical and biochemical analysis. Tissue culture systems are used to examine integrated functional properties and signalling. Interaction studies make use of two-hybrid systems and proteomics. Drug discovery activities involve the screening of chemical libraries to identify small molecules which disrupt protein interactions or which can act as chemical chaperones.

Lecturer E. Graciet MSc PhD

Protein degradation, ubiquitin system, biochemistry, plant molecular biology, plant development, plant-pathogen interactions

Our research focuses on the role of protein degradation in the regulation of developmental processes, as well as in the response of plants to pathogens. For this work, we use the model plant Arabidopsis thaliana in combination with biochemical, molecular, genetic and genomics approaches. More specifically, we aim at understanding how the nature of the N-terminal residue of proteins affects their stability and participates to the regulation of plant-pathogen interactions. Another aspect of the work aims at gaining further insights into the role of protein degradation in the regulation of transcription and developmental processes in plants.

Senior Lecturer

C.T. Griffin BSc PhD

Behaviour, Physiology, biological pest control, nematode, insect, climate change

Biological pest control in horticulture, forestry and agriculture, particularly using insect parasitic nematodes. Interactions between biological pest control agents and other organisms, and between different classes of biocontrol agent. Behaviour and physiology of parasitic nematodes. Insect behaviour. Biogeography and biodiversity of invertebrates. Effects of temperature on development in relation to climate change.

Senior Lecturer

G. Jones BSc PhD

Yeast, amyloid, prions, chaperones, protein folding, molecular biology, Aspergillus fumigatus, oxidative stress, adaptive response, alkylating agents.

Cellular factors that affect propagation and stability of prions in Saccharomyces cerevisiae, focusing mainly on the contributions of the protein chaperone Hsp70. Use of chaperone mutants to dissect differences between prion-related and essential cellular functions. Oxidative stress and alkylation DNA damage repair in opportunistic human pathogen A. fumigatus.

Senior Lecturer

K.A. Kavanagh BSc PhD

Aspergillus, Candida, Fungi, Innate immunology, Insect, Medical mycology, metal-cell interactions, Proteomics

Interactions of pathogenic fungi with host tissue. Epidemiology of pathogenic yeasts. Role of Demodex mites in the induction and persistence of Rosacea. Insect immune response to pathogenic fungi. Investigation of similarities between innate immune response of mammals and insect immune response.

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Title Name & Qualifications

Key Words Research Interests

Lecturer (contract)

G. Kinsella BA(Mod) PhD

G-protein coupled receptors and human dysfunction, Drug discovery, Chemical Biology, Computational biology; Protein modelling;

Research activities focus on protein structure prediction and the early stages of drug development for diseases encompassing Type II Diabetes, genetically pre-disposed obesity, auto-immune conditions and Parkinson’s Disease. An emphasis is placed on G-protein coupled receptors and experimental approaches used include protein expression and purification; binding and functional assays; computational modelling techniques. Studies involve the screening of chemical libraries to identify small molecules which disrupt protein interactions or which can act as pharmacological chaperones.

Professor J.O. McInerney BSc PhD DSc

Genome evolution, bioinformatics, molecular phylogeny reconstruction

Studies of adaptive evolution in protein-coding genes, synonymous codon usage variation and the application of this information to gene identification. Analysis of genome evolution, strain-specific sequence differences and the evolution of mutational biases in completed genomes. Development of bioinformatic software for the analysis of large genomic datasets. Phylogenetic analysis of Bacteria, Archaea, Eukarya and Multi-gene families.

Lecturer C. Meade BSc PhD

Ecology, Molecular Ecology, population genetics and systematics of plants

The natural history, biogeography and population genetics of Alpine plants in Ireland and Europe. Gene-flow in wild relatives of Irish arable crops. The ecological impact of conventional and genetically modified (GM) crops. Systematics and taxonomy of the Custard Apple family (Annonaceae). Flora of Ireland and tropical Southeast Asia.

Lecturer S. Miggin MSc PhD

Innate immunity, toll-like receptors, cell signaling, inflammation, molecular biology, Virus, antiviral immunity

Characterisation of the innate immune response via Toll-like receptors. Differential roles of the TLR adaptor molecules in innate immune signaling pathways. Anti-viral signaling. Identification of novel signaling pathways using proteomics. Interest in chronic inflammatory conditions including Rheumatoid Arthritis, Osteoarthritis and Type-2-Diabetes.

Professor P. Moynagh BA(mod) PhD

Molecular Immunology, Inflammation, Signal Transduction, Neuroimmunology

Signal transduction in inflammation. Regulation of gene expression. Identification of novel anti-inflammatory agents. Interactions between the immune and nervous systems (Neuroimmunology).

Lecturer N. Murphy, BA(mod) PhD

African trypanosomes, differentiation, cell signaling, vesicular trafficking, disease resistance, repetitive sequences.

Molecular mechanisms controlling population size and differentiation status in African trypanosomes; compartmentalization of proteins in vesicles and their transport in cells; differential gene expression during differentiaiton; mechanisms of resistance to trypanosomiasis in African wildlife species; host-parasite interactions; development of new therapeutics; minisatellite sequences and retrotransposons - their origins and evolution.

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Title Name & Qualifications

Key Words Research Interests

Lecturer

J.M. Nugent MSc PhD

Plant molecular, developmental biology

Basic research in the Nugent lab focuses on mechanisms of plant development and the evolution of plant morphology. In particular we are interested in understanding the evolution of novel developmental roles for flower shape genes in Plantago lanceolata. Applied research in the lab is focused on plant plastid transformation for plant-based therapeutic protein production (e.g. vaccines) using tobacco as a model system.

Professor K. Ohlendieck DipBiol PhD DSc

Muscle biology, biochemistry, proteomics

Biochemical and proteomic analysis of skeletal muscle transitions, degeneration and and aging. Molecular pathogenesis of muscular dystrophy and related neuromuscular disorders.

Senior Lecturer

S. O'Dea BSc PhD

Epithelial immunology, lung disease

Understanding mechanisms of lung regeneration in health and disease. Study of lung stem cells. Identification of key signals and pathways that regulate lung cell proliferation and function. Development of novel therapeutic strategies, including gene therapy and differentiation therapy, for treatment of lung disease.

Lecturer M. Schroeder BSc PhD

Pattern recognition receptor signaling, Host-pathogen interactions, type I interferons

Research in the lab centers on the recognition of pathogens, in particular viruses, by pattern recognition receptors. A particular focus is on the ensuing signaling pathways leading to type I interferon production, and viral evasion strategies targeting these signaling pathways. The aim is to define these signaling pathways in more detail and to identify novel regulatory components using proteomics techniques.

Lecturer F. Walsh BSc PhD

Antibiotic resistance, microbiomes, infectious diseases, bacteriology, metagenomics

Understanding antibiotic resistance from source to sink. The world of antibiotic resistance is not confined to human pathogens. The research of this laboratory investigates different microbiomes (animal and environmental) as reservoirs of current and novel antibiotic resistance mechanisms and traces these resistance mechanisms through the food chain or other pathways into the human microbiome. The goals include identifying reservoirs of current and future antibiotic resistance, understanding how these are selected and spread from outside the patient/hospital to within human pathogens and to provide answers to the questions: what and where are the origins of antibiotic resistances and how do they get from there to humans? Techniques include microbiology, molecular biology, metagenomics and functional metagenomics.

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WRITING A 4th YEAR DISSERTATION: ESSENTIAL INFORMATION Dissertation Writing: Your Responsibilities For all students writing an essay or dissertation the volume of material available on the internet/ digital media is almost limitless. With this abundance of source material it is essential that you, the student, prepare your work with due care – especially in ensuring that what you write is your own work and not a copy of someone else’s work (plagiarism). To assist with this task we provide you with two important aids: (i) an online self-assessment tool on moodle for checking the originality of your work, called ‘Turnitin’ (see below); and (ii) a clear guide to what is, and is not, acceptable in terms of originality: the NUIM Biology Plagiarism Policy (see below). Please read both very carefully as it is mandatory to follow the guidelines contained therein.

