Table of Contents

Staff Consultation Times ................................................................... 2

Schedule of Introductory Talks .......................................................... 3

Industrial Outplacement ................................................................... 4

Project/Report Deadlines .................................................................. 5

Staff Research Interests .................................................................... 6

Departmental Policy on Plagiarism.................................................... 11

• Plagiarism & the 4th year research project ............................... 13 • Writing a 4th year dissertation: essential information .............. 14 • How to submit an assignment to Turnitin ................................ 15

Guidelines for Literature Project (BI423) ........................................... 19

Literature Project Titles ........................................................... 21

Alltech Young Scientist Award Programme 2017 ............................... 22

Biochemical Calculations Website: BiochemicalcTM ........................... 23

Biotechnology Year Outline ............................................................... 24

Interviews with External Examiner .................................................... 24

Module Descriptors ........................................................................... 25

Examination Assessment Scale .......................................................... 29

Marking Scheme for Practical Element of Course .............................. 30

Lab Safety ......................................................................................... 31

Notification of Absence ..................................................................... 33

Sample Forms:

• Declaration of Originality ........................................................ 37 • Cover Sheet ............................................................................. 38 • Literature Review Form ........................................................... 39 • Absence Forms ........................................................................ 40

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MAYNOOTH UNIVERSITY DEPARTMENT OF BIOLOGY Information for Fourth Year Biotechnology Students 2016 - 2017

Please read this manual carefully and keep it safely so that you can refer to it during the year. The 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 DEPARTMENT OF BIOLOGY

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.

The fourth year programme in Biotechnology provides detailed discourse of modern biotechnological processes across a range of disciplines. In addition, a three-month industrial outplacement is incorporated both to provide the student with the skills required in the modern workplace and also to facilitate future career choice. Students will also undertake a literature review and practical classes in advanced laboratory-based procedures. Assessment will be a combination of end of Semester examination of the theory component and continuous assessment of practical work. There will be 7 theory papers counting 70% of the final mark. Practical assessment (30%) will be based on literature review and industrial outplacement. The industrial outplacement will be assessed by both a written report and oral presentation. Expenses associated with the industrial outplacement will normally be the responsibility of the student. Fourth Year Committee: The members will be Sean Doyle and 1 elected fourth year Biotechnology student. Problems and matters of interest will be discussed by the committee. If you have issues which you would like to be considered you should tell your representative.

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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. Conor Breen (CB) B2.06 conor.breen@nuim.ie Friday 11.00-13.00 Dr. Marion Butler (MB) B3.18 marion.butler@nuim.ie Wednesday 12.00-14.00 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) 2.35 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. Karen English (KE) B3.17 karen.english@nuim.ie Tuesday 11.30 -13.00 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 Tuesday 10.00-12.00 Dr. Christine Griffin (CG) 2.36 christine.griffin@nuim.ie Monday 14.00-16.00 Dr. Kevin Kavanagh (KK) 2.39 kevin.kavanagh@nuim.ie Mon & Wed 14.00-16.00 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 12.00-14.00 Prof. Paul Moynagh (PM) B1.21 paul.moynagh@nuim.ie Monday 14.00-16.00 (Head of Department) 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 12.00-13.00 Dr. Rebecca Owens (RO) F6 rebecca.owens@nuim.ie Wednesday 10.00-11.30 Ms. Teresa Redmond (TR) 1.21* teresa.redmond@nuim.ie During practical classes Dr. Martina Schroeder (MS) B2.18 martina.schroeder@nuim.ie Monday 15.00-16:00 Dr. Fiona Walsh (FW) B1.24 fiona.walsh@nuim.ie Thursday 11.00-12.30

*=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 Offices are open daily: 10am-12.45pm; 2-4pm Biology Office (room 2.41): Ms. Jean Burbridge (jean.burbridge@nuim.ie); Dr. Zoe Mulroy-Hehir (zoe.mulroy-hehir@nuim.ie) Departmental Administrator (room 2.40): Ms. Terry Roche (terry.roche@nuim.ie)

