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  Scientific Program

Final Program of PepCon - 2009

Theme: Life, Knowledge & Bio-Economy


Time: April 2-4, 2009
Venue: COEX Convention & Exhibition Center, Seoul, South Korea

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Opening Ceremony & Plenary Lectures

Time: April 2, 2009, Thursday 09:30-11:40

Place: Meeting Room 402
09:30-09:40
Chair's Opening Remark

Chair: Dr. Kyung-Soo Hahm, Professor, Cellular and Molecular Medicine, College of Medicine, Research Center for Proteineous Materials, Chosun University; President of the Korean Peptide Protein Society, South Korea

09:40-10:10

Title: Global Human Proteome Project and Future Direction in the Disease Proteomics Research
Dr. Young-Ki Paik,
President, HUPO and AOHUPO, Director of Yonsei Proteome Research Center/Biomedical Proteome Research Center, Yonsei University, Seoul, South Korea


Dr. Paik is a Professor of Department of Biochemistry and Director of YPRC/BPRC and has been actively engaged in the proteomics field by serving as a director of the Korean Human Plasma Proteome Project, a Senior Editor for PROTEOMICS, Editorial Board Member for MCP and Clinical Proteomics, and President Elect of HUPO and President of AOHUPO. His research interests are discovery of biomarker for HCC and regulatory molecules for aging (in animal model). He has established YPRC/BPRC as a flagship center in the nation and has carried out major roles in education, training, and technical services in the field of proteomics throughout the country since 1999.

10:10-10:40

Title: Mechanism and Inhibition of Collagenolytic Matrix Metalloproteinases
Dr. Gregg B. Fields,
Robert A. Welch Foundation Distinguished Professor of Chemistry, Department of Biochemistry, The University of Texas Health Science Center; President Elect of American Peptide Society (APS), USA


Fields has over 180 publications and 6 patents in the fields of extracellular matrix biochemistry and peptide synthesis methodology. His laboratory has been funded by the NIH and the American Cancer Society, and he has been profiled in Today's Life Sciences (1997), Boca Raton Magazine (2003), and Time Magazine (2004). Dr. Fields also serves on many editorial boards such as The Journal of Biological Chemistry, Current Protein and Peptide Science, Expert Opinion on Therapeutic Patent, The Journal of Peptide Research, Protein and Peptide Letters, and Letters in Peptide Science.

10:40-11:10

Title: Bio 2.0 for the Journey to the Protein Universe
Dr. Han-Oh Park,
CEO & President, Bioneer Corp., South Korea


Han-Oh Park has been dedicated in molecular biology research as well as in Biochemistry. He has carried on various studies related in both prospects in science and business development. He is the founder of Bioneer Corporation. He has earned his Ph. D. in Biochemistry in KAIST (Korea Advanced Institute of Science and Technology). His main focus is to provide total solution in molecular by providing from nucleic acid extraction, amplification, and analysis to increase accuracy and productivity, reduce operating costs for developing and under development countries . Bioneer Corporation currently owns many technologies (72 patents). While he is in position of CEO at Bioneer, he is also involved in various scientific organization committees. He is a Chairman of Bio-IT Industry Committee, Vice-President of the Korean Society for Biotechnology and Bioengineering.

11:10-11:40

Title: The Quest for Superior Product Quality – A Play between Enhancing and Selecting
Dr. Thomas Seewoester, Director, Process Development, Amgen Inc., USA

Thomas Seewoester is Director of the Cell Science & Technology organization at Amgen, Thousand Oaks. He is responsible for developing recombinant cell lines, clinical & commercial upstream processes for microbial & mammalian hosts, and overseeing process transfers to clinical GMP manufacturing sites. He is further engaged in strategic and efficient alignment of research, development and manufacturing activities and in creating operational strategies for future bioprocessing approaches.He received his Ph.D. in 1995 for developing novel two-phase production processes for CHO cells and the discovery of novel amino acid-inducible promotor systems for Boehringer Ingelheim Pharmaceuticals. As postdoc, Thomas developed new membrane-based high-cell density bioreactors for bioartificial liver systems.
Track 1: Human Proteome Technologies

Track 1-1: Functional Proteomics, Disease Proteomics, Proteome Biology and Systems Biology

Time: April 2, 2009, Thursday 13:30-16:15

Place: Meeting Room 310A

Session Chair:
Dr. Mu Wang, VP of R&D, Monarch LifeSciences, LLC., Director of Proteomics Indiana University, USA
Co-Chair:
Dr. Jason Yongsheng Chan, National University Medical Institutes, Oncology Research Institute, National University of Singapore, Singapore

13:30-14:00

Keynote Speech: Title: Proteomics at Large Scale and High Sensitivity
Dr. Larry Gold
, Founder, CEO & Chairman of the Board, SomaLogic, Inc., USA


Dr. Larry Gold is the founder, Chairman of the Board, and Chief Executive Officer of SomaLogic. Prior to SomaLogic, he also founded NeXagen, Inc., which later became NeXstar Pharmaceuticals, Inc. In 1999, NeXstar merged with Gilead Sciences, Inc. to form a global organization committed to the discovery, development and commercialization of novel products that treat infectious diseases. During nearly 10 years at NeXstar, Dr. Gold held numerous executive positions including Chairman of the Board, Executive VP of R&D, and Chief Science Officer. Before forming NeXagen, he also co-founded and served as co-Director of Research at Synergen, Inc., a pioneering biotechnology company later acquired by Amgen, Inc. During his prestigious career, Dr. Gold has received many citations including the CU Distinguished Lectureship Award, the National Institutes of Health Merit Award, the Career Development Award, and the Chiron Prize for Biotechnology. In addition, Dr. Gold has been a member of the American Academy of Arts and Sciences since 1993 and the National Academy of Sciences since 1995. Dr. Gold also serves on the board of directors of BioForce Nanosystems, BT Pharma, CompleGen, MicroPhage, and the scientific advisory board of Archemix.
14:00-14:30
Title: Targeted Assay Development Using Mass Spectrometry
Dr. Mu Wang, VP of R&D, Monarch LifeSciences, LLC., Director of Proteomics Indiana University, USA

Dr. Wang is the VP of the Monarch LifeSciences and Director of Proteomics at Indiana University School of Medicine. He has significant experience with all aspects of proteomics technologies. He was a founding Director of proteomics service CRO Monarch LifeSciences (formerly known as Indiana Centers for Applied Protein Sciences or INCAPS). His own research involves mechanistic study of drug resistance in ovarian cancer and DNA repair mechanisms in mammalian systems in response to genomic stresses. In his recent study in searching for biomarkers of cisplatin resistance in human ovarian cancer using a proteomic approach, he identified multiple pathways that may be involved in cisplatin resistance. His preliminary data suggests that SOD1 may be a key determinant of drug resistance. Through inhibition of SOD1 activity, the cisplatin resistant ovarian cancer cells were sensitized. He is in the process of finding a more specific inhibitor for SOD1 and validating the biomarkers in plasma samples from ovarian cancer patients. Dr. Wang was a recipient of the HUPO (Human Proteome Organization) 2004 Young Investigator Award.
14:30-15:00

Title: System-Level Analysis of Signal Transduction Networks by Quantitative Proteomics and Systems Biology
Dr. Masaaki Oyama, Assistant Professor, Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Japan

The mass spectrometry-based analysis of small proteins expressed in human K562 cells provided the first direct evidence of translation of upstream ORFs in human full-length cDNAs. In his recent work, he established an integrated framework for analyzing tyrosine-phosphoproteome dynamics through temporal network perturbation, which enabled us to obtain a system-wide view of regulatory network clusters involved in signal transduction.

15:00-15:15
Coffee Break
15:15-15:45
Title: Functional Proteomic Analysis Identifies Caspase-6 Activation as a Major Signalling Event in Colon Cancer Cell Apoptosis that May Be Targeted for Combination Chemotherapy
Dr.
Jason Yongsheng Chan, National University Medical Institutes, Oncology Research Institute, National University of Singapore, Singapore

P53 loss-related chemoresistance in colon cancer represents a major setback to its successful treatment. However, the underlying mechanisms remain poorly understood. In this study, the mechanisms of resveratrol (RSV) and 5-fluorouracil (5-FU)-evoked apoptosis were investigated in HCT116 p53+/+ and p53-/- colon cancer cell lines via a functional proteomic approach.
15:45-16:15
Title: An Integrative Systems Biology Approach for Discovering Breast Cancer Serum Markers
Dr. Daehee Hwang,
Assistant Professor, School of Interdisciplinary BioScience and Bioengineering, Pohang University of Science and Technology, South Korea
Track 1-2: Array Based Proteomics

Time: April 3, 2009, Friday 08:30-11:15

Place: Meeting Room 310A

Session Chair:
Dr. Jutta Bachmann, Principal and Founder, Bachmann Consulting, Norway
Co-Chair:
Dr. Xiaolian Gao, Chief Scientific Officer, LC Sciences, LLC, USA
08:30-09:00
Keynote Speech: Title: Recent Advances in ProteoChip Technology
Dr. In-Cheol Kang,
Professor, Department of Biological Science, Director of BioChip Research Center, CEO of InnoPharmaScreen Inc., South Korea


ProteoChip has been developed as a novel protein microarray technology. So far it has been applied in different protein expression profiles and molecular diagnostics and we expect its role to grow in the field of biology. Here, we investigated the application of ProteoChip in expression proteomics and intracellular kinase assa.
09:00-09:30

Title: Small is Beautiful: Protein Microarrays-an Array of Applications
Dr. Jutta Bachmann, Principal and Founder, Bachmann Consulting, Norway

Dr. Jutta Bachmann is principal and founder of Bachmann Consulting. She has been an advisor for microarray-related conferences and is the project manager of www.biochipnet.com as well as of an international portal on regenerative biology http://www.regenerationnet.com operated by BioRegio STERN Management GmbH, Germany.

09:30-10:00
Title: Proteomic Kinase Substrate and Phosphopeptide Chip Technology for Protein Profiling
Dr. Xiaolian Gao, Chief Scientific Officer, LC Sciences, LLC, USA

Dr. Gao is a Professor of Biology, Biochemistry and Chemistry, and is Director of the Keck/IMD NMR Center at the University of Houston. Dr. Gao holds a BS degree from the Beijing Institute of Chemical Engineering and a Ph. D. degree in Chemistry from Rutgers University ; she did post-doctoral work in NMR -based structure biology at Columbia University Medical School. Dr. Gao is the founder of several biotechnology companies and has extensive experience in commercialization of biotechnology products.
10:00-10:15
Coffee Break
10:15-10:45
Title: High-Content Protein Arrays for Discovery of Peptide and Peptoid Ligands and Nanoengineering of Reagentless Assays
Dr. Alexander N. Asanov, CEO and President, TIRF Technologies, USA

Total Internal Reflection Fluorescence (TIRF) combined with Electric field Control (TIRF-EC) is novel platform technology, which is sensitive down to single molecules and capable of monitoring and controlling the dynamics of biomolecular interactions. In this paper, we report on the development of TIRF-EC array technology for the rapid discovery of sequence-specific ligands from one-bead-one-compound (OBOC) combinatorial libraries of peptides and peptoids. We also describe novel application of TIRF-EC for nanoengineering of reagentless assays based on peptide and peptoid ligands equipped with fluorescence reporters.
10:45-11:15
Title: Predicting Anti-cancer Drug Sensitivity by High-dimensional Quantitative Protein Monitoring of Cellular Signal Transduction
Dr. Satoshi Nishizuka
, Assistant Professor and Chief Principal Investigator, Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Japan

Dr. Satoshi Nishizuka currently serves as Assistant Professor and Chief Principal Investigator in the Molecular Therapeutics Laboratory of the Department of Surgery at Iwate Medical University School of Medicine. He graduated from Iwate Medical University Graduate School of Medicine with M.D. (1994) and Ph.D. (1998) degrees. Originally trained as a surgical oncologist, he did postdoctoral research in the Department of Microbiology and Molecular Genetics at the University of California, Irvine. In 2001 he joined the Laboratory of Molecular Pharmacology at the U.S. National Cancer Institute (NCI) as a Research Fellow, where he developed a high-density "reverse-phase" protein lysate microarray (RPA) system using a NCI-60 cancer cell line panel in the context of drug sensitivity profiling at the protein level.

Track 1-3: Bioinformatics and Structural Proteomics

Time: April 3, 2009, Friday 13:30-17:10

Place: Meeting Room 310A

Session Chair:
Dr. Herbert Thiele, Director Bioinformatics, Bruker Daltonik GmbH, Germany
Co-Chair:
Dr. Huisheng Fang, Professor, Department of Bioinformatics, China Pharmaceutical University, China
13:30-14:00

Keynote Speech: Title: Metallomics by Imaging Laser Ablation Inductively Coupled Plasma Mass Spectrometry: New Analytical Directions in Brain Research
Dr. J. Sabine Becker,
Professor, Central Division of Analytical Chemistry, Research Centre Juelich, Germany

Dr. habil. J. Sabine Becker (head of Trace and Ultratrace Analysis, Research Centre Juelich, Germany) pioneered the quantitative bioimaging mass spectrometry of metals and non-metals in thin section of biological tissues, e.g., human and rat brain tissues by LA-ICP-MS (laser ablation inductively coupled plasma mass spectrometry) and combined to metallomics to study neurodegenerative diseases. She is author of the comprehensive handbook: Inorganic Mass Spectrometry: Principles and Applications, Wiley 2008, 514 pages (ISBN: 978-0-470-01200-0), of 295 scientific publications, 21 patents and serves in several boards e.g., of the Intern. J. Mass Spectrom. and J. Anal. At. Spectrom.
14:00-14:25
Title: A New Integrated Bioinformatics Platform for Advanced Protein Identification Strategies and Quantitative Proteomics Studies
Dr. Herbert Thiele
, Director of Bioinformatics, Bruker Daltonik GmbH, Germany


Dr. Herbert Thiele, Worldwide Head of Bioinformatics, work at Bruker Daltonics. He said, Bruker Daltonics is pursuing and will continue a strategy of differentiation built around excellence, including excellence in bioinformatics. We are going to maintain and even enhance our very innovative R&D and engineering processes, creating more differentiated high-performance, high quality products—further enhancing our excellent brand recognition position.
14:25-14:50
Title: An Efficient Method for Solving the Intractable Problem i.e. Protein Structure Prediction
Dr. Huisheng Fang
, Professor, Department of Bioinformatics, China Pharmaceutical University, China
14:50-15:15
Title: Probing Protein Environment in Enzymatic Process Based on Hybrid Computational Modeling: Case Study of Chorismate Mutase Catalysis
Dr. Toyokazu Ishida, Researcher Scientist, Research Institute for Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), Japan

The main focus of the work is to analyze the details of electrostatic stabilization, which is considered to be the major origin of the enzymatic catalysis, and to clarify how the electronic structure of proteins is polarized in response to the change in electron distribution of the substrate. By performing a systematic computational modeling analysis from a quantum chemical viewpoint, we clarified the relationship between the location of amino acid residues on the protein domain and the degree of electronic polarization of each residue. In this presentation, we'll discuss the following topics: (a) how to construct enzymatic process: QM/MM modeling and the energy component analysis (b) Comparative study of the enzymatic TS and the transition state analogue. (c) Role of Arg90: modeling and analysis of several mutant reactions.
15:15-15:30
Coffee Break
15:30-15:55
Title: The Proteome of Crocodile Egg White
Dr. Sompong Thammasirirak
, Associated Professor, Department of Biochemistry, Faculty of Science, Khon Kaen University, Thailand
15:55-16:20

Title: Classification of Proteins into Structured and Unstructured Regions
Dr.
Satoshi Fukuchi, Assistant Professor, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Japan

It has long been known that eukaryotic proteins have complex domain structures, and recently revealed that considerable number of eukaryotic proteins have the so-called intrinsically disordered (ID) regions, which occasionally extend more than a few hundred residues. Those proteins with long ID regions have been known to play crucial roles in the important cell activity such as signal transduction, transcriptional regulation etc. The structural domains homologous to those registered in PDB can be identified with highly sensitive homology searches such as PSI-BLAST and HMM, while ID regions can be predicted because of their biased amino acid composition in the sequence. We have constructed a pipeline, DICHOT, to divide a protein molecule into structural domains and ID regions, which consists of the standard procedure of domain assignment, the ID-region prediction by the DISOPRED program, and a newly developed program (CLADIST) that discriminates domains from ID regions. The reliability was tested with human transcriptional factors, which are one of the typical proteins with long ID regions, showing a plausible result by referring some of the published domain-ID partitioning. All human proteins in the SwissProt database are loaded into the pipeline. The results indicate that 37% of total residues belong to ID regions, while 63% fall in structural domains including 10% of unknown structure. These predicted novel structural domains are good targets of structural genomics.