Essay Preparation and Submission – the Turnitin facility All Biology dissertations at NUIM must now be submitted to the online Turnitin Facility on moodle. This portal allows you and your supervisor to confirm the originality of your written work. Turnitin compares your text with pre-existing texts (from a digital database of all published scientific research on the web) and highlights sections where you have used wordings and paragraphs that have been written before by other authors. When you receive this information you are able to make appropriate changes to ensure your written work is actually your own. Thus you can eliminate any accidentally plagiarised text, and ensure you are being understood correctly.

Please note • The onus is on you, the student, to validate your work using Turnitin.

• You should only submit your completed essay when you have checked it on Turnitin and are satisfied that your written work is truly your own and not a copy of something else

• Submitted essays that are deemed to contain copying/ plagiarism will be dealt with according to

the departmental policy on plagiarism (see page 24)

Using Turnitin on Moodle There are two steps to using Turnitin on Moodle. Once you have signed up for your Literature Review/ Laboratory Project Module, you will be able to access the Turnitin portal via the appropriate module page on Moodle. Turnitin self-check will be available on your dissertation module moodle page throughout semester I, Turnitin final submission will be available from two weeks before the final submission date.

Step 1. During essay preparation – use Turnitin self-check

Submit your draft essay to Turnitin self-check on Moodle to get an originality report (see description on next page). Ammend your text as appropriate. Step 2. When your essay is complete - use Turnitin final submission

(i) print out the final document as per the guidelines for the written text (see detailed description of the 4th year dissertation relevant to you) and submit the hard copy. (ii) submit an identical copy to Turnitin final submission on Moodle as a final text. The originality report for this submitted copy will only be available to your essay supervisor. At all times during the preparation of your dissertation you can access ‘Moodle and Turnitin Help for Students’ on the ‘My Courses’ bar at https://moodle.nuim.ie/2012/

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How to submit an essay/assignment to Turnitin

1. First, login to Moodle, and go to the module for which you have an essay/other assignment to hand in. 2. On the module homepage, you should see the link for submission of your work. If so, click this link. 3. If not, look at the Activities box on the left hand side of the screen, and you should see a link Turnitin

Assignments. Click on this link to locate the submission link you will need. 4. You should then see a screen like this one, giving the Summary details about the assignment:

5. You cannot submit your work on this page, so instead click on My Submissions – circled in the

image below:

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6. You should now see this screen, and you need to complete the empty fields (spaces) shown:

7. Once you have made your submission, you will be returned to the My Submissions screen, this time

showing that you have one item submitted, and that the Originality Report is Pending, shown circled in the screen shot below:

8. You may also have the opportunity to submit the work again, if your Lecturer has left the submissions open until the assignment deadline. The screenshot above shows this. But if you do not see the same settings, there is nothing to worry about – it is simply that your Lecturer has chosen to set up Turnitin for one submission only.

9. You will also receive an email to your NUI Maynooth email address confirming receipt of your work by Turnitin.

1. Give your submission a name. Your department may have told you a format for this.

3. Click/check the copyright box to confirm you agree to Turnitin’s terms of use.

4. Finally, click on Add Submission to submit/hand in your essay or assignment.

2. Browse to locate your file on your computer or memory

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10. If you return to the course homepage, and click on the Turnitin Assignment link again a little while later, you will be able to go to My Submissions to see the Originality Report. The screen will have changed and will show a result instead of the Pending message. This is shown below:

11. In the example shown on the previous page, we deliberately used a text that would have a high percentage result – this is just to show you how the results look. Most results will be for a much smaller percentage, and the colour code used will reflect this – it will be green, blue or yellow. Click on the colour code/percentage to see the full Originality Report from Turnitin.

12. The Report will open in a separate screen. Below, you can see a different example, this time the result

was 11% similarity to the Turnitin database.

13. The report can be read as follows: • Your essay is shown with different pieces of text highlighted in different colours on the left pane of

the screen. • The numbered list on the right of the screen shows where matching text might have come from,

and the colours are the same as those used on your work. • For example, Turnitin has highlighted a line in purple on the left, and given it number 11. On the

right, you can see that number 11 is at the bottom of the list, in the Match Overview. It links to portal-live.solent.ac.uk, where Turnitin found a match to this text.

• In this case, the matched text is unlikely to have been plagiarised. It talks about a well-known theory, and makes reference to the work of two writers.

14. If you are submitting coursework for a particular module, the Originality Report will also be available to your Lecturer. However, if you receive a 100% result because you already submitted a draft of your work to Turnitin, it is important to tell your Lecturer. He/she can exclude the drafts in order to produce a true result for your work. If you encounter problems using Turnitin, you can contact Moodle Support for further assistance using the email address moodlesupport@nuim.ie.

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Department of Biology Policy on Plagiarism

Definition of Plagiarism Plagiarism is the passing off of another person’s work as your own. It includes copying without acknowledgement from a published source (print or electronic), or from unpublished sources (e.g. another student’s essay or notes). Plagiarism occurs when material is copied word for word, but not only in that circumstance. Plagiarism also occurs when the substance or argument of a text is copied even with some verbal alterations, such as in paraphrase or translation, without acknowledgement. Plagiarism includes unacknowledged use of material from books or periodicals, from the internet, from grind tutors, or from other students, without full acknowledgement of the sources.

The policies of the University apply within the Department of Biology, as contained within the University Calendar (pp.90-91), informed by the following view: “Plagiarism is a form of academic dishonesty and will be treated with the utmost seriousness wherever discovered.” (NUI Maynooth, Calendar 2009-10, p.91). This policy will be implemented in the following manner: 1. Dealing with Suspected Cases of Plagiarism: Assignment markers will refer suspected cases of plagiarism to the Year Head (or in the case of practical assignments, in first instance to the Academic in charge of practical module); “Any student submitting written work for continuous assessment can be asked by the marker or the department to take a further test. This may take the form of an oral examination on the assignment in question and related issues, or the writing of a test paper in controlled conditions. Requiring a student to take such a test does not necessarily imply that plagiarism is suspected.” (NUI Maynooth, Calendar 2009-10, p.91). 2. Dealing with Proven Cases of Plagiarism: If there is evidence of plagiarism, the matter will be turned over to the Year Head, who will determine the disciplinary consequences following the guidelines outlined below. In each case the student may be invited to explain in person to the Module coordinator and/ or Year Head the origin of the material contained in the piece in question.

2a. Minor Plagiarism: In cases of minor plagiarism, the following University statues will apply: “In instances where an element forming part of an assignment (from a phrase or sentence up to a paragraph or two) is found to be plagiarised, marks will be deducted for that assignment, there will be no possibility of submitting a ‘make-up’ assignment, and previous and subsequent work submitted in connection with the course may be subject to particular scrutiny. While the amount of marks deducted will be proportionate to the extent of the plagiarised material, the deduction may be severe.” (NUI Maynooth, Calendar 2009-10, p.91). 2b. Major Plagiarism: In cases of major plagiarism, the following University statues will apply: “In instances where a significant part or all of an assignment is found to be plagiarised, zero marks may be awarded for that assignment, there may be no possibility of submitting a “make-up” assignment, and previous and subsequent work submitted in connection with the course may be subject to particular scrutiny. In serious cases the plagiarism will be reported to the Supervisor of Examinations and the Committee of Discipline.” (NUI Maynooth, Calendar 2009-10, p.91) In those instances in which a module contains both continuous assessment and a final examination, and the failed continuous assessment component constitutes a significant percentage of the overall mark, students may find that they are not advised to write the relevant Winter or Summer Examinations for that module, as any mark achieved on these exams would necessarily have to be foregone in order for the candidate to register for the Autumn Examination in the relevant module. Students will be permitted to repeat all module components in the Autumn examination period.

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2c. Postgraduate Students: Instances of postgraduate plagiarism will be referred directly to the project supervisor or member of faculty responsible for the relevant postgraduate programme. “Plagiarism in postgraduate or research material is a particularly serious offence. Penalties imposed may involve suspension or expulsion from the course and from the University, in addition to the deduction of marks. Early offenders may be required to attend educative classes.” (NUI Maynooth, Calendar 2009-10, p.91).