Programme Coordinators: OMNIBUS SCIENCE: Dr. Jackie Nugent BIOTECHNOLOGY: Prof. Sean Doyle SCIENCE EDUCATION: Dr. Jackie Nugent BIOLOGICAL & BIOMEDICAL SCIENCE: Dr. Kevin Kavanagh

MAP (Mature and Access Students) ACADEMIC ADVISOR: Dr. Christine Griffin POSTGRADUATE COORDINATOR: Dr. Martina Schroeder MSC IN IMMUNOLOGY & GLOBAL HEALTH: Dr. Sinead Miggin

For urgent matters the Programme Coordinators and/or Head of Department may be contacted in their rooms at any time. Please contact Jean or Zoe to make an appointment.

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4th BIOTECHNOLOGY INTRODUCTORY LECTURES *Mon. 19 September 1pm BSem Introductory Lecture (S.Doyle) Thurs. 22 September 5pm CB8 Options with your degree (incl. introduction

to career planning, postgrad study & employment) (E.Strain)

Fri. 23 September 9am JH4 Plagiarism/Turnitin (C.Meade) Tues. 27 Sept 1pm JH2 Accessing Information (F.Brady) Tues. 27 Sept 5pm CB9 Postgraduate Studies (M.Schroeder) *There will be an introductory seminar in the Biology Seminar Room (BSem) rm. 2.28 starting at 1.00pm on Monday 19 September. In addition you are invited (along with the rest of the 4th year classes) to meet the staff at coffee/tea at 4.15pm in the foyer of the Biosciences Building.

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INDUSTRIAL OUTPLACEMENT The Biology department will arrange an industrial outplacement of three months duration for each student in Fourth Biotechnology. This year, the outplacement will take place from Monday 30 January – Friday 21 April 2017. While the majority of placements will be in Ireland, it is possible that occasional placements abroad will be available. However, you will be notified of this well in advance. Financial costs associated with accommodation, subsistence and travel will be the responsibility of the student except in the case of placements abroad where an appropriate financial stipend will be made available.

In certain cases it may be necessary for you to attend for interview with a potential host company. To this end you have already been requested to submit a completed Curriculum Vitae (CV) to the Biology Department Office. You have been supplied with a template to assist you in this task. In general, host companies will come from the food, beverage, human and veterinary diagnostic and biopharmaceutical sectors. Students will be accommodated in their choice of area and geographical location as far as practicable, however the final decision with placement allocation will lie with the Biology Department.

In the majority of cases, the outplacement will be your first experience of working in a

scientific or laboratory environment. In addition to fulfilling the daily tasks assigned to you during this period, you should strive to familiarise yourself with all aspects of company operation and investigate alternative career options requiring scientific knowledge in areas such as quality control, technical marketing and clinical trials.

Upon completion of your outplacement you will be required to present both a written

report and a 10-minute oral presentation on your experiences, with an additional 5 minutes allowed for questions. This should cover the following aspects: Company description and organisation and a review of your work over the three-month period. You will have to be aware of company confidentiality in compilation of your report and presentation, and so you should obtain written permission from your employer for all information to be disclosed. Your audience will include the supervisor, one other member of staff, fellow fourth year students, where appropriate, and other research workers (postgraduate and post-doctoral fellows) from the Biology Department. Powerpoint and/or acetate presentations are acceptable. Students who choose to use powerpoint are responsible for procuring a computer for the presentation, for connecting the computer to the projector and for ensuring that it works before the time when the talks are scheduled to begin. 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.

Student Grants. The Fees and Grants Office have very kindly agreed to arrange payment of student grants, where appropriate, into student bank accounts upon provision of Bank details including address, account number and sort-code to the Fees and Grants Office. It is the responsibility of individual students to ensure that this information is made available to the relevant party.

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PROJECT/REPORT DEADLINES

Commence Final Thesis/Report to be submitted

BI423 Literature Project

3 October 2016

10 February 2017

BI430 Industrial Outplacement

30 January

2017

5 May 2017

BI423 LITERATURE PROJECT: • TWO typed, spiral or heat sealed (fast-back bound) copies of the final version of the BI423

Literature Project 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 38 of this manual. Cover sheets may

be obtained outside the Biology Office or online at the address below. Please type in the following: the title of your project, your name, student number, the name of your project supervisor. date.