16:20-16:45
Title: Gene Expression Profiles and Protein Features Effectively Complement Each Other in Gene Function Prediction
Dr. Krzysztof Wabnik
, Plant Systems Biology Department, University of Gent, VIB, Belgium

We explored the use of Rough Sets for a novel data integration strategy where gene expression data, protein features and Gene Ontology (GO) annotations were combined to describe general and biologically
relevant patterns represented by If-Then rules. The descriptive rules were used to predict the function of unknown genes in Arabidopsis thaliana and Schizosaccharomyces pombe. The If-Then rule models showed success rates of up to 0.89 (discriminative and predictive power for both modeled organisms); whereas, models built solely of one data type (protein features or gene expression data) yielded success rates varying from 0.68 to 0.78. Our models were applied to generate classifications for many unknown genes, of which a sizeable number were confirmed either by PubMed literature reports or electronically interfered annotations.
16:45-17:10

Title: Peptide Epitopes: Approach Fragment Based Drug Design from Plant Viruses
Dr. Virendra Gomase,
Department of Bioinformatics, Padmashree Dr. D.Y. Patil University, India

The new paradigm in vaccine design is emerging, following essential discoveries in immunology and development of new MHC Class binding peptides. MHC molecules are cell surface glycoproteins, which take active part in host immune reactions. The involvement of MHC class in response to almost all antigens and the variable length of interacting peptides make the study of MHC Class molecules very interesting. MHC molecules have been well characterized in terms of their role in immune reactions. They bind to some of the peptide fragments generated after proteolytic cleavage of antigen. This binding acts like red flags for antigen specific and to generate immune response against the parent antigen. So a small fragment of antigen can induce immune response against whole antigen. This theme is implemented in designing subunit and synthetic peptide vaccines. Adducts of MHC and peptides complexes elicit the immune response for clearing various intracellular infections. Prediction methods based on the specificity of immunological assessment of functionally active subunit vaccines and will complement the wet lab experiments and speed up the knowledge discoveries on the basis of computational algorithms. These peptides can initiate antigen processing by generating larger fragments containing antigenic epitopes, the respective fragments are subsequently trimmed to their final size by exopeptidases.

Track 1-4: Methodology or Technologies of Human Proteome Analysis

Time: April 4, 2009, Saturday 08:30-11:30

Place: Meeting Room 310A

Session Chair:
Dr. Chung Hsuan (Winston) Chen, Distinguished Research Fellow & Director, The Genomics Research Center, Academia Sinica, Taiwan
Co-Chair:
Dr. Yoshiya Oda, Director of Omics Group, Laboratory of Core Technology at Eisai Co., Ltd. and Associate Professor at Metabolome Laboratory, University of Tokyo, Japan
08:30-08:55
Keynote Speech: Title: Novel Mass Spectrometry Technologies for Ultra-sensitive Analysis
Dr. Chung Hsuan (Winston) Chen,
Distinguished Research Fellow & Director, The Genomics Research Center, Academia Sinica, Taiwan

His group developed mass spectrometry for DNA analysis and sequencing for Human Genome Project. They are the first to demonstrate large DNA fragments detection and sequencing by mass spectrometry. They are also the first to apply mass spectrometry for genetic disease diagnosis. In 1994, he was elected to be in editorial board in the journal of “Rapid Communication of Mass Spectrometry”. There are three high tech spin-off companies from his ORNL groups. His recent work at Academia Sinica has focused on the development of innovative mass spectrometry, microarray and nanobiotechnology. Among mass spectrometry research, siginificant effort was placed on biomarker search for various cancers which include breast, stomach, ovarian and prostate cancers.
08:55-09:15

Title: Novel Method to Elucidate Protein Interactions and Protein Kinases Based on Chemical Proteomics
Dr. Yoshiya Oda, Director of Omics Group, Laboratory of Core Technology at Eisai Co., Ltd. and Associate Professor at Metabolome Laboratory, University of Tokyo, Japan

Dr. Yoshiya Oda developed a widely used metabolic stable isotope labeling method for quantitative proteomics, which is featured in the most frequently cited article from the Proceedings of the National Academy of Sciences-Chemistry journal. He is also a famous as one of pioneers of phosphoproteomics and he developed a beta-elimination strategy to enrich phosphoproteins as well as efficient IMAC protocols. Dr Oda is now an editorial board member of Molecular & Celluar Proteomics. Dr. Oda is currently a Director of Omics group at Eisai Co., Ltd. Laboratory of Core Technology and a Associate Professor at Metabolome Laboratory, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, at the University of Tokyo. He has published numerous papers in the field of proteomics.
09:15-09:35

Title: Revealing Targets of the Low Abundance Proteome; The Essence of Biomarker Discovery
Dr. Dian Er Chen
, Principal Investigator, Proteomics R&D, Sigma-Aldrich, Inc., USA


Dr. Chen has significant multidisciplinary scientific research and management expertise gained through a career largely spent at Sigma-Aldrich Corporation. Dr. Chen's research experience is extremely broad, encompassing a range of disciplines including Organic Chemistry, Protein Chemistry, and Immunology-as well as other Life Sciences areas.

09:35-09:55
Title: The MAPPIT Toolbox: Strategies to Analyze Molecular Interactions in Intact Cells
Dr. Jan Tavernier, Professor, VIB Department of Medical Protein Research, Ghent University, Belgium
MAPPIT (Mammalian Protein-Protein Interaction Trap) is a cytokine receptor-based two-hybrid method that operates in intact mammalian cells. Modification-independent and tyrosine phosphorylation-dependent protein-protein interactions can be studied in their normal physiological context. Interactor hunts for novel protein-protein interactions can be performed using either a FACS-based protocol using complex cDNA libraries or using an array format. Most recently, we adopted MAPPIT for large-scale interactomics mapping in yeast, C. elegans and man.
09:55-10:15
Title: Phosphoproteome and Quantitative Proteome Analysis Revealed the Role of Nedd4 E3 Ligases in the Tgfbeta Superfamily Signalling Pathways
Dr. Je-Yoel Cho, Assistant Professor, Department of Biochemistry, School of Dentistry, Kyungpook National University, South Korea

His current researches include the development of lung cancer biomarkers using the enriched samples of glycoproteome and low molecular weight proteome and LC-ms/ms-based mass spectrometry. In this project, he utilizes non-labeling quantitative proteomics and subtractive and comparative proteomics approaches using clinical samples from various diseases.
10:15-10:30
Coffee Break
10:30-10:50

Title: Optimisation and Standardisation of Sample Preparation with the Bead-beating Technology in Proteomics Research
Ms. Elina Machefer
, Asia Area Manager, Bertin Technologies, Hong Kong

In the context of sample preparation and cell lysis, Bertin Technologies (France) has developed a technology dedicated to the homogenization and grinding of soft to hard materials. The goal is to improve the first critical step in any molecular biology process and follow the latest requirements of analysis equipments which have radically improved in terms of throughput, reproducibility, detection limits and linearity.Following specific mechanical engineering studies of bead beating technology, a high speed figure-8 multidirectional motion gives shaking energy to the beads that grind/homogenize samples in sealed tubes. This patented solution Precellys24 plays a large part in the analyse chain of rapid method to extract and detect or quantify DNA, RNA or proteins. Thanks to Cryolys option, temperature inside Precellys24 tubes is maintained at an optimal level during homogenization. Cryolys technology permits temperature-sensitive molecules to keep their native state for any analysis.

10:50-11:10

Title: Analytical Methods for Studying Physical and Chemical Instabilities of Lenograstim
Dr. Jasmina Tonic-Ribarska
, MSci. Pharm. Assistant, Center of Drug Quality Control, Faculty of Pharmacy, University “Ss Cyril and Methodius”, Macedonia

The stability of protein - based pharmaceuticals is significant in terms of their pharmaceutical quality and biological activity. A right choice of suitable analytical methods is needed in order to detect the early formation of degradation products or modified forms. Aggregation and oxidation are the dominant physical and chemical pathways that degrade protein molecules, leading to the inactivity of protein pharmaceuticals. Therefore, t he analytical methods for the assessment of the formation of aggregates in glycosylated form of recombinant human granulocyte colony – stimulating factor ( rHuG-CSF), lenograstim under physiological conditions and the investigation of the effect of hydrogen peroxide on oxidation of methionine residues in lenograstim will be discussed.

11:10-11:30

Title: Modern Optical Analytical Devices for the Express Peptide and Protein Discovering at the Diagnostics and Environmental Monitoring
Dr. Nickolaj F. Starodub,
Professor of National University of Life and Environmental Sciences of Ukraine, Kiev, Ukraine

N. Starodub and his colleagues have developed a number optical biosensors, in particular, based on the nano structured porous silicon, fiber optics, surface plasmon resonance and total internal reflection for the determination of specific antigens and antibodies as well as some mycotoxins and bacteria at the diagnostics of number of diseases (autoimmune status of diabetics, retroviral infections, influence, birds flu, heart failure and others) and monitoring of environmental objects. The last is connected with the revealing of nonylethoxylates and such mycotoxins as: T2, aflatoxins, patulin, searelenone and others. Among the developed biosensors there are principal new ones based on photoluminescence and light induced photoconductivity. To replace non stable biological materials at the formation of selective structures of biosensors and to express remove above enumerated toxic substances, in particular, from water resources it was proposed number of substances as calyx[4]arenas for the practical application. It is discovered a principal new way to modelling selective binding sites in the analytical devices and at the express decontamination of environmental objects, especially, water sources.

Track 2: Protein Sciences and Technology

Track 2-1: Biomarkers Discovery, Assay and Applications

Time: April 2, 2009, Thursday 13:30-16:15

Place: Meeting Room 310B

Session Chair:
Dr. Jong Shin Yoo, Vice President, Mass Spectrometry Analysis Group, Korea Basic Science Institute; President of KHUPO, South Korea
Co-Chair:
Dr. Hyun Joo An, Associate Specialist, Clinical Glycomics Mass Spectrometry Facility, University of California, USA

13:30-13:55

Keynote Speech: Title: Discovery of Glycoproteins as a Cancer Biomarker in Human Plasma by Mass Spectrometry
Dr. Jong Shin Yoo, Vice President, Mass Spectrometry Analysis Group, Korea Basic Science Institute; President of KHUPO, South Korea

Dr. Yoo joined the Mass Spectrometry Division at Korea Basic Science Institute in 1993, he served his presidency of Korean Society of Mass Spectrometry in 2006-2007. He is also join ing the presidency of Korean HUPO from 2008. Dr. Yoo pioneered a new technology for the high throughput analysis of human proteomes and identification of their post translational modification such as acetylation in 2001 and phosphorylation in 2007. This technology is capable of label free quantitation of the proteins in normal plasma as well as cancer case. It is expected that this work will lead to the development of novel biomakers linked to highly abundant proteins in human plasma. Concurrently, Dr. Yoo is appl ying ultra-high resolution mass spectrometry technology with 15T FTICR for the analysis of glycoproteins in human plasma for the biomarker discovery and validation.

13:55-14:20

 

Title: Multimarker Strategies and Data Integration: Are We Ready for Prime Time in Laboratory Medicine?
Dr. Damien Gruson, Medical Director, LABCO Diagnostics, Belgium

Laboratory Medicine represents a major component of healthcare and nowadays, is involved in more than seventy percent of medical decision. The evolution of this discipline is constant and an important motor for such evolution is the assimilation of new technologies for information and communication. Due to their incredibly fast development during the last decade, information and communication technologies (ICT) have been applied in numerous fields including life sciences and laboratory medicine. In fact, the integration of ICT and laboratory medicine represents a very attractive perspective which may lead to the generation of new tools to support current clinical evaluation and to apply in daily practice some multimarker strategies. Multimarker strategies (MS) consider the integration of different results from laboratory tests into a single score able to support medical decision or disease risk estimation. Some concrete examples exist since many years and have entered the current algorithms for prenatal diagnosis and estimation of a possible liver fibrosis. With the development of new biomarkers, MS is more and more consider as a real possibility to improve the diagnosis, prognosis and stratification of multifactorial diseases. Indeed, a potent advantage of MS is the possibility by combining different biomarkers from different physiopathological origin to improve the predictive and discriminatory power of these biomarkers. Furthermore, with the recent success of genomic, ICT tools will be able to enlarge the MS field and integrate data from genomic analysis and furthermore, data from imaging analysis. Consequently, MS through ICT and its application to laboratory medicine represent an opportunity to support medical decision but also to contribute directly to a more personalized diagnosis and treatment. In conclusion, a new area is open with the integration of ICT to laboratory medicine in its daily practice. One of the consequences of this integration is a more easy access to MS which will participate to the transformation of laboratory data into a global medical knowledge able to support medical decision and may participate to personalized care.