3. Reporting: All cases of plagiarism will be reported by the Course Leader to the Head of Department. 4. Recording: All cases of plagiarism will be recorded by the Course Leader on the student’s permanent record card. All members of the Department providing a reference for a student may be obliged to mention an instance of major plagiarism, or two or more instances of minor plagiarism, when providing a reference for the student. 5. Appeals Procedure: All students have a right of appeal to the Head of Department. Students may only appeal on the grounds that the allegation of plagiarism is unfounded, and appeals must be made in writing in the first instance. Medical, personal, or other circumstances do not constitute a defence in cases of plagiarism. In the case of an unsuccessful appeal of the Head of Department, the student has the right to appeal to the Examinations Appeal Board. Plagiarism & the 4th year research thesis

Your thesis will inevitably draw on the work of others. The effective use and evaluation of existing material are among the skills that you are expected to develop. In all cases, when you build on the work of others you must cite the source of the material (an idea or opinion, a quote, data, diagrams etc). It must be acknowledged in a standard form of referencing. Details of the referencing format are given later on, but here are some practical tips to help you:

• You must present a work of scholarship in your own words and diagrams. • If you state a fact or rely on data from another source, you must acknowledge that source in the

form of a citation in the text. Citations must be listed in a bibliography/reference list. • If you use a diagram or figure from another person’s work, you must cite this in the legend and the

bibliography. • If the exact words used by someone else are important to your argument, then you may use these

within quotation marks and must cite the source. • If you have paraphrased someone else’s argument, data or conclusions, then this must be

acknowledged by citation. • Paraphrasing that dominates your work, does not include your own intellectual input or is simply a

rewrite of another person’s effort is still plagiarism, even if you do use citations. You must provide an intellectual input that adds to the existing material. This point is particularly relevant to students wishing to follow postgraduate study. In summary, your work will rely on the work of others. You should understand that material and

think about it. Use your own words to describe the essential point that is relevant to your thesis, and cite your source in the text as well as the reference/bibliography section. If you are worried about what constitutes plagiarism, contact your project supervisor. When handing in your literature/laboratory project you will be required to sign a declaration stating that you have read and understand the department's Policy on Plagiarism, and that your project is your own work. Please see the sample declaration form on page 47, which will be available for you to download from the departmental website at the following address: https://www.maynoothuniversity.ie/biology/undergraduate/forms-coversheets-and-deadlinesThis must be downloaded, signed and placed into your project, directly after your project title page

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GUIDELINES FOR BI424 LITERATURE PROJECT The literature project is aimed at researching the literature in the area and discussing the topic under consideration, including reference to opposing views on the subject where appropriate. The thesis should not be simply a reproduction of information from review articles or book chapters, but should include your interpretation of the subject, organised to develop the reader’s understanding as you think appropriate and written with authority, by one who understands the evidence and issues. The thesis should be broken into sections which should have a General Introduction, Discussion (should be broken into subsections with appropriate subheadings for sections dealing with different topics), Conclusions and References. The Conclusions should draw together the discussion points made during the discussion. At the end of the assignment you should understand your topic fully and be capable of presenting the findings and defending your conclusions at a seminar on your thesis topic.

Understand the major points you wish to make order them logically and build towards each with evidence. Do not include empty material that is not helpful to the reader or part of your case building, no matter how impressive it looks.

THE LITERATURE PROJECT IS NOT TO EXCEED (3000 WORDS) INCLUDING REFERENCES, BUT NOT THE LIST OF REFERENCES AT THE END. Quotations. In general, use direct quotations only where the wording matters to your case, and always credit the author e.g. “Rowan (1932) described the elytra ‘in all cases strongly grooved and colourful’ but later work (Dods, 1946; Frish, 1983) suggests that the grooving is quite variable and in some cases the elytra are more dull than Rowan thought”. It is not acceptable to transcribe large tracts of text from reviews or journal articles. Write your literature survey in your own words. Reference Material. Familiarize yourself with the background literature relating to the project. You are expected to do a literature search using computers linked to the Internet, either in the Library or in certain cases in your supervisor’s laboratory. You should discuss the outcome of your literature review with your supervisor approximately 3 weeks after beginning the project. Your supervisor may provide you with additional reprints which may not be available in the library. However it is your task to research the literature and ask for specific references if available. Reference material that is not available from the library or from your supervisor can be obtained on inter-library loan through the Library. However there can be long delays in receiving these, so students are advised to make these requests early in the first term. Referencing. It must be possible to identify the source of all material which is not your own. • References are easier to revise and more informative if given in the form:

According to Jennings (1978) ----- Jennings (1978) stated that -----

• All references should be given fully, and in alphabetical order, in the reference list at the end of the literature survey. Follow the format described for the laboratory project thesis.

Diagrams. Should be made whenever possible. Where based in published illustrations/data these should be re-drawn by you to demonstrate the point you wish to make. The legend should contain a credit e.g. “Re-drawn from Stairs (1989)”, and of course Stairs will appear in the reference list at the end. If, for instance, your point concerns a few chemical groupings on a large molecule, you might consider using lines to pick out all or part of the overall shape of the molecule and draw in more fully the few groups that are essential to your discourse. Material beyond your competence. Where your presentation carries you into e.g. advanced mathematics or chemistry that you cannot reasonably be expected to master; deal only with the conclusions as set out by the author.

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Complex original ideas. Some topics allow you to develop ideas of your own. You may like to discuss them with your Supervisor before incorporating them in your essay. Typing. It is preferable to use a word-processing package so that you can easily rearrange sections. You should run a spell-checker. Recommended font is Times New Roman (size 12). The thesis should be double-spaced. Reprints. Where you order literature (on Inter Library Loan) that is not available at Maynooth, you should show (returnable book) or give a copy of it (paper) to your Supervisor. This will aid appreciation of how well you have done and contribute to the reference collections of the laboratories. Brief guide to literature searching Before beginning your literature review (or a review of literature associated with your lab project) you will be given clear guidance on how to proceed with literature searches for peer-reviewed material and so forth on the internet. Peer-reviewed material means material has been reviewed by scientists prior to publication in scientific journals. Indeed, one of the difficulties you may initially face when compiling reading material is ascertaining which material is peer-reviewed, and so, worthy for consultation as reading material for your literature review. You must exercise great caution in using reference material which is not found in peer-reviewed journals as this material can be subjective in nature and, on occasion, blatantly biased to promote a particular viewpoint! Listed below is a selection of websites which enable you to access peer reviewed journals, which can be searched using keywords or author names to help you begin the task of getting relevant and useful reading material. You should note that scientific articles are often presented as follows: Abstract, Introduction, Materials&Methods, Results and Discussion. Some of the databases/search engines will enable you to access the entire article while others will only give access to abstracts and you may then have to get the entire article either in library (paper or internet access to journals) or by inter-library loan. Literature search engines include Web of science (most complete): http://portal01.isiknowledge.com/ ScienceDirect: http://www.sciencedirect.com PubMed: http://www.ncbi.nlm.nih.gov/pubmed/ These (and others) can also be accessed by following the links on the library web page >databases and e-books…>..by subject.. >Biology You will be given further direction accessing literature by your project supervisor and in the talk on Tuesday 30 September at 1pm in JH2 on Accessing Information. The material presented above is for quick reference only. See page 24 for information regarding plagiarism.

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BI424 Literature Projects Antimicrobial Resistance and Microbiomes (Dr. Fiona Walsh) Antibiotic resistance as an emerging pollutant Behavioural Ecology & Biocontrol Laboratory (Dr. Christine Griffin) The importance of bacterial symbionts for insects Food caching in corvids Bioinformatics Laboratory (Prof. James McInerney) Mathematical modelling of infectious disease dynamics (Biomedical) Biotechnology Laboratory (Prof. Sean Doyle) Enzyme-mediated lignocellulose conversion to bioethanol Clinical Proteomics Laboratory (Dr. Paul Dowling) The role of Antibody-drug conjugates as a targeted therapy for cancer (Biomedical) The tumour microenvironment and cancer progression (Biomedical) Cell Signalling Laboratory (Dr. Marion Butler) Th17 cells and autoimmune disease Apoptosis and Cancer Fungal Genetics and Secondary Metabolism Laboratory (Dr. Ozgur Bayram) The mycotoxins: growing health hazard Genome Evolution Laboratory (Dr. David Fitzpatrick) Evolution of mating type loci in fungi Host-Pathogen Interaction Laboratory (Dr. Martina Schroeder) Sex differences in autoimmune disorders Immune Signalling Laboratory (Dr Sinéad M Miggin) Epstein Barr virus and innate immunity Medical Mycology Laboratory (Dr. Kevin Kavanagh) The insect immune response to microbial pathogens Membrane Biology Laboratory (Dr. Gemma Kinsella) GPR55 - a novel target for type 2 diabetes? neuronal Nitric Oxide Synthase (nNOS) - a target for neurodegenerative diseases? Molecular Ecology Laboratory (Dr. Conor Meade) Extra-terrestrial complex organic molecules Add maths and stir: Chaos, fractals and the evolution of organic life Molecular Immunology Laboratory (Prof. Paul Moynagh) The importance of ubiquitination in innate immunity Molecular Parasitology Laboratory (Dr. Noel Murphy) Transgenerational inheritance The origin and evolution of introns