• Extensions to these deadlines will not normally be granted. BI430 OUTPLACEMENT REPORT: • TWO typed, spiral or heat bound copies of the final version of the BI430 Industrial

Outplacement report must be presented to the Biology Office on or before the final deadline. These will be retained by the Department.

Remember to place a signed copy of the Declaration statement of originality (see page 37) at the front of your thesis, after the cover sheet (copy on page 38). These sheets are also online at: https://www.maynoothuniversity.ie/biology/undergraduate/forms-coversheets-and-deadlines

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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 (contract)

C. Breen BA(Mod) PhD

Membrane proteins, biochemistry, cellular metabolism, protein-protein interactions, bio-fermentation, mass spectrometry, proteomics, assay development, drug target identification

The Marie Curie Laboratory for Membrane Proteins was established with the goal of studying the role, structure and mechanism of action of integral membrane proteins. Recent research activities include: (a) fundamental studies on the structure and function of the human vitamin A transporter (STRA6) using high-cell-density protein expression and purification; (b) the discovery of novel STRA6-interacting proteins using affinity purification/mass spectrometry (AP/MS), membrane yeast two-hybrid (MYTH), co-immunoprecipitation (co-IP) and dual-luciferase reporter assays; and (c) the development of novel assays for drug target identification using chemical biology and spectro-fluorimetric techniques. A unifying theme in our research is the application of a wide range of biochemical and cell biological techniques to the study of systems important to human health.

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Title Name &

Qualifications Key Words Research Interests

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.

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.

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Title Name &

Qualifications Key Words Research Interests

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 K. English MSc PhD

Cellular therapy, mesenchymal stem cells, immune modulation, pre-clinical models of inflammatory disease, organ transplantation

Our research focuses on the translation of cellular therapies for the treatment of inflammatory disorders including graft versus host disease and organ transplant rejection. In addition, we also work on pre-clinical models of airway inflammation including asthma, chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Specifically, our objectives are to understand how cellular therapies (mesenchymal stem cells- MSC) mediate their anti-inflammatory effects and to use this knowledge to enhance the efficacy of cellular therapies for the treatment of patients. At the basic science level much of our efforts are focused on characterising the effects that MSC have on immune cells and how the inflammatory environment influences MSC protection in the context of disease.

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 and Phytophthora species. We use next generation sequencing, comparative genomics, and bioinformatics tools on completely sequenced genomes to identify genetic signatures that may be associated with particular phenotypes.

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 mediated by the ubiquitin system 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, but also crops such as barley and turnip, 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.

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Title Name &

Qualifications

Key Words Research Interests

Senior Lecturer

C.T. Griffin BSc PhD

Behaviour, symbiosis, physiology and biogeography of invertebrates (insects and their nematode parasites)

Current research of the Behavioural Ecology and Biocontrol lab explores the behaviour and use of entomopathogenic nematodes Steinernema and Heterorhabditis (which kill insects and are used to control pests). We study their dispersal and host-finding behaviour, both in the lab and the field (currently focussing on a forest ecosystem). We investigate the relationship between nematodes and their bacterial symbiont (essential partner for killing and digesting hosts) in an ecological context. We also interested in the behaviour of adult nematodes - including fatal fighting, mate attraction, and female-dependent male maturation, behaviours for which Steinernema is an ideal model organism.

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.

Lecturer C. Meade

BSc PhD

Ecology, Molecular Ecology, population genetics and systematics of plants

Evolution, phylogeography and population genetics of land plants. Adaptation to climate change in Alpine plants. Flora of Europe and tropical Asia. Gene-flow in wild relatives of Irish arable crops. The ecological impact of conventional and genetically modified (GM) crops.

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

J.M. Nugent MSc PhD

Plant molecular, developmental biology

Mitochondrial- nuclear interactions and the consequences for plant growth and development. Mitochondrial genome evolution in Plantago lanceolata. Plant plastid transformation for recombinant protein production (e.g. antigens).

