In Memoriam: John Dunn

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Posted: September 13, 2012

John Dunn

John Dunn, a senior scientist in the Biology Department, died on July 13, 2012. He was 68. A resident of Bellport, he is survived by his wife Orrell, his daughters Teresa and Heather, sons-in-law Joseph Gebbia and Michael Alpiner, granddaughter Emma Grace Alpiner, and his sister Mary and family.

Dunn joined BNL as an assistant microbiologist on July 1, 1972, after earning a bachelor’s degree from West Chester State College in Pennsylvania and a Ph.D. in microbiology from Rutgers University in New Jersey. On July 1, 1977, he was promoted to scientist with tenure, and on May 1, 1988, to senior scientist.

The following reminiscences and summary of Dunn’s 40 years of research at BNL are condensed and adapted from an article, “John Dunn, Scientist Extraordinaire,” by Bill Studier, former Biology Department chair and a longtime colleague and friend. The full article appears below.

John’s wide-ranging scientific curiosity was evident in conversation, his questions in seminars, and his many scientific collaborations, which typically involved application of methods he had developed or adapted. Throughout his career, he pursued collaborations within the Biology Department and with scientists elsewhere. He had an insatiable scientific curiosity and passion for discovery. When he got interested in something he pursued it tenaciously, using any technique at his disposal, whether he had to develop it himself, learn it from someone else, or find it in the literature.

John always had an interest in medical applications and in the late 1980s, was approached by a high school student who had the idea that bacteriophages, viruses that infect bacteria, might be used as a weapon against the bacterium that causes Lyme disease. This idea went nowhere but got John interested in producing surface proteins of Borrelia burgdorferi as potential vaccines against Lyme disease. He immersed himself in many aspects of Borrelia biology, including genome sequencing and evolution, determining structures of outer surface proteins, and vaccine development, primarily through a continuing collaboration of more than 20 years with physicians at Stony Brook Medical School who specialize in treatment and research on Lyme disease, particularly Ben Luft.

When John joined the Biology Department, he had already published a ground-breaking 1969 Nature paper with R. Burgess, A.A. Travers, and E.K. Bautz elucidating the role of sigma factor (a sub-unit of E. coli RNA polymerase) in controlling which genes are expressed. His biochemical expertise was an ideal complement to genetic and physiological work underway in my lab on bacteriophage T7, which infects E. coli. We immediately struck up a collaboration to study how gene expression is controlled during T7 infection.

This highly productive collaboration led rapidly to the discovery that RNase III, an E. coli enzyme, performs the final step in producing messenger RNAs of T7, the molecules that carry information for making specific proteins from T7 DNA to the ribosomes. We further found that RNase III has a similar RNA-processing role in producing the ribosomes themselves. John organized the 26th Brookhaven Symposium in Biology: “Processing of RNA,” held in May 1974, which brought together people working on all aspects of RNA processing and is remembered fondly by many.

When DNA sequencing became feasible, John adopted Maxam-Gilbert sequencing to determine the sequence of the entire 39,937 base pairs of T7 DNA, a tremendous accomplishment in the early 1980s, which he and Willie Crockett completed in less than two years. The sequence allowed us to identify all of the T7 genetic elements, making T7 one of the best-understood bacterial viruses. This basic understanding enabled the harnessing of T7 RNA polymerase and T7 genetic signals to direct the production of specific proteins from cloned coding sequences in E. coli, a technology successfully licensed by BNL.

Over the years, John served on review panels for the American Cancer Society and the National Institutes of Health Genome Study Section, was an associate editor of Virology and since 1992, executive editor of Protein Expression and Purification. Among his honors were the 1984 E.O. Lawrence Award “for fundamental contributions...to the understanding of the mechanisms by which DNA is transcribed and processed into functional messenger RNA” and the 2001 Energy 100 Award for his work on Lyme disease prevention and diagnosis, both from DOE; the Waksman Institute Medal on the 30th Anniversary of the Discovery of Sigma Factor (awarded to all four sigma paper authors); and Honorary Doctor of Science from Long Island University, Southampton Campus.