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Muscle Biology Laboratory (Prof. Kay Ohlendieck) The human proteome project: Recent progress Advances in biological mass spectrometry Pathogen Proteomics Laboratory (Dr. James Carolan) Plant defence mechanisms against insects Plant Biochemical Laboratory (Dr. Emmanuelle Graciet) Glucosinolates: biosynthesis and functions in plants Plant Cell Biology Laboratory (Dr. Phil Dix) Gravity perception in plant roots: the latest insights Mutants affecting auxin response in plants Plant Molecular Biology (Dr. Jackie Nugent) The chloroplast genome in parasitic plants Plant stem cells Yeast Genetics Laboratory (Dr. Gary Jones) Prions – Are they all bad news?

GUIDELINES FOR BI428 LABORATORY PROJECT Your project will provide you with an opportunity to get involved in real research, usually on some aspect of the research already ongoing in your supervisor’s laboratory. Your project also gives the examiners and future employers an indication of your ability and your initiative. But the other parts of your course are also very important so it is essential to remember this and not to spend most of your time doing project associated work. A. Choosing your project. Try to choose a laboratory which interests you and which suits your scientific

background and your general lab skills. B. Project organisation. Initial steps. • Familiarize yourself with the background literature relating to the project. Your supervisor may

provide you with a reading list or key review articles papers directly relevant to the project. However you are expected to do a literature searches using computers linked to the Internet, either in the Library or in certain cases in your supervisor’s laboratory.

• Become familiar with the equipment and experimental techniques that you will require for your project. It is essential that you become competent in all the research techniques to be used before you start proper experiments and make sure you understand the basis of the techniques.

C. Project organization. Lab work. • Plan experiments carefully following discussion with your supervisor. Make sure suitable controls are

included and sufficient replicates of the experiments are carried out. • Use booking sheets for the equipment in high demand. • Check time scale of experiments and make sure it fits in with your lecture schedule and the permitted

working hours in the laboratory. • Make note of all the experimental procedure, including calculations for making up solutions etc. • Never rely on your memory. Write your results into your notebook immediately; preferably a

hardbound notebook not on pieces of paper.

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• Analyse your results as you get them. Draw graphs, etc. now while the material is fresh in your mind and while you are not under too much pressure.

• Record the results from all experiments, even ones which did not appear to work. • See all experiments through to the end. • Show courtesy to other workers in your laboratory. Keep your work area clean and tidy; wash

glassware and return reagents to shelves, fridges or freezers immediately after use; respect other people’s laboratory property: glassware, stock solutions, media, etc.

D. Writing up your results. No matter how carefully you conducted and carried out your experiments and

how excellent your results are, your overall mark can be pulled down considerably by a poor write-up. Therefore, it is important to leave sufficient time for writing up the thesis.

Typing. It is preferable to use a word-processing package so that you can easily rearrange sections. You should run a spell-checker. Recommended font is Times New Roman (size 12). The thesis should be double-spaced. A research thesis should be no more than 3000 words of text for double honours students (including references in text, but NOT including the list of references at the end, tables, figures, table of contents, or abstract); in addition, the whole thesis should not exceed 30 pages. The thesis should be organised under the following sections:- Title page. Brief accurate title with scientific names of any organisms used Statement that the thesis is submitted in fulfillment of the requirements for the degree. Your name Address of the Department Date Acknowledgments page. Optional Declaration. Certification of originality. Table of Contents. All pages should be numbered and the Table of contents should have a list of all sections and subsections. You should also use a separate numbering system to denote each section and subsection as follows: 1. Introduction; 2. Materials and Methods 3. Results; 4. Discussion and 5. References. e.g. the first subsection within Materials and Methods would be numbered 2.1, with the appropriate page number in the right hand side. Abstract. This should be a maximum of one page and should briefly summarize the aims of the project, how the problem was tackled and the key findings from the research. This should have the basic content of the thesis without extensive experimental details. Introduction. This section covers the scientific background to your project and the rationale for the study. The Introduction should supply sufficient background information from your literature survey to allow the reader to understand and evaluate the findings of the study. Materials and Methods. A clear and concise description of the techniques you used in the project. This should include sufficient information to allow the experiments to be repeated.

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Results. The data is presented in this section in the form of Figures (graphs, histograms), Tables and drawings or photographs as appropriate, and a suitable text which should summarize the significant experimental observations and briefly explain the findings; reserve extensive interpretation of the results for the Discussion section. Each results sub-section should begin with text giving a brief description of the rationale and design of the experiments (not the methods as these will have already been covered under Materials and Methods) followed by details of the findings, referring to all the Figures and Tables. Figures must have a legend underneath with the Figure number and title; followed by a short description of the Figure to make the information displayed understandable without frequent reference to the text. Tables must have the Table number and title above the Table with the Legend underneath. Discussion. The Discussion should provide an explanation and interpretation of your results and the presentation of evidence (from your own project work and from the literature) which justify the explanations proposed. The significance of your findings should be discussed in the context of published work and should not contain extensive repetition of the Results section or reiteration of the Introduction. References. The reference section must contain all relevant sources (original articles from scientific journals, review articles and chapters from books). You must always reference original articles for techniques or statements of fact; reference to general textbooks and reviews can only be used when you are summarizing points in the Introduction and Discussion. All listed references must be cited in the text in parentheses after the relevant section of text. You should give the first name of the first Author and et al if more than two authors and the one or two first name(s) if only one or two authors, followed by the year of publication (e.g. Smith et al., 1995 or Smith & Jones, 1995). In the reference section arrange the citations in alphabetical order by first author and in chronological order if there are more than one article by an identical list of authors. The authors name(s) should be followed by initials (not first names in full), followed by the year of publication, the title of the article, the name of the Journal, the volume and the inclusive page numbers of the articles. You must give the complete title of the article or book chapter, but you can use standard abbreviated titles of journals. Examples below; note the reference to a book or book chapter differs in format from the reference to a periodical.

Mahon, B.P., Katrak, K. and Mills, K.H.G. 1992. Poliovirus-specific murine CD4+ T cell clones recognise serotype specific epitopes on VP1 and VP3 and cross reactive epitopes on VP4. J. Virol. 66, 1479-1481. Mills, K.H.G. 1996. Induction and detection of T cell responses. In: Vaccine Protocols. Methods in Molecular Biology. (Eds. Robinson, A., Farrar, G.H. and Wiblin, C.N.) Humana Press Inc., NJ, USA. pp. 197-221. Roughgarden, J. 1979. Theory of Population Genetics and Evolutionary Ecology: An Introduction. Macmillan, New York. At the start of your project you should devise a filing system (cards, files of reprints or computer programme) for references which will make it easy for you to collate them in alphabetical order in the final reference section. Appendix Tables These are optional and can be used to tabulate raw data which was used to generate the contents of Figures and Tables of analysed data in the results section. Fourth year projects vary greatly in the degree of difficulty of the techniques and the ease with which data are obtained. This is taken into consideration by the examiners. So there is no need to be anxious and upset if some of your colleagues are amassing large quantities of data and despite your best efforts,

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your project appears to be moving very slowly. Keep in contact with your supervisor and if your supervisor is satisfied with your rate of progress, then you shouldn’t worry too much about the progress of your colleagues’ research. Most people get great satisfaction from doing project work. It is our hope in the Biology Department that you too will enjoy the intellectual challenge of your project and that it will give you some valuable first hand experience of the procedures used in original research. Chapter 8 in Wedgewood, M.E. “Tackling Biology Projects”, Macmillan (1987) gives some very valuable advice on the writing of a project report.

