Category: The inside story

This is the penultimate chapter and is an account of my personal story and involvement in the Department. — My Story.

In the beginning …

Growing up in a well-to-do middle-class family in the wheat growing area of Saskatchewan, there never was any doubt that when I finished high school I would go on to university. Such were the expectations of my family and the friends of my family. I had a flare for chemistry and English literature and even did some acting in High School plays. When it came to choosing a direction, arts or science, it became a problem that led to a somewhat checkered academic beginning. I attended the University of Saskatchewan in Saskatoon in 1958 taking English and chemistry — putting off the decision of becoming a scientist or a writer. By the end of that year I was no further ahead in choosing which direction to take so I chose the glamorous route of being a poet and I headed off to the jazz scene in Vancouver. I spent a winter there doing poetry. During that time I met Lorene who would later become my wife and we put together a couple of self-published poetry books. The first one was called ‘Garbolish’ which is available as an ebook.

After running out of money for coffee, German Black Forest cake, poetry readings and rent, I decided to give journalism a try. I moved to Ottawa (capital of Canada) and enrolled at the Journal School at Carlton University. At that time Carlton University was pretty much a finishing school for the children of the civil servants who populated the city. After a while it didn’t suit my dissidence and anti-establishment temperament. I dropped out of university and got a job as a lab technician in a government research facility — primarily based on the chemistry courses I had taken. The work involved studying exotic animal viruses and the facility was the reference laboratory for the whole country. Working with viruses I became fascinated with the question of: where does chemistry end and biology begin? Viruses seem to sit somewhere on the boundary.

After working for two years as a lab technician, I enrolled (1962) for a BSc in microbiology at the University of British Columbia and was clever enough to get a Canadian government scholarship to do a PhD. I found a compatible PhD supervisor, Jack Tremaine, at the on-campus Agricultural Research Station. I embarked on the studies of a plant virus and an insect virus using the biophysical tools of the day. 

Along the way I acquired a wife, a house and two kids and a PhD. I managed to finish the PhD in 18 months, the minimum time allowed.

 

At the end of my PhD studies there was the usual problem of ‘finding a job’. Fortunately, this was delayed, in the short term at least, by being awarded a no-strings-attached post-doctoral fellowship, again courtesy of the Canadian government.  This was now the late sixties and my choices were either Mill Hill in London or the Molecular Biology lab at Berkeley, California. Needless to say the 'flower power' of Berkeley won.

In the autumn of 1968 we sold our house and bought  a VW Combie van that my father-in-law and I modified to provide camping facilities and we headed south along the coastal route to California.

Postdoc at UC Berkeley

The first priority for starting my postdoc at UC Berkeley was to find a place to live that was close to the UC Berkeley campus. We were directed by the University Accommodation Office to a new housing development in Richmond (an adjoining Bay city). Richmond was predominantly a black area and the Federal government, as part of the urban renewal plan, had built a housing estate which was to consist of 60% blacks, 30% whites and 10% others — to avoid it becoming another black ghetto. These were still the days when blacks were expected to sit at the back of the bus. Upon arriving at the office of this housing estate we were greeted with open arms since it meant that if we took a place, they could house two more black families. We were offered the pick of the bunch. The units were two-bedroom duplexes with adjoining garages, a front lawn and a fenced back yard. They were tastefully designed with polished concrete bench-tops and solid walls. Our neighbour was a fireman with a wife and two small kids.

Most of the people in the community were professional families: teachers, nurses, social workers. In general, it was the women of black families who had jobs while the men odd-jobbed or otherwise occupied their time with children and ‘hobbies’. This was the time of the Black Panther Party and the ‘Black is Beautiful’ movement. One evening we heard a loud knock and upon opening the door this huge African  American who filled the entire door frame asked if I wanted to buy a copy of the Black Community News (the Black Panther newspaper) — I said yes, I would have bought his entire stock if he asked.

As well as these challenges on the political front there was the ‘cultural revolution’ — the hippie lifestyle: free love, drugs, sex, music, a new way of thinking —  the dawning of the Age of Aquarius. Although the lyrics of the opening song in the musical Hair (1967)  were considered to be ‘astrological gibberish’, nonetheless the concept of the Aquarian age spread to young audiences around the world. The musical Hair defined the hippie culture. The musical's profanity, its depiction of the use of illegal drugs, its treatment of sexuality, its anti-Vietnam war, its irreverence for the American way of life and its nude scenes set the stage for the hippie counterculture.

The UC Berkeley campus was beautiful and spacious  and on the east side was Sproul Hall, the neoclassic administration building - the site many of the student protests.

The building in which I worked was called the Molecular Biology and Virus Laboratory Building. When it was built in 1952 in the gothic Soviet-Bloc Cold War style it was called the Biochemistry and Virus Laboratory Building. It was later renamed to Stanley Hall after Wendell Stanley, who won the Noble Prize in Chemistry (1946) for his work on TMV (tobacco mosaic virus). C Arthur Knight was one of his co-workers and it was in Knight’s lab that I did my postdoc.

The building was later demolished and a new Stanley Hall was opened in 2007. It became one of the newest buildings on campus and housed the Bioengineering Department, along with 40 research labs affiliated with the multi-campus California Institute for Quantitative Biosciences.

Lab space in C Arthur Knight’s lab was at a premium and I shared a bench with another postdoc, Leon Lewandowski. We struck up a great research partnership. He had just graduated from the University of Pennsylvania and knew of the recent

discovery that reovirus particles (dsRNA) contained an RNA-dependent RNA polymerase. I was carrying out some work on an insect virus that was also double-stranded RNA. The Question: Did it contain a similar RNA polymerase? After a crash course in how to rear this virus in silkworms we were able to get enough data to publish two papers on the properties of this insect virus RNA polymerase of the cytoplasmic polyhedrosis virus of silkworms.

Later Leon studied medicine and spent most of his career in Pharmaceutical Medicine/Pharmacovigilance (Drug  Safety). He ran Senior Health services, a New York State pro-bono "Charity", providing home-care visitation services to fulfil the critical role of helping older folks oversee their pharmaceutical needs. As Leon tells me: this is the closest he will ever get to fulfilling his Mom's dream of her being able to say, "her son, the Priest".

Throughout time spent at UC Berkeley there were a series of protests on campus. By and large we avoided the picket lines and the charges by state-troopers since our laboratory was located at the north end of the campus and we could ‘sneak in to work’ ,but there were major disruptions to classes and the normal student activities. The protests were similar to that of the guerrilla tactics used by the Vietcong— disrupt then melt into the surrounding student population. Activists would ‘occupy a building’ disrupting  normal activities — the authorities would send in the state troopers — the activists would blend in with the students — meanwhile another ‘occupation’ would occur at the other end of the campus.

Let’s go to New Zealand

I remember that it was a glorious sunny day in spring (April). We were having a picnic at the beach in Golden Gate Park in San Francisco. The kids were playing in the sand, the surf was gently rolling in, the bridge was beaming in the sun and all was well with the world.  We had decided to explore going to New Zealand since we heard from our neighbours at the housing estate of the beaches, the climate and the relaxed pace of life. It was reputed to be a great place to bring up kids. We were beginning to get weary of the racial tension and social unrest and worried about the effect this was having on us and the kids. I wanted a place to slow down and relax from the hectic pace of the last few years.

I decided to try for an academic position since I enjoyed working at a university, carrying out research, teaching students and being the conscience and social critic of society.  I did what is probably unthinkable today — I wrote a do-you-have-any-jobs?-letter and enclosed my CV. I addressed it care of the HOD Department of Microbiology to each of the six Universities --- not really knowing if they had a microbiology department or not. I did a similar thing for all the potential Biochemistry Departments since I could teach that as well, having taken as many biochemistry courses as microbiology.

About 3 weeks later a Teletext arrived from Professor John Miles, Department of Microbiology, University of Otago. It was a very cryptic message that said, we have an academic vacancy here teaching Microbiology to Science students – are you interested? I replied immediately and said, yes, I am interested, please send more details.

Then there was this long silence and I began to think, ‘I have blown that option’, then weeks later a Teletext arrived offering me the position at a lecturer’s scale at salary of NZ$3,000. I had no idea what this meant in terms of money or living costs or average salary.

We were living in a housing estate in the middle of a black ghetto in Richmond – which is just outside Berkeley. There was a New Zealand couple living there so we invited them over for dinner to get some information about living in NZ. The husband was studying city planning (which sounded promising) and his stunningly beautiful Polynesian wife was doing a sociology degree and ran the local kindergarten. His wife did most of the talking and the bloke just listened and drank beer. So towards the end of the evening I asked him, Is $3,000 enough to live on in NZ? His reply after pondering the question for awhile said, “Ah yeah mate, that’s enough to keep you in beer money.” His wife later translated that into – yes, you could live comfortably on that.

The next step was to get to New Zealand. I went to the NZ Consulate in downtown San Francisco and asked the Maori lady at reception: “What do I need to do to get to New Zealand?” She smiled back with the look of wild flowers growing near mountain streams and surf rolling in on sandy beaches and said, “Buy an air ticket.” Back in 1969 that was all that was required. I made some creative arrangements with a shipping company to pack all our household effects into the VW Combie van and ship it as a ‘container with wheels’. I also included some scientific supplies, not knowing what kind of place I was going to end up in.

We went back for a quick trip to the Canadian prairies to say our farewells and then boarded a plane in Vancouver bound for New Zealand.  In those days travel by air was very luxurious (no cattle class) and you were treated like royalty with plenty of leg room, wide seats, a five course meal and the clinking of champagne glasses over the Pacific.

During our approach to Christchurch, the pilot pointed out Mt Cook on the West Coast and reminded us to put our clocks forward by two hours and our years back by 20. That turned out to be quite a prophetic statement, but it didn’t bother me since I enjoyed the calm and secure pace of life of my childhood. On the connecting flight from Christchurch to Dunedin, we were warmly greeted by a distinguished English gentleman dressed in a 3-piece suit and carrying a copy of the General Journal of Microbiology tucked under his arm as an identity tag — this was Professor John Miles, HOD of the Department.

Arrival In Dunedin

It was customary for the University to arrange accommodation for arriving academics at Owen’s Motel until their household effects arrived or other arrangements were made. It had the classic NZ 1950s furnishings, but it was comfortable and allowed us to adjust ourselves to the place. It was only a five minute walk to the Medical School where the Microbiology Department was located.

Dunedin in 1969 was a mature city of 80,000 and many of the buildings were built as a result of the gold rush in the 1860s. By 1870 Dunedin was New Zealand’s largest and richest city with some of the finest architecture in the country. This ‘point of difference’ continues to the present day and it is one of the world’s greatest small cities. In 2014 Dunedin was designated as a UNESCO Creative City of Literature. — it “values and builds on its rich cultural heritage and supports the life of the mind and treasures its books and writers”  (but I digress). It is a city of natural beauty surrounded by hills, a harbour and stunning beaches that are only a few minutes from the Octagon, the city’s centre.

The Microbiology Department was located in the Medical School on the 3rd floor of the Hercus and the Scott Buildings. At that time there were 8 academic staff members and 4 research staff, as listed in the University Calendar.

We received a very warm welcome from the staff of the Department and were made to feel at home. We bought  a 3-bedroom house up North East valley which was surrounded on three sides by paddocks.

A seminar given in 2006 as Associate Dean, Website & Communications -- on developing a departmental intranet. For the full version see: vimeo.com/28964655

The occasion was the 150th anniversary of Darwin's Theory of Evolution (2009) -- some of the key concepts are still relevant today. For the full version see: vimeo.com/29203825

JK-LAB Gallery

The start of the new millennium was prefaced by the concern for the Y2K bug – but when the clock ticked Jan 1, 2000, no major problems were reported. Almost every bank worked fine, no major power outages were reported, airplanes still flew and the whole world went on with its normal life.

During this decade several staff members died, namely John Miles, Sheila Thompson, Sandy Smith and Glenn Buchan. New staff members were appointed: Alex McLellan, Ralph Jack, Sangsun Yoon, Peter Fineran and Roslyn Kemp. As the decade proceeded it was becoming more obvious that a changing of the guard was beginning to take place and the Department was losing its old ethos as new graduates and staff joined.