14:20-14:45

 

Title: Advances in Biomarker Verification / Validation Strategies Using QTRAP? LC/MS/MS System Technology
Mr. Byunghee Shin
, Mass Spectrometry System Division, Part of Life Technologies, Applied Biosystems, South Korea

As the study of protein biomarkers increases in importance, technical limitations to the detection of low abundance proteins and to high-throughput, high precision quantitation remain to be overcome. Targeted quantitation by multiple reaction monitoring (MRM) on triple quadrupole based MS systems is being used increasingly for quantitative monitoring of peptides/proteins in complex biological samples. Strategies for overcoming the key challenges (need for rapid assay development, need for higher multiplexing and need for assay robustness) are becoming critical. Solving these problems will require a combination of robust instrumentation, intelligent acquisition and processing software, and appropriate use of internal standard strategies. In this talk, we will discuss the new trends in targeted quantitative proteomics and the key tools available for performing high quality biomarker verification assays.

14:45-15:10

Title: Human Serum Glycome for Disease Biomarker Discovery
Dr. Hyun Joo An, Associate Specialist, Clinical Glycomics Mass Spectrometry Facility, University of California, USA

She and colleagues have established a company, Glycometrix Inc., to develop the patented technology in July 2004. She is a director, Technology development. She is currently working on the application of F ourier transform mass spectrometry in bio-analysis. Her specific research interests include oligosaccharide analysis (glycomics), biomarker discovery for infectious diseases and cancer and glycoprotein analysis (glycoproteomics) to determine the site specific glycosylation.

15:10-15:25
Coffee Break
15:25-15:50
Title: Translating Mass Spectrometry-Based Proteomics of Malignant Lymphoma into Clinical Application: Identification of Disease Biomarkers and Drug Targets
Dr. Megan S. Lim, Associate Professor and Director, Hematopathology, Department of Pathology, University of Michigan, USA

Dr. Lim is the recipient of several awards including the Young Investigator Award (2002) and the Translational Research Award (2004) from the Children's Oncology Group. Her research is supported by several grants from the National Cancer Institute. She is a member of several professional societies including the United States and Canadian Association of Pathology, American Association for Cancer Research, American Society of Hematology, American Society of Investigative Pathology and the Children's Oncology Group. She is a member of the Editorial Board for Laboratory Investigation and serves as a referee for a number of journals including the American Journal of Pathology, Leukemia and Lymphoma and Blood. She is board certified in Anatomic Pathology, Hematopathology and Molecular Genetic Pathology.
15:50-16:15

Title: Biochemical Markers of Bilirubin-Induced Neurotoxicity in Newborns; Tau and S100B Proteins
Dr. Nurullah Okumus, Specialist of Neonatology, Division of Neonatology, Dr. Sami Ulus Children's Hospital, Ankara, Turkey

Track 2-2: Biological Significances of Protein Aggregation, Folding/ Unfolding, and Signaling

Time: April 3, 2009, Friday 08:30-11:50

Place: Meeting Room 310B

SessionChair:
Dr. Matthias P. Mayer, Group Leader, Zentrum Fur Molekulare Biologie der Universitat Heidelberg, DKFZ-ZMBH Alliance, University of Heidelberg, Germany
Co-Chair:

Dr. Ching-Hwa Kiang, Professor, Department of Physics & Astronomy, Rice University, USA

08:30-08:55

Keynote Speech: Title: Analyzing Protein Conformations and Dynamics Using Amide Hydrogen Exchange Mass Spectrometry
Dr. Matthias P. Mayer, Group Leader, Zentrum Fur Molekulare Biologie der Universitat Heidelberg, DKFZ-ZMBH Alliance, University of Heidelberg, Germany

Upon completion of his doctorate in cell biology at the University of Freiburg in 1990 he joined the laboratory of C. Dale Poulter at the Department of Chemistry, University of Utah, Salt Lake City where he analyzed protein farnesylation and farnesyltransferases (Mayer et al. 1993). In 1992 he joined the laboratory of Costa Georgopoulos at the Centre Médical Universitaire, Université de Genève, Geneva, Switzerland working on chaperones and heat shock response. This work was continued in Bernd Bukau's laboratory at the University of Freiburg, Germany where he focused on the analysis of the molecular mechanism of Hsp70 proteins (e.g. Mayer et al. 2000). In 2002 he moved to the Zentrum für Molekulare Biologie der Universit?t Heidelberg where he became independent group leader in 2005. In Freiburg and Heidelberg his team established the amide hydrogen exchange mass spectrometry technology and applied it to several problems of molecular chaperones and heat shock response (e.g. Rist et al., 2003, 2005, 2006; Rodriguez et al. 2008)
08:55-09:15

Title: AFM Studies of the Resistance to Unfolding of Titin and Von Willebrand Factor (VWF)
Dr. Ching-Hwa Kiang, Professor, Department of Physics & Astronomy, Rice University, USA

Kiang's current research focuses on single-molecule manipulation. Kiang used single-molecule manipulation technique to stretch a protein and follow the trajectory to understand the folding pathways (Harris et al. 2007). Because protein misfolding may result in malfunction of biological processes and even disease, understanding how proteins fold into their correct shape may help us to develop strategies for treating diseases resulted from protein misfolding, such as Alzheimer's, Parkinson's, and mad cow diseases. The technique can also be applied to any proteins as well as RNA and DNA. Kiang won the 2007 Best of Small Tech Researcher of the Year award for this research accomplishment.

09:15-09:35
Title: Roles of p97/VCP, a Multifunctional AAA Chaperone, in Protein Oligomerization and Aggregation in Neurodegenerative Diseases
Dr. Teru Ogura, Professor and Director, Institute of Molecular Embryology and Genetics, Kumamoto University, Japan

In 1990, he started to study a membrane-bound ATP-dependent protease, FtsH, in E. coli, He has achieved a series of extensive studies on FtsH. His pioneered review on AAA+ superfamily proteins has stimulated the relevant field and has been cited over 350 times to date. In 2002, he promoted to a Professor of the Institute of Molecular Embryology of Genetics, Kumamoto University. A decade ago, he also set up a systematic study on AAA proteins using a sophisticated model animal, nematode Caenorhabditis elegans. The project aims to elucidate functions of AAA proteins in development and cellular functions of their human homologs related to diseases, and has revealed several implications of p97, spastin and fidgetin in C. elegans development (Sasagawa et al. 2007; 2007; Matsushita-Ishiodori et al. 2007) and disease-related functions of p97 and spastin (Yamanaka et al. 2004; Nishikori et al. 2008). Dr. Ogura has been the Director of the Institute of Molecular Embryology and Genetics, Kumamoto University since October, 2008.
09:35-09:55
Title: Assisted and Unassisted Folding – GroEL/ES and Cyp18 Action on Carbonic Anhydrase
Dr. Uno Carlsson, Professor, Division of Chemistry, IFM-Department of Physics, Chemistry and Biology
Linkoping University, Sweden

After completion of his doctorate in biochemistry at the University of Goteborg in 1975 he joined Linkoping University as an Assistant Professor. In 1981 he was Associate Professor and in 2000 Full Professor at this university. During the Ph.D. time he studied the protein folding mechanism and at Linkoping University he continued these studies, but also included studies of chaperone-mediated folding and other conformational related studies such as protein-surface adsorption and protein-protein interactions.
09:55-10:15
Title: Computer Simulations of Myoglobin
Dr. Alfredo Di Nola, Full Professor, Department of Chemistry, University of Rome "La Sapienza", Italy

He contributed to set up some of the most used algorithms in the MD field such as the temperature rescaling with coupling to an external bath, the high temperature sampling, for a rapid exploration of the configurational space allowed for a molecule, and an algorithm for the simulation of the interaction between a small ligand and a receptor (docking problem). He also studied methods to calculate the free energy in proteins and had contributed to a new statistical-mechanical theory, the Quasi-Gaussian Entropy (QGE) theory, that allows to predict the equation of state of fluids. He has also extended this theory to solutes. He has also collaborated at the formulation of a new quantum/classical method (the Perturbed Matrix Method) that allows the efficient and precise calculation of the electrinic properties in a molecule.
10:15-10:30
Coffee Break
10:30-10:50

Title: Unraveling Amyloidogenic Behaviour from Computational Analyses
Dr. Flavio Seno, Professor, Department of Physics, University of Padua, Italy

Upon completation of his Ph.D. on Critical Phenomena at the University of Padua, he joined in 1991 the Theoretical Physics Group in Oxford working on the magnetic properties of rare earth by using spin models with competing interactions. Afterwards he got a position as Researcher (1994) and as Professor (2001) at the University of Padua working first on equilibrium and non equilibrium statistical mechanics. The main results have been obtained in the topics of phase transitions and critical phenomena, of the renormalization group, of spin systems, of surface critical phenomena, of conformational properties of polymers and random surfaces. In the last years most of his research has been devoted to the application of tools of statistical mechanics to understand biologically inspired problems. Important results have been obtained in the modelling of single molecule experiments, particularly in understanding the unzipping and the overstretching conformational transitions. Other important results have been obtained on the inverse protein folding problem, in the analysis of topological models to mimic the folding problem and in developing an unifying framework to explain the reduced menu of protein folds. More recently he develops an algorithm “Pasta” (Prediction of Amyloid Structure Aggregation) which portions of a given protein or peptide sequence forming amyloid fibrils are stabilizing the specific inter-molecular pattern of hydrogen bondend amino-acids. The results of the whole research are contained in about 80 publications.

10:50-11:10
Title: Factors that Promote or Protect against Formation of Amyloid Fibrils by Folded Proteins
Dr. Daizo Hamada
, Assistant Professor of Medicine, Division of Structural Biology (G-COE), Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Japan

We have been focused on the mechanism of amyloid fibril formation in relation with structural and physicochemical properties of folded proteins including -lactoglobulin whose involvements in diseases are unclear. Results from these studies provided a significant insight into the role of dynamical properties of protein structures in the formation of amyloid fibrils and a fundamental concept for the negative design principle that is included in the folded protein to protect them against aggregation. We will also discuss the effect of protein aggregates on the structure of lipid membrane as to provide an insight into the mechanism of cytotoxic properties of protein aggregates.

11:10-11:30

Title: The Role of Phosphorylation Motifs in Dissecting MAP Kinase Signaling
Dr. Richard R. Vaillancourt
, Associate Professor of Pharmacology & Toxicology, Department of Pharmacology & Toxicology, University of Arizona College of Pharmacy, USA

Dr. Vaillancourt received his B.A. at St. Anselm College in Manchester , N.H. and Ph.D. from the University of Wisconsin-Madison. For his doctoral work, he did radiosynthetic chemistry and developed photoaffinity probes of NAD + to study the structure of the retinal G protein, transducin. As a post-doctoral fellow at the National Jewish Medical & Research Center in Denver , Colorado , he studied specific phosphorylation sites on the platelet-derived growth factor receptor tyrosine kinase and their regulation of the ERK MAP kinase pathway. At the University of Arizona , Dr. Vaillancourt has been studying the MAP3K family of serine/ threonine kinases. Specifically, his research group has identified phosphorylation sites on MEKK3 that are critical for activity. Serine 526 has been identified as an autophosphorylation site that is required for MEKK3 catalytic activity. In addition, serine 166 has been identified as a Pim kinase phosphorylation site, thus linking Pim kinase activity with MEKK3. On going studies are aimed at defining the role of phosphoserine 166 in MEKK3 activity.

11:30-11:50

Title: To Bind - or not to Bind: Differential Presentation of a Self-peptide by HLA-B27 Subtypes
Dr. Andreas Ziegler, Full Professor and Founding Director, Institute for Immune Genetics, Charite University Medicine Berlin, Germany

Andreas Ziegler studied genetics and biochemistry at the universities of Darmstadt and Heidelberg ( Germany ). He was trained at the Max Planck Institute for Medical Research in Heidelberg (diploma), the Basel Institute for Immunology (PhD dissertation, Basel, Switzerland), and the MRC Laboratory of Molecular Biology (post-doctoral research, Cambridge, UK). Following work at the universities of Tübingen and Marburg ( Germany ), he became full professor and founding director of the Institut für Immungenetik ( Charité-Universit?tsmedizin Berlin , Freie Universit?t Berlin ). He is interested in the biology of gene complexes, structure–function relationships of MHC molecules and selection processes that take place within the human immune and reproductive systems. Andreas Ziegler is the author of more than 200 peer-reviewed publications.

Track 2-3: Membrane Protein Structure and Functions

Time: April 3, 2009, Friday 13:30-17:30

Place: Meeting Room 310B

Session Chair:
Dr. Andreas Ziegler, Full Professor and Founding Director, Institute for Immune Genetics, Charite University Medicine Berlin, Germany
Co-Chair:
Dr. Toshiyuki Takai, Professor, Department of Experimental Immunology, Institute of Development, Aging and Cancer, Tohoku University, Japan
13:30-13:55
Keynote Speech: Title: Functional Proteomics of Membrane Protein Complexes and Associated Protein Networks
Dr. Uwe Schulte, Founder and CEO/CSO of LOGOPHARM GmbH, Germany


LOGOPHARM GmbH is a research-oriented biotech company that provides advanced solutions in proteomic target and biomarker R&D. It combines proprietary proteomic technologies, long-term experience in functional membrane protein analysis and innovative drug development concepts with focus on membrane proteins and protein complexes. Dr. Uwe Schulte's research topics include biochemical and functional characterization of ion channels and GPCRs (focus on pain and CNS disorders); development of methods for biochemical characterization and mass spectrometric analysis of membrane proteins and protein-ligand interactions; protein quantification techniques, antibody profiling, analysis of protein networks.
13:55-14:20

Title: Structure- function of the Calcium Release Channel by Cryo-electron Microscopy
Dr. Montserrat Samsó, Assistant Professor, Anesthesia, Pain and Perioperative Medicine, Harvard Medical School, USA

Dr. Samsó received her PhD degree in Biochemistry and Molecular Biology from the Autonomous University of Barcelona in 1993 and did her postdoctoral training at the New York State Department of Health ( Albany, NY ). Her research centered in the structure-function analysis of macromolecular complexes using single-particle electron microscopy with contributions such as the first structural determination of the molecular motor dynein (Samso and Koonce, 2004; Samso et al., 1998), the 3D mapping of physiological modulators of the calcium channel RyR1 (Samso et al., 1999; Samso and Wagenknecht, 2002), and the development of a novel classification method for electron microscope images (Samso et al., 2002). Dr. Samsó joined the Anesthesia Department at Harvard Medical School in 2004 where she is an Assistant Professor. Her current studies center on the structural study of membrane proteins using cryo-electron microscopy in conditions as close as possible to their native state in order to understand their function. For the calcium channel RyR1 she is elucidating the structure of its gating unit and the basis of its long-range alosterism. She has provided the first description of its ion pathway (Samso et al., 2005) and its detailed interactions with its associated subunit, the FKBP12 protein (Samso et al., 2006).