BI428 Laboratory Projects

Antimicrobial Resistance and Microbiome Laboratory (Dr. Fiona Walsh) Back to the roots of antibiotic discovery Soil microorganisms naturally produce most antibiotics currently used as medicines. Selman Waksman is one of the founding fathers of antibiotic discovery. His method of antibiotic discovery involved screening soil for bacteria capable of producing antibiotic compounds. This project will analyse soil in the same manner as Selman Waksman but with an added dimension. The soils will be analysed under a wide variety of growth conditions, including antibiotic selective pressure. The aims of this project are to identify bacteria capable of producing anti-bacterial compounds and then the compounds with anti-bacterial activities themselves. Once identified the compounds will be analysed further using protein analysis. How do bacteria react to very low concentrations of antibiotics? The natural concentration of antibiotics in soil is much lower than that used to treat infections. There have also been theories to suggest that natural antibiotics act as signalling molecules. This project will investigate the sub-lethal effects of antibiotics on bacteria and bacterial population dynamics and on the emergence of antibiotic resistant bacteria. Bioinformatics Laboratory (Prof. James McInerney) Comparison of two different methods of finding gene fusions In this study we will compare two different methods of identifying gene fusions in sequence similarity networks. These methods apply network mathematics in an effort to identify specific nodes that might indicate gene fusion. We will compare the two methods on a number of datasets and try to assess their efficiency (time and computational resources) and accuracy. We will also analyse the genes that are identified as fusions. Biotechnology Laboratory (Prof. Sean Doyle) Immunoproteomic investigation of Aspergillus fumigatus We have developed a novel immunoproteomic strategy to identify antigenic proteins in, and antibodies against, A. fumigatus. This project will involve purification of human antibodies and confirmation of immunoreactive protein presence in A. fumigatus. The student will gain expertise in modern immunoproteomics techniques and get to work in a vibrant and productive research environment. Specifically, the student will prepare affinity chromatographic resins, immunoaffinity purify antibodies from human serum, generate protein lysates from A. fumigatus mycelia and identify immunoreactive proteins. Proteins will be detected using tagged antibodies by Western blot analysis to identify the target protein and this will be further confirmed by protein mass spectrometry, using protein mass spectrometry. Overall, the student will help identify specific immunogenic A. fumigatus proteins. The project will improve our understanding of methods to diagnose infection with A. fumigatus. Techniques: ELISA, SDS-PAGE, Western blot, antibody purification and modification, protein identification by LC-MS mass spectrometry. Cell Signalling Laboratory (Dr. Marion Butler) TBK1 and IKKε and have emerged in recent years as ‘new players’ in the pathogenesis of cancer, including breast and ovarian cancer. Targets of IKKε of relevance to breast cancer include Akt, TRAF-2 and estrogen receptor alpha. IRAK1 shows abnormal expression in myelodysplastic syndromes and some B cell

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lymphomas. To date, few studies have explored the role of IRAK1 in cancer. This project will be examining the role of IRAK1, IKKε and TBK1 in a signalling pathway found deregulated in solid cancers. Techniques will include standard molecular biology techniques and cell culture work. Clement, J.F. et al (2008) The IKK-related kinases: from innate immunity to oncogenesis. Cell Res. 18(9): 889-99. Rhyasen et al (2013) Targeting IRAK1 as a therapeutic approach for Myelodysplastic syndrome. 24(1):90-104 Fungal Genetics and Secondary Metabolism Laboratory (Dr. Ozgur Bayram) Identification of AnSte11 and AnSte12 interaction partners by tandem affinity purification Aspergillus nidulans MAPK module consist of AnSte11 (MAP3K)-AnSte7 (MAP2K)-AnSte50-AnFus3 (MAPK) that shuttle between the plasma membrane and the nucleus. The MAPK module releases the AnFus3 to the nucleus where AnFus3 interacts and phosphorylates the AnSte12 that is homologous to yeast Ste12 transcription factor. Deletion of each component results in defects in sexual development and secondary metabolite production. Previously, we have identified interaction partners of AnSte7, AnSte50 and AnFus3. However, the proteins associated with MAP3K AnSte11 and the transcription factor AnSte12 remained to be shown. In this project, we aim to identify AnSte11 and AnSte12 associated proteins by using generic tandem affinity purification (TAP) method and GFP Trap. This project will also require some knowledge of microbiology, fungal biology, molecular genetics and biochemistry. Methods/Techniques: Growth tests on plates, expression studies, identification of interaction partners by mass spectrometry. Genome Evolution Laboratory (Dr. David Fitzpatrick) Is there evidence for recent horizontal gene transfer of fungal genes into Candida krusei Horizontal gene transfer (HGT) is defined as the exchange of genes between different strains or species. HGT introduces new genes into a recipient genome that are either homologous to existing genes, or belong to entirely new sequence families. Large-scale genomic sequencing of prokaryotes has revealed that gene transfer is an important evolutionary mechanism for these organisms. The process of gene transfer has been assumed to be of limited significance to eukaryotes. The availability of diverse eukaryotic genome sequence data is dramatically changing this view however. The rapid increase in fungal sequence data has promoted these species to the forefront of eukaryotic comparative genomics. This project will investigate the frequency of successful recent interdomain HGT events between bacteria and the fungal genome of Candia krusei. This project is completely computer based. Interested students should be computer literate but an ability to program is not essential. Techniques: Comparative genomics, phylogenetics, database searching. Host-Pathogen Interaction Laboratory (Dr. Martina Schroeder) A functional link between DDX3 and IKKε in breast cancer tumourigenesis? The project explores a potential functional relationship between the human DEAD-box helicase DDX3 and the kinase IKKε in breast cancer tumourigenesis. Both IKKε and DDX3 have independently been characterised as breast cancer oncogenes, and we have recently shown that there is a close functional link between these two proteins in innate immune signalling pathways leading to type I interferon (Schroder et al, EMBO 2008, Gu et al MCB 2013). Thus, this project will investigate whether a similar functional link exists for the expression of breast cancer relevant genes. In particular, we will investigate the effects of DDX3 and IKKε on the expression of E-Cadherin and on Estrogen Receptor-dependent gene expression. Techniques used for this project include mammalian tissue culture, transfection of mammalian cells with plasmids, reporter gene assays, shRNA knockdown, SDS-PAGE and Western Blotting. Immune Signalling Laboratory (Dr. Sinead Miggin Characterisation of novel modulators of TLR signaling (2 students) Toll-like receptors (TLRs) are generating intense interest amongst immunologists because of their clear role in the initiation of innate immunity during infection and their participation in inflammatory diseases. They

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all contain a Toll-IL-1 receptor (TIR) domain to facilitate receptor dimerisation and/or adapter molecule interaction. To date 5 adaptor molecules have been described in TLR signaling, MyD88, Mal, Trif, Tram and Sarm. MyD88 is used be all TLRs, with the exception of TLR3. In contrast, Mal only participates in signaling by TLR2 and TLR4. Trif appears to be the sole adapter used by TLR3, and signals to the transcription factor IRF3 via TBK-1. Trif is also used by TLR4 but appears to require Tram to function. Data generated from our lab has identified a number of proteins that modulate TLR signalling in a ligand-dependent manner. The project aims to establish a definitive role for the novel modulators in TLR signalling. To this end, functional analysis will be performed using biochemical techniques, including RT-PCR and immunoblot analysis. This project aims to gain an insight into the role of novel protein interactors in TLR signalling. Membrane Biology Laboratory (Prof. John Findlay) Influence of GPCR activity on Cellular Insulin Responses The project will involve the transfection of HEK293, myoblasts and/or macrophages with GPRs 21 and 105. The responses of the cells to insulin as measured by protein phophorylation and glucose transport, will be studied under conditions of activation/inhibition of these receptors. The effects of agents which produce insulin resistance and restore insulin sensitivity will be examined in the transfected cell lines. Membrane Biology Laboratory (Dr. Gemma Kinsella) GPR105, validation of a novel Diabetes target (to run alongside Prof. Findlay's lab project) Given the rapid escalation of type 2 diabetes (T2D), an effective strategy that will delay disease progression is urgent. This work is examining whether GPR105 is such a novel target. This protein is a member of the largest family of membrane receptors, G protein coupled receptors (GPCRs), many of which have been successfully addressed by molecular therapies. The promise of GPR105 lies in the observation that knocking out the protein in mice gives rise to increased insulin sensitivity and resistance to type 2 diabetes induced by high fat diets. A human knock-out is not possible and mutant versions of the gene are not so far reported but assessing the potential of this receptor can be addressed by strategies which correspond to future treatment regimes. An in-house GPR105 structural model has been constructed using the Modeller software. Utilising this developed model, virtual screening (VS) processes were implemented to examine large compound databases (e.g. Specs, Maybridge) in silico through docking studies (OpenEye, Fred). A ligand which blocks the constitutive activity of GPR105 could be a very powerful therapy. Additionally, the ligands will serve as tools to understand the mechanism of action whereby GPR105 generates insulin resistance. This project will examine Gα protein signalling and GPR105 ligand interaction through: 1) utilising a range of specialised yeast strains, each harbouring a specific humanised G protein which when activated, stimulates yeast growth and 2) mammalian systems where second messenger assays will be used e.g. for cAMP. Molecular Ecology Laboratory (Dr. Conor Meade) Economic systems and ecosystem laws (Suitable for Maths/Biology student Only) Ecosystems are governed by the competitive interaction of r- and K- selected species, with pioneering r- species beginning the process of ecosystem assembly, to be replaced by more competitive and dominant K-species. National economies develop along similar lines, with large companies gradually replacing multiple smaller companies as economies mature. This project will evaluate economic data from a number of different countries to determine how the patterns of succession compare between human economic systems and natural organic ecosystems. The objective is to determine whether economic development can be modeled in the same way as ecosystem succession. The project will use statistical approaches (ANOVA, correlation analysis, regression, multivariate analysis) to compare patterns in the two datasets. This project is relevant for careers in: statistics, comparative data analysis, economics.

