Helen Lawton Smith
email: h.lawton-smith@bbk.ac.uk

Rupert Waters+
email: rupert.waters@buckingham.ac.uk

NETWORKS AND REGIONAL INNOVATION SYSTEMS

Keywords: Scientific labour markets, networks and regional innovation systems scientific labour markets, regional innovation systems, Oxfordshire and Cambridgeshire

, the RIS literature has relatively neglected processes of labour force development. This paper addresses two questions (i) what is the role of labour markets in the making of regions as innovative systems and (ii) what is the role of labour markets in Regional Innovation Systems. The labour market and specifically the networks that exist between highly skilled workers are positioned at the centre of the analysis, using evidence from the UK high technology economies of Cambridgeshire and Oxfordshire.

INTRODUCTION

While quality of the labour force in a locality is the single most important component of local competitiveness [START_REF] Simmie | Innovation in Europe: A Tale of Networks, Knowledge and Trade in Five Cities[END_REF], the systems of innovation literature, including the regional innovation systems (RIS) literature, has devoted relatively little attention to processes of labour force development (see for example the neglect of labour by [START_REF] Cooke | Regional Systems of Innovation: Introduction to the concept[END_REF], CASPAR and VAN WAARDEN (eds) 2005, ASHEIM et al (eds) 2003). Yet a long line of studies dating back to [START_REF] Keeble | Entrepreneurship, high-technology industry and regional development in the United Kingdom: the Case of the Cambridge Phenomenon[END_REF], ANGEL 1991, through to SIMMIE et al 2002, BERCOVITZ and FELDMAN 2006[START_REF] Saxenian | The New Argonauts: Regional Advantage in a Global Economy Boston[END_REF] have focused both on cumulative, hence systemic processes, whereby the highly skilled are attracted to particular locations by the presence of other professionals whose movement between employers is a crucial factor in transferring technology within regions or localities. The argument is that the absorptive capacity [START_REF] Cohen | Absorptive capacity: a new perspective on learning and innovation[END_REF] of the highly skilled is crucial in drawing in, assimilating and translating new knowledge and applying it commercially, with the 'embodiment' of knowledge in the regional labour force being one of the primary mechanisms through which such localization occurs (HOLMEN and DOLEREUX 2003, 15-16).

As such concentrations of expertise develop greater demands for coordination within labour markets arise. Studies have shown that at the early stages of new concentrations self-organising processes emerge whereby informal institutions develop that help reinforce the impact of labour as a key component of the innovation process (see [START_REF] Garnsey | The Genesis of the High Technology Milieu: A study in Complexity[END_REF]. Later there is a demand for more formal initiatives designed to coordinate the supply and demand of skills, for example to ensure that there is a matching process between the career needs of individuals and the skill needs of firms. Under some conditions the former include the development of communities (BROWN and DUGUID 2000a) and 'learning communities' [START_REF] Benner | Learning communities in a learning region: the soft infrastructure of cross-firm learning networks in Silicon Valley[END_REF], while the latter might be skill specific training programmes. Therefore, if somewhere has a localised expert labour market system it is likely that there will be evidence of institutions, social as well as economic, which collectively comprise a system of governance within the localised component of a more geographically extensive highly-skilled local labour market.

Such fundamental issues of skill accumulation and the labour market mobility which lead to innovation through the transfer of knowledge are relatively neglected in the RIS literature. Taking coordination within localised labour markets as it theme this paper argues labour markets deliver innovation in particular places, driving regional innovation systems to a far greater extent than institutional arrangements -which rather than being instrumental in setting the climate for innovation, are reinforcing effects (see [START_REF] Garnsey | The Genesis of the High Technology Milieu: A study in Complexity[END_REF].

The paper addresses two questions (i) what is the role of labour markets in the making of regions as innovative systems and (ii) what is the role of labour markets in regional innovation systems. In particular, in relation to both questions, we are interested in how flows of people (and knowledge) through (local) space are coordinated.

Processes of coordination, we argue, are fundamental to understanding how regional labour markets contribute to knowledge transfer and learning. In this paper, we position the labour market and specifically the networks that exist between highly skilled workers at the centre of the analysis. We examine flows of people and knowledge through geographical space within local labour market for the highly skilled, using evidence from the high technology local economies of Cambridgeshire and Oxfordshire in the UK. The remainder of the paper is in three sections. In the first, the justification for the prioritisation of the role labour markers in RIS is reviewed. The second introduces evidence from a study of labour market mobility in the high-technology local economies of Oxfordshire and Cambridgeshire. The third draws some conclusions.

We argue that localised RIS in Oxfordshire and Cambridgeshire can be observed in patterns of intra and inter-regional mobility but that evidence of the localisation of national and global innovation systems is stronger.

CONCEPTUAL FRAMEWORK

Recent literature has focused on the interdependence of intra and inter-firm learning processes in firms [START_REF] Makinen | Intra-firm and inter-firm learning in the context of start-up companies The International[END_REF], in collective learning at the local/regional scale [START_REF]Innovation as an Interactive Process: from Userproducer' Induction to the National System of Innovation[END_REF], STORPER 1995[START_REF] Lawson | Territorial clustering and high technology innovation: from industrial districts to innovative milieux[END_REF] and in the institutions which emerge to sustain both [START_REF] Garnsey | The Genesis of the High Technology Milieu: A study in Complexity[END_REF][START_REF] Benner | Learning communities in a learning region: the soft infrastructure of cross-firm learning networks in Silicon Valley[END_REF][START_REF] Isaksen | Regional Clusters Building on Local and Non-Local Relations: A European Comparison[END_REF]. It is only recently that how labour markets contribute to both and hence to regional innovation systems has become the focus of attention. In part one of the literature review we consider the key concepts of regional innovation systems in order to identify where labour might fit into definitions of RIS, which we discuss in part two.

(i)

Regional Innovation Systems Regional innovation systems are extremely varied in form and as systems in process (see [START_REF] Cooke | Regional Systems of Innovation: Introduction to the concept[END_REF]. HOWELLS (1999) for example, points to three dimensions of RIS: regional structure -administrative, legal, constitutional and institutional arrangements; the long-term evolution and development of regional industry specialisation, and the additional core/periphery differences in industrial structure and innovative performance. The last relates to higher order versus lower order functions and activities and patterns of government expenditure. He also argues that RIS are One of the most difficult issues in identifying the existence of an RIS as opposed to an administratively defined area, is that of whether the system can be seen to have distinct features. For [START_REF] Edquist | Systems of Innovation -A Critical Review of The State of the Art' in Handbook of Innovation[END_REF][START_REF] Roper | The Scottish Innovation System: Actors Roles and Actions Report prepared by[END_REF], like HOWELLS, boundaries, functions and co-ordination are the identifiers of the existence of an RIS.

EDQUIST suggests that there are three criteria that must be met if an innovation system is said to exist in an area: coherence -demonstrated by feedback loops, common developmental trajectories and complementary competencies between agenda; unified function where there are identifiable objectives or aims to which all elements of the system contribute; and being bounded -creating the possibility of discriminating between the system and the rest of the world. Universities, whose contributions to the labour market are underplayed in regional innovation literature, therefore, might be expected to play an initial role in diffusing technological knowledge through graduate recruitment. In the latter the innovation process involves the application of existing sources of knowledge or new combinations of knowledge. This often occurs in response to the need to find technical responses to specific problems that emerge from interactions between clients and suppliers. In these conditions, labour market processes might be more interesting in the synthetic model as there is less reliance on codified knowledge, which is more important in the analytic model where universities might be expected to play a more downstream role (ASHEIM and COENEN, 2006).