John’s work was interrupted but not stymied for the last nine years by a continuing battle against cancer. His colleagues were devastated when he was unexpectedly felled by an aneurysm shortly after his 40th anniversary at BNL. We sorely miss his friendship, exuberance, and collaborative spirit.


John Dunn, Scientist Extraordinaire

May 29, 1944 – July 13, 2012

Reminiscences of John's 40 years of exhilarating scientific research at BNL
by Bill Studier, August 23, 2012

John Dunn joined the Biology Department at Brookhaven National Laboratory in July of 1972 as a skilled biochemist with an already impressive record of accomplishment. In his graduate work with Ekke Bautz at Rutgers, John had made the startling discovery that a dissociable subunit of E. coli RNA polymerase, sigma factor, directs transcription to specific sites in DNA, reported in the ground-breaking 1969 Nature paper by Burgess, Travers, Dunn & Bautz and succeeding papers. Moving with Bautz to Heidelberg for postdoctoral research, John studied the different specificities of phage T3 and T7 RNA polymerases, and experimented with cell-free protein synthesis. There he formed a lifelong friendship and continuing collaboration with fellow postdoc Bill McAllister. As John was beginning to look for a job, he gave a seminar at Cold Spring Harbor and luckily I went to hear it. He seemed a perfect fit for our department and we convinced him that BNL was a great place to work in a supportive research environment.

John arrived at BNL at the best possible moment for both of us. My work on bacteriophage T7 had reached the stage where all of the T7 early RNAs and proteins could be identified by gel electrophoresis and their genetic and physical locations in T7 DNA had been determined by analysis of deletion mutants. Transcription of T7 DNA by purified E. coli RNA polymerase had been shown by others to produce long RNAs that cover the entire early region, but our deletion and gel analyses showed that during T7 infection five smaller RNAs in tandem cover the early region. John’s own work on T3 DNA and that of others on T7 DNA suggested that the action of rho termination factor might be responsible for the difference.

John set out to reproduce the early RNA pattern seen during T7 infection, using purified E. coli RNA polymerase and rho factor to transcribe the T7 deletion DNAs and analyzing the resulting RNAs by slab gel electrophoresis. However, he was unable to match the in vivo patterns under any condition tested. Building on his previous experience, he then fractionated crude extracts of uninfected E. coli to search for a factor that, when added to the transcription reaction, would generate the in vivo pattern. He immediately identified and purified such a factor, and found that it acted by cutting the primary RNA at specific sites. Comparing this “sizing factor” to published properties of known E. coli ribonucleases, John established that the factor is in fact RNase III, an enzyme previously described as specific for double-stranded RNA. This remarkable achievement was accomplished and published in less than a year from John’s arrival.

Since RNase III processes early T7 RNA, we suspected that it may also process E. coli RNAs. As it happens, I had the good fortune to visit P.H. Hofschneider in Munich shortly after this work was completed and learned that he had isolated an RNase III mutant of E. coli, which he graciously supplied to us. As expected, John and I found that large early RNAs extending across the entire early region were made during T7 infection of this strain and not the discrete smaller RNAs found during infection of hosts with normal RNaseIII. More interesting, analysis of the E. coli ribosomal RNAs made in this strain revealed that RNase III processing is in the normal pathway to the 16S and 23S ribosomal RNAs. These were exciting times.

John had an insatiable scientific curiosity and passion for discovery. When he got interested in something he pursued it fearlessly and tenaciously, using any technique at his disposal, whether he had to develop it himself, learn it from someone else, or find it in the literature. He soon collaborated with Hugh Robertson at Rockefeller to further characterize RNase III and to learn RNA sequencing techniques to identify cut sites. John organized the 26th Brookhaven Symposium in Biology: Processing of RNA, held in May of 1974, which brought together people working on all aspects of RNA processing and is remembered fondly by many of them. He established early collaborations with Carl Anderson in our department and Eckard Wimmer at nearby Stony Brook University that extended over many years. Throughout his career John was a generous collaborator with anyone who shared a common interest, and he often had visitors working in his lab. His collaborations were invariably highly productive but were seen in the early days by some in the department as problematic in making the case for tenure. John was careful to publish a substantial single-author paper in the Journal of Biological Chemistry on the biochemical properties of RNase III, which he referred to as his tenure paper.