14:20-14:45
Title: Type IV Secretion Protein Complexes Required for Antibiotic Resistance Transfer in Human Pathogens
Dr. Elisabeth Grohmann, Group Leader, Department of Environmental Microbiology, Technical University of Berlin, Germany

In 2000 she started her molecular and biochemical studies on the type IV secretion system (T4SS) encoded by the multiple antibiotic resistance plasmid pIP501. The T4SS is responsible for DNA/protein transport during bacterial conjugation and similar T4SS in Gram-negative pathogenic bacteria are indispensable for toxin import into mammalian cells or effector secretion (Grohmann et al., 2003). Dr. Grohmann characterized the key players of this first T4SS encoded by Gram-positive bacteria (Kurenbach et al., 2002, Kopec et al., 2005, Kurenbach et al., 2006). In 2007 the group of Dr. Grohmann published the first molecular model of a T4SS encoded by Gram-positive bacteria (model host is Enterococcus faecalis ). The model of the multi-protein secretion complex is based upon in vivo yeast two-hybrid studies, pull down assays, cross-linking studies and immuno-localization of the secretion proteins (Abajy et al., 2007).
14:45-15:10

Title: X-ray Crystallographic Evidence for a Triple Conformation of An HLA-B*2705 -bound Self-peptide
Dr. Barbara Uchanska-Ziegler, Group Leader and Head of Structural Biology, Institute of Immunogenetics, Charité-University Medicine Berlin, Freie University of Berlin, Germany

Barbara Uchanska-Ziegler studied animal breeding and genetics at the Agricultural University of Warsaw ( Poland ). She was trained at the Nuclear Research Center in Warsaw and later at the Medizinische Klinik in Tübingen ( Germany ). She obtained her PhD degree in microbiology from the Biological Faculty of the university in Tübingen. She then worked as a post-doc at the Medizinische Klinik in Tübingen. Following work at the University of Marburg ( Germany ), she became group leader and head of structural biology at the Institut für Immungenetik (Charité- Universit?tsmedizin Berlin , Freie Universit?t Berlin ). She is interested in structure–function relationships of MHC molecules, using X-ray crystallography and spectroscopic techniques, and in producing and characterizing monoclonal and recombinant antibodies with T cell receptor-like specificity. Barbara Uchanska-Ziegler is the author of more than 80 peer-reviewed publications.

15:10-15:25
Coffee Break
15:25-15:50
Title: Augmented TLR9-induced Btk Activation in PIR-B-deficient B-1 Cells Provokes Excessive Rheumatoid Factor Production and Autoimmunity
Dr. Toshiyuki Takai
, Professor, Department of Experimental Immunology, Institute of Development, Aging and Cancer, Tohoku University, Japan

Dr. Toshiyuki Takai did his undergraduate work at Okayama University ( Okayama City ), where he received his M.Sc. degree in pharmaceutical sciences (1982). He did graduate work at Department of Medical Chemistry, Kyoto University (Ph.D., molecular biology, 1986, supervised by Prof. S. Numa). Dr. Takai stayed at Sloan–Kettering Institute for Cancer Research ( New York City ) as a visiting investigator for one and half year to study mouse genetic engineering (1992–1993, supervised by Dr. Jeffrey V. Ravetch) before joining to IDAC, Tohoku University in 1997 as Professor of Experimental Immunology. His research group, whose interest is focused on immunoregulatory cell-surface receptors, is currently supported by grants from the CREST Program, Japan Science and Technology Corporation.
15:50-16:15

Title: The EGFR-trypsin-PAR-2 Pathway in Cell Growth and the α4β1 Integrin/VCAM-1 Interactions in Pre-B Cell Repopulation Were Controlled by Fucosyltransferase
Dr. Akihiro Kondo
, Professor, Graduate School of Medicine, Osaka University, Japan

From 2002 to present, he was a Professor at Osaka University Graduate School of Medicine, Osaka , Japan . His works have been specialized in carbohydrate chemistry and analytical chemistry. Major works include ‘Oligosaccharide Analysis by Fluorescence Labeling' and ‘Development of the Test Method for Detection of Endocrine Disrupting Activity Using DNA Microarrays' in ‘Toxicogenomics'.

16:15-16:40
Title: Nature of Inter-NBD (Nucleotide Binding Domain) Communication in P-Glycoprotein, a Multi Drug Efflux Pump
Dr. S. L. N. Prasad Reddy, Assistant Professor, Pharmaceutical Biotechnology and Pharmacognosy, Krupanidhi College of Pharmacy, India

Several types of cancers are either resistant to chemotherapy or respond to chemotherapy initially, but acquire resistance in the long run. The best studied mechanism of resistance to chemotherapy is due to over-expression of an energy-dependent multidrug efflux pump, known as the multidrug transporter or P-glycoprotein (PGP). This protein is coded by the MDR1 gene and belongs to the family of ATP Binding Cassette Transporter proteins, known as ABC transporters. PGP contains two membrane spanning domains (TMDs) and two cytosolic nucleotide binding domains (NBDs). The TMDs form a pathway through which drugs are effluxed and NBDs energizes the drug efflux.
16:40-17:05

Title: Coarse-grained Molecular Dynamics Simulation of Membrane Proteins
Dr. Ken Takahashi
, Assistant Professor, Graduate School of Medicine, Nagoya University, Japan

Molecular dynamics simulation is a powerful tool to analyze functions of proteins. While conventional all-atom simulation requires massive computational cost, recently-developed coarse-grained simulation can analyze the dynamics of biological molecules up to microsecond order with less expensive cost. We report recent development of this state of the art technique by introducing a bacterial mechanosensitive ion channel MscL as an example.

17:05-17:30

Title: Bacterial F0F1-aTPase Association with Secondary Transport Systems and Membrane Ensymes under Fermentation
Dr. Armen Trchounian
, Professor, Department of Biophysics, Yerevan State University, Armenia

The experimental results, hypotheses and models allow to offer a novel look at the bacterial F0F1-ATPase associated with K+ transport system and/or enzymes of anaerobic oxidation-reduction (formate hydrogen lyase) under fermentation. Some evidence of cysteine-residue in F0 b subunit that can be involved in this association is also obtained. Regulatory pathways of such associations by one of the trk genes, by the Arc-system for control of synthesis of enzymes in aerobic (respiratory) metabolism as well as by environmental factors (pH, ionic content, osmolarity, temperature, redox potential etc) are being investigated.

Track 2-4: Micro-array and Protein Chip Technologies

Time: April 4, 2009, Saturday 08:30-11:40

Place: Meeting Room 310B

Session Chair
Dr. Steven Bodovitz, Principal and Co-Founder, BioPerspectives, USA
Co-Chair
Dr. Kwon-Soo Ha, Associate Professor, Department of Molecular & Cellular Biochemistry, Kangwon National University School of Medicine, South Korea
08:30-08:55
Keynote Speech: Title: Opportunities and Challenges in Multiplexed Diagnostics
Dr. Steven Bodovitz, Principal and Co-Founder, BioPerspectives, USA

Steven Bodovitz, PhD, is a Principal at BioPerspectives, a renowned research and strategy consultancy in San Francisco, California. He is an expert at analyzing markets and developing strategies for the biotechnology industry. He has worked with a range of companies, from start-ups to Fortune 500. He has published a guide on business plan writing for the biotechnology industry, and he has written more than 20 business plans for biotechnology companies encompassing diagnostics, therapeutics and tools. He has written 16 comprehensive market analysis reports on topics ranging from immunoassays to microarrays to proteomics to RNAi therapeutics. He has published articles in Trends in Biotechnology, Drug Discovery Today and Drug Discovery World . He has presented his market analyses at biotechnology conferences in the US, Europe, and Japan, and he has been quoted in Science, Nature Biotechnology and The Economist . In addition to BioPerspectives, Dr. Bodovitz also served as Interim CEO of AminoArrays, an early-stage company with a patented method for array-based amino acid analysis. Dr. Bodovitz took over a company without ongoing product development and without a sound financial position and engineered an international collaboration between the leading low-density microarray platform company and the world's leading expert in the biochemistry underlying the core technology. Prior to becoming a biotechnology analyst and strategist, Dr. Bodovitz received his PhD in neuroscience from Northwestern University, where he studied the molecular mechanisms of Alzheimer's disease.

08:55-09:20

Title: High-throughput Screening of Antibody-Mimic Peptide by Using Protein Microarray Chip
Dr. Soo-Ik Chang, Professor, Department of Biochemistry, Chungbuk National University, South Korea

By using ProLinkerTM as a new chemical surface technology, ProteoChipTM has been developed as a novel protein microarray chip. We investigated the application of ProteoChipTM in screening of antibody-mimic peptides which inhibits the antibody/antigen interaction. Anti-antigen antibody microarray immobilized on the ProteoChipTM was employed to screening novel peptides against antigen from multiple hexapeptide sublibraries of a positional scanning synthetic peptide combinatorial library (PS-SPCL). The anti-antigen antibody/antigen interaction was successfully demonstrated on the anti-antigen antibody microarray in a dose-dependent manner. Novel peptides which inhibit the interaction between anti-antigen antibody and antigen were identified from the peptide libraries with this chip-based screening system by a competitive inhibition assay in a simultaneously and high-throughput fashion. These results suggest that the ProteoChipTM is a promising tool for high-throughput screening of antibody-mimic peptides in new therapeutic antibody development.

09:20-09:45

Title: The Application of Microarrays in High-throughput Enzyme Profiling
Dr. Mahesh Uttamchandani,
Defence Medical and Environmental, Research Institute (DMERI) , DSO National Laboratories, Singapore

It has been estimated that 18-29% of eukaryotic genomes encode enzymes. However only a limited proportion of enzymes have thus far been characterized and little is understood about the physiological roles, substrate specificity and downstream targets of the vast majority of these important proteins. A key step towards the biological characterization of enzymes, as well as their adoption as drug targets, is the development of global solutions that bridge the gap in understanding these proteins and their interactions. I will herein present advances in catalomics that facilitate the study of enzymes and their properties in a high-throughput manner using microarrays. We have over the years introduced and developed a variety of such enabling platforms for many classes of enzymes including kinases, phosphatases and proteases. For each of these different types of enzymes, specific design considerations are required to develop the appropriate chemical tools to characterize each enzyme class. These tools include activity-based probes and chemical compound libraries, which are rapidly assembled using efficient combinatorial synthesis or “ click chemistry ” strategies. The resulting molecular assortments may then be screened against the target enzymes in high-throughput using peptide/small molecule microarrays, offering a powerful means to study, profile and also discover potent small molecules with which to modulate enzyme activity.

09:45-10:10
Title: Applications of Protein Arrays to Serodiagnosis and Enzyme Activity Assay
Dr. Kwon-Soo Ha, Associate Professor, Department of Molecular & Cellular Biochemistry, Kangwon National University School of Medicine, South Korea

Protein arrays have appeared as a key technology in proteomics and serodiagnosis, since the technology allows a high-throughput and large-scale analysis of protein interactions in a small sample format. Various kinds of protein arrays were prepared by immobilizing proteins or antibodies, and then analyzed with a spectral surface plasmon resonance ( SPR ) biosensor. The array-based SPR biosensor has been successfully applied to the rapid analysis of GST-fusion protein expression in Escherichia coli , protein interactions, infection of pathogens and blood proteins for serodiagnosis. Recently, the SPR-based array system was used to determine matrix-metalloproteinase (MMP)-3 activity using gelatin arrays. MMP-3 activity was dependent on Brij-35 and inhibited with GM 6001 in a dose-dependent manner. In addition, we effectively analyzed blood proteins and transglutaminase activity with fluorescence-based protein arrays. The proteins in human sera were quantitatively analyzed by a tagged internal standard assay.   Thus, protein arrays based on SPR biosensors and fluorescence detection can provide a useful system for the high-throughput analysis of enzyme activity and rapid serodiagnosis.
10:10-10:25
Coffee Break
10:25-10:50
Title: A Proteome Chip Approach Reveals New DNA Base Damage Recognition Activities in Escherichia Coli
Dr. Chien-Sheng Chen, Assistant Professor, Graduate Institute of Systems Biology and Bioinformatics, National Central University, Taiwan

Despite the fact that many genomes have been decoded, proteome chips composed of individually purified proteins have been reported only in the budding yeast, mainly because of the complexity and difficulty in high-throughput protein purification. To facilitate proteomics studies in prokaryotes, we developed a new high-throughput protein purification protocol that allows us to purify 4,256 proteins, encoded by Escherichia coli K12 strain, as HisX6 fusions within ten hours. The purified proteins were then spotted on glass slides to form the first E. coli proteome chips. To demonstrate its application in basic research, we established assays to identify proteins involved in the recognition of potential base damages in DNA using a group of DNA probes each containing a mismatched base pair or an abasic site. We found a handful of proteins that were able to recognize each type of probe with a high affinity and specificity. Two positive proteins, YbaZ and YbcN, were further evaluated with biochemical analysis. The assembly of libraries containing DNA probes with specific modifications and the availability of E. coli proteome chips hold promise to rapidly reveal important protein–nucleic acid interactions that are difficult to obtain with other techniques.

10:50-11:15

Title: Highly Enhanced Fluorescence Detection of Biomolecular Microarrays Using Large-area Metal Pattern
Dr. Hee-Tae Jung, Associate Professor, Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science & Technology, South Korea

Here, we significantly increase the sensitivity of MEF for biological molecule detection by using a combination of a large-area metal nanopattern and layer-by-layer assembly of polyelectrolyte (PET) films, in a development of a DNA microarray. To implement our strategy, w e used capillary force lithography (CFL) to fabricate nanopatterns with various feature sizes on large patterned area. F lexibility of generating various pattern sizes from a single prepattern makes this approach very attractive, and it has significant advantage of low cost and high-efficiency. The feature dimension variations of the resultant patterns are also obtained from the masters with many different dot sizes, periods and height.

11:15-11:40

Title: A Protein Chip Approach to Unraveling Networks and Pathways
Dr. Heng Zhu
, Assistant Professor, Department of Pharmacology & Molecular Sciences, The High-throughput Biology Center, Viral Oncology Center, The Johns Hopkins University School of Medicine, USA

The protein chip technology is emerging as a versatile tool in the field of proteomics. It provides an unbiased, high-throughput, and comprehensive platform to investigate various aspects of protein properties; the results from which greatly facilitate construction of networks and pathways on a global scale. Our group has established new assays and applied them to globally investigate protein posttranslational modifications, with focus on lysine residues. We have also built new protein chip platform to decode the DNA-protein interactome in humans. In this presentation, exciting new discoveries will be shared with the audience.