The distinction between analytic and synthetic clearly relates to boundaries, governance and industrial clustering and specialisation and the associated aspects interactive learning as it includes the recognition of the different research and institutional structures required to support the knowledge base in the cluster (WOLFE et al 2005). Thus in regional innovation systems based on analytical knowledge (hightech economies) there will be different processes of coordination between the various actors compared to those based on synthetic knowledge, in which the operation of labour markets will in turn differ in their significance. Table 1 here

Governance is a key element in the RIS concept as it is that which defines how a system is formally organized to overcome market (MALERBA 2002) and or system failures (WOOLHUIS et al 2005). It is expressed as both government and nongovernmental activities [START_REF] Stoker G | Introduction[END_REF]. With respect to scientific labour markets, formal policy structures include private sector organisations such as branches of industry associations and chambers of commerce which have responsibilities for addressing skills issues, and public organisations such as universities and polytechnics, regional ministries and skills councils with devolved powers concerning enterprise and innovation support, particularly for small and medium-sized enterprises (SMEs).

Universities' contribution to local labour markets, which might be expected to be pivotal in sustaining localised innovation systems, is problematic if the evidence from an OECD is accepted. This finds that although there is a positive correlation between secondary and tertiary educational attainment and economic performance, it is much stronger for secondary education, while 'university education makes a relatively modest contribution' (OECD 2001, 96). HOMMEN and DOLEREUX (2003, 18) comment, 'These results hardly bear out the expectation that 'elite' labour and higher education are vital for 'learning regions'. Further reference is therefore made to case study evidence on the importance of 'industry structure, the curriculum of [a region 's] universities, and the degree of co-ordination between education and industry'.

Moreover, while universities teach codified knowledge to students, there is no guarantee of a match between teaching and the kinds of students required by the firms Hence there is potentially a difference between universities with a regional mission (such as Newcastle University) and those without (such as Oxford University) and the types of universities needed in core and peripheral areas [START_REF] Benneworth | sessions on 'Universities and the Knowledge-Based Economy[END_REF]. In addition, there is no a priori assumption that the highly skilled will absorb the kinds of knowledge that have practical applications in the regional economy. (2002) argument that creative people are a key element of the contemporary creative city, argues that the production system is at the heart of understanding the system of employment which will attract, employ and train such people over any reasonably long run period. This complements HOWELL'S (1999) point about regional industrial specialisation as a feature of innovation systems.

Second, flows refer to both mobility of personnel within as well as into and out of a region. Both have implications for firms' organisational strategies and individual's career development [START_REF] Green | Geographical mobility: Family impacts London: Published in association with Joseph Rowntree Foundation GREEN, A[END_REF] as well as the human capital resources in particular cities and regions [START_REF] Champion T | Are our cities still losing human capital? The evidence of the 'moving group' data from the 2001 Census[END_REF]. Intra region mobility is both a competitive process and form of coordination of knowledge flows, both contributing to the creation of an RIS. MASSEY (1995) for example, argues that a better understanding of processes can be obtained by examining collective activity within high-technology labour markets. She describes how in such highly differentiated labour markets, a dynamic of competition is created in which it is necessary for both employers and employees to have a detailed knowledge of the staff plays an important role in the intra-regional transmission of expertise and fostering of inter-firm links'. While HENRY and PINCH (2000) suggests that the place is important, [START_REF] Keeble | Entrepreneurship, high-technology industry and regional development in the United Kingdom: the Case of the Cambridge Phenomenon[END_REF][START_REF] Segal Quince | The Cambridge Phenomenon: the Growth of High Technology Industry in a University Town Cambridge:SEGAL QUINCE and Partners[END_REF] show that it is through people that the place keeps ahead. With regard to the success of its high technology econony SEGAL QUINCE (1985, 33) noted that 'Cambridge is not only a good place in which to recruit, but of greater significance, also in which to recruit outstanding people' .

Flows of people into a region (and out of a region) are an important component on the making of a RIS, but as GREEN ( 2006) points out, is less well researched. This is particularly so with respect to international mobility within Europe, possibly because international mobility between European countries has not yet become a major pattern, the trend is still one of outflows to the US [START_REF] Mason | High-Level Technical Skills, Labour Mobility and Knowledge Transfer in Western Europe[END_REF]. More important is mobility between regions. As FLORIDA (2002) argues, the key to economic growth lies not only in the ability to attract the creative class, but also to translate that underlying advantage into creative economic outcomes in the form of new ideas, new high-tech businesses and regional growth. Other evidence while not wholly supporting FLORIDA's thesis, has identified that the tendency of initially skilled places to become more skilled over time [START_REF] Berry | The Divergence of Human Capital Levels Across Cities[END_REF] who emphasised the quality, mobility and flexibility of the labour market as being key to transferring ideas within industrial districts.

The attraction of various types of talent (students, researchers, IT specialists, research scientists etc.) is now a formal governance agenda. Measures include tax incentives, repatriation schemes and improving the attractiveness of academic careers (OECD 2004). BACHTLER (2004) proposes that attracting star academics, researchers and highly skilled knowledge workers is increasingly replacing inward investment as a key role for regional development agencies. He cites Quebec, where the government is offering five-year income tax holidays to attract foreign academics in IT, engineering, health science and finance to take employment in the region's universities. In Finland, Nokia invests in the cultural adaptation of foreign IT workers as a way to improve productivity but also to help to retain this 'talent' (OECD 2004).

Therefore, mobility is central to understanding co-ordination within the innovation process. Due to the fact that key industry clusters tend to be territorially based, talent attraction initiatives may be best designed by city and regional bodies that have strong industrial connections and a good knowledge of the local labour market (BACHTLER 2004).

Thirdly, networks are a key co-ordinating mechanism of information flows (LAMBOOY 2004). LAMBOOY argues that networks fulfil two functions: the first is facilitating the co-ordination of decisions made by separate entities (or nodes) of the networks and the second is the transformation of data, information and knowledge by using or making connections. These take the form of 'communities of practice' and 'learning communities; in local and regional settings (e.g. [START_REF] Brown | Mysteries of the region: Knowledge dynamics in Silicon Valley[END_REF][START_REF] Schoenberger | The firm in the region and the region in the firm[END_REF]BENNER 2004). training policy need to be taken into account. HOMMEN and DOLEREUX argue that such an approach is particularly needed as regional or local policy makers may underestimate the difficulties in developing cooperative governance structures. Such problems stem from macro-economic conditions and national state policies which influence regional or local labour markets.

The Rates of turnover exhibited in the UK labour market as a whole.

The pace of employment turnover in the UK overall is increasing. In their study of job tenure, GREGG and WADSWORTH (1999) found that the average job in Britain lasts for a little over 5 years. They additionally found that the average new job lasts for 15 months -that is to say that workers can be expected to continue to move between jobs before finding an appropriate job match. More recently, the Chartered 4 below.

Table 4 here

In IT and high-technology sectors CIPD data gives an average job tenure of 5.1 years.

The CIPD data therefore shows job tenures in the UK's high technology and IT sector to be longer than for professionals as a whole. In Motorsport Valley, a sectorally specialised cluster which includes Oxfordshire, the level of turnover is the highest recorded suggesting that there are important sectoral variations [START_REF] Henry | The) industrial agglomeration (of Motor Sport Valley): A knowledge, space, economy approach[END_REF] and possibly that skills are more easily transferred between very similar firms than between co-located firms even though they might have similarly well qualified workforces. In this sense, the networks that develop provide a means of coordinating knowledge flows within labour markets. likely to be a particular organisation rather than the cluster itself.

The survey of the highly skilled mapped the career trajectories of respondents. In both case studies it was most common for those currently employed to have previously worked elsewhere and to have subsequently moved into the areas. This was true for all three institutes. Although no statistics exist for the population of the UK as a whole, this situation is not unexpected, but does have implications for organisational strategies, where decisions to expand or remain may be affected by the propensity of individuals to move into the locality and the career development of individuals (cf GREEN and CANNY 2003).

The findings presented in Table 6 below offer limited support for making the case that Oxfordshire and Cambridgeshire are important world centres of scientific expertise.