When DNA sequencing became feasible, John adopted Maxam-Gilbert sequencing to determine more extensive sequences around RNase III cut sites. Once engaged, he went on to sequence the entire 39,937 base pairs of T7 DNA, a tremendous accomplishment in the early 1980s, which he and Willie Crockett completed in less than two years. The sequence allowed us to identify all of the T7 genetic elements, making T7 one of the best understood bacterial viruses.

T7 RNA polymerase is a highly active and selective enzyme that is key to directing E. coli to produce T7 proteins during infection, and the purified enzyme is a valuable research tool. Once Pari Davanloo, a postdoc, and Alan Rosenberg, our cloning virtuoso, succeeded in cloning the gene for T7 RNA polymerase, John was ready and able to purify the enzyme. He found that the E. coli strain we were using had an activity that put a specific nick in the enzyme during purification, but he developed a protocol that avoided the problem and produced large amounts of active enzyme. He later found other laboratory strains that did not have the nicking activity, and he and his student Jennifer Grodberg determined that the outer membrane protease specified by ompT is responsible. Having a limitless supply of purified T7 RNA polymerase, John put it to good use in collaborations with Wimmer to produce infectious poliovirus RNA and with Al Dahlberg at Brown to produce E. coli ribosomal RNA.

A primary motivation for cloning the gene for T7 RNA polymerase was to explore the potential of using T7 RNA polymerase to direct selective expression of cloned genes in E. coli. With the help of Barb Moffatt, a graduate student, I constructed E. coli BL21(DE3), which has in its chromosome the coding sequence for T7 RNA polymerase inducible from the lacUV5 promoter. This strain was able to maintain and express a variety of T7 genes that Alan had cloned, and it became the host for developing an inducible T7 expression system. Alan and John, with other members of both labs, constructed versatile suites of plasmid cloning and expression vectors, named pET vectors, that incorporated strong T7 signals for directing expression of target coding sequences. This expression system was adopted rapidly by the research community, and both John and Alan developed collaborations to help other labs express proteins of interest.

Although neither John nor I worked directly on eukaryotic systems, we recognized that T7 RNA polymerase might be useful for selective expression in eukaryotic cells. John modified the T7 RNA polymerase coding sequence to incorporate a nuclear localization signal at a site that had minimal effect on enzyme activity, and collaborated with Heiner Westphal at NIH to show that clones with mammalian expression signals produced T7 RNA polymerase that localized primarily to the nucleus of monkey kidney cells if the polymerase contained a nuclear localization signal but predominately to the cytoplasm if it did not. These clones continue to be freely distributed to other labs wanting to develop T7-based expression systems in eukaryotes.

John always had an interest in medical applications and, about this time, was approached by a high school student who had the idea that bacteriophages might be used as a weapon against the bacterium that causes Lyme disease. This idea went nowhere but got John interested in producing surface proteins of Borrelia burgdorferi in the T7 expression system as potential vaccines to protect against Lyme disease. He got his feet wet in a collaboration with Alan Barbour at Texas Health Science Center to express and purify a soluble form of OspA. This led to a continuing collaboration of more than twenty years with physicians at Stony Brook Medical School who specialize in treatment and research on Lyme disease, particularly Ben Luft. John immersed himself in many different aspects of Borrelia, including genome sequencing and evolution, determining structures of outer surface proteins, and vaccine development.

John’s wide-ranging scientific curiosity was evident in conversation, his pertinent and constructive questions in seminars, and his many scientific collaborations, often with colleagues in our department or at Stony Brook. These collaborations typically involved application of methods John had developed or adapted, and included analyzing mutations in mouse leukemic cells (Noy Rithidech); profiling microbial genomes (Niels van der Lelie) or transcripts in human platelets (Wadie Bahou); defining genome-wide DNA recognition sites in neuronal regulatory networks (Gail Mandel); determining sites of DNA binding by p53 in normal and cancer-derived human cells (Carl Anderson); and many others. John’s latest passion was developing methods to map epigenetic methylation and hydroxymethylation patterns in plant and human DNA, which brought him full circle to his early work with T-even phages, whose DNAs contain methylated and hydroxymethylated bases.