Track 2-5: Animal & Plant Proteins and Applications

Time: April 4, 2009, Saturday 08:30-11:15

Place: Meeting Room 314

Session Chair
Dr. Birgit Kersten, Head of the GabipD Team, Department Bioinformatics, Max Planck Institute of Molecular Plant Physiology Potsdam-Golm, Germany
Co-Chair:
Dr. Crispin R. Dass, Sen Res Officer and Lab Head, Department of Orthopaedics, St Vincents Hospital Melbourne, Australia
08:30-09:00
Keynote Speech: Title: Structure of a Secondary Vitamin D3 Binding Site of Milk-Lactoglobulin for Vitamin D Transport
Dr. Chun-Jung Chen
, Professor, Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Taiwan

Here he will discuss a major bovine milk protein -lactoglobulin ( -LG), containing primarily a calyx for vitamin D3 binding. Whether there are two binding sites in each -LG molecule has been a subject of controversy. Using X-ray crystallography and fluorescence spectral analyses, Dr. Chen and his collaborative group has identified the second vitamin D3 binding site that is near the surface at the C-terminus with a remarkable feature that it combines an amphipathic -helix providing non-polar residues and a -strand providing a non-polar and a buried polar residue and linked by a hydrophobic loop. This finding provides a new insight into the interaction between vitamin D3 and -LG, in which the exosite may provide another route for the transport of vitamin D3 in vitamin D3 fortified dairy products (Yang et al., 2008, 2009).
Dr. Chen received his Ph.D. in Crystallography from the University of Pittsburgh in 1999 and extended his scientific training as a postdoctoral research fellow at the Department of Biochemistry and Molecular Biology at the University of Georgia in U.S.A. Since 2001, Dr. Chen has been the faculty in National Synchrotron Radiation Research Center and the joint professor with National Tsing-Hua University and National Cheng-Kung University in Taiwan. His major research interest is the study, by synchrotron protein crystallography, of the structure and functional relations of biological macromolecules.

09:00-09:30
Title: Plant Phosphoproteomics – The Road Ahead
Dr. Birgit Kersten,
Head of the GabipD Team, Department Bioinformatics, Max Planck Institute of Molecular Plant Physiology Potsdam-Golm, Germany

Dr. Birgit Kersten is a biologist/biophysicist and has 8 years of experience in plant science research, especially in the fields of proteomics, phosphoproteomics and bioinformatics. She established her own independent research group at the Max Planck Institute of Molecular Plant Physiology in Potsdam-Golm in 2007. BK is a pioneer in the generation of plant protein microarrays and of their application in high-throughput phosphorylation studies. As a source of recombinant plant proteins she and her group generated cDNA expression libraries from Arabidopsis and barley. Based on cluster analysis of the sequences she created UniGene sets, which she used for high-throughput expression and protein purification. By arraying the purified proteins, she generated plant protein microarrays. BK used microarrays containing 1700 Arabidopsis proteins to analyze recombinant MAP kinases from Dierk Scheel's lab and was able to identify novel in vitro substrates. Since 2006, as head of the GABI Primary Database (GabiPD), she further developed GabiPD as an integrative omics-database of plant-specific data. In that context, BK and her group is performing new bioinformatic analyses of phosphorylated sequences in order to identify plant protein targets for in-deep phosphorylation analysis in vivo. Furthermore, BK is further developing array-based phosphoproteomic methods for the systematic detection of in vitro substrates for plant kinases together with bioinformatic tools for the proteome-wide prediction of kinase-specific phosphorylation sites in Arabidopsis proteins. By the synergistic connection of her proteomic and bioinformatic experiences she is interested in the analysis of signaling pathways and biological networks in plants.
09:30-10:00

Title: Identification of Putative Peptide Ligands and Receptors Involved in Control of Cell-separation Processes in Plants
Dr. Reidunn Birgitta Aalen, Professer, Department of Molecular Biosciences, University of Oslo, Norway

Upon completion of her doctorate in bacterial genetics at the University of Oslo in 1985 she switched to plant science. She worked as a Research scientist at Laboratory for Plant Molecular Biology, Agricultural University of Norway, focusing on the identification of tissue-specific transcripts expressed in barley grains. In 1989-99 Aalen had a research stay at the at Max-Planck-Institut für Züchtungs-forschung, Cologne, Germany, where she learnt plant transformation. She was appointed Associate Professor at the Department of Biology, Division of General Genetics, University of Oslo in 1991, and established Arabidopsis as a model organism at the Department. Aalen is since 1998 Professor, now at Department of Molecular Biosciences, University of Oslo. During the latest years she has pursued two lines of research. One is related to epigenetics where her lab has contributed to the identification of Arabidopsis counterparts of Methyl-CpG-Binding Domain proteins and histone methyltransferases (SET-domain Proteins). The other field is the elucidation of floral organ abscission and other cell separation events in plants, again using Arabidopsis as a model organism. Aalen 's lab identified the gene INFLORESCENCE DEFICIENT IN ABSCISSION ( IDA ) that is absolutely required for abscission to take place in Arabidopsis. Recently her lab provided genetic evidence suggesting that IDA is a small peptide ligand interacting with the Receptor-like kinases HEASA and HEASA-LIKE2.

10:00-10:15

Coffee Break

10:15-10:45
Title: PEDF: Steps Towards Clinical Evaluation of Anticancer Efficacy
Dr. Crispin R. Dass
, Sen Res Officer and Lab Head, Department of Orthopaedics, St Vincents Hospital Melbourne, Australia

Crispin Dass received his PhD from Charles Sturt University, Australia in 1999, in the field of cancer gene therapy. He has been at the Orthopaedics Dept, St. Vincent’s Hospital Melbourne, since 2005. Prior to that, he has had biotechnology research experience at at Johnson & Johnson Research Laboratories for four years. He has 13 years of medical biotechnology basic and applied research in cancer, 8 years of broad industrial experience mainly in cancer, ~90 papers published in the past 13 years, 12 years of in vivo (small animal) and cell culture testing experience, and biochemistry, molecular biology, nanoparticle formulation, and drug delivery skills.
10:45-11:15

Title: Pre-infectional Secretomics – Apoplastic Interaction of Rice and M. grisea Secretomes
Dr. Nam-Soo Jwa, Associate Professor, Department of Molecular Biology, College of BioScience, Sejong University, South Korea

Recently, Nam-Soo started to work on pre-infectional interactions of host-pathogen in the apoplastic region before fungal penetration into host cytoplasm. This work is focused on secretome analysis from two different organisms including host and fungal pathogen. He has applied LC-MS/MS based proteomic analysis for secretome identification for pre-infectional interactions and Yeast-Two Hybrid screening for MAPK cascade networking analysis for understanding of cytoplasmic networking. This work will be expected to lead broad understanding of host-fungal pathogen interactions and plant protections through pre-infection as well as cytoplasmic interactions during disease development.

Track 3: Protein Therapeutics Discovery and Development

Track 3-1: Protein Therapeutics for Immunologic & Inflammatory Diseases

Time: April 2, 2009, Thursday 13:30-17:15

Place: Meeting Room 310C

Session Chair
Dr. Charles J. Malemud, Professor of Medicine & Anatomy, Case Western Reserve University, USA
Co-Chair:
Dr. Xianzhong Meng, Professor, Director of Cardiothoracic Inflammation Research, Department of Surgery, University of Colorado Denver, USA

13:30-14:00

Keynote Speech: Title: A Novel Therapeutic Principle in Autoimmune Diseases
Dr. Peter Buckel, Chief Executive Officer, SuppreMol GmbH, Germany

Prof. Dr. Peter Buckel joined SuppreMol in October 2005. He spent most of his professional career in leading positions in Biotech and Pharma industry. Recently he served as CEO of Atugen AG, Berlin (since 2004), an RNAi company which was merged into SR Pharma, an AIM listed company in London. Before he was founder and CEO of Xantos Biomedicine AG, Munich, since 1999. Between 1996 and 1999 he was SVP Molecular Medicine at Boehringer Mannheim and Roche, responsible for establishing and managing and international network of joint venture companies in gene and cell therapy (Cytonet).He studied Microbiology and Biochemistry in Munich, Wuerzburg and Regensburg. Peter Buckel is author or co-author of 47 scientific publications, 4 book contributions and 58 patents.
14:00-14:30
Title: Is JAK/STAT Pathway Inhibition the Key to Suppressing Joint and Bone Destruction in Rheumatoid Arthritis
Dr. Charles J. Malemud, Professor of Medicine & Anatomy, Case Western Reserve University, USA
14:30-15:00
Title: Expression of Salivary Trefoil Factors in Patients with Chronic Periodontitis
Dr. Ponlatham Chaiyarit,
Associate Professor, Department of Oral Diagnosis, Faculty of Dentistry, Khon Kaen University, Thailand
15:00-15:15

Coffee Break

15:15-15:45

Title: Extracellular HSC70 as a Novel Mediator of Myocardial Inflammatory Response to Ischemia and Reperfusion
Dr. Xianzhong Meng, Professor, Director of Cardiothoracic Inflammation Research, Department of Surgery, University of Colorado Denver, USA

Cardiac surgery with obligatory global ischemia and reperfusion induces myocardial inflammatory response characterized by over-production of pro-inflammatory cytokines that suppress cardiac contractility. We discovered that the myocardium releases the 70 kDa heat shock cognate protein (HSC70) immediately after ischemia. Neutralization of extracellular HSC70 reduces myocardial expression of pro-inflammatory cytokines and improves cardiac function. Extracellular HSC70 activates the TLR4-mediated pro-inflammatory signaling through a mechanism requiring its peptide-binding domain. Thus, extracellular HSC70 functions as a novel mediator of myocardial inflammatory response to ischemia and reperfusion, and could be a therapeutic target for myocardial protection during cardiac surgery with ischemia and reperfusion.
15:45-16:15

Title: Heme Oxygenase-1: A Novel Therapeutic Target against Oxidative Tissue Injuries in Acute Inflammation
Dr. Toru Takahashi, Senior Assistant Professor, Department of Anesthesiology and Resuscitology, Okayama University Medical School, Japan  

Dr. Toru Takahashi was graduated from Okayama University Medical School, Okayama, Japan in 1982 to be given his M.D. degree. He was also awarded his Ph.D. degree from Graduate School of Medicine, Okayama University in 198 7. In 1988, he joined the Department of Anesthesiology, Okayama University Hospital as a staff Anesthesiologist. He was appointed as Assistant Professor of the Department of Anesthesiology and Resuscitology, Okayama University Medical School in 1993, and then became Senior Assistant Professor in 2005. He also acted as Visiting Research Associate in the Rockefeller University, New York, NY, USA in 1999.
16:15-16:45

Title: Discovery of Chemokines Mediating Fibrotic Complications in Renal Diseases in Humans
Dr. Frederick Wai Keung TAM, Imperial College Kidney and Transplant Institute, Renal Section, Imperial College London, United Kingdom

Fibrosis is a major cause of morbidity and mortality in patients suffering from chronic kidney diseases. Encapsulating peritoneal sclerosis (EPS) is a rare but live threatening complication in patients receiving long term treatment with peritoneal dialysis. We studied the cytokines in the spent dialysate from patients receiving long term peritoneal dialysis. Using specific ELISA, we detected increased concentrations of monocyte chemoattractant protein-1 (CCL2) in the spent dialysate. The amount of dialysate CCL2 correlated with the severity of peritoneal membrane dysfunction. In order to examine the cytokine network involved in this clinical complication, we used an antibody array to examine 120 cytokines simultaneously. We discovered very high concentrations of CCL18/PARC (Pulmonary and Activation Regulated Chemokine) in both spent dialysate and serum from patients receiving long term peritoneal dialysis. The long term clinical outcome of these patients has been followed up prospectively in our West London Peritoneal Dialysis Study. Interim analysis showed that patients had high concentration of CCL18 in dialysate or serum are more likely to develop EPS or technique failure requiring changing over to haemodialysis treatment.

16:55-17:15

Title: Development of a Novel DNA Vaccine Targeting Macrophage Migration Inhibitory Factor and Its Efficacy on Murine Models of Inflammatory Diseases
Dr. Shin Onodera
, Assistant Professor, Department of Sports Medicine and Joint Reconstruction Surgery, Hokkaido University Graduate School of Medicine, Japan

Dr. Shin Onodera was graduated from Hokkaido University School of Medicine, Sapporo, Japan in 1988 to be given his M.D. degree. He was also awarded his Ph.D. degree from Hokkaido University Graduate in 2001. In this year, he joined the Department of Orthopaedsics, Hokkaido University Hospital as a staff orthopedicist. He was appointed as Assistant Professor of the Department of Orthopaedsics, Hokkaido University Hospital in 2002. He then became Assistant Professor of the Department of Sports Medicine and Joint Reconstruction Surgery in 2005. Since 2007, he has also been acting as a research consultant of Napa Jenomics, a Japanese company engaged in the development of novel drug delivery system for the delivery of antisense oligonucleotides, siRNA, and DNA vaccines. Currently, Dr. Onodera's major areas of interest include: (1) the development of anti-cytokine vaccine for the prophylaxis and therapeutics of inflammatory diseases, (2) in vivo bioimaging of bone and joint diseases including arthritis and particle-induced osteolysis, and (3) the use of beta-D-glucan as DNA/RNA carrier.

Track 3-2: Protein Therapeutics for Cancers

Time: April 3, 2009, Friday 08:30-11:50

Place: Meeting Room 310C
Session Chair
Dr. Frank Grams, Business Development Director, Pharma Partnering Asia, Roche Global, China
Co-Chair:
Dr. Quintin Pan, Associate Professor, Director, Head and Neck Oncology Research Program, Otolaryngology-Head and Neck Surgery, the Ohio State University Comprehensive Cancer Center, USA

08:30-08:55

Keynote Speech: Title: The Rational Design of Fusion Proteins for the Treatment of Solid Cancers
Dr. Glen C. MacDonald
, Chief Scientific Officer & Vice President of Operations, Viventia Biotechnologies, Canada


Dr. Glen MacDonald is Viventia's most senior research executive and is responsible for the Company's overall research and operational activities at Viventia's Winnipeg facility. In regard to research, Dr. MacDonald oversees the management and implementation of Viventia's core technology platforms: Hybridomics, ImmunoMine, UnLock and Armed Antibodies, as well as Viventia's Process Sciences Department. In addition, Dr. MacDonald is responsible for the operational areas involved in the cGMP manufacture of Viventia's clinical products. Dr. MacDonald joined Viventia Biotech in July, 1997 and has held positions of increasing responsibility within the company becoming the Vice President, Research in 2004. Prior to joining Viventia Biotech, Dr. MacDonald was with The University of Manitoba Cancer Treatment Research Foundation, The University of North Carolina, Chapel Hill, and the Ontario Cancer Institute, Princess Margaret Hospital.
08:55-09:15
Title: Take the Challenge: Testing of Biologicals in Rodent Tumour Models
Dr. Ralf Brandt, CEO & Managing Director, vivoPharm Pty Ltd, Australia

A large amount of information exists on the testing of small molecules in rodent models. This knowledge includes distribution characteristics, membrane penetration, pharmacokinetics and toxicity. However, biologicals such as antibodies or peptides have raised a challenge to their development teams. These proteins or protein-like molecules behave quite differently compared to small molecules. Protein-based biologicals tend to be highly target specific, which therefore produce fewer side effects, with higher molar activity. However, the comparatively large size of antibodies negatively effects their distribution in the animal, and cell membrane penetration, thus slowing down delivery to the target.