Alex McLellan

Alex was appointed in 2003. He did his MSc at the                     University of Canterbury (Christchurch) and obtained a PhD from the Christchurch School of Medicine in 1998. He took up a postdoc in the Department of Dermatology at the University of Würzburg in Germany. He established links and collaborations with European institutions in Switzerland, Austria and Germany. He leads a research group studying the interaction of pathogens and cancer with the body's immune system. He enjoys teaching at all levels, including contributions to courses in continuing education, University of the Third Age, Health Sciences First Year and Pharmacy. The following was his response for the history project:

1. What was your academic background before joining the department?

BSc, MSc (Microbiology) Canterbury, PhD Otago (Dept. Pathology, Christchurch School of Medicine)

2. Why or how did you come to the University of Otago?

I applied for a lectureship following my postdoctoral training in Wuerzburg, Germany (1998-2002).

3. What do you consider your main achievement?

The discovery of soluble MHC class II in urine draining inflamed kidneys and the subsequent development of a non-invasive test for renal transplant rejection.

4. Any outstanding events in the Department during your time there?

Exceptional qualities of HOD leadership shown by Sandy Smith and Frank Griffin.

5. Any concluding comments?

The collegiality of the department is unrivaled by other institutes, universities I have worked in.

Alex McLellan explains innate immunity and the arrival of the adaptive immune system 500 million years ago.

His research focused on the role exosomes (extracellular vesicles that contain cellular components) played in the immune response  -- as possible cellular communications  systems.

In 2014 he was promoted to Assoc Professor and currently works on strategies to improve T-cell function against solid tumours using cytokines and chemokine receptors.

 

Ralph Jack

Ralph (far right) was appointed in 2003 after postdoc research in Prof. Hans-Georg Sahl’s laboratory in Germany. He was a graduate from the Department and his PhD supervisor was John Tagg. His research interests were the interactions and interplay that occur between commensals, pathogens and the host during both health and disease processes. He resigned in 2007 and took a position with Seperex Nutritionals Ltd, a New Zealand supplier of novel and innovative functional foods.

Sangsun Yoon

Sangsun joined the Department in 2007. Originally from Korea, he graduated with an MSc from the Korea Advanced Institute of Science and Technology and then completed his PhD at the University of Cincinnati Medical School. Prior to beginning at Otago, he was working as a postdoctoral fellow at Harvard Medical School and identified a group of novel bacterial proteins that stimulate host innate immune responses. He is also interested in anaerobic metabolism of Pseudomonas aeruginosa, a bacterium of clinical importance, especially to patients with cystic fibrosis. He resigned in 2009 and returned to take up a position in South Korea.

Peter Fineran

Peter was appointed in 2008. When asked to respond to the standard questions for the book: he provided the following biopic:

I did my undergraduate degree at the University of Canterbury (1997-2000) where I got a BSc(Hons) 1st Class in Biochemistry. I performed my honours research project in the laboratory of Professor Jack Heinemann investigating the phage-bacterium interaction of pseudolysogeny, a poorly understood phenomenon. Following my undergraduate degree I took up a research assistant position in the John Curtin School of Medical Research (JCSMR) at the Australian National University (ANU). I worked at ANU from 2001-2002 under the supervision of Professor Ian Young expressing, purifying and crystallising a IL-3 complex for structural studies.

Next, I took up a PhD position at the University of Cambridge in the Department of Biochemistry (2002-2006) where I was funded by a Bright Futures Top Achiever Doctoral Scholarship. There, I worked in the laboratory of Professor George Salmond where I investigated networks of gene regulation that control secondary metabolism and virulence in Serratia. This included the study of N-AHL quorum sensing and various other regulatory mechanisms. Following the completion of my PhD I took up a post-doctoral position at Cambridge supervised by Professor Salmond and Dr Kathryn Lilley (2006-2008). In this project I investigated a bacterial phage resistance mechanism known as abortive infection. 

After five and a half years in the UK and over 7 years out of New Zealand, I was interested in returning to New Zealand if a suitable job was available. I was fortunate to be offered the position of Lecturer, which I accepted. I had wanted to establish my own group so this was a perfect opportunity. I had met David Jones and Clive Ronson at different conferences in the UK and was aware of some of the research being undertaken at Otago. 

Fineran Lab - March 2009 (from left to right): Andrew McCaw, Peter Fineran, Tamzin Gristwood, James Clulow, Marina Iglesias Cans, Matthew McNeil and Ge (Annie) Huang.

My group is still being established as I have only been here a little over one and a half years. My main achievement to date was the research that I published as first author in PNAS in 2009 based on my work while a post-doc in Cambridge. This has also lead to a Marsden Grant in this area in collaboration with Professor Salmond. I am looking forward to continuing my research at Otago in the coming years."

 

In the above video Peter Fineran is introducing the virology course at the Microbiology and Immunology at Otago University -- circa 2010. This particular laboratory is an exercise in virology, taught at 3rd year level in which students isolate their own bacteriophage from a sewage sample. It has not changed in format since I first introduced it in 1971.

Peter carried on working with bacteriophages and focused on how bacteria acquire resistance to phage attack. In particular the research was on: 

1.  Abortive infection and toxin-antitoxin 'innate immune systems'
2. CRISPR-Cas 'adaptive immune systems'
3. Phages as antimicrobial agents

This research is part of ‘‘the biggest biological science revolution in recent decades’’ , which is enabling scientists to move on from reading the genome to potentially editing it.

Peter was promoted to Associate Professor in 2015 and appointed to Professor in 2018. He has won many awards for his work, particularly on the CRISPR-Cas systems. He is a frequent invited speaker at international scientific meetings and is an excellent science communicator (as seen below).

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Roslyn Kemp

Roslyn was appointed in 2009. She was a former undergraduate student in the Department and completed her PhD with Franca Ronchese at the Malaghan Institute of Medical Research at Wellington. She then embarked on a series of international fellowships including a postdoc with Richard (Dick) Dutton at the Trudeau Institute, followed by tuberculosis research in Oxford, UK, and with Ben Seddon at NIMR, London, before returning to New Zealand. Roslyn’s research is focused on CD8+ T cell memory and anti-tumour immunity.

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Comments on the 2000s

On April 1st, 2004 Sandy Smith stepped down as the Head of the Department and Frank Griffin took over the reins. Up until then Frank was not greatly involved in the day-to-day running of the department, concentrating instead on his Deer Laboratory, and immunological interests. Sandy continued to maintain his presence in the tearoom and during research seminars, always ready with witty and cutting remarks.

(L-R: Clive Ronson, Trish Smith, John Loutit and Sandy Smith – April 1st, 2004)

 

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Meanwhile on the local scene, in 2002 a government policy that had a profound effect on Otago University was the establishment of Centres of Research Excellence (CoRE’s). Universities were invited to bid for these Centres which carried with them a sizeable financial budget and funding for large innovative projects. It was assumed that Otago would get at least one of these CoRE’s given the presence of some high profile research groups on campus and the close proximity to the research station at Invermay (AgResearch).

For a variety of reasons, mainly the lack of strategic thinking, the University missed out. Following on from the days when Otago had the only Medical School, there was (probably still is) a feeling that Otago was the best and it was our entitlement to a lion’s share of any research budget. There was also a culture at Otago of supporting research ‘prima donnas’ which did not fit the government’s model of collaborative interdisciplinary research groups. The prima donnas could not get their act together – no CoRE was awarded to Otago. During this time Glenn Buchan was the President of the local branch of the Royal Society – the Otago Institute and became the spokesperson for supporting research in the University and attended meetings with government officials in Wellington, promoting Otago. In 2003 a second round of CoRE’s was called and again Otago failed to obtain one.

In 2003 another shock to the prestige of the University was the rating in the PBRF (Performance Based Research Funding) assessment with Otago coming in 4th place with Auckland University at the top.

David Skegg became the Vice-Chancellor in 2004 and refocused the University to research excellence.

Otago did recover its prestige somewhat after the second round of PBRF in 2006 ratings by coming to the top of the league table. 

In 2000, the Government of New Zealand appointed an independent Royal Commission on Genetic Modification to preside over an ambitious 15-month inquiry into genetic modification (GM). The Royal Commission heard testimony from hundreds of interest groups and experts, as well as the views of thousands of members of the general public. Staff members from the Department and the University participated in this exercise -- since making genetically modified organisms (GMOs) is what we do.

In July 2001, the Royal Commission on Genetic Modification reported to the Government and recommended a precautionary approach which preserved options for the future. The Green Party wanted to make New Zealand GE-free, and fortunately their views did not prevail. The effect on the working microbiologist was the need to keep records of every novel organism produced and to work in a PC-2 compliant laboratory. The compliance requirements have become more stringent with every safety audit and it has created a whole industry of its own.

In 2002 we had "Corngate", a political scandal which involved the suspected release of genetically modified corn seed in 2000. The possibility of the presence of a small percentage of GE corn in a seed shipment from the US was raised publicly by Nicky Hager in his book: Seeds of Distrust. The book was released a few months prior to the 2002 Parliamentary election. A select committee, including members of the Green Party, was formed to investigate the matter. The final report, released in late 2004, was inconclusive due to a lack of clear evidence, poor reporting of the original incident and the deletion of raw data critical for a full re-evaluation. The incident highlighted the problems of testing for the presence of GMOs when available detection methods have a relatively high base threshold before results become reliable.

During that time on the world scene:

* The first draft of the human genome was released in 2000, a race between private enterprise – Craig Venter and publicly funded research – Francis Collins.

* England had a foot-and-mouth disease outbreak resulting in 20 million animals being slaughtered and burnt.

* The September 11 terrorist attacks of 2001 on the Twin Towers in New York attack had long lasting effects and are still felt today. Ultimately it led to the United States, United Kingdom and other nations invading and occupying Afghanistan and Iraq, as well as implementing various anti-terrorist measures at home and abroad in what was known as the War on Terror.

 

* The Queen Mother died in 2002 (aged 101).

* Globalization continued to influence the world in the 2000s. The financial benefits were an increase in trade and linkages and technologies that benefited many countries, in particular China and India. China began to become an economic power and showcased its progress while hosting the summer Olympics in 2008. However, in other parts of the world such progress failed to address ongoing struggles with modernity, most notably characterized by the rise of al-Qaeda and other Islamist extremist groups. The economic growth due to globalization was shown to be vulnerable to global disruptions. This was illustrated by the financial crisis of 2007. A crisis was triggered by the lack of liquidity in the United States banking system caused by the overvaluation of assets (the packaging of subprime mortgages). This resulted in the collapse of large financial institutions, the bailout of banks by national governments and downturns in stock markets around the world (the vertical axis is the value of bad loans in billions). New Zealand did not escape –the global economic downturn meant less money for education and research and more students enrolling for university courses since there were fewer jobs.

 

* Barack Obama, the first African-American president of the United States, was inaugurated in 2009 -- with the “yes, we can” motto.

In 2008 work began on a $9 million upgrade of the Microbiology building which will be reclad, with windows replaced and air conditioning installed. The cladding had developed 'concrete cancer' due to reinforcing steel beneath rusting and cracking, causing pieces of concrete to fall from the cladding. The implementation of new Health and Safety Standards had meant that a number of laboratories required upgrading and renovation. The work was completed within the estimated two years.

There were several anniversaries during this decade -- the 50 years of NZMS (New Zealand Microbiological Society) in 2005 and an associated annual meeting, the Microbiology Alumni function, and 60 Years of the Virus Research Unit, along with celebratory dinners for the department, Sandy Smith and James Kalmakoff.

 

• 2002 -- 50th Year Microbiology Celebratory Dinner
• 2004 -- Name changed to Department of Microbiology and Immunology
• 2004 -- Sandy Smith Farewell Dinner
• 2005 -- 50 years of NZ Microbiological Society cocktail party
• 2005 -- Joint NZMS/NZSBMB scientific conference held in Dunedin -- Click here for photo gallery
• 2005 -- 50th Alumni Dinner at Staff Club
• 2008 -- 60 years of Virus Research Unit -- (Click here for previous posting)
• 2008 -- James Kalmakoff Farewell Dinner
  

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Galleries

2002 -- 50th Year Microbiology Celebratory Dinner

2004 -- Sandy Smith Farewell Dinner

 

2005 -- 50th Alumni Cocktail Party

 

2008 -- James Kalmakoff Farewell Dinner

 

In 1994 David Jones was away on sabbatical leave from May to February 1995 and I became the Acting HOD. During this time John Tagg and his team of happy microbe hunters began the publication of a Departmental newsletter. He recruited a team of news scouts from a representative of each floor and collected items of interest about the people whose home-base was that floor.