The proportion of the sample which had moved in and out of the respective local economies was highest in each of the institutes in Cambridgeshire than in Oxfordshire reflecting the smaller firm size in Cambridgeshire, and the large internal labour markets therefore available in Oxfordshire, and the shorter average job tenure [START_REF] Smith | Employment mobility in hightechnology agglomerations: the cases of Oxfordshire and Cambridgeshire[END_REF]. The table tells us who is there at the moment. 'One way' refers to moving into either Oxford or Cambridge, in and out means that they have taken a job outside the area and then returned. 'First job' means that this is their first career move. This provides some support for the [START_REF] Berry | The Divergence of Human Capital Levels Across Cities[END_REF] argument about the reinforcing effects of entrepreneurship on cluster development. Cambridgeshire had begun careers in that location and not left -ranging from 14 per cent for Oxfordshire physicists to 20 per cent for the county's chemists. This is in addition to the numbers who are still in their first job -regardless of time in that position which was 37 years in the case of one Cambridgeshire chemist. The IEE is the least qualified profile of the three institutes and so may not be in such global demand as for the physicist and chemists. But for the most highly qualified, Oxford and Cambridge are the places to be.

Validation for these findings is provided by the analysis of the 2001 UK Census presented in Table 7 below. This shows that the cities of Oxford and Cambridge respectively have the least and second least settled populations of all English local authorities and the 6th and 4th highest proportion of the present population to have been living outside the UK a year previously (at 3.8 and 4.1 per cent respectively).

Their respective labour markets for the highly skilled can therefore be seen to be located within counties used to exceptionally high levels of migration. Just under a fifth (17.4 per cent) of survey respondents had over the course of their careers previously worked abroad. The proportion varied by discipline ranging from 8 per cent of electrical engineers in Oxfordshire to 23 per cent for the same county's physicists.

Table 7 here

These findings are interesting when considered in conjunction with analysis of the results of where respondents would look for their next job. Where respondents would Respondents from the IEE were the most likely to only look for their next position within their own county, and accordingly the least likely to consider continuing their career overseas -with the US as the most common overseas choice, but recording only eight per cent of the stated locations. The table shows a UK focused labour market.

Chart 1 here

The advantages of carrying out a career in the Oxfordshire and Cambridgeshire as recorded by the survey of the highly skilled are presented in Chart 2 below. The effect of family ties is demonstrated by the response 'it is home' being the most common response in Oxfordshire and the second most common in Cambridgeshire.

However, 'career possibilities' and access to university research' were the other most popular responses, followed by 'ease of finding work', all of which suggest the presence of agglomeration economies within each regional innovation system (cf in the making of regions as innovative systems and (ii) what is the role of labour markets in regional innovation systems. We argue that that the coordinating role of labour markets is key to understanding both. The framework for analysing regional innovation systems from this perspective identified three common elements, boundaries, and industrial specialization/clustering and interactive learning, and governance, while the review of the literature on the role of labour markets identified four interrelated elements: stocks and flows of labour, networks, and informal and formal governance systems. Evidence from the two case studies has been used to explore these themes.

Defining the boundaries of RIS, industrial specialisations and clustering using labour market data of stocks of skills as indicators is always inexact. Instead, it maybe enough to point to the centre of labour markets, recognising that distance decay effects and centripetal forces draw in skilled people to and from particular locations, effects which contribute to the operation of regional innovation systems. We focus on industrial structures, using the distinction made by ASHEIM and COENEN (2006) Here we are interested in how flows of people (and knowledge) through (local) space which give rise to interactive learning and networks are coordinated. Mobility as a means of facilitating knowledge transfer, within and between spatial scales we argue, is essential in understanding how regional labour markets contribute to knowledge transfer and learning. The evidence points to considerable mobility into each region, supporting the argument that the agglomeration of skills [START_REF] Berry | The Divergence of Human Capital Levels Across Cities[END_REF] is the key component of the making of regional innovation systems. We show how the two counties -places which started with higher levels of human capital than most of the rest of the UK have attracted more skilled people over the last two decades, created by local entrepreneurs (Box 1 and Table 6), thus creating RIS of particular kinds -analytic knowledge in both cases with strong accumulations of codified knowledge. This is supported by evidence in Chart 1 which shows considerable reinforcing effects of a disinclination of the respondents to leave their county and region as a whole because of the career prospects.

In possibilities, backed up by ease of finding work -as well as it being home. This study, however, gives less support to the claims of the over-riding importance of networks as a key coordinating function. Chart 3 shows that the printed advertisement, particularly in Oxfordshire was considerably more important than word of mouth as a method of finding current employment.

In sum, we suggest that more attention is paid to how labour markets operate in understanding how regional innovation systems function. The findings also have important policy implications because the case studies highlight that even in such RIS as these that are characterised by the highly-skilled, that relative shortages in supporting skills may be inhibiting factors in the further success of local and regional economies.

ACKNOWLEDGEMENTS: We thank the two referees for their constructive comments on an earlier version of this paper. Source: Authors' survey

  localised learning and tacit know-how sharing -the informal links between key personnel. In spite of this variety, definitions of RIS have at least three points in common: they all stress boundaries, governance, and industrial specialization/clustering and associated interactive learning processes. We next discuss these points drawing on studies which have emphasized different aspects of each, to develop understanding of the RIS concept, in general and then specifically in relation to labour markets.

  ASHEIM and GERTLER (2005) address the issue of coherence from a rather different perspective on clustering and interactive learning, to the standard discussions of types of cluster specialisation (see for example the discussion in Martin and Sunley 2003.) In their categorisation of industries and their industrial contexts they distinguish those with an analytical knowledge base (most closely akin to high-tech sectors) or those with a synthetic knowledge base, the key features are presented in

  of the university -they are not necessarily mutually reinforcing.

  ANGEL (1991) MASSEY finds that scientific workers change jobs frequently. She also finds that they belong to a professional community which extends beyond and cuts across the confines of the firms that employ them. The professional labour market does not operate in terms of simple supply and demand, nor does it operate in terms of cost.MASSEY (1995, 138) argues it is a 'very individualistic labour market' in which particular people are sought, singled out by their possession of knowledge, a monopoly, she argues, they have developed through the separation of conception from execution. She notes that scientists are highly mobile, and that to a large extent they choose their employers, so that work follows them and not vice versa. MASSEY argues that the clustering effect caused by the locational preferences, for example of electronic engineers (citing KEEBLE 1976) is reinforced by the way in which the labour market for their skills operates. The labour market is able to operate in this fashion due to the nature of the electronics product market; firms compete through quality, innovation and new products at least as much as through cost so that 'what is being bought on the labour market is not just labour power but scientific knowledge'.Scientific knowledge is also transferred through recruitment by industry of graduates and employees from universities and other research institutions. In this respect, the scientific labour market can be seen as a 'bridging institution' between academia and industry for the co-production and transfer of knowledge and competences[START_REF] Lanciano-Morandat | The scientific labour market in international perspective: a 'bridging institution' between academia and industry for the co-operation and transfer of knowledge and competences[END_REF] Yet asMICHIE and SHEEHAN (2003) find, high commitment organisations or transformed workplaces are positively correlated with innovation(in ASHEIM and COENEN 2006). Thus barriers to technology transfer (LAWTON SMITH 1998) may be overcome by labour mobility.KEEBLE et al (1998, 20) emphasise the importance of the movement of the highly employers arguing that the 'local inter-firm movement of skilled

  governance systems sit along-side informal system of coordination through networks. Shortages of skills which arise when clusters become established create a demand for governance systems in the form of training and financial systems etc and so on. These present particular policy problems resulting from Myrdal-type polarisation effects whereby the rich get richer. Such policy implications are addressed byFLYNN (1988) in HOMMEN and DOLEREUX (2003). He emphasised the importance of adopting a life cycle framework in human resource planning arguing that institutional factors such as the mix and characteristics of firms and human resources, and the timing of adjustment to avoid shortages and surpluses of labour and of anticipating institutional conflicts and problems in education and