09:15-09:35

Title: In Search of Innovation from Asia
Dr. Frank Grams
, Business Development Director, Pharma Partnering Asia, Roche Global, China

Frank has been instrumental in setting up the newly formed Shanghai office of Roche Pharma Partnering. The office will further strengthen Roche's presence in the region and will be mainly responsible for partnering activities in Korea, Singapore and China, as well as Taiwan and Hong Kong. Prior to taking up this post, from 2006 Frank was Global Head, Drug Delivery Partnering, responsible for both the strategic and life-cycle management activities related to drug delivery partnering. Frank was a Global Alliance Director from 2002, managing pivotal research alliances such as Chugai, Evotec, SGX, Syrrx and Biotie. During the time of these two positions, he concluded more than 80 research and technology transactions. Frank joined the Roche Pharma Partnering team as Head of Opportunity Surveillance in July 2001, having previously worked in various research functions in Roche and at Boehringer Mannheim GmbH. Frank has a degree in chemistry from the University of Heidelberg and a Ph.D. from the Technical University of Munich within the group of Nobel laureate Robert Huber (Max-Planck-Institute for Biochemistry at Martinsried).
09:35-09:55
Title: A Mechanistic Based Novel Peptide Blocks Nuclear Import of RelB: p52 Dimer and Sensitizes Prostate Cancer Cells to Ionizing Radiation
Dr. William St. Clair, Associate Professor, Department of Radiation Medicine, University of Kentucky, Lexington, Kentucky, USA

Dr. St. Clair's laboratory is investigating the fundamental mechanisms by which reactive oxygen species (ROS) and reactive nitrogen species (RNS) contribute to normal tissue injury and cancer formation. The ultimate goal is to develop novel strategies for intervention and improvement of treatment. Several separate, but related areas of research are in progress.
09:55-10:15
Title: Protective Anti-tumor Immune Responses by Murine Dendritic Cells Pulsed with Recombinant CEA-Tat Derived from Escherichia Coli
Dr. Seung-Yong Seong, Professor, Department of Microbiology and Immunology, Seoul National University College of Medicine, South Korea


Carcinoembryonic antigen (CEA) is over-expressed on various human cancer cells and has been extensively studied in immunotherapy using dendritic cells (DCs) pulsed with RNA, peptide, adenovirus and vaccinia virus etc. Nonetheless, whole recombinant CEA protein – loaded DC vaccine has not been studied extensively. Considering that activated DCs do not phagocytoze soluble protein antigens efficiently and it is hard to get pure immature DCs ex vivo, we tried to load DCs with CEA which was conjugated with protein - transduction domains (PTD), HIV Tat. Using confocal microscope and FACS analysis, it was shown that the cytoplasms of DCs were full of recombinant CEA-Tat within 10 min, comparable to negligible staining of CEA-pulsed DCs even 30 min later. CEA-specific T cell proliferation and cytotoxic T cell responses were significantly enhanced in the mice immunized with CEA-Tat-pulsed DCs (DC(CEA-Tat)) compared with the mice immunized with CEA-pulsed DCs (DC(CEA)). Splenocytes from the mice immunized with DC (CEA-Tat) secreted more IFN-γ and less IL-4 than DC (CEA). In vivo, DC (CEA-Tat) vaccine significantly delayed tumor growth and prolonged survival of the mice. These results suggest that protective epitopes on CEA are well preserved on bacteria-derived recombinant CEA-Tat. In addition, the recombinant CEA-Tat could be efficiently delivered into the cytosol of DCs and could induces CEA-specific anti-tumor immune responses in vivo enough to protect mice. It might provide basic platform of cost-effective DC-based anti-CEA vaccines that can be combined with various immune-enhancing therapeutics.
10:15-10:30
Coffee Break
10:30-10:50

Title: Pre-clinical Development of a Bi-functional, Cancer Cell Homing, PKC Inhibitory Peptide for the Treatment of Head and Neck Cancer
Dr. Quintin Pan, Associate Professor, Director, Head and Neck Oncology Research Program, Otolaryngology-Head and Neck Surgery, the Ohio State University Comprehensive Cancer Center, USA

His research is focused on the genetic determinants of aggressive head and neck cancer to identify new “druggable” genes for the development of novel molecular-targeted anti-cancer therapeutics. Dr. Pan's laboratory has designed and developed a peptide therapeutic with two functional components to allow for the selective delivery of a PKC e inhibitor to tumor cells in vitro and in vivo . It is expected that this work will lead to the development of novel PKC e inhibitory peptidomimetics for the treatment of head and neck cancer.

10:50-11:10

Title: Fibrillar Protein rVP1 Induces Ovarian Cancer Cell Apoptosis via Integrin Signaling
Dr. Shu-Mei Liang, Deputy Director, Agricultural Biotechnology Research Center, Academia Sinica, Taiwan

Professor Shu-Mei Liang is currently the Deputy Director of Agricultural Biotechnology Research Center and Director of Office of Public Affairs, Academia Sinica. She received her doctorate in Biochemistry at University of Arkansas for Medical Sciences in 1978. Before joining Academia Sinica in 1998, Prof. Liang worked at biopharmaceutical companies such as Biogen S.A., and North American Vaccines, Inc., and also at FDA, USA. When she was at Biogen, she developed a simple and scalable novel process for isolating recombinant IL-2 which was successfully transferred to GSK. She also directed a team at North American Vaccines to produce recombinant porin conjugated vaccines which were then acquired by Baxter.

11:10-11:30

Title: A Novel HSP27-Targeted Heptapeptide for Overcoming Chemo- and Radioresistance
Dr. Yun-Sil Lee
, Chief, Division of Radiation Effect, Korea Institute of Radiological and Medical Science, South Korea

Heat shock protein 27 (HSP27) is highly expresed in human lung and breast cancer tissues and induces to cell death against various stimuli. We developed the heptapeptide of PKCdetla-V5 region, sensitized cancer cells through its interaction with HSP27, thereby sequestering HSP27. This heptapeptide may provied a novel strategy for selective nuetralizing of HSP27, which resulted in abolishing HSP27-mediated radio- and chemoresistnace.

11:30-11:50
Title: Acute-phase Protein Response: Can It Be Used as a Diagnostic Tool for Cancer?
Dr. Onn Haji Hashim, Professor & Head, Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Malaysia

The cure rate for cancer is strongly correlated with early diagnosis. Unfortunately many cancers are often diagnosed at their late stages and this is mainly attributed to the lack of efficient biomarkers for early detection. Our gel-based proteomic profiling analyses on unfractionated serum samples of cancer patients appear to demonstrate specific differential acute-phase response patterns in the different types of cancers studied. While the expression α1-antichymotrypsin (ACT) was upregulated in patients with breast cancer and epithelial ovarian carcinoma (EOCa), α1B-glycoprotein and antithrombin III were both overexpressed in sera of patients with endometrial adenocarcinoma (EACa), adenocervical carcinoma (ACCa) and squamous cell cervical cancer (SCCa). However, EACa was different from ACCa and SCCa in the expression of clusterin (CLU), leucine-rich glycoprotein (LRG) and zinc α-2-glycoprotein. Studies performed on sera of patients with germ-line ovarian cancer and EOCa demonstrated that the two cancers were similar in their up-regulated expression of CLU, LRG and haptoglobin (β chain) but different in their expression of ACT and ceruloplasmin. The latter also appeared to be the sole high abundance protein that was up-regulated in the sera of patients with nasopharyngeal carcinoma. In view of the unique and distinctive altered patterns of acute-phase response profiles obtained for the serum samples of the different cohorts of cancer patients that were studied, it is proposed that the acute-phase protein response may be used as an additional tool for cancer diagnosis.
Track 3-3: Promising Protein Therapeutics for CNS Disorders/ Neurodegenerations

Time: April 3, 2009, Friday 13:30-16:15

Place: Meeting Room 310C
Session Chair:
Dr. Elena V. Batrakova, Assistant Professor, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Center for Drug Delivery and Nanomedicine, USA
Co-Chair:
Dr. Yun-Ru (Ruby) Chen, Assistant Research Fellow, the Genomics Research Center, Academia Sinica, Taiwan
13:30-14:00
Title: Peptides Targeting Protein Kinases- A GSK-3 Story
Dr. Hagit Eldar-Finkelman
, Associate Professor, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel

Glycogen synthase kinase-3 (GSK-3) is emerging as a novel drug discovery target in neurodegenerative and psychiatric disorders. Many studies now suggest that GSK-3 activation is a critical step in brain aging and the cascade of detrimental events contributing to these pathological disorders. Therefore, therapeutics targeted at inhibiting GSK-3 may be a useful strategic approach. We focus on development of specific inhibitors for GSK-3 that in contrast to many other protein kinase inhibitors that are ATP competitive, are substrate competitive inhibitors. Accordingly, we developed a novel cell-permeable peptide inhibitor termed, L803-mts, based on the unique recognition motif of GSK-3.
14:00-14:30
Title: Therapeutic Proteins Delivered by Monocytes to the Brain in Parkinson's Disease
Dr. Elena V. Batrakova, Assistant Professor, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Center for Drug Delivery and Nanomedicine, USA


In 1987 Dr. Elena V. Batrakova obtained Ph.D. in Polymer chemistry at the Department of Polymers, MSU, Russia. Batrakova's aim is to extend and intensify the research in the developing of new drug delivery polymer-based systems for the chemotherapy and CNS disorders. Her resent project related to employing inflammatory-response cells as drug carriers to deliver RedOx enzymes to the brain and to decrease inflammation and produce neuroprotective effect in Parkinson disease, stroke, etc (Batrakova et al. 2007). These studies will provide a novel platform for the delivery of therapeutic proteins across the BBB in the treatment of neurodegenerative disorders.
14:30-15:00
Title: Bird Brains Throw Much Needed Light on New Treatments for Alzheimer's Disease
Dr. Radmila Mileusnic
, Reader in Neurobiology, Department of Life Sciences, The Open University, UK

The molecular and cellular mechanisms underlying the memory deficits in Alzheimer's disease are increasingly thought to be associated with faulty processing of APP. Following our earlier findings that it is possible to use the tripeptide RER (NH2-D-Arg-L-Glu-L-Arg-COOH, derived from the external domain of APP) to rescue memory in animal models, we report here that the diasteromeric (D/L) form of the acetylated tripeptide RER protects against A? induced memory loss for a passive avoidance task in young chicks and enhances retention for a weak version of the task when injected peripherally up to 12 hr prior to training.

15:00-15:15
Coffee Break
15:15-15:45

Title: A Novel Protein in Chick Retina Exhibits Bifunctional Activities: Glutamine Synthetase and Glutamate Decarboxylase
Dr. Nison Sattayasai, Associate Professor in Biochemistry, Faculty of Science, Khon Kaen University, Thailand

The protein was determined for its purity and characterized for its identification using SDS-PAGE, 2D-gel electrophoresis and LC-MS/MS. The purified protein was identified as a glutamine synthetase with four isoforms. Enzymatic reaction followed by paper chromatography confirmed the protein identification. The protein catalyzed the synthesis of glutamine from glutamate in the presence of ammonium ion and ATP. Interestingly, prolonging reaction time, γ-aminobutyric acid (GABA) was then detected in the reaction mixture. Reaction started with glutamate and glutamine, in the presence or absence of ammonium ion and ATP, GABA could be detected immediately in the reaction mixture. The results suggested that the 42 kDa biotin-coupled protein also exhibited glutamate decarboxylase activity. Both activities were inhibited by avidin. The 42 kDa biotin-coupled protein, therefore, is a bifunctional enzyme which behaves as both synthetase and carboxylase. Concerning the function of glutamate in the retina as a neurotransmitter and a neurotoxin, this enzyme may help balancing between glutamate and GABA in neural tissues.

15:45-16:15
Title: Conformational Stability and Aggregation Mechanism of Amyloid in Alzheimer's Diseases
Dr. Yun-Ru (Ruby) Chen, Assistant Research Fellow, the Genomics Research Center, Academia Sinica, Taiwan

The amyloidogenic protein, amyloid b peptide (A b) is composed of 40 or 42 amino acids and is a critical component in the etiology of the neurodegenerative Alzheimer disease (AD). A b is prone to aggregate and forms amyloid fibrils progressively in vivo and in vitro . A b 40 and 42 differed by 2 residues at the C-terminus posses different biochemical and physiological properties. A b 42 aggregates faster and is the main composition of senile plaques found in AD brains. Despite sporadic AD, familial AD containing autosomal mutation in A b (Flemish A 21G, Dutch E22Q, Artic E 22G, and Iowa D23N) causes early onset of AD. In addition, specific aggregates designated as spherical oligomers are considered as the toxic entity. Therefore, understanding the initial stages in the aggregation is pivotal to develop methods for prevention oligomer formation.

Track 3-4: Protein Therapeutics, Protein Formulation and Delivery Technology

Time: April 4, 2009, Saturday 08:30-11:25

Place: Meeting Room 313
Session Chair Dr. Radmila Micanovic, Research Advisor, Biotechnology Discovery Research, Lilly Research Laboratories, USA
Co-Chair
Dr. Bengt-Harald Jonsson, Professor, Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linkoping University, Sweden

08:30-09:10

Keynote Speech: Title: Delivery of Topically Applied Antibody Fragments to the Back of the Eye
Dr. Dominik Escher, Chief Executive Officer, ESBATech AG, Switzerland


Dominik Escher serves as CEO of ESBATech since its inception. He is a co-founder and the delegate of the board of directors of the Company. Dominik Escher obtained his Ph.D. from the University of Zurich. Dominik Escher was selected as "Swiss-Transatlantic Young Leader Entrepreneur" by the ETH Zurich and the Swiss Embassy in 1999. His achievements for the Company were honored in 2004 as the winner of the "Swiss Life Sciences Prize", in 2005 as a winner of the "Top 100 Private European Companies" and in 2006 as the winner of the "Top 50 Swiss Ventures". Dominik Escher served as an Advisory Board Member of the Swiss Biotech Forum and as Scientific Advisory Board Member of the Swiss Network for Innovation. Since 2002 he is a Board Member and Vice President of the Swiss Biotech Association (SBA), the biotech industry organization of Switzerland.
09:10-09:50

Title: Experimental Approach for Growth Inhibition of Human Malignancies by the Highly Efficient Transporter-mediated Anti-tumor Peptide Delivery System
Dr. Eisaku Kondo, Associate Professor, Department of Pathology, Okayama University Graduate School of Medicine, Japan

Upon completion of his doctorate in Department of Pathology at the Okayama University, Japan in 199 2, he started working as an instructor at the Dept. of Pathology there, where he proceeded basic cancer research mainly focusing on B-cell lymphomagenesis with molecular pathological methods such as mRNA in situ hybridization and so on. He was assigned for an associate professor of the department of Pathology, Okayama University Medical School in 2006, and he is still developing the research of medical technology for a future peptide-based therapy with a continued effort.