The idea was to present the news about visitors, new staff, social events and interesting stories about people -- to provide a sense of departmental identity and community -- the esprit de corps.  The newsletter provides the details of the Inside Story of the Department in a way that would not be otherwise possible -- warts and all.

The ethos of the Department in the 1990s shaped by the chairmanship of  David Jones and was carried on for the next two decades by the chairmanships of Sandy Smith and Frank Griffin. During the 1990s, several new academic staff were appointed and these included:

• Clive Ronson -- 1991
• Jurgen Thiele -- 1991
• Vernon Ward -- 1993
• Andrew Mercer -- 1993
• Robin Simmonds -- 1994
• Judith Bateup -- 1994
• Sam Hou -- 1994
• Heather Brooks -- 1994
• Margaret Baird -- 1998
• Gregory Cook -- 1998

Clive Ronson (Top)

Clive joined the Department in 1991 and soon established collaborations with scientists working on rhizobia at AgResearch Invermay. The collaboration led to a joint programme funded by the Foundation for Research, Science and Technology and to the discovery of a novel chromosomal genetic element his group termed a symbiosis island. This discovery led to new insight into the role of horizontal gene transfer (HGT) in microbial evolution and the work remains one of the best illustrations of HGT in the natural environment.

Clive Ronson was born in Kaikohe, and moved with his family to Palmerston North when he was five. He became interested in genetics through the influence of his biology teacher at Palmerston North Boys' High School. After completing his BSc(Hons) in Genetics at Massey University in 1973, he was awarded a National Research Advisory Council Scholarship and joined what was then Grasslands Division of the Department of Scientific and Industrial Research (DSIR) in Palmerston North. After a year there where he initiated his studies on the rhizobium-legume symbiosis, he undertook his PhD studies in Biological Sciences at the University of Warwick in Coventry, England. Upon graduating in 1979, he returned to Grasslands as a research scientist for six years.

His early study (at the DSIR) of mutants of dicarboxylate transport genes focused attention on 4-carbon dicarboxylic acids as the energy source that plants supply to the bacterium in rhizobial nitrogen fixation, and significantly altered understanding of the molecular events occurring during symbiosis. Stemming from this work (and perhaps his most important discovery) was the first two-component regulatory system in bacteria.  These systems, in which an environmental stimulus is sensed by one component in the bacterial cell and passed on to a second component, are now recognised as the major way in which bacteria sense their environments. This discovery was made during what was intended to be a one-year study leave at the Department of Molecular Biology at Massachusetts General Hospital in Boston. 

 The one-year stay in the Boston area stretched to six years when he joined a biotechnology company in Cambridge, MA. He became director of a large programme aimed at developing recombinant microbial inoculants for agriculture, and his experiences there included overseeing the second field trial of recombinant bacteria in the USA.

Clive has been involved in the teaching of genetics and was a member of the working party that led to the establishment of the Genetics Major in 2000. He was appointed to the inaugural Chair in Genetics in 2003 and Director of the Genetics Programme.

In 2007 Clive became a Fellow of the Royal Society of New Zealand.

In Oct, 2014, he became the Head of Department.

Gallery of lab photos

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Jurgen Thiele (Top)

Jurgen was appointed in 1991 and brought with him a very Germanic outlook on academia and science. His research activities were focused on the microbiology and biotechnology of industrial pollution control. He targeted pollutants that were toxic, persistent and only slowly degraded in nature. Four different pollutants were chosen: (i) fat, (ii) pesticides (DDT/DDE) in soil, (iii) PCB and pesticides in industrial effluents and (iv) the improved solid waste management (sewage).

He developed collaboration with the German Ministry for Science and Technology. Through this cooperation three German postgraduate students were chosen in 1992 and 1993 to study for a degree in environmental microbiology/biotechnology at the University. Since that time many postgraduate students have come to the Department to carry out studies in virology, bacterial physiology and immunology.

Jurgen was passionate about his research and soon became impatient with the many obstacles that were part of administrative academic life. He managed to alienate some of his colleagues and also his students for whom he had set very high expectations.

 

By 1996 he felt that he could best achieve his goals by establishing his own biotechnology company and consequently resigned from the Department. He continued to work in partnership with Waste Solutions at the MAF, Invermay research station on the development of biotechnology and bioprocesses to maintain a green and clean environment in New Zealand.

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Vernon Ward (Top)

Vernon was one of my PhD students and for more about his student days see "My Story" a chapter that will follow.

Vernon was appointed Assistant Lecturer in 1993 after spending six years on the postdoc circuit. In 1987 after graduating with a PhD from this Department he went to the Institute of Virology and Environmental Microbiology, Oxford and worked on tick-borne RNA viruses. He followed this with a postdoc at the Entomology Department, University of California at Davis from 1989 to 1993, working with Bruce Hammock’s group on baculovirus expression systems.

Upon his return to the Department he brought with him valuable expertise in baculovirus expression vectors and PCR cloning technologies. He took a leadership role in the local biotechnology developments and was the editor of Zealand Biotechnology Association Newsletter, 1995 – 1999. He was involved in the development of the Molecular Biotechnology major for University’s Applied Science programme.

Vernon always had the ambition to become an academic and this story is best told by his "My Brilliant Career" video. This video was made during a seminar organised by Heather Brooks for the 4th year students as part of her postgraduate teaching activities (see the section on Heather Brooks for further details).

 

 

Gallery of lab photos

A footnote: Vernon became a professor in 2011 and the Head of the Department in 2012. In August of 2014, he was appointed Dean of the School of Biomedical Sciences (formerly the Otago School of Medical Sciences). He was interviewed by TV Channel 39 shortly after his appointment.
 

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Andy Mercer (Top)

Andy has had a long association with the Department -- as an undergraduate student, as John Loutit’s Ph.D student and then after a period overseas, he returned in 1984 to the Virus Research Unit (VRU) as a post-doc. He is currently the Director of the VRU and holds the Chair of Viral Pathogenesis. In his own words he describes the activities of the VRU:

Terry’s recollections of the Virus Research Unit take us up to late 90’s. Since that time many things have changed but much of the essence is the same. Merilyn Hibma joined the VRU in the 1994, establishing a new and successful research direction for the group with her work on human papillomaviruses. Steve Fleming has developed our investigations of poxvirus factors that manipulate the immune system and Lyn Wise is leading our development of virus proteins that have exciting potential as new therapeutics in non-viral settings such as improved wound healing. We have remained reliant on external funding but diversified our sources of funding. In recent years these have included not only Health Research Council (HRC) but also the Foundation for Research Science and Technology, Cancer Society of NZ, local industry sources and international pharmaceutical industry. We have welcomed an increasing number of postgraduate students for MSc and PhD study, with many of these coming from other countries. We have also formed strong collaborative links with other labs in the Department and around the university. Currently these form an HRC-funded Programme that includes 10 University of Otago Principal Investigators supported by 8 technical staff and a similar number of postgraduate students. These come from 6 laboratories across the Departments of Microbiology & Immunology, Biochemistry and Pathology. In another illustration of the continuing evolution of the VRU and its role within the Department, in 2010 I was appointed to the inaugural Chair of Viral Pathogenesis. Despite these changes much remains as Terry recalls it. Social activities remain a big part of the VRU, even if the parties are quieter these days. And for me, like Terry, the VRU is, at heart, a great group of people and a great place to work.

Photo Gallery

The VRU remained somewhat aloft from the day-to-day running of the Department and the teaching programme. But it did feature large in taking on students for postgraduate training and supervision. Since the scientists in the VRU were carrying out research and were not distracted like the rest of us with teaching, it became an attractive place for students to work and the VRU usually had the pick of the bunch when it came to attracting the best students. 

Andy Mercer proved to be very competent director of the Virus Research Unit and faced the troubles of the world with a quiet and engaging smile. He always seemed to be the person who was at the right place at the right time.

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Robin Simmonds (Top)

Robin wrote the following description of himself for the 1994 Microbiology newsletter.

Undoubtedly the greatest influence on my research career has been an insatiable curiosity and the need to know why things happen. These traits have provided a motivating force in an unorthodox and seemingly chaotic path to my present position.

I was born a tradesman’s son. and long before I journeyed to university I was skilled with my hands. These skills found a ready application in microbiology and my curiosity an outlet in research. I graduated with a PhD from the Department of Microbiology. University of Otago in 1982 and immediately began postdoctoral studies at Baylor College of Medicine in Houston, Texas.

I returned to New Zealand late in 1985 to be confronted with the mindless violence of the Rainbow Warrior bombing and post Muldoon inflation. New Zealand as I remembered it no longer existed. Rather than return immediately to research I decided to use this opportunity to acquire new skills and in 1986 I enrolled at Auckland College of Education to study for a Dip. Teach. The ensuing three years saw a return to “the trade”, great for character building, lousy for the publication record.

1990 brought the chance to return to active research in Dunedin, working with John Tagg on bacteriocin-like inhibitory substances (BLlS). A remarkably peaceful two and a half years was spent on this project before a career move took me to Pitman-Moore in Upper Hutt to work on the development of small animal vaccines. Unfortunately this was followed very swiftly by another move back to Dunedin when Pitman-Moore decided it was no longer interested in maintaining research facilities in New Zealand.

As of July 1 1994 I have been appointed as Assistant Lecturer in Microbiology and I am looking forward to the challenges that I know this will bring. In the next three years I hope to continue my research on BLIS and to put into practice those teaching skills learned in the classroom.

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Sam Hou (Top)

Sam was appointed in 1994 and in 1997 resigned to take up a position of Group Leader at Edward Jenner Institute for Vaccine Research, UK. He provided a description of himself for the 1994 Departmental newsletter.

I was born in Hong Kong and moved to Dunedin with the entire family when I was three. After developing a reasonable Kiwi accent and completing a MSc degree in the Department of Microbiology in the University of Otago I decided to add a little Aussie slang to my repertoire and moved to Melbourne to complete my doctorate in the Department of Veterinary Preclinical Science in the University of Melbourne.

Not feeling satisfied with this addition, I decided to add a Southern drawl and moved to Memphis, Tennessee U.S.A. to work with Dr Peter Doherty in the Department of Immunology at St Jude Children's Research Hospital. But after 5 years, it was time to retrieve the original Kiwi intonations, my vowels had softened too much and you can only take so much of Southern fried chicken, and I returned "Home" to take up a lecturing position in Immunology in the Department of Microbiology in the University of Otago.

After ten years away, it’s good to be back. I am very interested in the mechanism(s) involved with the maintenance of T cell memory, particularly to viral infections. The work begun in Memphis using a mouse model for a respiratory parainfluenza infection hinted at possible answers and it is this area of research in which I would like to continue and expand in my studies in Dunedin, perhaps moving to a bacterial infection (tuberculosis).

Photos of Sam Hou's Farewell

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Heather Brooks (Top)

Heather was appointed in 1994 and as an introduction to her seminar “The Search for E. coli 0157” the following article was written for the 1994 Departmental newsletter (for more see her ‘My Brillant Career’ video).

Heather Brooks joined the Department of Microbiology as a Teaching Fellow in June 1993 and was elevated to the rank of Lecturer in February 1994. A graduate of Surrey University, UK, she developed an interest in E. coli as a urinary tract pathogen whilst studying for her PhD under Professors Frances O'Grady and Bill Cattell at St Bartholomew's Hospital, London.

Her interest in urinary tract pathogens continued during her time at Massey University. Heather's career was then punctuated by several years out of the work force bringing up a family. On returning to the world of microbiology she decided to redirect her research interests - same bug, different disease.

Preview of Heather's seminar.

One of the more exciting developments in medical microbiology in the past decade has been the discovery of a new class of intestinal pathogens; the Enterohaemorrhagic E. coli (EHEC). Spectacular outbreaks of food poisoning due to EHEC serotype 0157 have occurred in the USA in recent years, mainly due to the consumption of contaminated, undercooked hamburgers sold by fast food outlets. A common pathogen in the UK and Canada also, EHEC 0157 gained a certain amount of notoriety because of potentially fatal sequelae. EHEC 0157 has become the unacceptable face of food poisoning causing a disease which may he fatal to otherwise normal healthy children.

