UCD School of Chemical & Bioprocess Engineering

• Engineering Education
• Engineering Outreach
• Biochemical Engineering - shear sensitivity of biological systems

Research Support

RESEARCH SUMMARIES

Peer-Assisted Learning:

'Learning from others', variously implemented as Supplemental Instruction (SI), Peer-Assisted Learning (PAL) and Peer Assisted Study Sessions (PASS) is widely and successfully used in higher education, across a range of disciplines. Over the past two years, with the assistance of the UCD Centre for Teaching & Learning, I have introduced a related 'small group, cross-year tutoring' initiative to the Chemical Engineering curriculum.

Peer-Assisted Tutorials (PATs), a form of Peer-Assisted Learning (PAL), were implemented, as part of a core undergraduate module (CHEN30020: Unit Operations). I had previously delivered the module via lectures, with a small number of lecturer-directed tutorials. For 2008-09, I introduced weekly PATs, in addition to lectures. PATs were designed to support students in becoming more self-directed in their learning, to develop student confidence in tackling Chemical Engineering problems and to promote effective group work. For each PAT, 3rd Year students (Tutees) worked together in groups of 5-6, led by a trained Peer Tutor, a 4th Year student who had previously taken and passed the Unit Operations modules. PATs were well-structured, with each session involving two parts: (i) review of a previously assigned homework problem and (ii) introduction and group discussion of a new homework problem. PATs were evaluated on the basis of feedback from both Tutees and Tutors. PATs attracted high participation rates and yielded high levels of Tutee and Tutor satisfaction, in terms of student perceptions of their understanding of relevant material and enhancement of professionally relevant transferable skills.

Based on the success of the process, for the 2009-10 academic year, an associated module was developed for Tutors, who will receive credit for their efforts; additionally, with the direct involvement of Dr Dermot Malone, the PATs were extended to a computer-based core module (CHEN30160: Computational Methods in Chemical & Bioprocess Engineering).

This PAT system was specifically developed for a Chemical Engineering module. However, the approach, in which a group of Tutees, under the guidance of a Tutor from a slightly more advanced stage of the same academic programme, work together on the exploration and solution of discipline-specific problems, is readily adaptable to almost any subject area; it is particularly applicable to quantitatively-based subjects. 

Responses of Plant Cell Systems to Hydrodynamic Stress:

Commercially viable exploitation of biocatalysts to produce valuable pharmaceuticals depends crucially on the ability to speedily and reliably scale-up a biological process from the laboratory bench to the production floor. At the heart of almost every bioprocess - and posing the most severe scale-up challenges -  is the bioreactor, the vessel in which the organism is cultivated and/or product formation occurs. The bases for scale-up are poorly defined and loss of productivity on scale-up is common. A key theme, worldwide and within our group, is the interaction between suspended cells and the hydrodynamic environment prevailing in the bioreactor.

Plant cell culture technology facilitates the production of valuable chemicals (including, for example, Taxol, the anti-cancer agent) under controlled and reproducible conditions. However, given the diversity of phytochemicals, the range of products commercially produced via this route is extremely limited, due to economic feasibility which, assuming that a market for a plant product exists, derives from a combination of biological and process-based factors. Plant cells, in common with mammalian cells, are sensitive to the hydrodynamic stresses in bioreactors.

Figure 1. Submerged jet apparatus used to subject cells to well-defined levels of shear.

Although most research emphasis has focused on lethal effects of shear stress, sub-lethal phenomena are of particular importance for process optimisation. Our work has involved the identification and analysis of post-stress responses exhibited by cell suspensions exposed to well-defined levels of shear (e.g. in capillary and submerged-jet devices (Figure 1)) and to less well-defined, but more practically relevant cultivation conditions (in a bioreactor), with a long-term view to ultimately elucidating the mechanism(s) by which hydrodynamic stress is sensed and trandsuced within the cell.