09:50-10:05
Coffee Break
10:05-10:45
Title: FGF21 as a Novel Metabolic Regulator
Dr. Radmila Micanovic, Research Advisor, Biotechnology Discovery Research Division, Lilly Research Laboratories, USA

Doctor Radmila Micanovic is currently a Research Advisor at Lilly Research Laboratories, Lilly Corporate Center in Indianapolis. Radmila leads a team of scientists in the BioTechnology Discovery Research Division, focusing on identification, characterization and optimization of novel large molecule therapeutics and antibodies. Radmila has been with Lilly for 11 years and has lead or been a team member on a variety of programs targeting metabolic diseases, inflammation and cancer. Previously, Radmila has worked at Bristol Myers Squbb Pharmaceutical Research Institute in Princeton, NJ and at the former Roche Institute for Molecular Biology in Nutley, NJ, as a postdoctoral fellow. Radmila received a Ph.D. in Biochemistry from the University of Wyoming in Laramie, WY, and a B.S. degree in Molecular Biology from the University of Belgrade, in Serbia (Eastern Europe).
10:45-11:25

Title: Design of Functional Peptide-nanoparticle Complexes for Applications in Medical Imaging and Targeted Drug Delivery
Dr. Bengt-Harald Jonsson, Professor, Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linkoping University, Sweden

Track 4: Bioengineering or Bioprocessing: Protein Downstream Technologies

Track 4-1: Cell Line and Cell Culture Development & Protein Expression, Purification and Lyophilization

Time: April 2, 2009, Thursday 13:30-16:15

Place: Meeting Room 313

Session Chair
Dr. George Lovrecz, Principal Research Scientist and Project Leader, Molecular & Health Technologies, CSIRO, Australia
Co-Chair
Dr. John H Chon, Director, Upstream Process Development, PERCIVIA PER.C6® Development Center, LLC., USA

13:30-14:00

Keynote Speech: Title: New Strategies for Efficiently Producing Repetitive Proteins - Spider Silk as an Example
Dr. Sang Yup Lee, Distinguished Professor and Dean, LG Chem Chair at Department of Chemical and Biomolecular Engineering, KAIST, South Korea

He is Distinguished Professor and LG Chem Chair Professor; Dept. of Chemical & Biomolecular Engineering, KAIST, Korea; Dept. of Bio and Brain Engineering, KAIST; Dept. of Biological Sciences, KAIST; Dean, College of Life Science and Bioengineering; Head, Matabolic and Biomolecular Engineering National Research Laboratory; Director, BioProcess Engineering Research Center; Director, BioInformatics Research Center; Co-Director, Institute for the BioCentury. He has received numerous awards and honors including the First Young Scientist's Award from the President of Korea, the Scientist of the Month Award from the Ministry of Science and Technology, the Best Patent Award (SejongDaewang Award) from KIPO, the Citation Classic Award from ISI, USA, and the First Elmer Gaden Award (1999 Best Paper Award) from Biotechnology and Bioengineering (John Wiley & Sons, USA) at the ACS National meeting. In 2001, Prof. Lee has received the National Order of Merit from the President of Korea, for his contribution to the advancement of science and technology.
14:00-14:30

Title: Mammalian Cell Cultures: How the Glycosylation Pattern Can be Influenced by Various Scale-up Methods
Dr. George Lovrecz,
Principal Research Scientist and Project Leader, Molecular & Health Technologies, CSIRO, Australia

Dr George Lovrecz is a Senior Principal Research Scientist at CSIRO Molecular and Health Technologies with 25+ years experience in fermentation, specialising in mammalian cell cultures. His early projects involved the development of an on-line computer-linked control for bioreactors using novel techniques and the scale-up and GMP production of human growth hormone (hGH) at the University of New South Wales in conjunction with Commonwealth Serum Laboratories (CSL) and the Garvan Institute. Later he become responsible for the operation of the Recombinant Products Laboratories at UNSW. He joined CSIRO in 1995 as the Head of the Fermentation Group in Parkville. George provides expertise in the area of large-scale production, optimisation, development and characterisation of recombinant proteins for internal and external research collaborators such as programs from CSIRO, WEHI, LICR, PHI, Agenix, etc. He had an integral role in the development of a large-scale production system for mammalian cell receptor glycoproteins, as part of a collaborative effort. The resulting achievements of this work included the 3D structure of hIR and EGF receptor fragments the first published instance from this receptor family. George also has been involved in several patents/publications and teaching and training and various organisations.

14:30-15:00

Title: PER.C6® Technology: A Human Cell Line for Recombinant Protein Production at Extreme Levels
Dr. John H Chon, Director, Upstream Process Development, PERCIVIA PER.C6® Development Center, LLC., USA

Today's biopharmaceutical market requires manufacturing processes that are flexible, robust, cost-efficient, and deliver consistent product quality. A process that is capable of producing large amounts of the product quickly is valuable not only for preclinical and early-phase clinical material generation it also has great advantages in late-clinical and commercial manufacturing arena. PER.C6 cells are of a human cell line that has been used for years for production of vaccines. In the past few years, however, this cell line has become a popular platform for the production of recombinant proteins and monoclonal antibodies as well. Our research areas are focused on improving the yields of recombinant proteins by combination of PER.C6® cell line genetics, cell csulture medium optimization, and development of best practices to produce recombinant proteins in cell culture.

15:00-15:15

Coffee Break

15:15-15:45
Title: Largest Comparative Study on Expression Improvement by Gene Optimization Clearly Demonstrates Superiority over Wildtype Gene Approach
Dr. Max Mühlig-Versen, Senior Manager Scientific Sales, GENEART AG, Germany

The positive effects of silent mutations for improved gene expression have so far been demonstrated only on select genes. The current study describes a large scale comparison of wildtype and expression - optimized versions of 100 human genes selected from the NCBI Entrez database in mammalian expression systems. All optimized sequences were synthesized de novo, cloned into expression vectors and expressed protein levels compared to those of the respective non-optimized genes. In the vast majority of cases, expression optimized constructs outperform their native counterparts in protein yield with unaltered protein functionality, clearly demonstrating the benefits of sequence adaptation to the desired application compared to working with the natural sequence.

Dr. Max Muehlig-Versen, Senior Manager Scientific Sales, is responsible for the sales and marketing operations in the Africa–Middle East–Asia-Pacific region. In addition, he oversees the operations in the Northern European countries.
15:45-16:15
Title: The Removal of Aggregation during Process Purification
Dr. Faisal Uddin,
Biopharmecutical Development Department, MedImmune Ltd, United Kingdom

The presentation will discusses factors that play important role in effecting aggregation and how to avoid aggregation during different process purification steps and highlight which different types of techniques that are available to remove aggregation as well as method to find best final buffer choice in preventing aggregation in term long stability of the your antibody product.

Track 4-2: Recombinant Monoclonal, Antibodies, Protein-based Vaccine Bio-engineering and Protein Product

Time: April 3, 2009, Friday 08:30-11:25

Place: Meeting Room 313

Session Chair
Dr. Thomas Seewoester, Director, Process Development, Amgen Inc., USA
Co-Chair
Dr. Sang-hoon Cha, Professor of Molecular and Medical Biotechnology, Kangwon National University; President of IG Therapy Co., South Korea

08:30-09:10

Keynote Speech:
Title: Engineering Solutions to Improve Recombinant Protein Production - From Genetic Engineering to Process Engineering
Dr. Xuefeng Yu, Director, Process Development Department, Sanofi Pasteur, Canada

He obtained his PhD in Microbiology from McGill University in 1997. He joined IBEX Technologies inc. in Montreal as a research scientist in 1996. He was responsible for therapeutic enzymes products development. Dr. Yu joined sanofi pasteur in 1998 as a process development scientist. Since 2001 he has held director and corporate platform leader position in Process Development Department. In this role, he is responsible for local bacterial vaccine upstream process development and coordination of global activities across three R&D sites. He has played key roles in multiple new vaccines process development, GMP production as well as regulatory submission. Dr. Yu also has played leadership role in new GMP facility validation and technology transfer. As a corporate platform leader, he is also responsible for new technology and technical competency development.
09:10-09:50
Title: A Versatile Dual-vector Phage Display System Enabling Reliable Isolation of Specific Human Monoclonal Antibodies
Dr. Sang-hoon Cha
, Professor of Molecular and Medical Biotechnology, Kangwon National University; President of IG Therapy Co., South Korea

We believe that the DVS-II may provide a valuable tool in constructing a combinatorial phage-displayed Fab library with large diversity which is readily applicable in isolation of desired antibody clones based upon the L chain promiscuity of antibodies in determining antigen-binding specificity, and the DVS-III provides a convenient way to achieve light chain shuffling with any given heavy chain, leading to the identification of optimal light chain counterparts, which ultimately leads to in vitro affinity maturation of an antibody molecule. In addition to creating a huge combinatorial Fab diversity with great ease, another unique advantage of our hierarchical approach using the DVS-II and DVS-III over a conventional one-phagemid system has is its versatility in that the same human H and L chain sub-libraries created in the DVS-II or DVS-III, respectively, that used for construction of a 'single pot' human antibody library can be utilized in guided-selection or chain shuffling of mAbs of non-human origin instantly.

09:50-10:05
Coffee Break
10:05-10:45
Title: Development of Target Specific Recombinant Polyclonal Antibody Products
Dr. Torben P. Frandsen, Director, Antibody Chemistry, Symphogen A/S, Denmark

Torben P. Frandsen is Director for the Antibody Chemistry Team in Symphogen. He is responsible for the development of analytical technologies allowing characterization of recombinant polyclonal antibody products. He has been involved in the development of new mass spectrometry based methods to identify individual antibodies in such products. He also has the responsibility for development of manufacturing processes and CMC analytical release and characterization assays in collaboration with different CMO's. He received his Ph.D in 1997 for structure and function studies in different industrial enzymes. Torben P. Frandsen worked at Novozymes and other Biotech companies, prior to joining Symphogen in 2002.
10:45-11:25
Title: Therapeutic Potentials of Anti-Tn-antigen Antibodies: IGF-I Receptor Down-regulation as a Cancer Growth Inhibition Mechanism
Dr. Yoko Fujita-Yamaguchi, Professor, Applied Biochemistry, Tokai University School of Engineering, Japan

Tn-antigens are generally masked by covalently linked carbohydrates but exposed in most primary and metastatic epithelial malignant tumors, providing sensitive markers for detection of carcinoma. I will present our recent work which focused on tumor-associated carbohydrate antigen-specific antibodies as potential cancer therapeutics. MLS128, an anti-Tn monoclonal antibody, binds to a carbohydrate epitope (Tn3) consisting of three consecutive Tn-antigens (GalNAc -Ser/Thr). MLS128 treatment significantly inhibited colon and breast cancer cell growth. MLS128 bound to 110-210kD glycoproteins on the cell surface.
Track 5: Peptide Structure and Functions and Therapeutic Designs

Track 5-1: Peptide Conformations, Stability and Functions

Time: April 2, 2009, Thursday 13:30-16:25

Place: Meeting Room 314

Session Chair
Dr. Young Kee Kang, Professor, Department of Chemistry, Chungbuk National University; Secretary General of Korean Peptide-Protein Society, South Korea
Co-Chair
Dr. Norio Matsushima, Professor of Division of Biophysics, Center for Medical Education, Sapporo Medical University, Japan
13:30-14:10
Keynote Speech: Title: Conformational Design of Cyclic Bioactive Peptides: Restrictions via Cyclisation and N-methylation
Dr. Horst Kessler, Carl von Linde Professor, the Technische Universitat Munchen, Germany

Horst Kessler became full professor for organic chemistry at the J. W. Goethe University in Frankfurt in 1971. In 1989 he moved to the Technische Universit?t München. He also was head of the Bavarian NMR Center. Since October 2008 he is Carl von Linde Professor (Emeritus of excellence) at the Institute of Advanced Studies of the TUM. He has published over 630 papers in the field of NMR spectroscopy, organic chemistry and medicinal chemistry.
14:10-14:50

Title: Flexible and/or Disordered Structures of Tandem Repeats in Proteins
Dr. Norio Matsushima
, Professor of Division of Biophysics, Center for Medical Education, Sapporo Medical University, Japan

Tandem repeats occur in 14% of all proteins. The repeat unit lengths range from a single amino acid to more than 100 residues and the repeat number is sometimes over 100. Understanding the structures, functions, and evolution of these repeats is a significant goal in both proteomics and genomics. There are two general classes of tandem repeats in proteins. Some consist of globular domains, such as EF-hands, WD repeats, leucine rich repeats, and ankyrin; some of these domains associate to form helical structures. There are two subclasses of non-globular repeats. The first, such as collagen, form stable helices. The second, the focus of this review, are flexible and somewhat disordered both in vitro and in vivo.

14:50-15:05
Coffee Break
15:05-15:45

Title: Conformational Preferences of Bioactive Peptides Studied by Quantum-Chemical Methods
Dr. Young Kee Kang
, Professor, Department of Chemistry, Chungbuk National University; Secretary General of Korean Peptide-Protein Society, South Korea

Upon completion of his doctorate in physical chemistry at the Korea Advanced Institute of Science and Technology in 1983, he joined the faculty at the Department of Chemistry, Chungbuk National University, Korea. Dr. Kang spent two years as a postdoctoral fellow with Dr. Harold A. Scheraga at Cornell University for 1985-1987, where he developed a method to calculate the hydration free energies of peptides and proteins during their conformational changes. After returning to Korea, he has interested in developing the parameters for the molecular force field and applied his methods to study the conformational preferences of bioactive peptides, especially in aqueous solution. In particular, he has focused on the cis-trans isomerization of prolyl peptide bond and the puckering of prolyl ring since 1990. He has also served as the president of the Korean Biophysical Society (2005-2006), a steering committee member of Asian Biophysical Association (2007-present), and the Secretary General of Korean Peptide-Protein Society (2006-present).