The problem is considered to be so serious in the USA that legislation banning both the sale and import of meat containing EHEC 0157 is being considered. With its repercussions for the meat industry in NZ, EHEC seemed to be a worthwhile area of research. Very little is known about these organisms in NZ and a small grant from the Dean’s fund enabled me to conduct a survey over the summer months to find out if 0157 was present in the Dunedin population.

The results of the survey were both unexpected and intriguing - but if you want to hear more you will have to come to the seminar.

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Heather has been a consistent favourite in receiving the Otago University Medical Students' Association (OUMSA) Teaching Excellence Awards. In 2014 it was the sixth consecutive year that she received the award for the second-year programme and one of the several years she received both the second and third-year awards. 

An example of her inclusive teaching style is a seminar for the 4th-year postgraduates entitled "My Brilliant Career" in which Vernon Ward and Robin Simmonds participated.

 

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Judith Bateup (Top)

Judith joined the Department as a teaching fellow after spending her undergraduate and postgraduate years in Microbiology. Below are her microbiological memories:

I was born and bred in sunny Nelson, attending Nayland College. As Nelson is not a University-city, those wishing to undertake further study must move, most go to Christchurch to attend Canterbury University. I wanted to apply for entry into the School of Pharmacy, so I came to Otago in 1987 to undertake Pharmacy Intermediate (very similar to the current HSFY [Health Science First Year]). I was offered a place in the second year Pharmacy intake, but by then I had found Microbiology and the change in career was permanent. In 1991 I graduated with a BSc (Hons) First Class and enrolled in studying for a PhD. I chose Gerald Tannock as my supervisor, both for my interest in gastrointestinal research and also for his amazing teaching style. After three and a half years studying the bile salt hydrolase enzyme in lactobacilli I graduate with a doctorate. I had got married to Phil Page (also a Nayland College ex-student) in my final year of PhD study. Phil, a law student, used to come into the lab on particularly long days and wash my glassware for me (probably frowned upon in these days of Health and Safety).

In 1994, at the conclusion of my PhD I was offered a Teaching Fellow position in the department, initially involved in the teaching of the new BIOL115 paper (the precursor to HUBS) with John Cross, and 200-level Microbiology. After about five years I took up more Microbiology teaching and left BIOL115.

Now in my seventeenth year of teaching I have amassed a variety of responsibilities - from chairing the departmental teaching committee to convening two papers - MICR221 (Microbes to Medicine) and PHCY219 (Microbiology and Immunology for BPharm) - the girl who came to study Pharmacy Intermediate has come full circle! Along the way I have gained three gorgeous children and still haven't acclimatised to the Dunedin winters!

My current passion is liaising with secondary school teachers in the Dunedin and Otago region to help provide teaching resources and knowledge to ensure that Microbiology is well taught at the secondary school level. Many of the secondary schools in Dunedin bring classes into the department for year 11 workshops during the mid-semester breaks.

The staff in the Department of Microbiology and Immunology are its greatest resource and are professional and knowledgeable colleagues. Each year brings in a new cohort of young microbiologists. I often wonder who will be the groundbreaking researchers of the future.

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In 2016 Judith received both a University of Otago Teaching Excellence Award and a National Tertiary Teaching Excellence Award. She modestly said that the awards reflect the contribution the Department makes to the teaching of undergraduate programmes at Otago. Over the years, Judith has made the second-year microbiology laboratory exercises a positive learning experience and has mentored the students in a caring way.

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Margaret Baird (Top)

Margaret was appointed in 1998 but she had previous connections with the Department. The following is an excerpt from the newsletter in 1994:

If you've got it, flaunt it! - Dendritic Cells as Antigen Presenters'" Dr Baird has sent the Newsletter a brief preview of the seminar she will be presenting today. "Dendritic cells are the most potent of the cells that present antigen in a recognisable form to the immune system. Indeed, recent evidence suggests that they are essential for the initiation of an immune response. This seems extraordinary in view of the fact that they are present at very low frequency in most tissues. This seminar will cover work carried out over a four year period in which the activities of these cells have been investigated in a number of different contexts.

Glenn Buchan presented this profile for the seminar: "Dr Margaret Baird was in fact an early product of the Diploma of Immunology Course run by the Department of Microbiology. She was one of the "class of 78” - the first year the course was run. Other (now famous) graduates that year included Drs Ken Beagley and Glenn Buchan. Margaret survived her 4th Floor experience and moved on to do a PhD with Professor Barbara Heslop. She worked on the immunological response behind transplant rejection. Her interest in dendritic cells developed long before they became 'voguish' and she has made considerable contributions to both transplantation and dendritic cell research. Following Barbara’s retirement. Margaret has assumed the mantle and currently holds a Health Research Council grant to enable her to study the role of dendritic cells in the activation and regulation of immune responses to mycobacterial antigens. Over the years Margaret has taken an active role in promoting women in science and her talks are always a joy to attend."

Upon the request to provide information for this book, Margaret replied to the following questions:

What was your academic background before joining the department?

Although joining the department in 1998, my associated goes back to the 1960’s when as a Zoology student I took a course in microbiology. I remember the vibrancy and enthusiasm of Molly Marples (also Brian her husband who was in the Zoology department) and lectures by Sheila Thompson who elegantly sat on the edge of the desk with long legs crossed explaining recent ideas on bacterial genetics.

Upon returning to academic study in 1978, I enrolled in the inaugural Diploma in Immunology course taught by Frank Griffin and Bruce Gibbins. Although it was only a class of nine, it had four members who went on to have academic careers in immunology: myself, Kevin Mariarty, Glenn Buchan (also a Zoology student) and Ken Beagley. Upon completion of the course I was offered a PhD scholarship by Barbara Heslop in the Pathology department and carried out research on histocompatibility in inbred strains of rats. I continued working in Pathology until joining the department in 1998.

Why did you choose to join the department?

One of the unique features of the department is the ability to collaborate with a wide variety of disciplines and skills – from virology, gut ecology, genetics and other immunologists.

What do you consider your main achievement?

My research concentrated on the earliest stages of the immune response, particularly on the dendritic cell. This cell was relatively unknown to immunology but now it is recognized as being the key ‘decision maker’ of the immune response: they determine whether or not an immune response is initiated to foreign material or ‘altered self’ detected in the body. I am proud to be recognized and associated with that development in immunology.

Any outstanding events in the department during your time there?

As convener of the postgraduate students, I have been able to share many of the ‘highs’ and the ‘lows’ of the students who have come through the department. I feel honoured to have been part of their lives and to see many of them develop into world-class scientists and to continue to maintain links with them.

Any concluding comments?

One of the issues that I feel strongly about is the gender balance in the university. Whereas there is a greater than 50% enrolment of females in university courses, there is a very small percentage of women in senior academic positions.

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Margaret was very popular with the graduate students in the Department and became the postgraduate co-ordinator. She devoted a great deal of time helping young students and researchers. She hosted an annual breakfast at her home for all the new departmental postgraduate students at the beginning of the academic year. They loved coming to her home and being hosted -- that personal touch which showed she cared. She was known for her "distinctive laugh" and her boundless energy and enthusiasm. 

In May of 1964 while studying for a BSc in zoology at Otago, she met her husband-to-be Stephen Baird, in the chorus of that year's Capping Concert and they also took part in a spoof skit based on a current TV show, Dr Kildare. The relationship grew and they were married in January, 1967. After completing her degree in zoology in 1967, she taught science at St Hilda's Collegiate School for three years. In the 1970s, she accompanied her husband, Stephen, when he taught mathematics in the British Solomon islands and later in England. As already mentioned above in 1978 she took the Diploma of Immunology Course and went on to pursue a PhD in pathology under Barbara Heslop. 

In 2012 she retired from the Department and took up a part time research position back in the pathology department, working with Anthony Braithwaite on tumour-suppressing proteins. In 2013 she received the Derek Rowley Medal for services to the Australasian Society for Immunology.

In September of 2016 she died after a brief illness with cancer, aged 71. She is survived by her husband Stephen, their daughters Sophie Baird and Harriet Pope, and grandchildren Dan, Alex, Lucy and Daisy.

Gallery of Lab Photos

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Gregory Cook (Top)

Greg was appointed in 1998 and provided the following information for the book.

What was your academic background before joining the department?

I completed all my degrees (BSc, MSc(Hons) First Class, DPhil) at the University of Waikato (1984-1991). My DPhil was completed in the Thermophile Microbial Biochemistry Unit at the University of Waikato and focused on Ethanol production by thermophilic microorganisms and how this process was regulated. I then headed to Cornell University in Ithaca New York (1992) for my first postdoc with Professor Jim Russell focusing on rumen bacteria and control of energy source utilization. I stayed in Ithaca for 3 years and absolutely loved the place for its high-powered University, beautiful scenery and interesting people. It was a shame to leave, but I had become more interested in microbial genetics and molecular biology and needed to head in this direction. I went to Kings College in London in 1992 for a postdoc with Professor Robert Poole to studying a putative haem transporter in E. coli. I learnt a lot of molecular techniques, including attending the Advanced Bacterial Genetics Course at Cold Spring Harbor Laboratory. Rob Poole accepted a position at the Krebs Institute in Sheffield and that is where I stayed until 1997. In late 1997 I was offered the position of lecturer in Environmental Microbiology at the University of Otago.

Why or how did you come to the University of Otago?

I was encouraged to come to the University of Otago through interactions I had with Professor David Jones. I had never been to Dunedin before I took the position here and I instantly liked the place. I wanted to return to New Zealand for an academic post and my goal was to always gain a position at Otago.

What do you consider your main achievement?

The awarding of my personal chair in 2009. This was my number 1 goal since I can remember so it was nice to make the milestone.

Any outstanding events in the Department during your time there?

The most outstanding event during my time in the Department was the agreement reached between the Departments of Biochemistry and Microbiology to fund the Centre for Protein Research.

Any concluding comments?

I have enjoyed my time in the Department since 1998 and the key to staying fresh and focused has been the 3 sabbaticals I have had during this period. I have no regrets about coming to Otago and I look forward with great anticipation to the years ahead.

Gallery of lab photos

In 2014 Professor Greg Cook was featured in the November issue of the University of Otago Magazine.

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Closing Remarks for the 1990s

At the departmental level the 1990s were a time of growth and vibrancy as the new staff brought with them their energy and enthusiasm. The change to a free market economy previously mentioned by David Jones had an impact on university student fees, which resulted in student protests, disruption to University Council meetings and a two-day occupation of the Registry. The ‘management style’ of Graeme Fogelberg, the new Vice Chancellor, tended to inflame employment conditions and caused hostility in settling staff salary and wage negotiations.

In 1996 when David Jones took up the Deanship of the Otago Medical School, Sandy Smith became the Chairman of the Department. Since the Department was in good shape financially and well organised from the efforts of David Jones, Sandy took a minimalist view and let the Department run on its own momentum and intervened only when necessary. He became famous for his photocopied handwritten agendas for the weekly staff meetings.

On the world scene the Soviet Union dissolved -- On December 25, 1991, Gorbachev resigned as president of the USSR, declaring the office extinct and ceding all the powers still vested in it to the president of Russia: Yeltsin. On the night of that same day, the Soviet flag was lowered for the last time over the Kremlin. In 1994 Nelson Mandela became the president of South Africa, ending apartheid.

And finally in 1999 President Clinton visited New Zealand and made this famous comment about Queenstown: "Let me say from the bottom of my heart, this has been a magical trip. I think every person, when he or she is young, dreams of finding some enchanting place, of beautiful mountains and breathtaking coastlines and clear lakes and amazing wildlife, and most people give up on it because they never get to New Zealand. This has been an amazing thing for me and for all of us."

In the next chapter we will explore the social life of the Department during these times.

When I was collecting material for the departmental archives, I had asked the staff to provide some information about themselves and suggested  answering some questions:

* What was your academic background before joining the department?
*  Why did yoy choose to join the department?
*.What do you consider your main achievement?
* Any outstanding events in the department during your time there?
* Any concluding comments?

Some of the staff did not reply, some answered the questions directly, some replied in their own way and some like David Jones gave a detailed reply that covered the broader picture with a critical analysis of the issues involved. This was typical of David's response to all things -- a fully professional approach to life.