Plants have developed an array of defense mechanisms which afford them protection against pathogenic attack. One of the first measurable responses to infection, occurring within a few minutes of stress imposition, is the production and release of active oxygen species (AOS), known as the oxidative burst (OB). Our work has shown that the OB also occurs in response to non-pathogenic stimuli, including hydrodynamic stress (Figure 2) and, further, that hydrodynamic stress stimulates transcription-level responses. The OB is only one in a series of stress responses, which may culminate in commitment to a programmed cell death (PCD) pathway (Figure 3), similar to that exhibited by mammalian cells and which seriously undermines system productivity. The ultimate objective of this strongly inter-disciplinary work is the development of a rational approach to scale-up, based on a comprehensive understanding of the interactions between the cell and its cultivation environment.

Figure 2. DNA and RNA confocal scan images showing evidence of increased RNA levels (red) in Arabidopsis thaliana cells (a) after cultivation in a bioreactor, relative to (b) cells from control cultures. Images by Paul Jeffers; A. thaliana generously provided by Dr. Paul McCabe.




Figure 3. Morinda citrifolia cells (x 100 magnification, stained with acridine orange), 5 hours post-shear (submerged jet, 0.85 bar), showing condensed chromatin, characteristic of PCD. Images by Paul Jeffers; M. citrifolia generously provided by Dr.Graham Wilson. Morinda citrifolia cells

Peer Review

Member, Editorial Board, Process Biochemistry, 2007 to date

Reviewing and External Examining

• Member, Engineering Programmatic Review, Peer Review Group, Cork Institute of Technology, 2007
• Invited Reviewer, Czech Science Foundation (GACR), 2007
• Invited Reviewer, German Federal Ministry of Education & Research (BMBF), GABI-FUTURE: Plants as a Basis for Life – from Genome Analysis to Product Innovations, December 2006
• Member, Engineers Ireland (formerly IEI) Accreditation Panel, Cork Institute of Technology BEng (Hons) Chemical & Process Engineering, October 2005
• Invited Reviewer, Australian Research Council (ARC) Discovery Projects, 2005
• Invited Reviewer, Enterprise Ireland Basic Research Grants Scheme, 2001, 2002
• Member, Evaluation Panel, Enterprise Ireland International Collaboration Scheme, 2002
• Reviewer, FP5 Marie Curie Fellowships, Brussels, November 2000
• Research Article Reviewer, Biotechnol Bioengng, Biochem Engng J, Education for Chemical Engineers, J Chem Technol Biotechnol, Enzyme Microb Technol, J Plant Physiol
• Doctoral Dissertation External Examiner, University of Birmingham (UK), Adelaide University (Aus), Dublin City University (Ireland), University College London (UCL, UK)
• MEngSc Thesis External Examiner, University College Dublin (while employed in DCU)

Conferences/Meeting Organisation

• Dr Geraldine O'Neill,  UCD Centre for Teaching & Learning: Introduction of problem-based learning to engineering curricula; development of group-based problem-solving skills
  
• Dr Eilis Hennessy, Dr Charo Hernandez, Dr Henry McLoughlin: Student & staff experiences of non-programme electives; the effects of modularisation on assessment - student & staff perspectives
  
• Dr Paul McCabe, UCD: Sub-lethal stress responses in plant cell suspension cultures
  
• Dr Brian Glennon and Dr Susan McDonnell, UCD: Development of in-line methodologies for bioprocess characterisation - plant and mammalian systems
  
• Dr Kevin O Connor and Dr Dermot Malone, UCD: Characterisation and optimisation of liquid-liquid bioreaction systems
  

• Dr Rosaleen Devery, DCU: Sub-lethal stress responses in plant cell suspension cultures
  
• Mrs Ingrid Hook, TCD: Optimsation of secondary metabolite production by plant cell suspension cultures
  

Teaching Responsibilities

• CHEN20020: Chemical & Bioprocess Engineering Measurement
  
• CHEN20040: Chemical & Bioprocess Engineering Laboratory I
  
• CHEN30020: Unit Operations I
  
• CHEN30040 Commerical Phamaceutical & Bioprocess Technology
• CHEN40200: Chemical Engineering Research Project
  
• CHEN40210: Advanced Experimental Design: Group-based Problem-Solving for Engineers
  
• CHEN40430: Peer-Assisted Tutoring in Chemical Engineering
  

Teaching Initiatives

• Problem-Based Learning
  
• Peer-Assisted Learning
  
• Group-Based Problem Solving for Engineers 
  

3 PhD, 1 MEngSc, 3 MSc candidates supervised to completion