Over the years, John served on review panels for the American Cancer Society and the NIH Genome Study Section, was an Associate Editor of Virology and, since 1992, Executive Editor of Protein Expression and Purification. Among his honors were the E. O. Lawrence Award of the Department of Energy; the Waksman Institute Medal on the 30th Anniversary of the Discovery of Sigma Factor (awarded to all four sigma-paper authors); Distinguished Alumni Award from West Chester State University, Pennsylvania; and Honorary Doctor of Science from Long Island University, Southampton Campus.

John's work was interrupted for the last nine years by a continuing battle against colon cancer. However, after each round of surgery or chemotherapy he came back to enthusiastic pursuit of his scientific passion of the moment, until the next disappointing scan put him through another cycle of treatment. He remained optimistic and highly productive throughout the repeated ordeals. His colleagues were stunned and devastated when he was suddenly and unexpectedly felled by an aneurysm shortly after he passed his fortieth anniversary at BNL. We sorely miss his friendship, exuberance and collaborative spirit.


The following In Memoriam article comes from the family of John Dunn.

Dr. John J. Dunn, 68, died on Friday July 13, 2012, after a noble and valiant battle with cancer. Dr. Dunn was a renowned and respected Senior Research Scientist in Microbiology at Brookhaven National Laboratory, impacting countless lives through his discoveries, research, publications, and collaborations. In 1970, he earned his doctorate in Microbiology from Rutgers University. Following his two-year post-doctorate work at Heidelberg University, Dunn began his 40 years of tireless and dedicated service at BNL where he worked until his death.

He won the prestigious Lawrence Award in 1984, and holds numerous patents for discoveries in his field. Dr. Dunn’s distinguished accomplishments include involvement in the discovery of Sigma Factor, the co-development of the T7 expression system that revolutionized biology and recombinant DNA technology, as well as his ongoing research on Lyme disease and vaccine development. Dr. Dunn took pride in unraveling the mysteries of the invisible, sharing his expertise to those new to the field, serving as mentor to students, and inspiring many new scientists over the decades. Dunn’s passion to unlock what was hidden within strands of DNA fostered the growth of modern genetic technologies that have immeasurably impacted human life and modern medicine.

Dr. Dunn was preceded by his parents, Robert and Mary Dunn who raised him and his sister Mary Roberta in the underprivileged coal mining town of Minersville, PA. There, the seeds of his character were born. Beneath the dark clouds of coal dust and the post-war economic challenges, John found his calling for science after working in the local hospital lab. In 1963, while a student at West Chester University, he met Orrell Bietz, his zoology lab partner, who would later become his wife. While living in New Brunswick, NJ, they had two daughters, Teresa and Heather. In 1975, the family settled in Bellport, NY.

Although so much of Dr. Dunn’s time revolved around scientific research, he never neglected to be a constant and loving influence within his family and household. He enjoyed the sounds of Celtic music from his ethnic roots, folk melodies from the days of his youth, easy listening as the backdrop to dinnertime, and even memories from Lake Woebegon Days as he sat in the den by the fireplace with his family. He enjoyed the thrills from a spy novel as much as he did the challenges of the NY Times Crossword puzzle. He found peace jogging through town and down to the bay where gulls circled overhead like halos. He would then return home to feed the finches and enjoy his blossoming red hollyhocks. Dr. Dunn made a forever lasting impression on both the invisible and the visible worlds.

Dr. Dunn is survived by his loving and selfless wife Orrell, his beloved daughters Teresa and Heather and their respective husbands, Joseph Gebbia and Michael Alpiner. He leaves behind one granddaughter, Emma Grace Alpiner, for whom he will always be called Poppy, and who, at six years old, also calls herself a scientist. Dr. Dunn is survived by his sister Mary Roberta, her husband Owen Higgins and their family. He leaves behind a retinue of family, friends, colleagues and neighbors who will all dearly miss his presence.

Last Modified: September 13, 2012