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Molecular Immunology Laboratory (Prof. Paul Moynagh) We have initiated studies to characterise the important interplay between obesity and inflammation. This project will extend these studies and assess the anti-inflammatory potential of specific hormones that are deficient in obese conditions with a view to evaluating a new therapeutic regimes in inflammatory diseases. Molecular Parasitology Laboratory (Dr. Noel Murphy) Immunophilins of African trypanosomes (two students focusing on different immunophilin genes) Immunophilins are chaperone proteins involved in a range of cellular processes. Cyclophilin A, the best characterized representative, is the major cellular target for the immunosuppressive drug cyclosporin A which is used to prevent tissue rejection in transplant patients. Cyclophilins have been implicated in modulating the immune system and in the infection processes of pathogens, including HIV. African trypanosomes contain a large family of immunophilin-like protein genes – 20 cyclophilins, 6 FK506-binding proteins and 3 parvulins. We are interested in these genes as possible modulators of the immune systems of the vertebrate hosts that African trypanosomes infect, including humans. Recently we have found evidence for differential splicing of some of these immunophilin genes at different stages of the parasite life cycle. This is unusual in unicellular eukaryotes. The project which will be conducted by two students will involve the analysis of these genes, their protein products and other proteins they may interact with using simple bioinformatic programmes. This will be followed by cloning and analysis of the transcripts of the genes of interest. If time permits. expression constructs will be generated to produce recombinant immunophilin proteins and these will be used to trap associated trypanosome proteins that may be involved in the immune modulation of vertebrate hosts. Plant CellBiology (Prof. Philip Dix) The fate of guard cell chloroplasts during leaf senescence Senescence is the ageing process in leaves. A host of controlled biochemical changes is accompanied by the loss of chlorophyll, and the breakdown of chloroplast structure, leading to the yellowing of the senescent leaves. Guard cell chloroplasts have an essential function in controlling stomatal aperture, and therefore the control of both photosynthesis and water retention. It is reasonable to suppose that the need for these processes may be retained even when the photosynthetic capacity of the mesophyll cells of the leaves is severely diminished. This hypothesis will be explored through examination of the fate of guard cell chloroplasts during the senescence of both attached and detached tobacco leaves. Exploration of the membrane integrity of the chloroplasts will be facilitated by the use of transplastomic plants expressing green fluorescent protein (GFP) in their chloroplasts. The project will combine microscopic investigations with the molecular characterisation of the GFP expressing plants. Plant Biochemical Laboratory (Dr. Emmanuelle Graciet) Interaction between PROTEOLYSIS 1 (PRT1) and a proteasome subunit In the model plant Arabidopsis thaliana, PRT1 has been shown to recognize directly a subset of N-terminal residues and catalyze the conjugation of ubiquitin to the corresponding proteins. Mutant plants for PRT1 do not show any phenotypic abnormalities and hence its functions have remained largely elusive. A previous yeast-2-hybrid screen that was carried out in the laboratory suggested that PRT1 could interact with a subunit of the proteasome. The aim of this project is to further our understanding of this interaction using different molecular and biochemical methods. Techniques involved: yeast-2-hybrid, measurement of β-galactosidase activity in the yeast Saccharomyces cerevisiae and split luciferase and/or split GFP assays in plants.

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Plagiarism & the 4th year research thesis Your thesis will inevitably draw on the work of others. The effective use and evaluation of existing

material are among the skills that you are expected to develop. In all cases, when you build on the work of others you must cite the source of the material (an idea or opinion, a quote, data, diagrams etc). It must be acknowledged in a standard form of referencing. Details of the referencing format are given later on, but here are some practical tips to help you:

• You must present a work of scholarship in your own words and diagrams. • If you state a fact or rely on data from another source, you must acknowledge that source in the

form of a citation in the text. Citations must be listed in a bibliography/reference list. • If you use a diagram or figure from another person's work, you must cite this in the legend and the

bibliography. • If the exact words used by someone else are important to your argument, then you may use these

within quotation marks and must cite the source. • If you have paraphrased someone else’s argument, data or conclusions, then this must be

acknowledged by citation. • Paraphrasing that dominates your work, does not include your own intellectual input or is simply a

rewrite of another person's effort is still plagiarism, even if you do use citations. You must provide an intellectual input that adds to the existing material. This point is particularly relevant to students wishing to follow postgraduate study. In summary, your work will rely on the work of others. You should understand that material and

think about it. Use your own words to describe the essential point that is relevant to your thesis, and cite your source in the text as well as the reference/bibliography section. If you are worried about what constitutes plagiarism, contact your project supervisor. When handing in your literature/laboratory project you will be required to sign a declaration stating that you have read and understand the department's Policy on Plagiarism, and that your project is your own work. Please see the sample declaration form on page 47, which will be available for you to download from the departmental website at the following address: http://biology.nuim.ie/studentregistrationforms/index.shtml This must be downloaded, signed and placed into your project, directly after your project title page.

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LITERATURE AND RESEARCH PROJECT DEADLINES

BI424 BI428 Literature Project Commence

Finish 6 Oct

21 Nov --- ---

Project lab work-Sem.1 Commence Finish

--- ---

6 Oct 21 Nov

Seminar Week of 24-28 Nov 24-28 Nov Final thesis to be submitted 5.00pm 19 Dec 5.00pm 19 Dec

Double Honours Chemistry students whose Chemistry projects take place in Semester 1

BI424 BI428

Literature Project Commence Finish

3 Feb 14 Mar

--- ---

Project lab work-Sem.2 Commence Finish

--- ---

3 Feb 14 Mar

Seminar Week of 10-14 Mar 10-14 Mar Final thesis to be submitted 5.00pm 3 Apr 5.00pm 3 Apr

• TWO typed, heat sealed (fast-back bound) copies of the final version of each thesis must be presented

to the Biology Office on or before the final deadline. The Department will retain these. • Fast back (heat) binding must be done in either the machine room in the John Hume Building or the

machine room of the old campus, which is located behind post room, at a cost of approx. €1.60 to €1.80 depending on size. Please allow yourself plenty of time to get this done, as you may have to leave the thesis and return the following day if the machine room staff are very busy.

• A sample cover sheet for your project is included on page 48 of this manual. Cover sheets may be obtained outside the Biology Office, or from the Biology webpage. Please type in the following: the title of your project, your name, student number, the name of your project supervisor, date.