 

Personal Memories of Microbiology -- David Jones

• Academic background prior to joining the Department of Microbiology
• Move to University of Cape Town
• Appointment to the Chair of Microbiology at the University of Otago
• Tenure as Head of the Department of Microbiology (1989-1995)
• University management structure
• Changes within the education science and health care sectors
• Subsequent changes to the University management structure
• Departmental structure within the Otago Medical School
• Challenges as the incoming Head of Department
• Staffing issues
• Financial issues
• Academic issues
• Research issues
• Personal teaching activities
• Personal research activities
• Personal professional activities
• New challenges

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Academic background prior to joining the Department of Microbiology

I gained my initial training as a microbiologist when I undertook a qualification in medical laboratory technology – initially majoring in general clinical pathology followed by a specialist diploma in microbiology. At this time I was employed by the University of Natal Medical School located in Durban, South Africa. During my initial training I first worked in a routine hospital laboratory associated with the medical school and subsequently transferred to a position in the Department of Medical Microbiology at the University. I was then appointed as a technical research officer at the Institute for Parasitology while undertaking an honours degree in Biological Sciences at the University of Natal.

I was subsequently appointed as a lecturer in microbiology in the Department of Biological Sciences and undertook a PhD in microbiology through Rhodes University. While finishing my doctorate I accepted a position at Rhodes as a senior research fellow. My original field of research was in medical microbiology with as focus on anaerobic bacteriology. During the period I was in the Microbiology Department at Rhodes University we were approached by National Chemical Products (NCP), a large South African chemical and industrial fermentation company, seeking assistance to help them deal with a phage infection which had decimated their commercial Acetone Butanol Ethanol (ABE) fermentation process. I became involved because of my experience with phages infecting anaerobic bacteria. This initial contact lead to the establishment of a research group at Rhodes University funded by NCP and its holding company Sentrachem to pursue a number of fundamental research areas with relevance to their industrial fermentation processes. I accepted appointment as the NCP/Sentrachem research group leader.

Move to University of Cape Town (top)

At the end of 1979 the then Head of the Department at Rhodes, Professor David Woods was appointed to the Chair of Microbiology at the University of Cape Town. This was a large, well-established department, but due to a set of unusual circumstance that included the retirement of a number of senior staff there were very few members of staff holding tenured positions at the time. This provided David Woods with a unique opportunity to offer positions to almost the entire team from Rhodes.

Very generous start-up funding from UCT enabled us to establish well equipped, state-of-the-art facilities for microbial genetics, anaerobic microbiology and biotechnology. With the move to Cape Town our industrially funded research groups underwent a major expansion and it proved to be an exciting and productive time for our research. I was appointed as a senior lecturer and a few years later I was promoted to associate professor, but still continued in my role as the NCP/Sentrachem research group leader.

During this period we worked closely with the company’s research and development department and I was able to spend quite extensive periods working at the plant which provided me with hands on experience with the industrial ABE fermentation process. South Africa was one of the last countries in the western world to continue to run the ABE process which was initially developed during WW I for the production of munitions. This unique experience stood me in very good stead for my continuing involvement in this complex, fascinating and challenging fermentation. The main focus of the research group at UCT was on the improvement of solvent-producing clostridial strains through genetic and physiological manipulation and improvements in fermentation process technology. The group also undertook research on industrial enzymes and yeast used for ethanol production.

Appointment to the Chair of Microbiology at the University of Otago (top)

During the period 1984/1985 a spent a year sabbatical study leave as a visiting fellow at Oxford University. During this time I worked in the laboratory of Professor Joel Mandelstam, who was one of the world leaders in the genetics of sporulation. This proved to be a very productive year for me as I was involved with the development of a phage cloning vector which subsequently enable the majority of the genes know to be involved in sporulation to be cloned and sequenced. Professor Mandelstam had previously acted as a referee for my promotion to Associate Professor and as a result, he had a copy of my CV. In 1987 (which was the year he retired) he was asked to act on a UK search committee for the chair in Microbiology at Otago by Sir Robin Irvine who was the VC at that time. He took it upon himself to put my name forward for the position as I was travelling in Europe on conference leave at the time. When I met up with him at his retirement function he told me that he had submitted an application on my behalf and that obviously I could withdraw this if I was not interested.

At this time I had been appointed as the acting head of the Microbiology Department at the University of Cape Town as David Woods had accepted promotion to one of the Deputy Vice Chancellor position at UCT. At the beginning of 1988 I was invited to come to New Zealand to interview for the position at Otago. The interviews for the position of Head of Department at UCT were held two weeks later. David Woods and I worked closely together as colleagues and were also good personal friends and I knew that he was very keen for me to take over the department that he had been so successful at building up. As I had already served for a year as the acting head of department I felt that there was a very strong likelihood that I would be a strong contender for the position at UCT. Before I departed from my interview visit to New Zealand I was offered the position at Otago. This created a real dilemma as there seemed to be no point in going through with the appointment process at UCT if my decision was to accept the position at Otago. In effect I had less than two weeks to make a decision.

After weighing up all of the factors, we as a family decided to accept the position in New Zealand. On this basis, I withdrew my application for the post advertised at UCT. My obligation to work out my notice coupled with the complexities of emigrating from South Africa to New Zealand at that time meant that I was only able to take up my new appointment in February of 1989.

During 1987 and 1988 Sandy Smith served was as the acting head of department at Otago.

Tenure as Head of the Department of Microbiology (1989-1995) (top)

One of the main factors that attracted me to the position at Otago was that I saw this as offering a greater challenge for me personally than the appointment at UCT. At the time the department at UCT was the premier microbiology department in the country with an excellent international reputation. It was well organised, well funded and had been very well lead. The challenge as the incoming head of the department would have been trying to maintain the department in this position when there were already strong indications that circumstances both at UCT and in South Africa generally would make this increasingly difficult to achieve. My impression of the department at Otago at this time was that it had been through a long period of stability but to some extent had lost direction since the retirement of John Loutit as Head of Department. I was very impressed with quality of both the academic staff and the general staff in the Department but felt that the Department as a whole was not achieving its full potential and the recognition it clearly deserved.

My arrival coincided with a period of major change in New Zealand society and politics with particularly rapid changes taking place in the education, science and the health care sectors. The University of Otago had been through a period of sustained growth leading to an increased complexity and this had begun to impinging on the way the University was being managed and organised. Taking up the appointment as HOD was a daunting challenge for me personally as the academic staff in the department included five well established senior academic staff with a similar status to my own. It therefore seemed obvious to me that although I had been appointed to lead the department a consensus style of management would be required to achieve the necessary buy-in and support to bring about the changes that I considered needed to be made to allow the department to achieve its potential.

University management structure (top)

It did not take long to discover that the way that OU was run and managed differed in a number of significant aspects from the institutions that I had been acquainted with in South Africa. From my perspective the management style in operation at Otago at the time was tailored to a small elitist academic institution run along the lines of a close-knit family business, with the boss (VC) very much in charge. It also seemed apparent to me that this management style, that had obviously worked very successfully when the university had been small and more intimate, was starting to encounter some difficulties. The reason for this were both internal and external. Internally the University had expanded in both size and complexity. This had lead to divisionalization and greater diversification within the University. The significant expansion in student and staff numbers meant the informal top-down management approach with few standard operational processes, that had worked effectively in the passed, were proving inadequate in the new climate.

Changes within the education, science and healthcare sectors (top)

Externally the rapid shift to an open free market economy in NZ had a major flow on effect for the universities. Funding of universities moved to an EFT based funding model with student fees becoming and increasingly import component. The science sector was restructured on a competitive business model, the old DSIR was disestablished and a number CRI’s were established in its place and funding for science became contestable. Hospitals were also re-cast as business units that were expected to make a profit. This new model made no provision for the funding of medical research or teaching. This coincided with the old MRC that had been responsible for the funding of medical research being abolished and a new HRC set up in its place. Accompanying this was a strong focus by government on establishing a competitive environment with increased accountability and compliance within the university sector.

Subsequent changes to the University management structure (top)

Sir Robin retired from the position of VC and Graham Fogelberg was appointed in his place. He appointed two deputies from Australia. At this time the universities in NZ voluntarily established an internal quality audit program, that involved a rigorous internal self review process, to avoid pre-empt the government imposing a more rigorous accountability and auditing process. The combination of these extensive and rapidly introduced changes and the associated greatly enhanced processes that ensued had a demoralising effect on the university, science and health care sectors. Not surprisingly, within the university, these changes had huge flow down effect through the divisions and schools to individual departments.

Departmental structure within the Otago Medical School (top)

At the time I took up my appointment in the Department of Microbiology it was just one of several dozen departments of disparate sizes making up the Otago Medical School. Departmental funding came in the form of a confidential, annual, top-down allocation which was barely sufficient to meet the basic costs of teaching. Staffing salaries were paid for, and staffing appointments made via the Otago Medical School. The securing of funding to undertake research was basically the responsibility of individual staff members to obtain from whatever limited sources of external funding that was accessible at this time. There was no centralised research infrastructure or funding support within the University or the Division and only limited support was available from the Otago Medical School. Applications for the contestable funding of capital equipment were handled centrally though a small committee consisting of long serving senior academics. Health and safety and bio-safety and bio-security was left up to individual department and was of a very rudimentary nature or in some instances non-existent. The running of the department finances was in the hands of the aged storeman. About 15% of the departmental expenditure could be accounted for in detail with the remainder simply disappear down a black hole with little or no control or information on what it had been used for. General staffing matters were mainly an internal responsibility dealt with via the chief technician while processes for academic staffing and leave were mostly of an informal nature. Promotions were handled at the School level while senior promotions were dealt with by the VC with input from his advisory committee.

Challenges as the incoming Head of Department (top)

During the first few years there were a daunting range of challenges and issues to be addressed. Rather than rushing in an making immediate, sweeping changes I made a conscious decision to move more slowly and put my effort into first dealing with the most pressing issues. During my first year, to a large extent I maintained the status quo while I got to grips with how the system worked at the departmental, school, divisional and central university levels.

It seemed to me that it would be counterproductive and detrimental to try and tackle all of the issues head-on at the same time. I outlined the approach that I intended to take to the department, which was to prioritize those aspects and systems in most need of revision and focus on those first. Those areas that were working reasonably well could be left for a later time to be worked through systematically. My approach has always been to try and do things properly and to avoid tinkering or making, ad hoc changes unless these are absolutely necessary. As a consequence the changes and upgrades to the departmental systems essentially took five years to work though.

Staff issues (top)

One of the most immediate challenges involved staffing promotions. A lesson learn from experience and reinforced by my mentors is that good staff are the key to success. If a department can appoint and retain top quality academic and general staff then quality research and teaching follows automatically. Three senior academics, Frank Griffin, Gerald Tannock and John Tagg were all log-jammed for promotion to Associate Professor. Their cases for promotion were being compromised by competing against each other. The solution prove to be to establish an order of priority which enabled all three to receive their long overdue promotion over the next three years. The retirement of Mani Pillai followed by that of professor Margaret Loutit provided opportunity to make valuable new appointments. These were Clive Ronson and Jurgen Thiele. The ability to make limited term assistant lecture appointments coupled with the resignation of Bruce enabled the recruitment of additional staff that included Glenn Buchan and Vernon Ward. Other later appointments to assistant lecture positions included. Robin Simmonds and Heather Brooks.

Financial issues (top)

A second major challenge involved securing sufficient flexible funding to make changes and implement new developments needed to build up the departmental infrastructure and equipment. Adequate funding was also required to support research and postgraduate teaching. One of the immediate challenges was to put in place financial management system to manage the departmental finances. I devised a system that fitted my responsibilities as HOD and financial services were very helpful and supportive in implement the system This lead to the appointment of departments first financial administrator Ronnie Bell. The timing proved to be very fortuitous as shortly after the University changes to a budget driven allocation model. The new system provided all the information needed for the new funding model and as a result the annual budget almost doubled. Widespread budget inflation practices by departments across the university soon resulted in a shift to EFT based formulae funding. The bulk EFT funding model implemented by government to fund universities was never intended for internal use and Otago was the only university that elected to implement this as it internal funding model. This policy had many adverse effects as it led to cut-throat competition between the newly established cost centres to maintain and increase their EFT numbers at the expense of others. It did have the positive advantage of being transparent and providing competitive drivers to improve performance. The introduction of contestable research funding at the national level also had a similar effect. This generated enhanced research productivity until demand greatly outstripped the amount of funding available and individual success rates drop to levels that became little more than a lottery.