  Institute of Professional Development (CIPD) Labour Turnover Survey for 2000 (CIPD, 2001) recorded an average overall turnover rate for full time workers of 21 per cent (giving an average job tenure of 4.6 years). A comparison of average job tenures from recent studies is presented in Table

  from three postal surveys of the highly skilled between November 2000 and August 2001. Questionnaires were sent to the members of the Institute of Electrical Engineers (IEE), the Institute of Physics (IOP) and the Royal Society of Chemists (RSC) in the two case study areas. These three institutes represent the scientists and engineers of the case study areas. As far as we were able to ascertain, a biological sciences institute does not exist and as much of the science behind biological sciences is chemistry-based, for example bio-chemistry, many working in that field belong to the RSC. A total of 6,099 questionnaires were sent out to institute members in Oxfordshire and Cambridgeshire yielding 831 usable responses. The returns by institute and case study are presented in Table5below.

  their previous job histories suggest that these answers are not entirely aspirational, rather they reflect a realisation of their worth in the wider hightechnology labour market. However, the proportion of respondents who would look locally is notable given the previous geography of their employment, perhaps reflecting the need to consider family and the practicalities of repeated moves for homeowners may be reflected in the high proportion of respondents who would look locally, reflecting the quasi-immobility[START_REF] Camagni | Local 'milieu', uncertainty and innovation networks: towards a new dynamic theory of economic space[END_REF] of the highly skilled despite the global demand for their labour. The results of the analysis by location are presented in Chart 1 below.

  2005). Other results from the survey included an appreciation of the natural and built environment. This suggests evidence of coordination, through the local knowledge of career opportunities and scientific networks which link university research to the high-tech cluster.Chart 2 here Chart 3 below presents the means by which the highly skilled in Oxfordshire and Cambridgeshire found their current job. Despite the clustering effects noted above, it is the printed advertisement that is overwhelmingly the most common way to have found employment, ahead of word of mouth in both case studies. Hence on this indicator, networks are not a major source of coordination within the labour markets, and that the interactive RIS model of associationalism is limited in this respect at least.When the stage of career is considered different findings emerge. For those in their first job formal methods of job searching -printed advertisements and particularly direct applications to companies -are the most common forms, however the informal mechanisms we would expect to be visible in regional innovation systems are still prevalent, suggesting a strong link between the education institutes of Oxfordshire and Cambridgeshire and their local high technology local markets. With the exception of the Oxfordshire's electrical engineers respondents in their first jobs had made found their current positions by being contacted by their employers directly or through the use of employment agencies, highlighting the importance of the networks developed by individual scientists and engineers through work.

  we set out to address two questions (i) what is the role of labour markets

  of analytic and synthetic knowledge, arguing that Oxfordshire and Cambridgeshire are exemplars of the former. Here we show that the stocks of the highly-skilled (scientifically qualified and professionals) in each county marks them out as distinctively different to other locations, particularly in the cities of Oxford and Cambridge and show evidence of specialised clustering and the reinforcing effects identified by[START_REF] Berry | The Divergence of Human Capital Levels Across Cities[END_REF]. Both locations appear to be focal points wide labour markets for chemists and physicists. It is also shown that the RIS what appear to be very similar locations have differing characteristics. This is because their hinterlands are different. Cambridge as more of a stand-alone city-type innovation system whereas in Oxfordshire there is more evidence of a more geographically unified scientific/professional labour market, with generally stronger patterns of in-mobility.

  answer to the second question, what is the contribution of labour in RIS -we suggest labour markets are critical to coordination of economic activity, through the career mobility of individuals and the networks that they take with them. Chart 2 illustrates the advantages of current location for individuals, particularly career

  P. (1991) High-technology agglomeration and the labor market: the case of Silicon Valley, Environment and Planning A, 1991, Vol. 23 pp. 1501 -1516 ASHEIM B., and GERTLER M. (2005) 'The geography of innovation: regional innovation systems' In FAGERBERG J., MOWERY D.C., and NELSON R.R. (eds) The Oxford Handbook of Innovation Oxford: OUP ASHEIM B., & COENEN L. (2006) "Contextualising Regional Innovation Systems in a Globalised Learning Economy: On Knowledge Bases and Institutional Frameworks", Journal of Technology Transfer 31, pp 163-173 BACHTLER J. (2004) 'Innovation-led Regional Development: Policy Trends and Issues' Paper presented at the OECD conference on Innovation and Regional

Table 1

 1 biotech, where the production process draws on sources of knowledge, and tend to draw upon research results from universities or national laboratories.

	as IT and
	F o r
	P
	e
	e r
	R
	e
	v i e
	w
	O n l
	y
	6

below. The former are those industries that rely on scientific knowledge such

  of the better training of undergraduates, graduates, and other employees in industry -necessary if SMEs are to recruit graduates and make the best use of them. Such intervention could strengthen the links between further and higher education sectors and the local economy and ensure a strong value chain of skills. among the fastest growing centres and have dense populations of research activity and highly skilled people in high-tech SMEs and research institutions. They are both exemplars of foci of analytic knowledge-based systems and interactive RIS. The two counties are both located about 50 miles from London, Cambridgeshire to the North and Oxfordshire to the West. They are similar in size and population. Research Councils Rutherford Appleton Laboratory. Since 2007 the CCLRC has become the Science and Technology Facilities Council, STFC) while Cambridge has a higher number of multinational research laboratories than Oxford. In Cambridge they include Schlumberger, SmithKline Beecham, Toshiba, Sony and Microsoft, and in Oxford, Sharp, Dow Elanco and Esso (GARNSEY and LAWTON SMITH 1998). Hampshire and the London region have more very highly skilled people.

	Cambridgeshire covers 1300 square miles and has a population of 684,000; Oxfordshire's area is 1000 square miles with a population of 598,000. Both have Each county therefore has high and growing concentrations of indigenous high-tech firms formed by local, often academic, entrepreneurs in diverse sectors. In particular both are leading growth centres for the UK's biotechnology industry. CHADWICK ET AL (2003) show that the number of firms and employment in key high-tech residents holding degree level qualifications, East Cambridgeshire is the next strongest performer in the county with a national ranking of 136 th . In Oxfordshire, the fall is not so sharp between districts, with all of the counties' local authorities scoring above the national figure. Oxford City and Cambridge City rank respectively 1 st and facilitating the provision Central to these activities are (i) the identification of where Higher Education historic and influential universities and the residential attractions of cultural centres. sectors in Oxfordshire in descending order is Software, Web/internet and other 2 nd in England and Wales for the proportion of residents qualified to NVQ level 3
	Institutes (HEIs) jointly can offer training and (ii) an intelligence gathering role about Scientific and technological resources are concentrated in their university and computer Services (635 firms employing 7,900), Other R&D activities (44, 5,900), Given this mix of institutes and small firms, both counties can be classified as with 19.0 per cent and 18.0 per cent respectively.
	F o r vacancies and availability of personnel which span the city-region and its hinterland. In conclusion, the selection of the empirical material which follows is based on the F o r government laboratories, providing centres of knowledge capable of supporting high-tech commercial activity. F o r Instruments, Medical and Optical Equipment (112, 5,000), Biotech, Pharmaceuticals & Medical Diagnostics, (73, 3,300) and Technical Consultancy and Testing (317, F o r 'interactive RIS' (COOKE 1998) (i.e. degree of 'associationalism' higher than average, mixture of large and small firms and public and private R&D) F Although the proportions show the bias in favour of 'knowledge workers', it is o r important to put these proportions into perspective. The actual numbers are less
	P e e r R e v i e P e e r R e v i e P e e r R e v i e 3,300). Similarly the IT sector is the predominant sector in the Cambridge Cluster P Stocks of human capital impressive than the proportions but are a truer reflection of scale. Other counties such P (160, 4,200), with Biotechnology (153, 5,300) and Electronic Equipment & Instruments (106 3,000) the second and third largest number of firms (LIBRARY HOUSE 2003). Hence both locations are dominated e e r e e as Berkshire, Table 3 shows the occupational structure of the two counties based on Standard r by computing/physics/engineering/chemical skills and illustrate BERRY and R e Occupational Classifications (SOC) 1 . The counties of Oxfordshire and R Cambridgeshire rank 2 nd and 3 rd respectively of the 42 NUTS 2 regions in England e GLAESER's (2005) point about increasing agglomeration economies, whereby initially skilled places become more skilled over time (see also Table 2). v i e and Wales behind Inner London, while the cities of Oxford and Cambridge rank v i e respectively 3 rd and 2 nd of the 376 local authorities in England and Wales with 28.0
	w w w w w per cent and 23.4 per cent of residents respectively employed in professional
	O n l O n l O n l O n l occupations (SOC2) compared to the national average of 11.2 per cent. Table 3 does however highlight the relative shortage of associate professional and technical O n l workers in both local economies.
	y y Cambridgeshire County Council 2002). CHADWICK ET AL (2003) using the y has retained the position it held in the 1970s and early 1980s as a leading centre for y y
	second approach demonstrate that a difference between the two counties was in the the personal computer and software sectors (KEEBLE and KELLY, 1986), although
	Their importance in the UK's 'knowledge-economy' as a whole and in particular
	rate of growth. Oxfordshire had the highest percentage rate of growth in high-tech Oxfordshire is home to the largest UK manufacturer of educational computers
	sectors such as bioscience has been recognised by central government (see for
	employees of all English counties in the period 1991-2000 (141 per cent) compared to (Research Machines). With regard to the research base, Oxfordshire has a greater
	example SAINSBURY 1999; TRENDS BUSINESS RESEARCH for the DTI 2001
	Cambridgeshire which was eighth with an increase of 53 per cent.
	and the LAMBERT REVIEW 2003).
	14 15 16 18