15:45-16:25

Title: Chemokine Peptide-mediated Migration Control of Osteoclast Precursors Visualized by in Vivo Bone Imaging: A Novel Point of Regulation for Osteoimmunology
Dr. Masaru Ishii, Associate Professor, Chief of Laboratory of Biological Imaging, Immunology Frontier Research Center (IFReC), Osaka University, Japan

Chemokines are a family of small cytokines, consisting of approx. 100-polypeptides. The major role of chemokines is to act as a chemoattractant to guide the migration of cells. Although a variety of chemokines have been shown to control cells of the immune system, chemokine-mediated control of other biological systems is less demonstrated. Here I show for the first time that chemokines, such as CXCL12 and sphingosine-1-phosphate (S1P), dynamically controls migration of osteoclasts, special cell types for destroying bone tissues, and thus regulates bone homeostasis.

Track 5-2: Peptide Synthesis and Peptide Combinatorial Chemistry

Time: April 3, 2009, Friday 08:30-11:40

Place: Meeting Room 314

Session Chair
Dr. Seung Bum Park, Associate Professor, Department of Chemistry, College of National University, Seoul National University, South Korea
Co-Chair
Dr. Chien-Chen Lai, Associate Professor, Institute of Molecular Biology, National Chung Hsing University, Taiwan
08:30-08:55

Title: Simultaneous Qualitation and Quantitation of Peptides by Liquid Chromatography/ Mass Spectrometry with Electron Transfer Dissociation Technology
Dr. Chien-Chen Lai,
Associate Professor, Institute of Molecular Biology, National Chung Hsing University, Taiwan

08:55-09:20

Title: Current Drug Discovery Approaches Using Molecular Diversity and Chemical Biology
Dr. Seung Bum Park, Associate Professor, Department of Chemistry, College of National University, Seoul National University, South Korea

Upon completion of his doctorate in bioorganic chemistry at Texas A&M University in 2001, Dr. Seung Bum Park extended his scientific training as a postdoctoral research fellow at Harvard University under the guidance of Prof. Stuart L. Schreiber (2001-2004). Then, he joined the faculty of Chemistry department at Seoul National University. His research interest is following: Diversity-Oriented Synthesis and Chemical Biology, Rational Designed Drug Discovery, Bioimaging and High Throughput Screening, Proteomics screening using small molecule microarray, and NanoBioTechnology (NBT) for smart drug delivery system.

09:20-09:45
Title: Syntheses and Evaluation of Peptide Aldehyde as an Inhibitor for SARS 3CL Protease
Dr. Hiroyuki Konno, Assistant Professor, Department of Chemistry, Kyoto Prefectural University of Medicine, Japan

His research interest is following: natural product synthesis, solid phase peptide synthesis, synthetic methodlogy, drug discovery based on proteolysis mechanism.
09:45-10:10

Title: Inhibitory Effect of Oligopeptide on Cbl-b-mediated Ubiquitination and Degradation of IRS-1
Dr. Takeshi Nikawa
, Professor, Department of Nutritional Physiology, Institute of Health Biosciences, the University of Tokushima Graduate School, Japan

The down-regulation of IGF-1 signaling by Cbl-b, a RING-type ubiquitin ligase, contributed to bone loss and skeletal muscle atrophy during unloading. Cbl-b ubiquitinated IRS-1, an important intermediate of IGF-1
signal transduction, and enhanced its degradation. Since Cbl-b deficient mice were resistant to muscle atrophy and osteopenia induced by unloading conditions, we hypothesized that inhibition of IRS-1
ubiquitination promised to prevent unloading-mediated bone loss and muscle atrophy. In this study, we found that a synthetic oligopeptide with specific amino acid sequences effectively inhibited the Cbl-mediated ubiquitination of IRS-1 (patent pending). We also suggest that specific oligopeptides may be available as potent inhibitors against ubiquitin ligases, which are the rate-limiting enzymes of the ubiquitin-proteasome proteolytic pathway.

10:10-10:25

Coffee Break

10:25-10:50
Title: Ribosome Display Selection of Target Binding Peptides from Artificial Peptide Library
Dr. Akira Wada
, Research Scientist, Nano Medical Engineering Laboratory, Advanced Science Institute, RIKEN, Japan

Recently, I have developed a ribosome display technology for in vitro selection of target binding peptides from artificial peptide library. By use of this technology, I actually isolated and characterized new peptides with specific affinities for proteins, metal ion, metal biomaterial, and chemical compound. In my speech, I will present the details of the original technology, functions of target binding peptides, and bio-applications of them.

10:50-11:15
Title: Profiling Specificity of Deubiquitylating Enzymes Using Peptide-and Protein-based Probes
Dr. Holger Kramer, Department of Clinical Medicine, University of Oxford, UK

The ubiquitin-proteasome system (UPS) fulfills essential functions of protein degradation within eukaryotic cells. This pathway was found to be altered in diseases such as neurodegeneration, cancer and infectious diseases. Therefore the development of pharmacological intervention strategies are highly desirable and can be achieved at various levels: In the UPS both conjugation and deconjugation of ubiquitin (Ub) to substrate proteins are processes that are tightly controlled by the corresponding ligases (E1s,E2s,E3s) and Deubiquitylases (DUBs).
11:15-11:40

Title: Development of a Microwave-assisted Synthesizer for Polymer Supported Peptide Synthesis, and Its Application
Dr. Hiroki Shimizu, Research Institute of Genome-based Biofactory, Hokkaido Center, National Institute of Advanced Industrial Science and Technology (AIST), Japan

Microwave has well known as an effective heating tool and recently applied for chemical synthesis. Nevertheless this situation, we have focused on microwave non-thermal effect in the synthetic chemistry field, especially in peptide and carbohydrate syntheses. Based on our studies, we have developed a new semi-auto synthesizer which can be applied for polymer supported peptide synthesis as being able to control a reaction temperature rigidly and shake a reaction flask effectively. By use of this machine, we have synthesized some of bio-active peptides as ten, fifteen and thirty amino acid residual peptides easily and effectively, and even a sixty nine amino acid residual protein, verotoxin1 B subunit, is on the target of our chemical synthesis.

Track 5-3: Peptide Therapeutic Designs by Peptidomimetics and Peptidomics

Time: April 3, 2009, Friday 13:30-16:15

Place: Meeting Room 314

Session Chair
Dr. Kyung-Soo Hahm, Professor, Cellular and Molecular Medicine, College of Medicine, Research Center for Proteineous Materials, Chosun University; President of the Korean Peptide Protein Society, South Korea
Co-Chair
Dr. Yoshiki Katayama, Professor, Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Japan
13:30-14:00
Keynote Speech: Title: Synthetic Peptides for the Multi-drug Resistat and Bio-film Forming Bacterial Infections
Dr. Kyung-Soo Hahm, Professor, Cellular and Molecular Medicine, College of Medicine, Research Center for Proteineous Materials, Chosun University; President of the Korean Peptide Protein Society, South Korea
14:00-14:30

Title: Intracellular Signal-Responsive Gene Regulation System for Cancer Cell-Specific Gene Therapy by Using New Class of Peptide-Polymer Conjugate
Dr. Yoshiki Katayama, Professor, Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Japan

fter back to Dojindo Labs in 1991, Dr. Yoshiki Katayama then joined the faculty of Kyushu University. A t first, he pioneered a new technology for SNP analysis or biosensors for the detection of cyclic nucleotide ( Katayama et al. 200 0 ). From 1999-2002, he accomplished the research project of JST (PRESTO) for the research of intracellular signal-responsive DDS (Katayama et al. 2001, 2002). This technology is capable of signal-responsive drug release or gene activation. This work was developed by the next project of JST (CREST) from 2004-2008. The concept was successfully applied to living cell and animals and established a new concept of DDS (J-H. Kang et al 2008, J. Oishi et al. 2006 etc). He also developed a new peptide array for comprehensive analysis of intracellular signals or repid screening system of such signals using gold nanoparticles (K. Inamori et al. 2008, J. Oishi et al. 2007). He is now professor in Kyushu University from 2003.

14:30-15:00
Title: Discovery of Ss-peptides: Novel Opioid Analgesics and Mitochondria-Targeted Antioxidants
Dr. Peter W. Schiller
, Director of the Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal; Professor of Pharmacology at University of Montreal, Canada


Dr. Schiller holds a concurrent position as Professor of Pharmacology at the University of Montreal and is a Fellow of the Royal Society of Canada. During the past 33 years his research efforts have been focussed on structure─activity relationships in the area of peptide hormones and neurotransmitters. He uses an interdisciplinary research approach, incorporating organic synthesis, peptide chemistry, pharmacologic testing and conformational studies, to develop new concepts in peptide drug design. In particular, Professor Schiller's research efforts in the opioid peptide field resulted in the discovery of highly receptor-specific agonists and antagonists, and of novel mixed agonist/antagonists. Some of these compounds are widely used as pharmacological tools in opioid research or are being pursued as analgesic drug candidates. He has authored or co-authored over 360 publications and 12 patents.
15:00-15:15

Coffee Break

15:15-15:45

Title: Molecular Hiving Technology Bringing a New Innovation to Peptide Based Therapeutics
Mr. Yusuke Kohno
, Director, Department of Business Development, Jitsubo Co., Ltd., Japan

Mr. Kohno is appointed as a Director of b usiness development at Jitsubo Co., Ltd. in Jul y 2007. He re ceived his Msc and Bsc in Organic chemistry from Tokyo University of Agriculture and Technology in 2002 on efficient peptide synthesis with thermomorphic solvent system. For 3 years f rom 2002 to 2005, he was with DIC Corporation as a chemical specialist focusing on the process developmen t of the biomaterials and macro molecular for industry use. And then he was invited to join Jitsubo in 2005 and dedicated himself to establish Molecular Hiving? platform in collaboration with Tokyo university of Agriculture and Technology. In last 2 years he made up a number of collaborations with academia, biotech and pharmaceutical companies as a business development

15:45-16:15

Title: Endomorphins: Potent Anti-inflammatory Drugs in Arthritis
Dr. David S. Jessop
, Department of Medicine, University of Bristol, UK

Dr. Jessop was awarded his PhD from the University of London in 1988 for endocrine studies performed at St Bartholomew's Hospital. Since then he has worked at Westminster Hospital, London, and the University of Bristol in the UK. He was the first to identify the novel opioid peptides endomorphins in the mammalian immune system and demonstrate their anti-inflammatory activities. His current interests are the synthesis of endomorphins in immune cells and the therapeutic application of these compounds, and their long-acting analogues, to the treatment of arthritis. Dr Jessop was awarded an honorary Professorship in Neuroimmunology by the Hong Kong Polytechnic University in 2004.

Track 5-4: Peptide Therapeutics Pipeline and Successful Case Studies

Time: April 3, 2009, Friday 13:30-16:40

Place: Meeting Room 313

Session Chair
Dr. Andreas Brust, Reasearch Manager Chemistry, Xenome Limited, Australia
Co-Chair
Dr. Eagle Yi-Kung Huang, Associate Professor, National Defense Medical Center, Taiwan
13:30-13:55
Keynote Speech: Title: Research and Development of Biofunctional Peptides ~Antimicrobial Peptides, Angiotensin Converting Enzyme Inhibitor, and Enzymes for Cosmetics Application~
Dr. Shann-Tzong Jiang,
National Chair Professor & Vice President, Providence University; President of Nugen Bioscience (Taiwan) Co. Ltd., Taiwan
13:55-14:20

Title: Conopeptide to Drug: Structure and Activity Studies Central to the Development of Xen2174
Dr. Andreas Brust
, Reasearch Manager Chemistry, Xenome Limited, Australia

Dr. Andreas Brust obtained his Ph.D. degree in organic chemistry from the Technical University of Darmstadt ( Germany ). His work was focused on the synthetic evaluation of the use of carbohydrates as renewable resource for the chemical industry; Postdoctoral research into the biosynthesis of sponges including synthesis ( 14 C -labeled), isolation and structural determination of marine natural products at the University of Queensland braught him to Australia. In 2002 he joined Xenome Ltd.. As Research Manager (Chemistry) he is part of Xenome's Drug Development Team working closely with pharmacology and preclinical development.

14:20-14:45

Title: Behaviour of Neuropeptides in a Healthy Population: A Study on Neuropeptide EI
Dr. María Ester Celis, Professor, Laboratory of Physiological Sciences, Cátedra of Bacteriology and Virology Faculty of Medical Sciences, University of Córdoba, Argentina
14:45-15:10
Title: Structural and Functional Studies of the Antimicrobial Peptide Histatin-5 and Its Analogue, TOAC 0 -Histatin-5, in Solution and upon Interaction with Biomimetic Systems
Dr. Shirley Schreier, Professor, Department of Biochemistry, University of Sao Paulo, Brazil

Shirley Schreier obtained her Ph. D. in Physical Biochemistry at the University of S?o Paulo, Brazil, where she presently is Professor of Biochemistry at the Department of Biochemistry. Dr. Schreier worked as a Visiting Scientist at the National Research Council of Canada, the National Biomedical EPR Center of the Medical College of Wisconsin, and the Université Pierre et Marie Curie, in Paris. Dr. Schreier started her research on structure, dynamics, and physical chemistry of model membranes making use of spin labeling EPR spectroscopy.
15:10-15:25
Coffee Break
15:25-15:50
Title: Biological Roles of Angiotensin II and Its Receptor Blocker in Human Prostate Cancer
Dr. Hiroji Uemura, Associate Professor, Graduate School of Medicine, Yokohama City University, Japan

To date we have reported biological roles of angiotensin II (Ang-II) and Ang-II receptor blockers (ARBs) in prostate cancer. The prostatic renin-angiotensin system related to cell proliferation and angiogenesis has the potential especially in carcinogenesis of prostate and ARBs can suppress them by inhibiting signal transduction pathways or angiogenesis through AT1 receptor. Clinically, we demonstrated the administration of ARBs for hormone refractory prostate cancer patients induced the decline and stabilization of serum prostate specific antigen. We have clarified the molecular mechanism of ARBs which repress androgen receptor protein expression and induce apoptotic cell death.
15:50-16:15
Title: A Different View in Searching for A New Drug Target: Insulin-regulated Amino Peptidase (IRAP)
Dr. Eagle Yi-Kung Huang, Associate Professor, Department of Pharmacology, National Defense Medical Center, Taiwan

Dr. Eagle Yi-Kung Huang received his Ph.D. in Neuropharmacology from Dept. of Physiology & Pharmacology, University of Southampton, UK in Oct. 1997. He was Assistant Professor in Dept. of Pharmacology, National Defense Medical Center, Taiwan during Feb. 2001 – Jul. 2005. From Aug. 2005 to present he is Associate Professor in the Dept. of Pharmacology, National Defense Medical Center, Taipei, Taiwan.
16:15-16:40
Title:  Development of Novel Candidate Peptides for Antiangiogenic Applications
Dr. Berrin Erdag, Project Director, Immunogenetic Laboratory, the Scientific and Technological Council of Turkey, Genetic Engineering and Biotechnology Institute, Turkey

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