Academic issues (top)

At the time of taking up appointment the academic sciences courses in the department had not been updated for some time with mainly ad hoc changes made to the original design. In particular the practical course had languished and no longer had a coherent structure. A programme was implemented to upgrade the undergraduate lecture courses and practical classes with the aim of improving course ratings and recruiting more students. The structure of the honours course was also revamped with the specific aim building up research student numbers. The fact that many of these changes were already well underway by the time EFT based funding was introduced positioned the department to compete effectively in the new environment. A second area of attention was the duplication of teaching at the undergraduate level. In particular this entailed building bridges with Biochemistry in to avoid overlap in the teaching of molecular and microbial genetics and microbial biochemistry and physiology. This initiative led to the introduction of an interdisciplinary course in genetics which was eventually expanded into a full academic programme. There were a number of other academic initiatives that the department was actively involved in including the introduction of a first year health science course that had to be taken at Otago. A new four year interdisciplinary programme in Medical Laboratory Science was established and of a distance taught postgraduate programme in Biotechnology was introduced. During this period the teaching of microbiology and immunology to medical, pharmacy and dental students underwent major revisions.

Research issues (top)

During this time a number of initiatives to help strengthen research in the department were also implemented. These included strengthening the links with the virus research unit and the Deer Research Laboratory. The establishment of a university wide Centre for Gene Research that included a service section that included DNA sequencing service and other molecular genetic technologies. The department had a number of expensive specialised support services and facilities that included a fully equipped workshop and EM unit that were not being fully utilised. The department was involved in a series of negotiations that lead to the establishment of communal services to replace these. The replacement of old equipment and the provision of new equipment was greatly improved by including this in the department budget with only very large items of equipment remaining contestable and the university level. Improvements in the organization and accountability of the general staff were introduced and improvements and upgrades of student and staff health and safety procedures and biological compliance practices were also implemented. One area that remained a problem was funding for research and postgraduate teaching. The EFT based funding model made no provision for research and with the introduction of the full cost recovery policy for research that taking on of valuable marginally funded research grants were discouraged by the central university. However, despite these stringent limitations research output of the department showed a significant increase and postgraduate student number continued to grow. The good social atmosphere that prevailed in the department no doubt played a significant role in attracting and recruiting students.

Personal teaching activities (top)

During the initial period while major changes were being made to the undergraduate microbiology courses I took on quite a large teaching load. As part of the restructuring I taught a wide range of topic that included bacterial structure, function and systematics, microbial physiology, molecular biology and genetics, applied and industrial microbiology and contribution to the teaching on microbiology to pharmacy students. As time went on my teaching commitments reduced and my teaching became focused in the areas of microbial gene regulation and biotechnology. In particular I enjoyed developing the case based teaching approach in the biotechnology course.

Personal research activities (top)

In hindsight, I think that I should have put more time and effort early on into establishing my own research base instead of putting most of my energy and effort into dealing with the broader challenges and issues. A circumstance that prevailed at that time did not assist in this regard. There were no formal establishment or start-up grants and research funding was hard to come by. I was provided with adequate funding to buy the equipment required for my research but it took a full year while the equipment was ordered, purchased and installed before my laboratory became operational. In the mean time I was limited to writing up papers on research undertaken at UCT. I made the decision to continue with my main area of research which was the solvent-producing clostridia used in the industrial acetone butanol fermentation process. I was warned that research funding would be difficult to obtain in this area but this was the area that I had become established in internationally. I should have pushed for more support to enable me to get my research established but funding at the time was very tight. The initial area of research that was undertaken focused on a study of effects of phage infections in the industrial fermentation process and involved the characterization of a number of lytic, lysogenic and defective temperate bacteriophages. An investigation of phage host ranges served to confirm that the taxonomy of the solvent-producing clostridia confused and incorrect. Later research encompassed the molecular taxonomy, phylogeny and characterization of the solvent-producing clostridia. This lead on to genetic mapping of the newly established Clostridium saccharobutylicum species and an investigation into the comparative genomic structures of the four major species of industrial solvent-producing clostridia. Comparative fermentation studies and studies on lytic degeneration in industrial solvent-producing strains were also undertaken.

Personal professional activities (top)

I joined the NZ Microbiology Society and served on the committee and I was also one of the founder members of the NZ Biotechnology Association and later served a term as president. I was also involved in the establishment of BioSouth biotechnology cluster. Being somewhat of an outsider, I never really felt comfortable in the national professional science arena. The majority of my professional activities were in the area of international science. I served as an IUMS representative on both the Bacteriology and Applied Microbiology Division and the International Committee of Systematic Bacteriology. I also served on the advisory board for the International Clostridium Workshops on the regulation of metabolism, genetics and development of solvent and acid producing clostridia. I was a member of the International Commission for Genetics of Industrial Microbiology, the international scientific board for GIM symposia and the editorial board of Trends in Biotechnology.

New challenges (top)

During the second half of 1994 I was granted a six month sabbatical leave. On my return I was looking forward to expanding my research activities. At this time there had been a growing dissatisfaction amongst the heads of the five preclinical departments with the structure of the Otago Medical School and we established an informal group to look after our specific interests. This culminated in changes being made to the structure which resulted in the establishment of three clinical schools of medicine and the Otago School of Medical Sciences within the Faculty of Medicine. It never entered my mind to apply for the position of dean and I served on the initial selection committee. Both an external and internal candidate were short listed but in the end it was decided not to make an appointment. It came as a complete surprise when I was summonsed by VC and DVC and asked if I would consider taking on the position. Opportunities like this only come once and although I had reservations I decided to accept the position. I stood down as head of department at end of 1995 and Sandy Smith was appointed to take my place I took up the position as Dean from beginning of 1996 and served in this role for eleven years until my retirement at the beginning of 2007. During this time I retained my appointment as a professor in microbiology and continued with some teaching and research, although it became increasingly difficult to meet these commitments as time went by.

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Comments

David summarized many of the significant changes that occurred within the University and the Department in the 1990's. We were very fortunate to have his leadership during that time. He was like an Old Testament prophet leading the way through the chaos and change that was occurring around us. Not being part of the local, inbred, university culture, he was able to see the bigger picture and implement policies and strategies that made Microbiology a preeminent department at the University. It challenged, in a friendly way, the position that Professor Petersen and the Biochemistry department had previously held.

Among the important factors was the doubling of the departmental budget brought about by a change in the funding model for EFTS and the estimate of the actual costs of running the courses. The budget proposals were managed by Ronnie Bell, our financial advisor who came from the commercial world. She didn't last long: she was subsequently snapped by the Registry to assist in their financial woes, but she did us a great favour. The other main factor was the revamping of the practical microbiology classes in the 2nd and 3rd years -- they became more of a hands-on fun to learn set of practical exercises which explored the microbial world around us. Also at this time we happen to have a very social group of postgraduate students (more about this later) who were the tutors and demonstrators for these courses. They gave the overall message that Microbiology was a fun place to be. This word-of-mouth communication meant that many bright and able students were attracted to take postgraduate study in the Department. 

 

2010 - Commemorative unveiling of David Jones' portrait

Addendum

DAVID JONES'  INVOLVEMENT WITH THE INDUSTRIAL ACETONE BUTANOL FERMENTATION

"My initial involvement with the industrial Acetone Butanol Ethanol (ABE) fermentation process began in 1977 when a South African chemical and fermentation company, National Chemical Products (NCP), approached the Microbiology Department at Rhodes University for assistance. This company had been operating a commercial ABE fermentation plant since 1935 and they were experiencing recurrent problems with phage infections at the factory. At this time my research interests had been focused on the developmental biology and sporulation in Bacillus and subsequently on the genetics of obligate anaerobic bacteria of medical importance, including some studies on phages.

National Chemical Products plant

We were able to assist the company with their problem and this led to them, funding some contract research on phages, bacteriocins and autolysins. This resulted in the NCP and their holding company Sentrachem, deciding a fund a research group at Rhodes University and in 1979 I was appointed as NCP/Sentrachem Research Group Leader. At the beginning of 1980 almost the entire department at Rhodes transferred to the University of Cape Town (UCT). I was appointed to the position as the Deputy Director of the Genetics & Industrial Microbiology Research Unit and the NCP/Sentrachem Research Group Leader. Subsequently, I was promoted to Associate Professor.

In addition to programs on yeast and industrial enzyme, the program on the solvent-producing clostridia was focused on developing of genetic systems for stain improvements. This included the development of gene transfer and protoplast fusion systems as well as the cloning and sequencing solvent pathway, cellulase and nitrogen uptake genes. The second major focus was on developmental biology, sporulation, metabolic regulation and the use of developmental pathway mutants for fermentation. We also had projects on nitrogen uptake and regulation - sugar uptake, fermentation optimisation and strain characterisation. The earlier work on bacteriophages, lytic systems, autolysis and strain degeneration was also continued.

In conjunction with Chemical Engineering Dept. at UCT we undertook work on continuous fermentation and cell immobilisation systems and the use of genetically modified strains for fermentation. We co-operated closely with the NCP Research and Development Division on projects that included nutrient requirements, alternative substrates and fermentation optimisation. We also assisted the NCP factory with the various problems they encountered, including stuck fermentations,  bacteriophage and bacterial infections. I was very fortunate that this involved me spending time at the NCP plant. In Germiston that enable me to gain valuable hands-on experience with the large scale industrial fermentation process.

During my time at UCT I also became Involved with the French National IFP Programmes for the production of butanol as a fuel blending agent, as well as South African National Programme for the conversion of biogasses to ethanol and ABE.

Another piece of good fortune was that the Head of Department, David Woods, and I were invited by Microbiological Reviews to write a major review to be entitled, Acetone Butanol Fermentation Revisited. David took over a most of the responsibility of running the group while I spent almost 6 months tracking down, abstracting and collating scientific and engineering papers relating to the ABE fermentation. The aim was to try and cover every publication in the field that existed up until that time. This review subsequently became the main benchmark publication in the field and has been cited hundreds of times in scientific publications as well as numerous times in technical reports and articles. (The review is available here: Butanol revisited.)

A large amount of the research on the ABE process had been undertaken during the first half of the 20th century but had tapered off after the industrial process had been phased out in most western countries after WW2 due to competition from petrochemical processes. At the time of writing the review the number of groups working in the field was quite modest and we were able to establish personal contact with virtually every group. This led to the setting up of an international meeting for all those involved. This was a great success and resulted in the setting up of the Clostridium International Workshops on the Genetics of Solvent Producing Clostridia, which have continued to be held every two years right up to the present time. I was able to attend all of these meetings and the members of the community established long standing friendships that resulted in collaborations and the exchange of information, strain and materials. This facilitated the movements of students, postdocs and the appointment of external examiners and referees. These international links lead to my involvement with the International Commission for Genetics of Industrial Microbiology, the Scientific Advisory Board GIM International Symposia and the Editorial Board of Trends in Biotechnology.

At the end of 1988 I left UCT to take up the appointment of Professor in the Department Microbiology at Otago and served as Head of Department for seven years. At Otago research was focused on clostridial bacteriophage and bacteriocin biology, the molecular taxonomy and phylogeny of solvent-producing strains and species, along with genomic mapping and comparative genomics. During this period my group maintained links with the engineering group in Vienna lead by Richard Gapes and fermentation technology group at Massey University led by Ian Maddox.

After NCP closed their process I was able to acquire both the strains and a large amount of archival material, including the origin of the strains, specifications and production data etc. As part our project on the molecular taxonomy and phylogeny of solvent-producing strains and species I was able to acquire examples of virtually all of the strains of the solvent-producing clostridia lodged in all of the major international culture collections world wide. This resulted in me assembling the largest and most comprehensive strain collection of solvent producing clostridia in existence.

In 1996 I was appointed as the Dean of the School of Medical Sciences and served in the position for the next eleven years. During this time I continued as a Professor in the Department and managed to maintain a small research group, although funding to continue with ABE research continued to be increasingly difficult to come by. Although the results of our research were reported at international scientific meetings it is with great regret that much of this work was never submitted for publication.

When my term as Dean came to an end at the beginning of 2007 I was now at the nominally retirement age of 65. The eleven years in the Dean's job had been quite demanding and stressful. At this point both my previous postdocs had departed and the department was very short of accommodation and I had become distanced from the students so decided that I did not want to go back to a position in the Department. As there was no one in the department that was remotely interested in Clostridium or my culture collection the question was what was to become of it.