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Title Name &

Qualifications

Key Words Research Interests

Professor K. Ohlendieck DipBiol PhD DSc

Skeletal muscle biology, proteomics, biomarker discovery

Proteomic profiling and biochemical characterization of skeletal muscle adaptations, degeneration 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 (Contract)

R. Owens BSc PhD

Pathogenic fungi, secondary metabolites, proteomics, comparative metabolomics

Systems associated with secondary metabolites produced by pathogenic microbes such as the fungus Aspergillus fumigatus. Utilising mass-spectrometry based analysis, pathways affected by perturbations in these systems can be identified, as well as novel intermediates. Our work employs proteomic and metabolomics investigations to profile these changes on a system-wide level, leading to enhanced understanding of the cross-talk between secondary metabolite clusters as well as identifying links to primary metabolism.

Lecturer M. Schroeder BSc PhD

Pattern recognition receptor signaling, Host-pathogen interactions, type I interferons, breast cancer, drug development

Research in the lab centers on the recognition of pathogens, in particular viruses, by pattern recognition receptors and the ensuing signaling pathways leading to type I interferon production. We are particularly interested in the role of DEAD-box proteins in innate immunity and the regulation of translation initiation, and are exploring potential links between these two functions of DEAD-box helicases.

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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Department of Biology Policy on Plagiarism

Definition of Plagiarism Plagiarism involves an attempt to use an element of another person’s work, without appropriate acknowledgement in order to gain academic credit. It may include the unacknowledged verbatim reproduction of material, unsanctioned collusion, but is not limited to these matters; it may also include the unacknowledged adoption of an argumentative structure, or the unacknowledged use of a source or of research materials, including computer code or elements of mathematical formulae in an inappropriate manner.

The policies of the University apply within the Department of Biology, as contained on the Maynooth University website (https://www.maynoothuniversity.ie/university-policies/rules-regulations-students). Plagiarism is a form of academic dishonesty and will be treated with the utmost seriousness wherever discovered. 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 Module Coordinator (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. 2. Dealing with Proven Cases of Plagiarism: If there is evidence of plagiarism, the matter will be turned over to the Course Coordinator, 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 Course Coordinator the origin of the material contained in the piece in question. "Procedures

i. Where a marker (or course coordinator) believes that a case of plagiarism has been identified, the matter shall be referred to the Head of Department with a written report outlining the reasons for suspecting that the work has been plagiarised.

ii. The Head of Department shall then make an initial finding as to whether or not plagiarism has occurred, taking account of factors including, but not confined to, the extent of the plagiarism, indications of intent to deceive, the student’s prior history in this regard, practice within the discipline, and the level at which the student has submitted the work. The Head of Department will not take account of extenuating medical or personal circumstances in making a decision.

iii. If the Head of Department is the marker who suspects plagiarism has occurred, he or she shall delegate responsibility to a nominee in that department to follow the procedures laid down in this policy

iv. Where the Head of Department determines that plagiarism has not occurred but there are indications of incorrect citation, the work shall be awarded a grade that takes account of the failure to cite sources correctly, within the overall context of the work as a whole.

v. Where it is considered right to do so, the Head of Department shall confirm the determination that plagiarism has occurred by making a record of the decision setting out the reasons. At this point, the Head of Department shall consult the Registrar’s Office, informing the Registrar of the finding, and requesting any information on previous findings in relation to the student. Should prior findings exist, the procedures in xi and xii shall apply.

vi. Where the Head of Department determines that plagiarism has occurred, a meeting with the student shall be convened to inform the student of the finding.

