Pre-meeting Workshops
Sunday, July 29
1. Fermentation Basics
Organizer: Carol Baker, Pfizer
Summary: In response to requests for an introductory fermentation
workshop we have put together a one day dry workshop on fermentation. The workshop will
include the demonstration of lab scale equipment to help familiarize attendees with the
various parts of a fermentor and the important aspects of each part. Discussions will include
topics such as aspect ratios, agitators, spargers, ports, sterilization etc. This will be
followed by a lecture dealing with the actual operational issues of fermentation. Included
will be discussions about media considerations, foam control strategies, shear, mixing,
aeration, feeds and different types of fermentations and the controls involved. The workshop
will finish with a discussion of the issues involved in scale-up to production size fermentors
Topics will include head pressures, equipment limits, sterilization issues, evaporation,
seasonal differences, etc.
The workshop will include the demonstration of lab scale equipment to help familiarize
attendees with the various parts of a fermentor and the important aspects of each part.
Discussions will include topics such as aspect ratios, agitators, spargers, ports,
sterilization etc.
Presenter: Dr. Ernest L. Stadler, Sartorius BBI Systems, Inc.
Actual operational issues of fermentation. Included will be discussions about media
considerations, foam control strategies, shear, mixing, aeration, feeds and different
types of fermentations and the controls involved.
Presenter: Mark Berge, Amgen, Inc., Thousand Oaks, CA
The workshop will conclude with a discussion of the issues involved in scale-up to
production size fermentors Topics will include head pressures, equipment limits,
sterilization issues, evaporation, seasonal differences, etc.
Presenter: Robert Schwartz, Abbott Laboratories (ret.)
Workshop Bios:
Mark Berge
2006-Current: Scientist at Amgen Inc. in Cell Science & Technology group developing processes for therapeutic protein production using fermentation.
1999-2005: Sr. Scientist at Pfizer Inc. in Global Biologics division developing processes for therapeutic protein production using cell culture.
1995-1999: Process Engineer at FermPro Manufacturing in deep tank toll manufacturing for varied customers of food grade materials.
MS & BS in Chemical Engineering from University of New Hampshire
Robert Schwartz, PhD
Dr. Robert D. Schwartz recently retired as a Senior Development Scientist
in Fermentation Development at Abbott Laboratories, North Chicago, IL.
Bob received his BS in biology from Brooklyn College (1964), MS in
microbiology from Long Island University (1967) and PhD. in microbial
genetics from the Waksman Institute of Microbiology, Rutgers University
(1969).
Before coming to Abbott (1987) he worked at: the Germfree Life Research
Center (1969-1970) doing cancer research; Exxon Research and Engineering
Co. (1970-1976) working on petroleum microbiology; Union Carbide
(1976-1979) developing fermentation processes for producing specialty and
commodity chemicals; Stauffer Chemical Co. (1979-1987) developing
fermentation processes, based on dairy solids, for the food industry. At
Abbott (1987-2007) Bob’s responsibilities included fermentation
development and process support for bio-rational pesticides, (DiPel,
XenTari, VectoBac, VectoLex), plant growth regulators and other Ag
related processes. As a fermentation microbiologist with interest
primarily in industrial microbiology, Bob holds 12 patents and has 35
publications.
Bob is a member of SIM, ASM, AAAS, BIOT division of ACS and Sigma Xi. A
member of SIM since 1973, his service includes: President (1991-1992);
Director (1983-1986); Editorial Board member (1985-1996) and Senior Editor
(1996-present) JIMB. Bob received the SIM Charles Porter Award in 1989
and was elected SIM Fellow in 1994. Bob has also been a member of the
Advisory Board (1989-1993) and Associate Editor (1993-present) of Enzyme
and Microb. Technol., and served on the Editorial Board of Appl. Environ.
Microbiol. (1980-1985).
Ernest L. Stadler, P.E.
Ernest L. Stadler is Director of Bioprocess System Sales at Sartorius BBI Systems, Inc, a leading manufacturer of fermentors, bioreactors, automation software / hardware, and other related bioprocess laboratory and custom large scale equipment. A member of ASME, ISPE, and PDA, Mr. Stadler is a registered Professional Engineer in PA and NJ, holding a BS in Mechanical Engineering from NJIT and has done graduate studies at Lehigh University in biotechnology. Mr. Stadler has broad based expertise in automation, process and mechanical design for variety of Bioprocess equipment having served the biotechnology industry for over 21 years. He is a frequent speaker, teacher, and workshop leader on the design and application of fermentors and bioreactors particularly relating to biotechnology process scale-up and optimizing performance. Ernest served as Course Director, Lecturer and Workshop Leader for over 12 years with the ASME BioProcessing Technology Seminar series. He has authored articles and papers and was awarded the 1998 Article of the Year by Pharmaceutical Engineering Magazine, a publication of the ISPE. He has served the past 5 years on the Board of Directors for the SBP being a founding member and has supported the merger of the SBP within ISPE. Mr. Stadler can be reached via email at ernest.stadler@sartorius.com.