Things suddenly took a new direction half way through 2006 when there was a resurgence in interest in the ABE fermentation process. Due to my specific background and experience I was contacted by a number of companies and the next few years were something of a roller coaster that involved a number of consulting and scientific advisory appointments with the following companies.

* DuPont - Wilmington, USA
* Lanzatec - Auckland, New Zealand
* Bayer/LanXess - Leverkusen, Germany
* LanXess - Sarnia, Canada
* Gevo - Pasadena, USA
* Aquaflow Bionomics - Nelson, New Zealand
* H-C Sucroqumica - Campos, Brazil
* Green Biologics - Didcot, UK
* NCP Alcohols - Durban, South Africa
* Green Biologics, UK and Butylfuel - Columbus, USA

Through consulting involvements with Gevo and Lanzatech I agreed to concede commercial rights for the use of the culture collection which was to be maintained as an independent scientific collection with free access to all who want to use strains for legitimate scientific research. On the surface this seemed to be a sensible and satisfactory arrangement, but in reality the scientific community found it extremely difficult to gain access to the collection.

At this time both Gevo and Lanzatech changed direction and I was asked by Gevo to meet with people from Green Biologics (GBL) in the UK as potential partners. There was a natural fit with GBL and with their agreement I terminated my consulting contracts and transferred my contract to GBL in 2008. I have been involved with them as a scientific adviser ever since.

I also had a unique opportunity to become involved with the commissioning of a new ABE plant that had been built in Brazil by a privately owned sugar company (HC-Sucroqumica – (2007-2010). They contacted me because they could not get their process to work. I spent three extended periods working in Brazil and providing assistance and I was able to get the commercial process working successfully for them. It was a great opportunity to be able to apply the knowledge from both my research and my previous practical experience with an industrial scale ABE plant NCP. I also gained a huge amount of new experience and knowledge and the family were a delight to work with.

In 2009 I spent a short sabbatical working at the GBL facility in Dicot and I also travelled to China with them as part of their involvement with existing and new ABE plants which had started up. Just prior to this, I have continued my association as scientific and technical adviser to Green Biologics, UK and USA. Recently I spent time in the US advising them on their pilot scale, demonstration scale and full production scale ABE plants. These developments have led to the conversion of a large commercial ethanol distillery in the US which is now producing butanol and acetone using modified strains and modern state-of-the-art process technology.

Photo Gallery

Glenn was initially a zoology student, but in 1978 he took a postgraduate diploma in immunology and became interested in immunology. He completed a PhD in the Department in 1984 and took up a postdoctoral fellowship at University College, and later at Charing Cross Medical Research Centre from 1985 to 1987 where he worked on the immunology of autoimmune diseases. In 1988 he returned to New Zealand on a Research Fellowship in the then Microbiology department's Deer Research Laboratory.  In 1993 he was appointed to the academic staff as a lecturer in immunology and was promoted to senior lecturer in 1996 and associate professor in 2002. His rising career was cut short by liver cancer and he died in 2008 at the age of 51.

His early research activities were focussed on the immune response to chronic disease and infection. Special areas of interest were the development of vaccines to tuberculosis and making vaccines work more effectively by manipulating the immune response with immune hormones or cytokines. He worked towards cloning and expressing cytokine genes and using these products in vaccines. The major research aim was to produce better vaccines by immunotherapy. In collaboration with MIT in Boston, a new recombinant BCG vaccine was being developed. This was tested in the USA for its protective effect against bladder cancer. Controlled field trials began in New Zealand in 1996-97 to determine its efficacy against tuberculosis.

Obituary

Here is the obituary prepared in 2008 by Sarah Young, President of Otago Institute, Dunedin branch of the Royal Society of New Zealand -- a colleague and close friend.

Buck completed a Postgraduate Diploma in Immunology followed by a PhD in Immunology at the Department of Microbiology and Immunology, University of Otago. He spent from 1985 -1987 as a Postdoctoral Fellow at University College London and Charing Cross Hospital under the guidance of Professor Marc Feldmann, one of the world's leading Clinical Immunologists. During this time Buck began the research which eventually led to the development of the anti-TNF antibody therapy for rheumatoid arthritis. This antibody is now used as a front-line treatment for the control of Rheumatoid arthritis - over 6 billion doses of the antibody has been administered worldwide.

In 1988 Buck returned to the University of Otago and spent the next four years building a research platform in Molecular Immunology. In 1993 he was appointed Lecturer in Immunology in the Department of Microbiology, where he continued to advance his career, being promoted to Senior Lecturer in 1996 and Associate Professor in 2002. His most recent research focused on the development of new generation vaccines for chronic diseases of humans and animals.

Buck published more than 100 scientific articles in Immunology. He has worked closely with other leading Immunologists throughout New Zealand and internationally in Australia, Belgium, Japan, UK, Switzerland, USA.

His expertise in Immunology led him to act as a Consultant, Technical Advisor and Research Provider for the New Zealand Ministry of Health (immunization), Foundation for Research, Science and Technology, AgResearch, New Zealand Dairy Group, Fonterra, Lactopharma, NZ Animal Health Board and the Ministry of Agriculture. In addition, he was the NZ councillor on the Australasian Society for Immunology from 1998 until 2002, he was a former president of the Otago Institute, and he was founder and co-chair of Immunet (the University's special theme in Immunology).

As well as being a leading researcher, Buck made a pivotal contribution to the development of undergraduate theory and laboratory courses in Immunology throughout the curriculum at Otago. While he was an inspiring and effective lecturer he was at his most effective as a small group teacher and as a mentor and postgraduate supervisor. The commitment to his postgraduates is legendary, nobody showed more loyalty for their students or advocated with greater passion on their behalf.

Buck is survived by his wife, Kerry, and four sons, Tom, Sam, Charles and Jack.

In his later years Glenn became something of a media star and gave of his time and energies to local issues and newsworthy events. He had championed the twin causes of early childhood vaccination and increased funding for scientific research. His leadership qualities were reflected in the large number of governmental agencies and professional bodies of which he was a spokesman, negotiator and administrator. From 2003 he was elected Associate Dean of Research for the Otago School of Medical Sciences. His influence as an academic will forever remain embedded within the culture of the Department.

 

 Photo Gallery

Newspaper clippings from the Otago Daily Times

Funding boost -- Funding boost urged for science • Policy progress reliant on reforms

Cell sorter -- Cell sorter valuable addition

Epidemic should help -- Epidemic should help vaccination

Science needed -- Science needed, Hodgson told

Researchers given -- Researchers given grants worth $6.6m

Job losses at IRL -- Job losses at IRL ‘tragedy’ for science

Meningococcal B-vaccine -- Some facts: the vaccine’s safe, we need it, it works

 

 
 
Mike Holmes joined the Department in 1976. Upon arrival, he reminded one of King Henry VIII -- in physical stature, majestic manner, intellectual and artistic abilities and temperament. He and his statuesque wife Ann (who was also a microbiologist) infused the place with English charm and their dinner parties and barbeques were legendary. 

They bought a baronial villa built from Oamaru stone with huge bay windows overlooking Northeast Valley below. It was in a slight a state of disrepair which only added a certain charm - it had the mandatory open fireplaces and a large dining and living room for entertaining guests. On the walls were some of Mike's artwork and in the hallways, his fishing gear. The Holmes' would invite everyone in the Department to their banquets/barbeques where the booze flowed freely - Mike was famous for his "leg opener" punch.  During the course of the evening, Mike would bring out his guitar and entertain us with well-known folk songs and Irish ballads. We managed to sing along in one way or another. On many occasions I was among the last to leave, whereupon he would produce his finest single malt whiskey. The living room couch was my bed on more than one occasion.

Profile in 1979 - Epidemiology of human Viruses

Prior to his appointment, Dr Holmes spent nine years in epidemiological research on criteria for the transmission and severity of acute human respiratory virus and mycoplasma infections. The work was carried out at the WHO-MRC Common Cold Unit, Salisbury (UK), the NIMR laboratories Holly Hill, Hampstead, the Clinical Research Centre, Harrow, NASA-Ames Research Center, California and included three years in Antarctica. His main project comprised a series of comparative human volunteer studies in England and in polar isolation, investigating the progressively increased vulnerability to acute respiratory disease of men in isolated communities. The local and systemic immune responses of both groups were compared and the kinetics of transmission and persistence of a range of viruses and mycoplasmas in the isolated communities were examined. During the two years before he came to New Zealand, Dr Holmes took over the NASA Lunar Biology laboratory at Moffett Field where he worked on the infectivity of airborne rhinovirus in the human environmental milieu and the microclimates of the human respiratory tract.

The Antarctic studies are being extended here at Otago University, where related collaborative work with the University of Oklahoma and the US Office of Polar Programs has already been in progress for four years. It is hoped that these studies can be further developed to include "antigenically naive" isolated Pacific communities.

In the last two years, human volunteer and laboratory studies of the local immune responses of the nasopharynx have been funded by the MRC. These are aimed at clarifying the nature, extent and roles of the components involved, the persistence of local immunological memory and the degree of autonomy from the systemic immune response. To date, studies have concentrated on the development of the technology for assay work in humans correlated with animal model studies being carried out under the direction of Dr Griffin. So far, this laboratory has been successful in developing the first atraumatic sampling system for the extraction of mucosal lymphoid cells from humans and is presently delineating the extent of the total nasopharyngeal lymphoid resources. Armed with these procedures, the project work has now reached a stage where systematic human studies on local mucosal immunity can begin.

Profile - Departmental Newsletter - 1994

"I was born on December 6, 1941 (the night of Pearl Harbour and the Russian counter-attack at Stalingrad), at Tettenhall, a village near the edge of the 70-mile-diameter industrial complex known as the 'Black Country' in central England, I won a scholarship for the sons of war-widows to a very minor public school, catering to children of scrap-iron merchants and war profiteers and left at 16 to take a job as a brick-layer's mate building a power station in Barcelona (this being as far away from Teltenhall as I could gel at the time). After misunderstandings with the Spanish Authorities I retreated tactfully to a village high in the Catalonian Pyranees where the prime occupation was transporting French cigarettes and contraceptives across the Spanish border. Some months later I was traced from England and learned that my practice A-levels had come up lucky. After a year as a hospital porter, I was fired for overturning a trolley by the lift shaft on the top floor (it carried the day's milk supply for the hospital). I then spent 6 happy years getting my license-to-kill at Liverpool Medical School - at this time we could hire the Beatles for £50 a gig.After my MB I, took a year off to do my first bit of research, looking for evidence of certain characteristic b-haptoglobins in the blood of the inhabitants of remote fishing communities in the outer Canary Islands, Here I developed my abiding hatred of camels. After my registration year in 1966, during which I was Prof Pat Molloy's houseman, I joined the British Antarctic Survey. I spent three of the next seven years at the dog-driving base of Stonington Island on the Antarctic Peninsula and the rest between the Common Cold Unit at Salisbury, Flying-Doctor in the Falkland Islands and the Clinical Research Centre at Harrow. This was all under the direction of David Tyrrell, FRS and Bar, who inherited the mantle of Sir Christopher Andrewes, daddy of English virology. In 1972 I married, we had a son and then in 1974 we submitted our MD and PhD theses a day before leaving for California. There, for two years, I ran the duplicate Moon-Lab facility for NASA, working on Viking until they abandoned the manned Mars shot, when I applied for the job here. My interview with Prof John Miles took place at midnight on the 12th floor of the Oklahoma City Hilton and began stylishly when he suggested a night-cap, opened a bottle of single malt and chucked the cork out of the window.

Following an extended holiday with old mates homesteading in Northern Alberta on the edge of the Arctic Circle, we came to Otago in 1976 and here we have raised our family in a big, shabby old villa up the NE valley. My research interests and training are in clinical immunovirology, particularly at a mucosal level and for the past 8 years I have become focused on Chronic Fatigue Syndrome or Tapanui 'Flu, trying to find out if it has an infectious aetiology."

Profile - Departmental website - 1995

Mike Holmes' current research is aimed at attempting to isolate the causative agent of Chronic Fatigue Syndrome, and the development of a diagnostic test for its detection. These studies are being undertaken in collaboration with the HRC Virus Research Unit. Investigations are under way to develop a cell culture system for the isolation of a retrovirus. Multi factorial analysis of data bases compiled from white blood cell tests has been utilised in an attempt to develop a diagnostic test. Immmunovirological studies aimed at identifying target cells are under way. Purification, characterisation and studies of the in vitro effects of a new reverse-transcriptase inhibitor are in progress. The reverse transcriptase inhibitor may be a representative of a new class of these compounds and the mode of inhibition suggests that it could act synergistically with the di-deoxynucleoside analogues currently employed in the treatment of AIDS. Since resistant strains of HIV develop rapidly, the therapeutic potential of the compound could be high if it can be used in rotation/combination regimes.