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vii. The student shall be advised of the determination by the Head of Department and of the consequences that may unfold and that a response should be received by the Head of Department from the student within ten working days from the date the determination was confirmed.

viii. The student shall be advised that failure or refusal to respond within the designated period of time, or failure or refusal to attend for any meeting requested by the Head of Department, will result in the matter being referred to the Academic Discipline Board of Maynooth University in like manner as if the student had chosen not to accept the findings of the report.

ix. Where the student chooses not to accept the findings of the report, the matter shall be referred to the Academic Discipline Board of Maynooth University together with all relevant documentation and reports.

x. Where the student accepts the findings of the report, the student shall be asked to sign the report. The Head of Department shall then countersign the report. The Head of Department will then give the work a mark of 0. The student will be allowed to redo the assignment before a designated deadline prior to the next Examination Board meeting, if it is practical to do so. The mark for the resubmitted work will be capped at 40%. A record shall be kept in the Department of the incident, and this shall be forwarded to the Registrar’s Office.

xi. In the case of a second finding of plagiarism in relation to a student, the matter is automatically referred to the Academic Discipline Board, who shall notify the student that the matter has been brought to its attention.

xii. A “second finding” in this regard may refer to findings made in the current academic year or in previous academic years, and it may refer to findings made by more than one Department."

-(Maynooth University Policy on Plagiarism)

2a. Minor Plagiarism: In cases of minor plagiarism, the following 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. 2b. Major Plagiarism: In cases of major plagiarism, the following University statutes will apply: In instances where a significant part or all of an assignment is found to be plagiarised, the Department will "award a mark of zero in the assignment, with no chance to resubmit in the current academic year" (Maynooth University Policy on Plagiarism), and previous and subsequent work submitted in connection with the course may be subject to particular scrutiny. In serious cases the plagiarism will be referred to the Academic Discipline Board. 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. “Instances of plagiarism among postgraduate research students will be treated as being particularly serious. The Board will not take into account extenuating medical or personal circumstances in making its decision..” (Maynooth University Policy on Plagiarism).

3. Recording: All cases of plagiarism will be recorded by the Course Coordinator 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.

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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 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 37, 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-deadlines This must be downloaded, signed and placed into your project, directly after your project title page.

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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 Maynooth University Department of Biology Plagiarism policy. 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 Maynooth University 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 11)

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://2017.moodle.maynoothuniversity.ie/course/index.php?

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Please refer to Understanding Turnitin Originality Reports for more information

If you encounter problems using Turnitin, you can contact Moodle Support for further assistance using our email address moodlesupport@nuim.ie

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GUIDELINES FOR BI423 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 (5000 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 27 September at 1pm in JH2 on Accessing Information. The material presented above is for quick reference only. See pages 11-14 for information regarding plagiarism.

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BI423 Literature Projects Antimicrobial Resistance and Microbiomes (Dr. Fiona Walsh) Bacteriophages as therapeutic tools Behavioural Ecology & Biocontrol Laboratory (Dr. Christine Griffin) Replacing meat for future planetary needs Biotechnology Laboratory (Prof. Sean Doyle) 1. Synthetic Biology: reality or illusion? 2. The role of primary metabolism in antibiotic biosynthesis Cell Signalling (Dr. Marion Butler) Immunotherapy Chemical Microbiology (Dr. Rebecca Owens) Harnessing fungi for plant biomass degradation: Recent developments and applications Clinical Proteomics Laboratory (Dr. Paul Dowling) Anti-cancer monoclonal antibodies and their production Fungal Genetics and Secondary Metabolism Laboratory (Dr. Ozgur Bayram) 1. Biotechnology of fungal secondary metabolites 2. Use of fungi and their enzymes in food production industry Genome Evolution Laboratory (Dr. David Fitzpatrick) Genome-wide association studies and the prospect of personalized medicine Host-Pathogen interaction Laboratory (Dr. Martina Schroeder) 1. Food-derived anti-inflammatory compounds 2. Functional foods Immune Signalling Laboratory (Dr. Sinéad Miggin) Rheumatoid Arthritis and DMARDs Medical Mycology Laboratory (Dr. Kevin Kavanagh) Is Bioremediation effective and environmentally sustainable? Membrane Biology (Dr. Conor Breen) Advances in fluorescent protein technology Molecular Immunology Laboratory (Prof. Paul Moynagh) Ubiquitination as a target for new drug discovery Muscle Biology Laboratory (Prof. Kay Ohlendieck) Biomarker discovery using mass spectrometry-based proteomics Applied Proteomics Laboratory (Dr. James Carolan) Plant mediated RNAi as a method for controlling crop pests Plant Biochemical Laboratory (Dr. Emmanuelle Graciet) Improving crop resistance to pathogens: new methods and targets Plant Molecular Biology Laboratory (Dr. Jackie Nugent) The use of mitochondrial DNA in forensic identification

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Alltech Young Scientist Award Programme 2017 Alltech Biotechnology have announced the Alltech Young Scientist Award Programme 2017 whereby undergraduate students may submit a 3000-3500 word essay on an area relevant to Alltech business - see http://education.alltech.com/alltech-young-scientist/how-participate 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 2016 and further information is available on Departmental noticeboards.