Remember to place a copy of the Declaration statement of originality at the front of your thesis, after the cover sheet (copy on page 47). https://www.maynoothuniversity.ie/biology/undergraduate/forms-coversheets-and-deadlines • Extensions to these deadlines will not normally be granted. If you have a serious problem concerning the fulfillment of any of these deadlines, please consult Professor Moynagh. SEMINARS. Students will be asked to make a 10-minute presentation with an additional 5 minutes allowed for questions on their literature or laboratory project. The audience will include the supervisor, one other member of staff and all of the fourth year students and other research workers (postgraduate and postdoctoral fellows) from the relevant laboratory. You are required to e-mail your presentation (usually in powerpoint form) to your supervisor at least two days before your talk. Your supervisor will transfer the file to a CD or USB stick for presentation on the computer projector. If you have any questions about these talks please contact your project supervisor. A proportion of the practical marks will be awarded for each of these presentations.

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Alltech Young Scientist Award Programme 2015 Alltech Biotechnology have announced the Alltech Young Scientist Award Programme 2015 whereby undergraduate, MSc or PhD students may submit a 3000-5000 word essay on an area relevant to Alltech business - see http://www.alltech.com/education/alltech-young-scientist/about This competition is open to all students, especially those in 3rd and 4th year who can, in principle, submit their course literature reviews (BI305, BI423), if relevant, for the competition. See above link or contact youngscientist@alltech.com for further details. The deadline for submission is 31 December 2014 and further information is available on Departmental noticeboards.

-Professor Sean Doyle

September 2014

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Biochemical Calculations Website: BiochemicalcTM

http://www.biochemicalc.com

Students in the Department of Biology now have access to BiochemicalcTM. This website, developed by Professor Sean Doyle (Biology) and Mr Dermot Kelly (Computer Science), allows students to: 1. Learn the fundamental concepts of biochemical calculations such as:

What are moles, nanomoles and micrograms? Why do I need to use moles in my calculations? How do I make up laboratory solutions such as buffers? What is molarity?

2. Use online calculators to help solve biochemical problems.

The online calculators allow students to calculate the weights (in mg or g) of reagents required for making up laboratory solutions of defined molarity, calculate the volume of stock solutions required for preparation of a more dilute reagent, carry out %(w/v) dilutions, work out how to do serial dilutions etc…

3. Practice online questions to test their understanding of biochemical calculations.

BiochemicalcTM offers a suite of pre-formatted questions to help students judge if they understand key concepts required for becoming proficient at undertaking laboratory calculations. These questions are of varying difficulty and style, and are designed for use in association with the online calculators on the BiochemicalcTM website.

Although primarily designed for students in the 3rd and 4th years of our degree programmes, it will also be of assistance to students at earlier stages of study. Indeed it may be of use to students taking Chemistry, or any subject requiring knowledge of laboratory calculations. Postgraduates may also find aspects of BiochemicalcTM beneficial to their own research projects and also find use of its functionalities a useful “double-check” for their own laboratory calculations. We encourage you to use BiochemicalcTM and please tell others if you’re happy with it. If not, please email: biochemicalc@gmail.com

BiochemicalcTM was funded by the NUI Maynooth CTL Fellowship Programme 2011

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EXAMINATION ASSESSMENT SCALE

Letter Grade

Descriptive Heading Representative %

Class

A++

Answer which could not be bettered.

100

I

A+ Exceptional answer displaying unexpected insight.

90 I

A Undoubtedly first class, flawless answer, demonstrating originality.

80 I

A- Almost flawless answer demonstrating some originality

70 I

B+ Extremely high competence, perhaps displaying limited originality or technical flaws or minor errors

68 II-1

B Fundamentally correct and demonstrating overall competence.

65 II-1

B- Competent performance, substantially correct answer but possibly containing minor flaws or omissions.

60 II-1

C+ Awarded on the basis of the answer being somewhat better than a C but below a B-.

58 II-2

C Basically correct, answer with minor errors or one major error/omission.

55 II-2

C- Awarded on the basis of the answer being somewhat below a C but better than a D+.

50 II-2

D+ No more than adequate answer. 48 III D Adequate answer with serious errors or

omissions. 45 III

D- Lowest passing grade, barely deserving to pass. 40 P

E+ The answer is inadequate and does not deserve to pass.

38 F

E The answer fails to address the question properly but displays some knowledge of the material.

35 F

E-

Fails to address the question. 30 F

F+ Little relevant or correct material but some evidence of engagement with question.

20 F

F Very little relevant or correct material.

10 F

F- Totally irrelevant answer.

0 F

41

BIOLOGY LABORATORY SAFETY For the protection of yourself and others please read the following notes carefully and obey the instructions implicitly. FIRE: You should be aware of the positions of emergency exits. Specific instructions will be given in the event of evacuation. Your assembly point is Fire Assembly Point C (see map - inside front cover). Bags and coats must be stored at the coat hanger area of each laboratory. PERSONAL PROTECTION: Smoking, eating, drinking, chewing gum are prohibited in the laboratory. Storage of food and drink and food is prohibited by law in all laboratories. You are required to wear a white laboratory coat at all times. Laboratory coats may be available for hire from the Biology Department. Laboratory coats must be worn fastened at all times. You must also wear safety glasses at all times. Please contact your demonstrator if you need to purchase a pair. Gloves are also provided for personal protection. Unfortunately they only protect the wearer and can easily contaminate surfaces. Remove all gloves before leaving the laboratory, even if for a brief period. Remove gloves while using laboratory equipment unless there are specific hazards present. Do not wear gloves when using Bunsen burners unless specifically instructed by the lecturer in charge. If you need to transfer samples or equipment to another laboratory, remove one glove and used the ungloved hand to open doors etc. Sandals, flip-flops and other open footwear are prohibited when chemical and biological agents are used. Long hair must be tied back. You must wash your hands immediately at the end of the practical. In accordance with university regulations, you will be expelled from the practical session if you do not conduct yourself in an orderly manner or deliberately act in an unsafe manner. PERSONAL INJURY: Cuts or grazes must be covered with a plaster. Please inform your demonstrator. First aid cabinets are supplied in all teaching laboratories. Any accident or injury however trivial must be reported to a demonstrator. If a particular practical has specific hazards or disposal methods, these will be explained to you. You must follow these instructions carefully. Please inform your demonstrator if you have any concerns relating to a pre-existing medical condition or if any pre-exisitng medical condition may be impacted by chemical/biological agents used in a practical session.

42

GENERAL SAFETY: In accordance with university regulations, you will be expelled from the practical session if you do not conduct yourself in an orderly manner. Students are normally allowed in the teaching laboratory only for timetabled laboratory sessions. You may not use the laboratory at other times unless permission has been obtained from the technician in charge. Undergraduate students should not enter the preparation laboratory, research laboratories, growth rooms, storerooms etc. without permission. Proper regard to the correct use of equipment is required from all staff and students. Intentional interference with safety signs and safety features of any equipment is a criminal offence. Students are expected to leave their bench place, including sink, clean and tidy. It is particularly important that microscopes are put away correctly:

• slides must be removed. You will be instructed by your demonstrator on how to dispose of slides and coverslips

• a check must be made that a low power lens is in the viewing position • all lenses must be cleaned with lens tissue • the microscope must be unplugged and the flexes wound neatly, but not tightly. • the microscope must be covered

You should be aware that chemicals and biological materials are frequently transported around the department, therefore it is very important that you walk slowly and carefully in the corridors. N.B. The instruction of your demonstrator must be followed at all times. Please check with your demonstrator if you have any doubts or questions in relation to safety. Please notify your demonstrator or senior demonstrator if you are pregnant or have any health issues which you feel may be impacted by any practical.

43

NOTIFICATION OF ABSENCE

It is the responsibility of all students to be available for class throughout Semester I and Semester II between the hours of 0900-1800 Monday to Friday, in addition to occasional classes outside these hours (eg. field trips, academic visits). If you are unable to attend Laboratory practicals, workshops or tests for whatever reason you must advise the Department of Biology by completing the relevant Notification of Absence Form which is available on MOODLE or from the Biology Office or Senior Demonstrator. This must be submitted to the Biology Office, room 2.41 Callan Building, or to your Senior Demonstrator, together with the relevant supporting documentation either before your absence or within FIVE working days of the end of the period of absence. Failure to do so may result in the absence being counted as unacceptable and you will be given a mark of zero.

No more than two absences per semester will be accepted. If you lodge more than two absence certificates in a semester, or if the period of absence extends to three weeks, you will fail the practical component of the course, thereby incurring an automatic fail in the module, and you may be referred to the Academic Advisory Office, Student Services; or to an appropriate member of staff in the department.