Some of Mike's handiwork

Epilogue

Mike resigned in 2002 after an extended period of ill health - involving complications with inflammatory bowel disease (IBD). I don't think the backbiting and the nit-picking nature of academic life suited MIke's temperament. He would have been much happier as a country doctor in some small town in Central Otago where he could spend more time fishing, hunting, driving his 4X4 LandRover off road and being the centre of the community. This was suggested to him by some of his colleagues, but he found the challenge of being an academic more compelling. He passed away, at Dunedin Hospital, on July 4, 2016; aged 74. He is survived by his sons Kevin and Robin and his daughter, Elin and his former wife, Ann.

John joined the Department in 1975 after completing a postdoc fellowship with Lewis Wannamaker at the University of Minnesota. He brought with him a ‘passion for streptococci’ and a very engaging teaching style. The following are excerpts from his NZMS Oration given in 2005:

A passion for Streptococci - Confessions of a streptophile

"As far as I now recall, my first significant encounter with the “bad” streptococci was when, as a 12-year old living in suburban Melbourne, a series of sore throats culminated in me developing rheumatic fever. I still remember anxious parents, aching limbs, visits to cardiologists - but most of all, those penicillin tablets: twice a day for 10 years they were a recurring reminder that the streptococcus had got the better of me. From a more positive perspective it seemed that, unlike the case for so many of the other youngsters world-wide who succumb to rheumatic fever, for me there had been no apparent residual heart damage. This, I was reminded, was further incentive to adhere to my daily dosing regimen, since it was known that recurrences of rheumatic fever were far more likely to “bite” the heart. Small compensation that was for a teenager who had soon tired of persistently peeing and perspiring penicillin – it just seemed there had to be a better way to keep the streptococcus at bay.

At Melbourne University

Following high school, I had the opportunity to study at Melbourne University and it was there, in the second year of a science degree, that I was strongly influenced by a truly remarkable teacher, Dr Nancy Millis of the Microbiology Department. Nancy de-mystified microbes for me and I quickly developed a keen appreciation for them and for the central role they undoubtedly played in maintaining the health of humans and indeed of planet earth. We all have special individuals (I think of them as “signpost people”) we meet along the way who clearly make a difference to the path we take. For me, Nancy Millis was one such person. Another was Dr Rose Mushin. With the encouragement of Nancy Millis I had decided to major in Microbiology and a defining experience in final year practical classes was the introduction that Rose Mushin gave to us about the concept of utilising bacterial interference as a means of infection prevention.

I decided to study towards an MSc with Dr Mushin, learning some of the tools of the trade of a researcher. My project concerned the bacteriocins of Pseudomonas aeruginosa, termed pyocins (based on their original species epithet, Ps. pyocyanea). My mission was to develop a practical pyocin typing scheme and to apply this in an investigation of the epidemiology of Ps. aeruginosa infections in Melbourne hospital). In my spare time, I developed strategies for purification of several pyocin molecules and to my surprise found some of them to be the tail components of defective bacteriophages.

At Monash University

Armed now with a range of basic laboratory skills and unexpected new self-belief I turned my attention to my nemesis, S. pyogenes. Nobody at Melbourne University had appropriate research programmes for a fledgling student focused entirely upon gaining knowledge of S. pyogenes and of its role in rheumatic fever. Enquiries of the Microbiology Departments of Monash and LaTrobe Universities drew similar responses. However, in the Pathology Department at Monash Professor Ritchie Nairn, who was skilled in the “art” of immunofluorescence microscopy, suggested a PhD project relating to the role of autoimmunity in rheumatic heart disease. I thankfully accepted, nevertheless quietly convinced that it was the role of the streptococcus in the disease process (not the host response) that I wanted to investigate.

Lewis Wannamaker - University of Minnesota

It was time now to undertake a post-doctoral apprenticeship, and from my reading of the streptococcal literature I knew where I must go. Dr Lewis Wannamaker at the University of Minnesota had established a leadership role in the field and indeed he had been instrumental in helping to develop the guidelines for use of penicillin to provide protection against rheumatic fever recurrences. In 1972 he hosted a workshop “Streptococci and Streptococcal Diseases” at the University of Minnesota attended by all of the leading investigators in the field. In his summing up of the week's proceedings Dr Wannamaker commented that “working with the streptococcus is like a love affair, which I guess explains why so many of us find it difficult to give up”. I found that I could relate comfortably to this sentiment and wrote to him asking if he (for me the “King of the Streptococci”) would consider allowing me work with him, looking for an alternative to penicillin for rheumatic fever prophylaxis. Three heady years of complete research immersion followed and Lewis (signpost person No 3) was generous in his encouragement of me to seek an anti-S. pyogenes BLIS, at the same time cautioning that what the streptococcus really needed was understanding – not extermination. Before leaving Minnesota I wrote (together with Lewis and Adnan Dajani) the first major review in the field of bacteriocins of gram-positive bacteria and upon purifying streptococcin A-FF22 predicted it may belong to the same family as nisin, the best-known and most widely-applied of all the bacteriocins of gram-positive bacteria.

A real job - University of Otago

Now the need was to find a “real” job and although the homing instinct was strong there appeared to be no appropriate job for me in Melbourne at that time. There was one at the University of Otago however, and that seemed close enough to serve as a temporary stepping stone for the inevitable return to Melbourne when the right opportunity arose. The job was mine and I suspect that my PhD supervisor Roy McGiven, a kiwi who had just returned to New Zealand to head the Pathology Department at the Christchurch Clinical School, must have made some helpful recommendations about me to Professor John Miles, then head of the Microbiology Department at Otago.

At this time (1975) the Microbiology Department was in the midst of a substantial growth spurt, having just moved into expansive new quarters and mine was just one of a cluster of new appointments. The life of a young academic at Otago was great - teaching loads were light, research funding was abundant and it appeared relatively uncomplicated to obtain and manage, there was time for reflection and my new colleagues were very supportive. Spirits were high and Dunedin seemed to be a great place to raise a family. Buoyed by this, my wife and I set about raising four sons.

Bacteriocin - chain gang 

However, the core agenda for me was still to find a way to tame the streptococcus and it appeared that interest in rheumatic fever in New Zealand was high, since Maori and Pacific Islanders are particularly prone to this disease. Two approaches were taken to finding an antagonist of S. pyogenes. While in Minnesota, I had met many members of an international streptococcal club of sorts, named the Lancefield Society in honour of that venerable lady of streptococcal classification Rebecca Lancefield. I wrote to many colleagues in the club (sometimes known as the “chain gang”) asking that they send me their favourite streptococci so that I might test them for bacteriocins. The response was enthusiastic and we set about systematically screening them against a set of nine standard indicator strains according to a very simple deferred antagonism method similar to the pyocin typing method that I had devised years previously for Ps. aeruginosa. When this bacteriocin production (P) –typing was combined with testing of the streptococci for their sensitivity to a panel of nine different bacteriocin-producing strains (S-typing) it was referred to as bacteriocin “fingerprinting”. Although now probably considered quaintly low-tech and intrinsically simple this procedure has survived as the preliminary screen for all candidate bacteriocinogenic strains entering my laboratory. It soon became clear that most (if not all) streptococci produce bacteriocins of some type and over the succeeding years dozens of post-grads, post-docs and technical support staff have adopted inhibitory streptococci (or sometimes their staphylococcal and lactococcal cousins) and been charged with responsibility for assessing the biochemical and/or genetic basis of their antagonistic behaviour. What transpired was the (sometimes) systematic discovery and categorization of a remarkably heterogeneous array of proteinaceous inhibitory agents, ranging from nisin-like post-translationally modified (the lantibiotics) or non-modified small peptides to larger proteins, some of them muralytic and others having unusual circular conformations. Follow-up reviews have highlighted the profusion and variety of these molecules: streptococci, especially those of the species uberis, mutans and salivarius appear to have been particularly inventive and acquisitive of bacteriocin loci. Recently, we have discovered that S. salivarius utilise very large plasmids as transmissible genetic receptacles for these loci.

Streptococcus salivarius

The second approach to identifying a S. pyogenes antagonist came in the form of a 6-year prospective study of one-hundred 5-year old Dunedin schoolchildren. The aim was to regularly document the composition of the childrens’ oral microflora throughout the course of the study and in particular to note if and when each child acquired S. pyogenes. The striking outcome was that many of those children who experienced relatively few S. pyogenes acquisitions had large populations of BLIS-producing S. salivarius on their tongues, especially of the P-type profile known as 677. These strains were shown to produce salivaricin A, a lantibiotic inhibitory in vitro to most S. pyogenes. This was very promising, because S. salivarius has had an almost blemish-free record in its association with humans – indeed it is the most common bacterium found in the human mouth and its closest relative is the copiously consumed dairy species, S. thermophilus.

BLIS-ful Beginnings

So, things were looking good for S. salivarius as the prime candidate for a bacterial interference approach to the prevention of S. pyogenes infection and it got even better when we discovered a few strains (including S. salivarius K12) that produced in addition to salivaricin A a second lantibiotic (salivaricin B) that appeared to kill all tested S. pyogenes strains, with no sign of any resistance development. It was about now that John Scandrett (signpost person No 4), then director of the University’s Commercial Office, intervened. John quickly realized that I was quite naïve about the practical realities of product development and advised that a patent be put in place on salivaricin B. That done, he arranged for a meeting with the late Howard Patterson, an entrepreneur who at that time had masterminded the funding of several fledgling biotech companies in Dunedin. What followed over the next weeks is still a bit of a blur, but the outcome was formation of BLIS Technologies Ltd in August 2000. Within a short time a CEO (Kelvin Moffatt), a Scientific Director (Chris Chilcott) and a Board of Directors were appointed and the company was listed on the NZ Stock Exchange in July 2001.

As a result of their efforts the first product BLIS K12 Throat Guard appeared on the shelves of pharmacies in early 2002. Several more products have followed and overseas sales are steadily increasing. Further tests are planned to simplify the colonization protocol (powder, lozenge and chewing gum formats have already been developed for different applications) and prospective trials are planned (some back in Australia) to further document the efficacy of this world-first bacterial interference approach to the reduction of streptococcal disease. I feel extremely privileged to have been able to follow my quest for such a long time. My parents, family, colleagues, students and staff, as well as the funding agencies have made it all possible.

May the BLIS be with you all.

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60 Minutes programme produced by Brent Fraser - John Tagg and BLIS

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While Tagg couldn't be more serious about his subject, when the lecture room doors close he admits that sometimes the clown in him comes out to ease the path to learning. Tagg discovered microbiology by accident when he signed on for a paper just because it fitted a gap in his timetable. He was inspired by his tutor, Nancy Millis, "whose lecturing style was off-beat, candid, natural and entertaining".

"I attribute a lot of my enthusiasm for Microbiology and my teaching style to her. Although I started in research, the more I taught the more I enjoyed it. And the more I grew in confidence the more my teaching style began to mimic that of my old professor".

Many students have benefited from Tagg's offbeat approach. "The point of a lecture is not the communication of facts. That's what libraries are for. It's an opportunity to motivate. And if I'm not having fun in a lecture it's probably not working for the students either."

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An example of his teaching style can be seen in this TEDxDunedin video:

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Each summer, Otago opens its doors to senior high school students for Hands-On Science: a week of field exercises, lab testing, and practical learning aimed at encouraging talented young New Zealanders to consider a career in science. The popular programme celebrated its 25th anniversary in 2014. John Tagg, who has been involved with the programme since the beginning, was one of the principal organisers of the event. He was most happy when during the ‘Hands on Science’ sessions he would lead a bevy of students down some path of discovery much like the pied piper of Hamelin.

A gallery of lab photos

John was a very active member of the NZ Microbiological Society (NZMS) and was president from 1994 - 1996. He also contributed to the organization of several international scientific meetings. He has a keen interest in the history of microbiology in New Zealand and has been instrumental in providing some of the archival material used in this book.

Below are some photos from the 2005 meeting of the Microbiological Society at which John gave the Microbiology Oration with which this chapter began.

NZMS meeting 2005