-Professor Sean Doyle

September 2016

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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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FOURTH YEAR BIOTECHNOLOGY LECTURE MODULES 2016/2017 Students are required to take ALL courses listed below. Module No. Name Semester Exam BI403 Plant Biotechnology Semester 1 BI412 Bioethics & Biobusiness Semester 1 BI415 Biotechnology Processes 2 Semester 2 BI416 Genomics & Proteomics Semester 2 BI417 Food Biotechnology Semester 2 BI423 Literature Project 1 -- BI430 Outplacement -- The following modules are optional [Those in brackets are timetabled against each other. You will need to pick one from each grouping.]: Module No. Name Semester Exam BI405 Advanced Immunology Semester 1 BI441 Fungal & Bacterial Secondary Metabolism Semester 1

BI407 Tumour Biology Semester 1 BI443 Clinical Proteomics: Discovery, Validation & Medical Utility Semester 1 Each examination will be of two hours duration. A summary of course contents and a lecture timetable is appended. 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 7-16 June). If you have particular difficulty about being available at that time please discuss the matter with Professor Moynagh. Copies 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. Past examination papers can be obtained from the Quicklinks section (lower left hand side of the page) of the Maynooth Library web page. (web address: https://www.maynoothuniversity.ie/library/exam-papers

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4 BIOTECHNOLOGY MODULE DESCRIPTORS BI423 Literature Project 1 A 12 academic 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 and an oral presentation of the research topic. BI403 Plant Biotechnology (Prof. Phil Dix) 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 (Dr. Martina Schroeder / Dr. Marion Butler) 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. BI407 Tumour Biology (Dr. Marion Butler) This course will explore the mechanisms that underlie cancer, and examine the rationale behind the technologies used in the diagnosis and treatment of this disease. The course consists of lectures, extra reading and is supported by additional on-line resources. Initially we address the question "what is Cancer?" examining the experimental data that has led to our current understanding of tumorigenesis, and acquiring the specialised terminology of the field. The roles of genes and environment will be covered before an in depth study of the control of cell division and cell death. A major section of the course will cover the molecular genetics of cancer, focusing on key oncogenes and tumour suppressor genes. Having grasped the detail of the genetic "lesion|" that is central to carcinogenesis, we will examine the human body's intrinsic defences

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against cancer before studying the details of diagnosis and clinical therapy. Special reference will be made to novel approaches such as anti-angiogenesis therapies. In the final lectures, and support material, the knowledge acquired above will be brought together in two "case-studies"; breast cancer and lung cancer. Study of this course should provide students with a solid understanding of cancer, and provide a foundation for postgraduate studies in tumour biology or for students intending to follow careers in biomedical industries. 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. BI412 Bioethics & Biobusiness (Prof. Martin Downes/Dr. Ciaran Walshe/Dr. Brian Kelly Undergraduates as well as graduates are constantly faced with decisions for which they may be blamed, or for which they may blame themselves. What help has western ethical thought (in particular) to offer you for such things as

personal justification management of decisions on technology and business public acceptance of choices avoiding ethically naive responses to criticism