2. Organizing and Analyzing Data in a Microbial Culture Collection
Organizer: Micah I Krichevsky, Bionomics International, Rockville, MD
Summary: The need for more effective microbial collections increases
with the proliferation of activities in biotechnology, other R&D, biosafety and
research efforts. Key to maximizing effectiveness is enhanced management of primary
data and their analysis. A one day workshop will emphasize concepts and practical
techniques for organizing and analyzing collection data. The workshop will involve
presentations and discussions on improving collection information operations for any
size collection. Participants will form small groups to choose case study topics on
data management. Using the Internet, each group will analyze their chosen topic. The
groups will present short reports of their findings for discussion by all. The workshop
is jointly sponsored by the US Federation for Culture Collections and the Society for
Industrial Microbiology.
Database construction
Data types; key organizing index; taxonomy, ecology, time; phenotypic sequences
Presenter: Micah I. Krichevsky, Bionomics International, Rockville, MD
Nomenclature
Taxonomy vs identification; nomenclature codes; sources of accepted names
Presenters: Micah I. Krichevsky, Bionomics International, Rockville, MD and Paul De Vos,
University of Gent, Gent, Belgium
Culture collection information on the internet
World Federation of Culture Collections; world Data Center; patent deposition, shipping and receiving
cultures, safety
Presenter: Paul De Vos, University of Gent, Gent, Belgium
Data analysis tools
Hierarchical clustering; cladistics; identification revisited
Presenter: Peter Dawyndt, University of Gent, Gent, Belgium
Case studies setup (Choose group topic)
Case studies and reports
Workshop Bios:
P. Dawyndt
Peter Dawyndt got the degree of M.Sc. in Mathematics in 1997 and M.Sc. in Computer Science in 1999, both from the Ghent University in Belgium. During the period 1999-2006 he worked at the Laboratory of Microbiology of the Ghent University, helping to establish a symbiosis between mathematics, computer science and the life sciences, as a means to further explore the diversification processes that drive evolution. In December 2004 he was assigned Doctor (Ph.D.) in Sciences, option Computer Science. Through his long-standing collaborations with Bernard De Baets, he also joined the research unit Knowledge-based Systems (KERMIT) at the Ghent University in 2005.
His research career somewhat became full circle, when in 2006 he was appointed as professor at the Department of Applied Mathematics and Computer Science of the Ghent University, where he is currently teaching courses in computer science.
He is the author of several peer reviewed papers published in international research journals, showing his main research interest in the design of a self-learning reasoning system for landscaping the bacterial diversity, used as a figure of speech for taxonomic modelling. Achieving this goal yet means that several major technical hurdles need to be overcome, including advancing the barriers of global data sharing, identify and come up with new ways to fill the gaps of observational efforts, and explore the possibilities of novel data mining techniques to the benefits of understanding microbial diversification. He is also regarded as the founding father of the StrainInfo.net bioportal (www.StrainInfo.net).
Paul De Vos, PhD
Paul De Vos, Full Professor, Laboratory for Microbiology, University of Gent, Belgium, received his Ph. D. from the University of Gent (1980). His interests include bacterial biodiversity, evolution, taxonomy, identification and detection. Research includes bacterial denitrification and nitrification; role of Bacillus and related organisms in various niches; role of plantpathogenic pseudomonads/xanthomonads. He is Director of BCCM/LMG Bacteria Collection; Secretary, Belgian Committee on Microbiology; member, Judicial Commission, International Committee of the Systematics of Prokaryotes, and Member, Bergey's Trust.