Please read and take note of your responsibilities relating to absence as, in signing a Notification of Absence Form, you agree that you have read and understood them.

It is your responsibility to: • Advise the department of any absence. • Submit a Notification of Absence Form to your department together with the relevant supporting

documentation either before your absence or within FIVE working days of the end of the period of absence.

• Keep in touch with your department should you be absent for a prolonged period. • Make up any work you have missed due to your absence. • Agree a revised deadline with your department for any missed assessment(s) due to your absence.

Note that alternative arrangements for a missed test will only be made if a medical certificate is supplied.

• Recognise that submission of a Notification of Absence Form does not automatically mean that the absence is acceptable and that it is at the discretion of the department as to whether any absence is deemed acceptable or unacceptable. If the absence should be deemed as unacceptable it will be recorded as such and count against the minimum attendance level.

• Recognise that, although a specific individual absence may be deemed acceptable, if your overall attendance and submission of work drops below the minimum level prescribed by your department, then disciplinary procedures will still be followed.

• Recognise that notification of absence, whether it is deemed acceptable or unacceptable, does not constitute grounds for appeal against a course or programme failure or failure to progress to the next stage of study.

1. Notification of Absence Forms

Reason for absence Documentation required Illness up to and including 5 consecutive term-time days (excluding Saturdays and Sundays)

Completed Absence due to Illness Form

Illness for more than 5 consecutive term-time days (excluding Saturdays and Sundays)

Completed Absence due to Illness Form plus Formal Medical Certification signed by the Medical Centre, your GP or hospital consultant

44

Unrelated to sickness Notification of Absence Form plus supporting evidence

2. Supporting evidence

The following table gives examples of the kind of supporting evidence that you may be required to provide as justification of absence.

Absence Evidence Illness of LESS THAN FIVE consecutive term time days

Self-certification, which must be submitted to the department within 5 working days of the end of the period of absence. Should students submit repeated self-certifications, the department will require students to produce formal Medical Certification. Note that alternative arrangements for a missed test will only be made if a medical certificate is supplied.

Illness of MORE THAN FIVE consecutive term time days

Formal Medical Certification signed by the Health Centre or your GP or hospital consultant

Outpatient’s appointment Letter from outpatients or appointment card Doctor or dental appointment

Appointment card

Documented personal problems

Letter from someone, e.g. counsellor, who has direct knowledge of the problem and/or is involved in supporting you

Illness of dependent or family member

Medical Certification and statement explaining illness and why personal attention is necessary

Bereavement Formal certificate or note from family member who can vouch for the situation Severe transport problem A copy of online or newspaper reports on the problem to be submitted to the

department within 5 working days of the problem having occurred Court attendance Official correspondence from the Court confirming attendance requirement Victim of crime Statement of events, police report and crime reference number Involvement in a significant/prestigious event

Letter of invitation from the relevant organising body

Sport commitment at national/county level

Official correspondence from the relevant sporting body confirming the requirement to be available on specified dates

The following table gives examples of the kind of circumstances where absence may be deemed as ‘acceptable’ and ‘unacceptable’ for non- attendance. This is for general guidance; it does not represent an exhaustive list. All absences will be reviewed on a case by case basis. If possible you should try to arrange to attend a different session rather than be absent for a lab session.

Acceptable Unacceptable • Illness • Hospitalisation • Out patients appointment (where possible you

should try to make any appointment outside of your class commitments

• Doctor or dental appointment (you should try to make any appointments outside of your class commitments)

• Documented personal problems • Illness of dependent or family member (until

other arrangements can be made) • Bereavement

• Oversleeping • Misreading the timetable • Paid employment and voluntary work • IT and/or computer problems • Minor transport problems, e.g. being stuck

in normal rush hour traffic, not permitting enough time in travel plans for minor unanticipated delays, missed public transport

• Holidays • Family celebrations • Weddings

45

• Severe transport problems (e.g. severe disruption of train travel due to signalling failure or track problems or major traffic incident on motorways, which can be verified by online or newspaper reports)

• Court attendance or victim of crime • Representing College/county/ country at

significant or prestigious event or sport commitment or involvement in such an event

• Accommodation issues, e.g. moving house • Extra-curricular sports activities • Driving test • Lack of awareness of attendance

requirements and College Regulations in this regard

Completed forms should be handed into the Biology Office (room 2.41, Callan Bld), or directly to your senior demonstrator. Forms not requiring supporting documentation may be e-mailed to biology.department@nuim.ie. Useful links: Medical Centre

• Telephone: (01) 708 3878 Academic Advisory Office

• Telephone: (01) 708 3368 • Email: advisory.office@nuim.ie

Student Services • Telephone: 01 708 4729 • Email: student.services@nuim.ie

Maynooth Access Programme • Tel: 01 708 6025 • Email: access.office@nuim.ie

Late Assignments Late assignments will not be accepted. Computers crash, printers run out of ink, dogs eat lab reports, but these are not acceptable excuses for handing in a late assignment. In the case of illness late assignments may be submitted with documentation OR a signed declaration from your assignment supervisor. For other circumstances please see the Senior Demonstrator or Academic Supervisor, as appropriate. Make sure you back up your computer files often, and also on a separate storage device so that you avoid losing hours of work in the event of a computer crash. Leave plenty of time for printing your report since printer problems are as common as computer crashes.

46

Registration for Modules SUBJECT: BIOLOGY Year of Study: 4th Qualification: BSc (Double Honours)

You must take all compulsory modules listed below. Tick the box opposite each optional module, which you have selected to take in Semester 1 and Semester 2. You must take a total of 30 Credits. MODULE NAME Credits Semester Module

code Tick Selections here

Semester 1 – Compulsory Modules You are required to take all compulsory modules

Research Methodology 2 2.5 1 BI422 √ Semester 1 – Compulsory Modules (to add up to

7.5 credits). You are required to take either: BI424 and BI426 OR BI428.

Literature Project 2 5 1&2 BI424 Advanced Practicals/Professional Modules 2 2.5 1&2 BI426 Laboratory Project 2 7.5 1&2 BI428 Semester 1 – Optional Modules Select 1, 2 or 3 modules from the following Group:

Environmental Field Studies (not offered this year) 5 1 BI401 Plant Biotechnology 5 1 BI403 EITHER Advanced Immunology OR 5 1 BI405 Fungal & Bacterial Secondary Metabolism 5 1 BI441 EITHER Tumour Biology OR 5 1 BI407 Clinical Proteomics: Discovery, Validation & Medical Utility

5 1 BI443

Organelle Genome Evolution 5 1 BI409 Bioethics & Biotechnology 5 1 BI411 Semester 2 – Optional Modules Select 1, 2 or 3 modules from the following Group:

Behavioural Ecology 5 2 BI406 Plant Developmental Biology 5 2 BI410 Molecular Ecology and Biogeography 5 2 BI435 EITHER Medical Mycology* OR 5 2 BI436 Antibiotics: Discovery, Modes of Action & Resistance 5 2 BI439 EITHER Neuromuscular Biology OR 5 2 BI437 Control of Protein Activity 5 2 BI440 Human Genetics 5 2 BI442 Latest Dates for Changing Optional Modules: Latest date for change of optional modules in Semester 1 is the Friday of Week 3 of Semester 1 and the latest date for change of optional modules in Semester 2 is the Friday of Week 2 of Semester 2. No changes allowed after these dates. It is your responsibility to inform the Student Records Office of all changes to your module selection.

47

DECLARATION

I have read and understood the Departmental policy on plagiarism.

I declare that this thesis is my own work and has not been submitted in any form for

another degree or diploma at any university or other institution of tertiary

education.

Information derived from the published or unpublished work of others has been

acknowledged in the text and a list of references is given.

Signature: .....................................................................................................

Date: .............................................................................................................

48

SAMPLE COVER SHEET

Maynooth University Department of Biology, 2014-2015

BI428 LABORATORY PROJECT 2

The Isolation of Recombinant DNA Clones Containing Microsatellite DNA Sequences of the

Nematode Heterorhabditis sp K122

This thesis is submitted in fulfillment of the Double Honours Biology Degree.

SUBMITTED BY: Eimear Quinn

STUDENT NO: 66218606

SUPERVISOR: Dr. David Fitzpatrick

DATE: 19 December 2014