policy dilemma at the local level is that graduate recruitment and retention means both finding local jobs for people from the universities and recruiting new students from the local population into the region's universities. Particular problems lie in matching supply to the demand for skills. While some parts of an economy may have a high demand for graduates and technicians such as high-tech SMEs and research institutions, other firms, particularly low-tech small firms, are not able to meet the challenges presented by new technologies. In the UK for example, a general weakness of SMEs is insufficient training and graduate recruitment. Nationally, between 30 per cent and 40 per cent of firms employ no graduates

[START_REF] Curds | North East Graduate Labour Market Report Executive Summary 1999-2000[END_REF]

. Thus there is a role of governance in co-ordinating appropriate responses to this problem by key points made above. These are that RIS are constructed through labour market processes in which stocks of highly-skilled labour are accumulated and flows of knowledge are facilitated through career mobility, networks and interactive learning.

These comprise informal systems of governance and which may create a demand for intervention by formal institutions. This paper now explores these aspects of RIS development, focusing particularly on stocks and flows of the highly-skilled, particularly with respect to career mobility and the means by which this is facilitated.

THE CASE STUDIES: OXFORDSHIRE AND CAMBRIDGESHIRE

The two counties, although not the largest concentrations of high-tech activity in the UK, are Comparisons of levels of extent of entrepreneurship in high-tech economies depend on the definition of high-tech. For example CHADWICK ET AL (

2003

), using the Eurostat definition finds that Oxfordshire has 54,600 employees in 1,936 firms in 2002. However, using a more realistic and narrower Butchart-based approach using official statistics -for example excluding motor vehicle manufacture, but including Motorsport, 36,682 were employed in 1,400 firms, accounting for 12 per cent of employment in the county. Using their own broad definition but based on Eurostat, the estimate for Cambridgeshire for the end of 2001 was 48,300, about 13 per cent of employment in an estimated 1,526 'establishments'. The method of selecting firms on a case-by-case basis and non basic sectors such as wholesale and retail are discarded hence the Eurostat definition is not followed exactly (Personal communication They differ in that there is a higher proportion of small firms in the Cambridge region and a higher proportion of larger firms in Oxfordshire; Cambridge is more serviceorientated while Oxford has a greater orientation to manufacturing and Cambridge has a concentration of technical consultancies while there are none in Oxford. Cambridge density of public sector research laboratories, for example in atomic energy (UKAEA Culham) and scientific research (CCLRC, Council for Central laboratories of the Both Oxfordshire and Cambridgeshire have high proportions of well-qualified residents compared to the rest of England & Wales. Table

2

shows that 27 per cent of Oxfordshire residents and 25 per cent of Cambridgeshire residents are qualified to degree level (National Vocational Qualification (NVQ) level 4+) to rank as the 2 nd and 6 th most qualified counties respectively in England and Wales. These figures mask the range of performance recorded for the local authorities that make up the counties. Cambridge City is the strongest performer with 41 per cent of residents qualified to degree level to rank 8 th of the 376 local authorities of England and Wales while in Oxford City the proportion is 36.8 per cent to rank 12 th .

Table

2

here Outside the cities, South Cambridgeshire, which surrounds Cambridge City, also has a highly qualified workforce ranking 29 th in England and Wales with 29.8 per cent of

Table 3 here

 3

	F o r
	P
	e
	e r
	R
	e
	v i e
	w
	O n l
	y

1 For a full explanation see www.statistics.gov.uk/methods_quality/soc/structure.asp

Table 5

 5 However in contrast to Motor Sport Valley, the optimum place of work is

	here
	The response rate of 14 per cent is typical for this type of survey providing
	sufficiently large samples for both case study areas and institute membership to allow
	analysis by both place and branch of science and compares favourably with previous
	studies of high-technology local economies. For example, ANGEL's 1991 study of
	Silicon Valley was based on a postal survey of 67 firms (representing a 14 per cent
	response rate), SEGAL QUINCE WICKSTEED'S (2000) update to the Cambridge
	Phenomenon was based on a study of 12 firms, while HENRY & PINCH (2000)
	based their study on the careers of 100 engineers employed in Motorsport Valley.

"Motor Sport Valley acts as the epicentre of a global, yet highly spatially defined labour market ... As an individual in motor sport, it is rare that you do not at some point in your career, spend some time within Motor Sport Valley ... essentially this is about joining the knowledge community of motor sport production. Yet opportunities exist in this highly mobile industry to sell your knowledge elsewhere and many do so ... Thus few stray away from the Valley for long, returning once more to reconfigure their position within the community of knowledge".

Table 6

 6

	here

Table 1 :

 1 One of the problems of becoming a specialist is that the number of posts available is automatically narrowed. In my area of expertise there are probably 200 relevant jobs world wide. About ten of them are probably in Southern England but that is almost a fluke. Having got a job that fits me this well, I am very unlikely to voluntarily change my post'. 'Mobility is limited because when (a) one strives to be the best in one's research and (b) one is at the strongest UK university for one's research, why should one move? Only the US would represent a step up for me. Nowhere else in the UK is sufficiently attractive'. 'Interesting point about Cambridge -I believe many skilled engineers live in the area despite no ties and not particularly liking the area -its the career prospects and access to starting companies that keep us here'. 'Telecoms is a very incestuous market. The same faces keep appearing on projects around the world. It has a very specific skill set and a global market so skilled people can choose where they work and how much they get paid to do so'. Characteristics of synthetic and analytic knowledge bases

	F o r
	P
	e
	e r
	R
	e
	v i e
	w
	O n l
	y

Table 2 :

 2 Educational Attainment in Oxfordshire and Cambridgeshire

			Percentage					Total
		NVQ Level 3	NVQ Level 3	(Rank of 376)	NVQ Level 4+	NVQ Level 4+	(Rank of 376)	NVQ Level 3	NVQ Level 3	(Rank of 376)	NVQ Level 4+	NVQ Level 4+	(Rank of 376)
	East of England	7,9	4 (of 9)	18,1		4 308.581		4 (of 9) 704.743			4
			4 (of					21 (of
	Cambridgeshire	9,5	42)	25,2		6 38.458		42) 102.528			17
	Cambridge	18,0		2	41,2		8 15.324			40 35.145			45
	East
	Cambridgeshire	7,2	210	20,2	136 3.842		313 10.712		278
	Fenland	5,0	370	9,5	370 3.014		339 5.681		358
	Huntingdonshire	8,0	142	20,0	140 9.096		111 22.726			98
	South
	Cambridgeshire	7,6	175	29,8		29 7.182		152 28.264			67
	South East	9,2	2 (of 9)	21,8		2 530.682		1 (of 9) 1.253.917		2
			1 (of					15 (of
	Oxfordshire	10,8	42)	27,7		2 48.177		42) 123.323			14
	Cherwell	7,7	169	20,0	139 7.329		147 19.169		128
	Oxford	19,0		1	36,9		12 19.763			21 38.301			38
	South Oxfordshire	8,9		94	28,3		39 8.222		129 26.261			76
	Vale of White Horse	8,7	106	28,2		41 7.234		151 23.576			87
	West Oxfordshire	8,2	130	23,3		79 5.629		213 16.016		169
	England	8,3		-	19,9		-2.962.282		-7.072.052		-
	England and Wales	8,3		-	19,8		-3.110.135		-7.432.962		-
	Source: Census, ONS, 2001