The ethics element of this module comprises lectures and case history analysis as well as recommended reading. The biotechnology industry comprises a broad group of organisations ranging from the production of animal feeds to speciality biopharmaceuticals. All biotechnological organisations have one common thread insofar as they are based on the commercialisation of biological organisms or products. This course will examine the diverse nature of the biotechnology industry and the commercial constraints in which it operates; particular emphasis will be paid to income generation for start-up enterprises, specific difficulties encountered and their circumvention. Introduction to, and detailed discussion of, quality management systems (ISO9000, cGMP and MDD) and the role of quality management systems in the manufacture of biopharmaceutical and in vitro diagnostic products. BI415 Biotechnology Processes 2 (Prof. Sean Doyle/Dr. David Fitzpatrick) This course will comprise of a detailed examination, and examples of, the physical and chemical processes underlining bioprocess operations including fluid dynamics; heat and mass transfer in bioreactors; homogenous and heterogenous bioreactions. Specifically, we will examine fluid classification, viscosity and non-newtonian fluids. In addition, factors affecting media broth viscosity and the rheological properties of fermentation broths will be discussed. Cell growth kinetics, rate of substrate utilisation and product formation in homogenous and heterogenous systems will be examined. Finally, a detailed discussion of selected examples of large-scale prokaryotic and eukaryotic cell culture systems for recombinant protein production will be undertaken with reference to recent reviews in the area. The use of a range of enzymes is critical to the success of many pharmaceutical, biotechnological and industrial processes. Microbial enzymes are used in a variety of foods, beverages and diagnostic procedures and, as such, their production and purification is extremely important. This course will examine factors affecting the use of micro-organisms for the production of native and recombinant enzymes. An examination of the role of thermophilic proteases in industry will be made and the ability to engineer subtilisins to withstand a variety of adverse conditions will be used as an example of enzyme engineering. Discussion will also focus on factors affecting the

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production of recombinant chymosin and the use of immobilisation technology for the long-term use of enzymes in industrial processes. BI416 Genomics & Proteomics (Dr. Rebecca Owens/Dr. Ozgur Bayram) The genomics component will cover methods of genome sequencing and emerging technologies that increase throughput and reduce costs. Experimental methods for genome analysis including microarrays and functional genomics will be covered. Students will be introduced to methods for probing the molecular biology databases and the impact of the genomics revolution on biology. The proteomics section of the course will comprise brief revision of protein mass spectrometry (MS), a detailed discussion of tandem mass spectrometry and daughter ion fragmentation patterns. Close inspection of current literature to understand the application of protein MS in modern laboratories will be undertaken. BI417 Food Biotechnology (Dr. Rita Dempsey) The importance of the Agri–Food industry is seen in the fact that in 1997/1998 this sector of industry accounted for 12.7% of GDP, representing 12% of total exports. There are 176,000 people employed or 11.8% of total employment (source CSO figures 1997/98). The course will commence with an introduction into the major food components such as proteins, carbohydrates, lipids, and water and the behaviour of these food components on subsequent processing, storage, and cooking. Foodborne disease and the microbial spoilage of food results in the failure or inability to control micro-organisms at one or more stages in the food chain from raw material production to consumption of the final product. Details of the major food spoilage micro-organisms as well as those causing foodborne illness will be discussed. The course will detail some industrial preservation methods which extend the shelf life of foods by inhibiting microbial growth or biochemical changes. The final lectures will examine the Hazard Analysis Critical Control Points (HACCP) system which is used to identify, assess, and control health hazards in food. Relevant food safety legislation will also be examined. BI430 Industrial Outplacement The student will work in a biotechnology company (e.g., diagnostic assay manufacturer, clinical trial co-ordinator, pharmaceutical drug manufacturer etc.) in a research, manufacturing, quality or clinical trials function. The student will be required to compile a detailed report on the outplacement, upon completion of same, and also give an oral presentation based on their outplacement experience. BI441 Fungal & Bacterial Secondary Metabolism (Dr. Ozgur Bayram). 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.

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BI443 Clinical Proteomics: Discovery, Validation & Medical Utility (Dr. Paul Dowling). 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: Total marks 100%; 80% for two hour written examination at the end of the semester; Continual Assessment 20% (made up of 2 MCQ’s – 10% each, the first MCQ in the middle of the lecture series and the second MCQ at the end).