Contact information: Paul De Vos, Laboratory for Microbiology, University of Gent, K.L. Ledeganckstraat, 35, B-9000 Gent, Belgium, Phone: 32 9 264 5110 Fax: 32 9 264 5346
E-mail: Paul.DeVos@UGent.be
Micah Krichevsky
Micah Krichevsky (micahk@bioint.org) is Chairman of Bionomics International, a not for profit research and educational organization. He retired from the National Institutes of Health in 1992 after 33 years of research and development activities. He received his MS (1955) and PhD 1958) degreed in Dairy Science (Microbiology) from the University of Illinois, Champaign-Urbana, and his BA degree in Microbiology from The University of Connecticut in 1952. Dr. Krichevsky is President of the United States Federation for Culture Collections.
3. Working with Extremophiles
Organizer: Frank Robb, UMBI, Baltimore, MD
Summary: Extremophiles are able to grow at temperatures from 4°C up to 110 °C
and at extremes of pH (acidophiles and alkaliphiles) are an interesting source of stable enzymes
(extremozymes). These are in general superior to the traditional biocatalysts, because they provide
proteins with unique properties and many show activity even at 120 °C, at pH values between 0-3, pH
9-11 and in the presence of organic solvents. The ability to carry out cloning and sequencing is
dependent on the protein engineering and directed evolution of the stable DNA and RNA modifying
enzymes. Microorganisms living in extreme habitats are an ideal source for polymer degraders, which
allow to perform biotransformation reactions under non-conventional conditions under which many
proteins are completely denatured. There is an increasing interest in the utilization of renewable
sources to satisfy the exponentially growing energy needs. Therefore, efficient and stable enzyme
systems are also needed for the breakdown of plant biomass, which contains complex substrates such a
cellulose, hemicellulose, lignin, fats and oils is of high interest.
Presenters:
Alexei Slesarev, Fidelity Systems, Inc.
Eric Mathur, J. Craig Venter Institute
Andrew Gardner, New England Biolabs
Jocelyne Di Ruggiero, Univ. of Maryland
Workshop Bios:
Jocelyne DiRuggiero, PhD
Dr. Jocelyne DiRuggiero is an assistant professor in the Department of Cell Biology and Molecular Genetics at the University of Maryland, College Park. She obtained her Ph.D. at the University Claude Bernard in Lyon, France and came to the United States with a Fulbright fellowship. She was a postdoctoral fellow at the Center of Marine Biotechnology before moving to the University of Maryland. Her main research interests are in microbial genomic, diversity and evolution in extreme environments. She is particularly interested in the mechanisms of DNA repair and stress response to changing environmental conditions and in the mechanisms that drive genome evolution in response to those environmental changes.
Andrew Gardner, PhD
Andrew Gardner has focused on hyperthermophilic DNA polymerase discovery, characterization and modification at New England Biolabs for twelve years. After participating in a workshop "Microbial Ecology of Hot Springs and Geothermal Areas in Iceland" in 1997, he has continued microbial field work in the United States and internationally to identify novel DNA polymerases and restriction enzymes from environmental samples. In 2000 and 20005, he participated in field microbiology at the International Workshop on “Biodiversity, Molecular Biology and Biogeochemistry of Thermophiles” in Petropavlovsk-Kamchatksky, Russia. In addition, he has studied DNA polymerase structure and function to define determinants of nucleotide discrimination. From these biochemical studies, novel DNA polymerases have been engineered for genotyping and DNA sequencing applications. Andrew is also studying genome replication of an extremophilic virus, Sulfolobus
islandicus rod-shaped virus 2 and hopes to uncover novel replication mechanisms. He looks forward to combining microbiology and biochemistry to discover novel enzymes and mechanisms from extremophiles.
Eric J. Mathur, PhD
Eric J. Mathur currently serves as Vice President of Metagenomics at Synthetic Genomics, Inc.; he was responsible for establishment of the Company’s La Jolla-based biological research laboratories. Eric also holds a Visiting Distinguished Scientist non-paid position at the J. Craig Venter Institute. Prior to working with Dr. Venter, Eric served as Vice President of Scientific Affairs & Molecular Diversity at Diversa Corporation where he developed the Company’s metagenomics (gene recovery from the environment), high throughput cultivation and biodiversity access discovery programs. Eric was the first employee and a scientific founder of Diversa and at various times during his 12 year tenure, had direct oversight for the majority of the research organization – including microbial diversity, enzyme discovery, gene evolution, gene expression, metabolic engineering, sequencing, bioinformatics and process development. Prior to Diversa, Eric was a founding scientist at Stratagene Cloning Systems where he discovered and developed Pyrococcus
furiosus (Pfu) DNA polymerase. Eric has published over 60 scientific papers, is named inventor on more than 50 issued US and World patents and has been invited to present over 100 scientific lectures.