Table 3 :

 3 Managerial, Professional and Technical Workers in Oxfordshire and Cambridgeshire (% of respondents)

			SOC1		SOC2		SOC3	SOCs 1-3
		%	Rank	%	Rank	%	Rank	%	Rank
	East of England	16,3	3 (of 9) 10,8	3 (of 9) 13,6	4 (of 9) 40,6	3 (of 9)
	Cambridgeshire	16,4	15 (of 42) 14,7	3 (of 42) 13,8	14 (of 42) 44,9	7 (of 42)
	Cambridge	13,2	275 28,0	2 14,2	116 55,3	15
	East Cambridgeshire	17,3	93 10,9	156 12,7	223 40,9	140
	Fenland	12,8	285	6,7	355 10,8	349 30,3	348
	Huntingdonshire	18,1	70 10,5	169 14,7	94 43,2	113
	South Cambridgeshire	18,2	68 16,6	21 14,9	87 49,7	42
	South East	17,4	2 (of 9) 12,1	2 (of 9) 14,6	2 (of 9) 44,2	2 (of 9)
	Oxfordshire	17,4	7 (of 42) 15,0	2 (of 42) 15,2	6 (of 42) 47,5	4 (of 42)
	Cherwell	17,0	103 10,3	182 14,4	101 41,7	127
	Oxford	12,8	284 23,4	3 15,8	50 52,0	31
	South Oxfordshire	20,8	24 14,3	49 15,4	63 50,6	35
	Vale of White Horse	18,6	64 15,6	31 14,3	107 48,5	48
	West Oxfordshire	17,4	87 11,4	137 16,0	43 44,8	86
	England	15,3	-11,2	-13,8	-40,3	-
	England and Wales	15,1	-11,2	-13,8	-40,1	-
	Source: Census, ONS, 2001

Table 4 :

 4 Comparative mean job tenureSource:CBI, 2002, CIPD, 2001[START_REF] Henry | The) industrial agglomeration (of Motor Sport Valley): A knowledge, space, economy approach[END_REF]

		Average Job Tenure
	Territory	(Years)
	UK overall (2001)	6,7
	UK SOC 2	4,6
	UK IT & high technology	5,1
	Motorsport Valley (UK, 2000)	3,7

Table 5 :

 5 Responses to the survey of the highly skilled

		IEE	IOP	RSC	Total
	Oxfordshire	62	282	83	427
	Cambridgeshire	105	182	115	402
	Total	167	464	198	829
	Source: Authors' survey

Table 6 :

 6 Overview of the careers of the highly skilled

		IEE	IOP	RSC
	Cambridgeshire
	All in Cambridgeshire	-	19,2	19,0
	In & Out	12,1	11,6	9,5
	One Way	62,6	46,6	52,4
	First Job	25,2	22,6	19,0
	Oxfordshire
	All in Oxfordshire	-	15,8	23,3
	In & Out	8,1	8,5	6,8
	One Way	75,8	50,6	56,2
	First Job	16,1	25,1	13,7

Table 7 :

 7 Migration in Oxfordshire and Cambridgeshire

		Lived at same address one year ago	Lived elsewhere -outside the UK
		No.	%	Rank (of 376)	No.	%	Rank (of 376)
	East	4.764.140	88,4	5 (of 10)	36.577	0,7	3 (of 10)
	Cambridgeshire	472.471	85,5	33 (of 34)	7.894	1,4	2 (of 34)
	Cambridge	81.810	75,1	375	4.423	4,1	4
	East
	Cambridgeshire	64.373	87,9	251	705	1,0	74
	Fenland	73.683	88,2	233	186	0,2	321
	Huntingdonshire	137.985	87,9	252	1.287	0,8	87
	South
	Cambridgeshire	114.620	88,1	239	1.293	1,0	68
	South East	6.984.762	87,3	8 (of 10)	71.285	0,9	8 (of 10)
	Oxfordshire	512.874	84,7	34 (of 34)	9.675	1,6	1 (of 34)
	Cherwell	114.972	87,2	284	977	0,7	99
	Oxford	100.144	74,6	376	5.158	3,8	6
	South Oxfordshire	112.451	87,7	268	1.130	0,9	79
	Vale of White Horse	100.842	87,2	288	1.714	1,5	29
	West Oxfordshire	84.465	88,3	220	696	0,7	102
	England	43.124.923 87,8	-	360.511	0,7	-
	England and
	Wales	45.703.875 87,8	-	370.430	0,7	-
	Source: Census, ONS, 2001

Where Oxfordshire and Cambridgeshire scientists will look for their next position

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				Oxon Cambs

http://mc.manuscriptcentral.com/cres Email: regional.studies@fm.ru.nlRegional Studies

< O -Economic Development, Technological Change, and Growth, O31 -Innovation and Invention: Processes and Incentives < O3 -Technological Change|Research and Development < O -Economic Development, Technological Change, and


Mark Melville
email: mark.melville@pfizer.com

Dr Padraig Doolan
email: padraig.doolan@dcu.ie

William Mounts

Niall Barron
email: niall.barron@dcu.ie

Louane Hann
email: louane.hann@pfizer.com

Mark Leonard
email: mark.w.leonard@pfizer.com

Martin Clynes
email: martin.clynes@dcu.ie

Tim Charlebois
email: timothy.charlebois@pfizer.com

Both

Development and characterization of a Chinese hamster ovary cell-specific oligonucleotide microarray

Keywords: Affymetrix, Chinese hamster ovary, microarray

des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Introduction

One of the most commonly used cell types for the manufacture of protein therapeutics is the Chinese Hamster Ovary (CHO) cell as they offer many advantages (adaption to suspension culture, growth in the absence of serum, relatively genetically stable, capable of secreting high levels of protein) over other cell lines for this kind of commercial application. Despite its widespread use, the molecular mechanisms via which CHO achieves these goals remains largely unknown. To address this, several laboratories have begun applying "omics" tools, primarily genomics and proteomics, broadly to the field of process development, and specifically to CHO cells, to better illuminate the molecular mechanisms that underlie cell culture processes [START_REF] Wong | Transcriptional profiling of apoptotic pathways in batch and fed-batch CHO cell cultures[END_REF][START_REF] De | Comparative transcriptional analysis of mouse hybridoma and recombinant Chinese hamster ovary cells undergoing butyrate treatment[END_REF], reviewed in [START_REF] Gupta | Genomics and proteomics in process development: opportunities and challenges[END_REF]. Detailed examination of the CHO transcriptome, however, has remained largely underdeveloped due to the lack of available tools for such experiments.