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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

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MARKING SCHEME FOR PRACTICAL ELEMENT OF 4TH YEAR COURSE Practical elements of the course are as follows: BI423 Literature Project BI430 Industrial Placement (70% written report, 20% oral presentation, 10% feedback from

Outplacement Supervisor) Theses will be handed up as completed work, with no first drafts reviewed by the supervisors. Theses will be marked by the supervisor and one other staff member. The seminars will be marked by the supervisor and one other member of staff (one staff member will second mark all seminars from one laboratory; a different staff member will second mark the thesis). In the marking of seminars, emphasis will be placed on displaying an understanding of the subject and clarity and relevance of the material presented, rather than the quality of the overheads used for the presentation. Students are advised that it is important to perform well in all components of the course and not to neglect either the practical or lecture elements. This is particularly relevant to students who may fall on the borderline between two grades where small numbers of marks may make a difference in the final degree class attained.

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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.

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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.

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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. This must be submitted to the Biology Office, room 2.41 Callan Building, 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. NOTE THAT BACKDATED MEDICAL CERTIFICATES WILL NOT BE ACCEPTED FOR ANY REASON. 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.

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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 issued and dated during the period of illness and signed by the Medical Centre, your GP or hospital consultant

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 normally only be made if a medical certificate is supplied.

Illness of MORE THAN FIVE consecutive term time days

Formal Medical Certification issued and dated during the period of illness and 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

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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 • 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

• 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 • 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 directly to your senior demonstrator at the next practical/workshop or into the Biology Office (room 2.41, Callan Bld). Forms not requiring supporting documentation may be e-mailed to mailto:zoe.mulroy-hehir@nuim.ie

Multiple Choice Questionnaires and Notification of Absence Throughout the year you will sit a number of Multiple Choice Questionnaires (MCQs) which are generally comprised of questions that cover a significant proportion of the module. Some of these are held online and conducted during a scheduled practical or lecture time. The remainder are machine readable and are held during a lecture time slot. It is important that you view the MCQs as official exams and are aware that different policies exist for missing an MCQ than for a practical. In addition, Maynooth University Exam policies and regulations will apply and be enforced during MCQs. All MCQs are compulsory and failure to sit these exams will result in a zero grade. If you foresee that you may not be able to sit an MCQ it is imperative that you contact the lecturer who is setting the exam BEFORE the MCQ. Individuals who miss an MCQ may be permitted a resit if they have an acceptable reason and provide the appropriate evidence. Individuals who miss an MCQ without an acceptable reason

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and who did not contact the lecturer who has set the exam prior to the MCQ will not be offered a resit and will consequently be awarded a zero grade. MCQs are exams and Maynooth University Exam policies and regulations apply during these. The Maynooth University Exam policy can be viewed at the Examinations and Timetabling Office Webpage under “Policies and Regulations”.

Medical Certification You are reminded of our policy on medical certificates (page 33). NOTE THAT IF YOU ARE SUBMITTING A MEDICAL CERTIFICATE, THE CERT MUST BE ISSUED DURING THE PERIOD OF ILLNESS. BACKDATED CERTIFICATES WILL NOT BE ACCEPTED UNDER ANY CIRCUMSTANCES.

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.

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SAMPLE DECLARATION OF ORIGINALITY FORM

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: .............................................................................................................

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SAMPLE LITERATURE PROJECT COVER SHEET

Maynooth University Department of Biology, 2016-2017

BI423 LITERATURE PROJECT

Protein Secretion in Eukaryotes: The Mechanism of Protein Targeting and the use of the Baculovirus

system for the Secretion of Recombinant Proteins

This thesis is submitted in fulfillment of the Biotechnology Degree.

SUBMITTED BY: Eimear Dennehy

STUDENT NO: 93189606

SUPERVISOR: Prof. Sean Doyle

DATE: 10 February 2017

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SAMPLE LITERATURE REVIEW FORM

4th Biotechnology 2016-2017

LITERATURE REVIEW FORM

Student Name: ____________________________ Student Number: ____________________ Literature Review Selection (please select your top three choices of topic): 1._________________________________________ 2._________________________________________ 3._________________________________________ Please complete and return to Professor Sean Doyle by 5pm Friday 23 SEPTEMBER 2016.

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