We report here the development of the first oligonucleotide microarray built upon the Affymetrix GeneChip platform specific to the expression profiling of CHO cells (US patent application US20060010513 A1). The CHO microarray was designed using a combination of publicly available hamster sequences and sequences derived from proprietary CHO cDNA libraries. Until recent years, lack of available sequence from CHO cells has presented a significant barrier to broad spectrum genomics studies. A small number of independent efforts have lead to development of similar tools, most notably the Consortium for CHO Cell Genomics (headed by the laboratory of Wei-Shou Hu at the University of Minnesota, Minneapolis, MN), where sequence mining led to the development of a cDNA microarray platform [START_REF] Wlaschin | EST sequencing for gene discovery in Chinese hamster ovary cells[END_REF], and more recently a microarray constructed on the Affymetrix platform [START_REF] Kantardjieff | Developing genomic platforms for Chinese hamster ovary cells[END_REF]. Several studies in this area have attempted to utilize commercial microarrays from related species, such as mouse, with some success [START_REF] Ernst | Evaluation of a genomics platform for cross-species transcriptome analysis of recombinant CHO cells[END_REF][START_REF] Yee | change differences in two sample sets. Table 1. Summary of WyeHamster2a microarray comparisons with mouse and rat microarrays[END_REF]. However, while there may be applications where this approach is applicable, we demonstrate here that a more specific tool is necessary when one is attempting to dissect alterations in specific, individual genes.

The work here describes the characterization of the CHO microarray developed at Wyeth/Pfizer and its utility as a laboratory reagent. The microarray has been used to study the effects of overexpression of soluble PACE on CHO cells expressing a transgene for bone morphogenic protein-2 [START_REF] Doolan | Transcriptional profiling of gene expression changes in a PACE-transfected CHO DUKX cell line secreting high levels of rhBMP-2[END_REF], predicting productivity in CHO [START_REF] Clarke | Predicting cell-specific productivity from CHO gene expression[END_REF], as well as to identify genes linked with the ability of CHO cells to modulate their rate of growth [START_REF] Doolan | Microarray and proteomics expression profiling identifies several candidates, including the valosin-containing protein (VCP), involved in regulating high cellular growth rate in production CHO cell lines[END_REF].

Materials and methods

Library Construction

CHO cDNA libraries were derived from total RNA collected from Wyeth proprietary CHO DUKX B.11 cells cultured in defined medium lacking animal products, and harvested during the log phase as well as the lag phase of growth. The libraries underwent 4 rounds of normalization, and achieved an average of 5.2 x and 2.5 x for the log phase and lag phase, respectively (Cell and Molecular Technologies, Inc.) Bacterial colonies containing library-derived plasmids were picked and subjected to 3"-sequencing.

WyeHamster2a oligonucleotide microarray

A total of 12,288 clones from CHO libraries were sequenced, and the results were combined and processed with CAT (DoubleTwist), a sequence clustering and alignment tool to firstly identify homologous sequences through clustering and secondly to align all sets of homologous sequences to produce one or more representative consensus sequences (contigs) for each set. These clusters and alignments were manually examined to remove artifacts and ensure quality of the contigs.

Ultimately, 2835 unique sequences were compiled from the library sequencing efforts. At the time of the construction of the microarray, there were 732 public sequences available in GenBank, resulting in 3,567 total hamster sequences which were used. In addition, 122 control sequences were added to the array for sample preparation, hybridization, and normalization quality control. Finally, 25 product-specific and proprietary sequences were also included in the design. These were primarily molecules associated with the biotherapeutic pipeline within clinical development (including monoclonal antibodies, fusion proteins, and other recombinant proteins), but also included several CHO genes that had been sequenced internally. The total microarray thus consisted of 3,714 sequences. Probe sets contained 55 probe pairs on average and were designed as normal RNA expression profiling probe sets containing both a perfect match and mismatch probe pair for each probe selected [START_REF] Lockhart | Expression monitoring by hybridization to high-density oligonucleotide arrays[END_REF]. The array is an 18 m standard-sized array. The experimental design of the WyeHamster2a microarray, detailing the EST-sequence data collected from CHO libraries, is illustrated in Supplementary Figure 1.

Results and discussion

The WyeHamster2a microarray is a precise, reproducible, and specific reagent The WyeHamster2a microarray was constructed using sequences derived from public databases as well as EST-sequence data collected from CHO libraries generated in-house, as described in the Material and Methods and Supplementary Figure 1. To test the quality of the microarray, we analyzed sets of biological replicates to assess reproducibility. Biological replicates, as we defined them, were derived from a single culture vessel that was used to seed three or four parallel "daughter" cultures. The examples shown in Supplementary Figure 2 are the scatter plots of 4 biological replicates of parallel cultures (cells harvested, RNA purified, processed and hybridized to microarrays, as outlined). The data were plotted on a log-log scale using only valid values, as determined by expression level in the Expressionist tool. For each of the pair-wise comparisons, we observed very little signal scatter or skewing. Similar data were compiled for 100 scans, comprised of 28 triplicate and 4 quadruplicate biological replicate sample sets. The average R 2 value calculated for the entire set of scatter plots was 0.98152 (Supplementary Figure 2), indicating a high degree of correlation between all replicates examined. These analyses indicate that the method as a whole (culture replicates, sample preparation, and microarray scanning) is highly reproducible.

Reverse Transcription Quantitative PCR results validate microarray profiles

From the comparison of the transcriptional profiles, we selected 12 sequences that were differentially expressed to varying degrees between 2 sample sets of same CHO DUKX cell line cultured at different temperatures and which we felt would provide a wide range of differential expression with which to test the predictive accuracy of the array to the betterestablished qPCR technique. The targets ranged from 1.3-to 42-fold different by microarray analysis, and in all cases met a p-value cutoff of <0.05. The sequences were selected because they represented a range of differential expression, as opposed to having any particular identity or significance. Each of the 12 targets was assayed by RT-qPCR, utilizing in vitro transcript standard curves designed for each target. For 11 of the 12 targets tested, the direction and approximate fold change observed by microarray was confirmed by RT-qPCR (Figure 1). At the low end of the fold-change spectrum we did observe some variability in that one of the two sequence targets that had a 1.3-fold change in the microarray experiment was not confirmed by RT-qPCR. This could imply that the lower level of accurate differential measurements by microarray is at or near a 1.3-fold change; however more experimentation would be necessary in order to determine this for certain, and thus define the true lower limit of accuracy. Nonetheless, the balance of the experiment demonstrates that the microarray returns results that are generally consistent with RT-qPCR measurements.

Alternate species microarrays will significantly under-report the complexity of the CHO transcriptome

To identify if oligonucleotide microarrays directed against different, but related, species (such as mouse and rat) are viable alternatives for the quantitative characterization of transcripts in CHO cells, we compared expression results for an identical, triplicate set of CHO RNA samples run on the WyeHamster2a microarray and the Affymetrix MOE430A and RAE230A microarrays. The experiment had two main features; firstly, the subset of probe sets that are relevant for study were identified through sequence analysis, while the second part involved hybridization of CHO RNA to the WyeHamster2a, MOE430A and RAE230A microarrays. These comparisons of the WyeHamster2a array revealed 2385 common homologous probe sets with the MOE430A array and 2230 common homologous probe sets with the RAE230A array. For CHO RNA samples run on both the WyeHamster2a and MOE430A arrays, 1462 of the homologous hamster probe sets were identified as being present (by Affymetrix MAS5.0 algorithm) on all of three replicate WyeHamster2a arrays and 458 (31%) homologous mouse probe sets were identified as being present on all of three replicate MOE430A arrays. Of the 458 mouse homologous probe sets identified, 386 (84%) were also identified on the hamster array (Table 1).

These data show a 56% false negative rate and a 16% false positive rate when running CHO samples on a mouse array.

When comparing CHO RNA samples run on both the WyeHamster2a and RAE230A arrays, we found a 57% false negative rate and a 12% false positive rate (Table 1). These results demonstrate that alternate, commercial mouse or rat microarrays will significantly under-report the complexity of the CHO RNA sample. That said, of the sequences that are identified, approx. 85% of them would be predicted to approximate the homologous CHO gene. If one were to extrapolate to the entire mouse or rat microarray, however, it is difficult to predict from these data which sequences are/are not accurately reporting expression values.

From this study, we were also able to estimate the total number of transcripts present in our sample, as well as extrapolate the complexity of the CHO transcriptome (Table 1) by utilizing the calculated true positive rates in conjunction with the 6 total number of mouse and rat probe sets that were detected as being present. By these calculations, we estimate that were we to use a microarray of the same complexity as the RAE230A or MOE430A arrays, we would detect 10,000 -13,000 transcripts, with an overall complexity of 16,000 -21,000 potential expressed sequences. Our estimate from these experiments is somewhat lower than recent articles published on deep sequencing of the hamster transcriptome [START_REF] Kantardjieff | Developing genomic platforms for Chinese hamster ovary cells[END_REF]. It is likely that these recent efforts have increased our understanding of the complexity of the transcriptome by identifying expressed sequences with little or no homology with other species, as well as splice variants, all species of which may be underestimated in our projections.

Annotation and Ontology of WyeHamster2a Array

As the WyeHamster2a microarray contained only a subset of the total number of genes expressed in CHO cells, and the libraries generated for sequencing were from a limited set of physiological conditions, we wanted to determine 1) the level of coverage of the microarray, in an overall biological context and 2) as a means to identify potential bias in other experiments in which the WyeHamster2a microarray was used in conjunction with such informatics tools. In order to generate an accurate functional classification for the WyeHamster2a array, the full in-house annotated transcript list was submitted to the PANTHER database [START_REF] Thomas | PANTHER: a library of protein families and subfamilies indexed by function[END_REF]) and re-annotated using the NCBI mouse database. A total of 31 Biological Processes were identified to be impacted by this list and are detailed in Table 2. As can be seen, there is a clear functional bias towards protein (>22% of genes submitted) and nucleic acid (>19% of genes submitted) metabolism genes, together with signal transduction genes (>15% of genes submitted) on the chip. Additionally, over 18% (317 genes) of the annotated transcripts contained on the chip have not been classified with any biological function to date.

In a similar, complementary analysis, Gene Ontology (GO) modeling using GOstat [START_REF] Beissbarth | GOstat: find statistically overrepresented Gene Ontologies within a group of genes[END_REF]) was utilized to identify annotation categories that are overrepresented on the array, thus elucidating the functional focus of the chip with reference to the gene ontology vocabulary. GOstat analysis identified a total of 256 GO categories that were overrepresented on the array, of which the top 35 (ranked by p-value) specific, filtered biological processes are outlined in Supplementary Table 1. As can be seen, the WyeHamster2a microarray is enriched for ontologies linked to biosynthesis (particularly cellular biosynthesis, protein biosynthesis and macromolecule biosynthesis), as well as categories related to translation, catabolism, cell cycle and the endoplasmic reticulum. Similarly highly represented categories linked to specific components of cell architecture include the GO categories cell organization and biogenesis, organelle part and intracellular organelle part, cytosol, organelle membrane, mitochondrion and ribosome. Also, several categories relating to nuclear activity were identified in the top 30 processes, namely RNA metabolism and binding, ribonucleoprotein complex, nucleoside-triphosphatase activity, ATP binding, nucleotide binding, purine nucleotide binding and adenyl nucleotide binding. The results from the PANTHER and GOstat functional annotation surveys should be considered when performing such analyses on data sets generated from the WyeHamster2a microarray. This paper describes the first generation CHO-specific oligonucleotide microarray , WyeHamster2a, the studies designed to characterize it, the analyses used to confirm its utility and some of the considerations one must bear in mind when analyzing data derived from its use. The results generated, on a technical level, can be viewed with high confidence, as the microarray is specific for CHO, and has demonstrated considerable fidelity in validation experiments using RT-qPCR. We have also presented a functional annotation of the genes and that are represented on the microarray which is helpful as a guide to using and analyzing data generated, and interpreting the significance of the biology of any subsequent findings. full-length sequences and vice versa. Any hamster qualifier whose top BLAST hit is the original hamster qualifier (reciprocal BLAST hits) is defined as a hit.

2 A true positive is a sequence that is called present on both the WyeHamster2a array and the corresponding rodent array for a matched probe set.

3 A false positive is a sequence that is called absent on the WyeHamster2a array, but present on the corresponding rodent array for a matched probe set. 4 True positive rate is the ratio of true positive hits (2) to matched mouse or rat probe sets present. 5 A false negative is a sequence that is called present on the WyeHamster2a array, but absent on the corresponding rodent array for a matched probe set. 6 A true negative is a sequence that is called absent on the WyeHamster2a array and the corresponding rodent array for a matched probe set. 7 True rodent (mouse or rat) present calls is the product of the True Positive Ratio (4) and the total rodent present calls.

8 Based on ratio of true positive hits (386 for mouse or 402 for rat) to the product of 'matched hamster probe sets present' and true positive present calls (5). 10 9 Based on ratio of true positive hits (386 for mouse or 402 for rat) to the product of rodent (mouse or rat) probe set hits (1) and true positive present calls (5). BPs identified by PANTHER analysis (Protein ANalysis THrough Evolutionary Relationships) (http://www.pantherdb.org/). 3,714 WyeHamster2a IDs were annotated to 2005 NCBI mouse Genbank gene symbols using a combination of an in-house annotation tool and PANTHER. Processes are sorted according to "Percent of gene hit against total # genes", then "# genes", then "Category name (Accession)"

Fig1.

  Fig1. Comparison of fold change values derived from the WyeHamster2a microarray (CHO Chip) and RT-qPCR (TaqMan).

Table 2 .

 2 List of 31 Biological Processes impacted by the member-annotated WyeHamster2a transcript list.

			Percent of gene	Percent of gene
			hit against total #	hit against total #
	Category name (Accession)	# genes	genes	Process hits
	Protein metabolism and modification (BP00060)	385	22.60%	13.80%
	Nucleoside, nucleotide and nucleic acid metabolism (BP00031)	339	19.90%	12.20%
	Biological process unclassified (BP00216)	317	18.60%	11.40%
	Signal transduction (BP00102)	258	15.20%	9.30%
	Developmental processes (BP00193)	155	9.10%	5.60%
	Immunity and defense (BP00148)	152	8.90%	5.50%
	Cell cycle (BP00203)	142	8.40%	5.10%
	Intracellular protein traffic (BP00125)	133	7.80%	4.80%
	Transport (BP00141)	117	6.90%	4.20%
	Cell proliferation and differentiation (BP00224)	95	5.60%	3.40%
	Cell structure and motility (BP00285)	95	5.60%	3.40%
	Lipid, fatty acid and steroid metabolism (BP00019)	95	5.60%	3.40%
	Apoptosis (BP00179)	67	3.90%	2.40%
	Carbohydrate metabolism (BP00001)	66	3.90%	2.40%
	Other metabolism (BP00289)	59	3.50%	2.10%
	Oncogenesis (BP00281)	45	2.60%	1.60%
	Electron transport (BP00076)	39	2.30%	1.40%
	Neuronal activities (BP00166)	35	2.10%	1.30%
	Cell adhesion (BP00124)	31	1.80%	1.10%
	Amino acid metabolism (BP00013)	30	1.80%	1.10%
	Protein targeting and localization (BP00137)	31	1.80%	1.10%
	Homeostasis (BP00267)	17	1.00%	0.60%
	Muscle contraction (BP00173)	15	0.90%	0.50%
	Sensory perception (BP00182)	15	0.90%	0.50%
	Coenzyme and prosthetic group metabolism (BP00081)	14	0.80%	0.50%
	Phosphate metabolism (BP00095)	11	0.60%	0.40%
	Miscellaneous (BP00211)	11	0.60%	0.40%
	Sulfur metabolism (BP00101)	7	0.40%	0.30%
	Blood circulation and gas exchange (BP00209)	6	0.40%	0.20%
	Non-vertebrate process (BP00301)	2	0.10%	0.10%
	Nitrogen metabolism (BP00090)	1	0.10%	0.00%

A hit is determined by BLAST analysis of WyeHamster2a full-length sequences vs. MOE430 (mouse) or RAE230 (rat)

Acknowledgements

: This work was supported by funding from Science Foundation Ireland (SFI) grant number 07/IN.1/B1323 and the Irish Higher Education Authority (HEA) PRTLI Cycle 4.